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Conserved domains on  [gi|93102371|ref|NP_060783|]
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protein polybromo-1 isoform 2 [Homo sapiens]

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 44-156 3.21e-67

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 221.82  E-value: 3.21e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   44 VDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNA 123
Cdd:cd05524    1 LDPIAVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNA 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 93102371  124 KSYYKPDSPEYKAACKLWDLYLRTRNEFVQKGE 156
Cdd:cd05524   81 KAYYKPDSPEHKDACKLWELFLSARNEVLSGGE 113
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 519-622 1.46e-62

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 208.07  E-value: 1.46e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  519 RKQRMKILFNVVLEAREpGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNAR 598
Cdd:cd05518    1 RKKRMLALFLYVLEYRE-GSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNAR 79

                         90       100
                 ....*....|....*....|....
gi 93102371  599 HYNEEGSQVYNDAHILEKLLKEKR 622
Cdd:cd05518   80 HYNEEGSQVYEDANILEKVLKEKR 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 383-484 1.86e-59

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99951  Cd Length: 103  Bit Score: 199.10  E-value: 1.86e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  383 SNPFYQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRY 462
Cdd:cd05520    2 SNPLWQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRY 81

                         90       100
                 ....*....|....*....|..
gi 93102371  463 NVPNSAIYKRVLKLQQVMQAKK 484
Cdd:cd05520   82 NVPNSRIYKDAEKLQKLMQAKK 103
Bromo_polybromo_VI cd05526
Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which ...
 775-882 1.44e-58

Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99956  Cd Length: 110  Bit Score: 196.82  E-value: 1.44e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  775 TLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIP--AVDPNFPNKPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERAR 852
Cdd:cd05526    1 QLLVQELLATLFVSVMNHQDEEGRCYSDSLAELPelAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 93102371  853 RMNRTDSEIYEDAVELQQFFIKIRDELCKN 882
Cdd:cd05526   81 RLSRTDSEIYEDAVELQQFFIKIRDELCKN 110
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 1130-1248 1.60e-58

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


:

Pssm-ID: 240068  Cd Length: 121  Bit Score: 197.04  E-value: 1.60e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371 1130 DMWLKVGDCVFIKSHG-LVRPRVGRIEKVWVR-DGAAYFYGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1207
Cdd:cd04717    1 GLQYRVGDCVYVANPEdPSKPIIFRIERLWKDeDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 93102371 1208 CAVLSFKDFLSCRPTEIPENDILLCESRYNESDKQMKKFKG 1248
Cdd:cd04717   81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIKT 121
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 658-762 2.27e-58

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99946  Cd Length: 105  Bit Score: 195.99  E-value: 2.27e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  658 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 737
Cdd:cd05515    1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                         90       100
                 ....*....|....*....|....*
gi 93102371  738 YNEPESLIYKDALVLHKVLLETRRD 762
Cdd:cd05515   81 YNEPDSQIYKDALTLQKVLLETKRE 105
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 182-284 1.79e-55

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99948  Cd Length: 103  Bit Score: 187.65  E-value: 1.79e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  182 LKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKT 261
Cdd:cd05517    1 LKQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKT 80

                         90       100
                 ....*....|....*....|...
gi 93102371  262 YNEPGSQVFKDANSIKKIFYMKK 284
Cdd:cd05517   81 FNEPGSQVYKDANAIKKIFTAKK 103
BAH super family cl02608
BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). ...
 957-1049 2.91e-39

BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.


The actual alignment was detected with superfamily member cd04717:

Pssm-ID: 470629  Cd Length: 121  Bit Score: 142.34  E-value: 2.91e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  957 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSA-------------------------EKEVFKSDYYNKVPVSKILGKCV 1011
Cdd:cd04717    3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDgekfffgcwfyrpeetfheptrkfyKNEVFKSPLYETVPVEEIVGKCA 82

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 93102371 1012 VMFVKEYFKLCPENFRDEDVFVCESRYSAKTKSFKKIK 1049
Cdd:cd04717   83 VMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIK 120
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 1328-1383 4.22e-28

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


:

Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 108.10  E-value: 4.22e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 93102371 1328 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGMMGGY 1383
Cdd:cd21984    1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQ 56
 
Name Accession Description Interval E-value
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 44-156 3.21e-67

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 221.82  E-value: 3.21e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   44 VDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNA 123
Cdd:cd05524    1 LDPIAVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNA 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 93102371  124 KSYYKPDSPEYKAACKLWDLYLRTRNEFVQKGE 156
Cdd:cd05524   81 KAYYKPDSPEHKDACKLWELFLSARNEVLSGGE 113
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 519-622 1.46e-62

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 208.07  E-value: 1.46e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  519 RKQRMKILFNVVLEAREpGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNAR 598
Cdd:cd05518    1 RKKRMLALFLYVLEYRE-GSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNAR 79

                         90       100
                 ....*....|....*....|....
gi 93102371  599 HYNEEGSQVYNDAHILEKLLKEKR 622
Cdd:cd05518   80 HYNEEGSQVYEDANILEKVLKEKR 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 383-484 1.86e-59

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 199.10  E-value: 1.86e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  383 SNPFYQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRY 462
Cdd:cd05520    2 SNPLWQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRY 81

                         90       100
                 ....*....|....*....|..
gi 93102371  463 NVPNSAIYKRVLKLQQVMQAKK 484
Cdd:cd05520   82 NVPNSRIYKDAEKLQKLMQAKK 103
Bromo_polybromo_VI cd05526
Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which ...
 775-882 1.44e-58

Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99956  Cd Length: 110  Bit Score: 196.82  E-value: 1.44e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  775 TLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIP--AVDPNFPNKPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERAR 852
Cdd:cd05526    1 QLLVQELLATLFVSVMNHQDEEGRCYSDSLAELPelAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 93102371  853 RMNRTDSEIYEDAVELQQFFIKIRDELCKN 882
Cdd:cd05526   81 RLSRTDSEIYEDAVELQQFFIKIRDELCKN 110
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 1130-1248 1.60e-58

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 197.04  E-value: 1.60e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371 1130 DMWLKVGDCVFIKSHG-LVRPRVGRIEKVWVR-DGAAYFYGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1207
Cdd:cd04717    1 GLQYRVGDCVYVANPEdPSKPIIFRIERLWKDeDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 93102371 1208 CAVLSFKDFLSCRPTEIPENDILLCESRYNESDKQMKKFKG 1248
Cdd:cd04717   81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIKT 121
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 658-762 2.27e-58

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 195.99  E-value: 2.27e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  658 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 737
Cdd:cd05515    1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                         90       100
                 ....*....|....*....|....*
gi 93102371  738 YNEPESLIYKDALVLHKVLLETRRD 762
Cdd:cd05515   81 YNEPDSQIYKDALTLQKVLLETKRE 105
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 182-284 1.79e-55

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 187.65  E-value: 1.79e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  182 LKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKT 261
Cdd:cd05517    1 LKQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKT 80

                         90       100
                 ....*....|....*....|...
gi 93102371  262 YNEPGSQVFKDANSIKKIFYMKK 284
Cdd:cd05517   81 FNEPGSQVYKDANAIKKIFTAKK 103
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 957-1049 2.91e-39

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 142.34  E-value: 2.91e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  957 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSA-------------------------EKEVFKSDYYNKVPVSKILGKCV 1011
Cdd:cd04717    3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDgekfffgcwfyrpeetfheptrkfyKNEVFKSPLYETVPVEEIVGKCA 82

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 93102371 1012 VMFVKEYFKLCPENFRDEDVFVCESRYSAKTKSFKKIK 1049
Cdd:cd04717   83 VMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIK 120
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 1131-1247 3.48e-32

BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.


Pssm-ID: 460207  Cd Length: 120  Bit Score: 122.03  E-value: 3.48e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   1131 MWLKVGDCVFIKSHG-LVRPRVGRIEKVWVRDGA--AYFYGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1207
Cdd:pfam01426    1 ETYSVGDFVLVEPDDaDEPYYVARIEELFEDTKNgkKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 93102371   1208 CAVLSFKDFLSCRPTEIPENDILLCESRYNESDKQMKKFK 1247
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEPDDFFCELLYDPKTKSFKKLP 120
BROMO smart00297
bromo domain;
651-763 1.95e-30

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 116.22  E-value: 1.95e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     651 KSKYMTPMQQKLNEVYEAVKNYtdkrgrRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVM 730
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSH------PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNL 74

                            90       100       110
                    ....*....|....*....|....*....|...
gi 93102371     731 MFNNACTYNEPESLIYKDALVLHKVLLETRRDL 763
Cdd:smart00297   75 MFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107
BAH smart00439
Bromo adjacent homology domain;
1132-1247 1.77e-29

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 114.31  E-value: 1.77e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371    1132 WLKVGDCVFIKSH-GLVRPRVGRIEKVWVRDG---AAYFYGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1207
Cdd:smart00439    1 TISVGDFVLVEPDdADEPYYIGRIEEIFETKKnseSKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 93102371    1208 CAVLSFKDFLSCRPTEIP-ENDILLCESRYNESDKQMKKFK 1247
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSIgEPDVFFCESAYDPEKGSFKKLP 121
BROMO smart00297
bromo domain;
519-625 1.35e-28

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 111.22  E-value: 1.35e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     519 RKQRMKILFNVVLEAREpgsGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNAR 598
Cdd:smart00297    4 LQKKLQELLKAVLDKLD---SHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100
                    ....*....|....*....|....*..
gi 93102371     599 HYNEEGSQVYNDAHILEKLLKEKRKEL 625
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEKFFEKKLREL 107
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 411-761 1.95e-28

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 119.14  E-value: 1.95e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  411 LPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLEcDLNLMFENAKRYNVPNSAIYKRV--LKLQQVMQAKKKELa 488
Cdd:COG5076   43 EGSKNLFQKQLKRMPKEYITSIVDDREPGSMANVNDDLE-NVGGITYSPFEKNRPESLRFDEIvfLAIESVTPESGLGS- 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  489 rrddiedgdsmISSATSDTGSAKRKSKKNIRKQRMKILFNVVLEAR--EPGSGRRLCDLFMVKPSKKDYPDYYKIILEPM 566
Cdd:COG5076  121 -----------LLMAHLKTSVKKRKTPKIEDELLYADNKAIAKFKKqlFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPM 189

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  567 DLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKekrKELGPLPDDDDMASPKLKlsrksg 646
Cdd:COG5076  190 DLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFL---KLIEEIPEEMLELSIKPG------ 260

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  647 ispKKSKYMTPmqqklnevyeaVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVE 726
Cdd:COG5076  261 ---REEREERE-----------SVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVR 326

                        330       340       350
                 ....*....|....*....|....*....|....*
gi 93102371  727 DFVMMFNNACTYNEPESLIYKDALVLHKVLLETRR 761
Cdd:COG5076  327 DAKLFFDNCVMYNGEVTDYYKNANVLEDFVIKKTR 361
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 1328-1383 4.22e-28

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 108.10  E-value: 4.22e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 93102371 1328 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGMMGGY 1383
Cdd:cd21984    1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQ 56
BROMO smart00297
bromo domain;
181-287 5.77e-27

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 106.59  E-value: 5.77e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     181 YLKEILEQLLEAIVVatnpsgRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAK 260
Cdd:smart00297    7 KLQELLKAVLDKLDS------HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100
                    ....*....|....*....|....*..
gi 93102371     261 TYNEPGSQVFKDANSIKKIFYMKKAEI 287
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEKFFEKKLREL 107
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 956-1049 1.43e-26

BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.


Pssm-ID: 460207  Cd Length: 120  Bit Score: 105.85  E-value: 1.43e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371    956 SMYHVGDYVYVEPAEANLQPHIVCIERLWEDS--------------------------AEKEVFKSDYYNKVPVSKILGK 1009
Cdd:pfam01426    1 ETYSVGDFVLVEPDDADEPYYVARIEELFEDTkngkkmvrvqwfyrpeetvhragkafNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 93102371   1010 CVVMFVKEYFKLCPENFRDEDVFVCESRYSAKTKSFKKIK 1049
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEPDDFFCELLYDPKTKSFKKLP 120
BROMO smart00297
bromo domain;
384-487 4.18e-26

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 103.90  E-value: 4.18e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     384 NPFYQLYDTVRSCRNNQgqLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYN 463
Cdd:smart00297    6 KKLQELLKAVLDKLDSH--PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|....
gi 93102371     464 VPNSAIYKRVLKLQQVMQAKKKEL 487
Cdd:smart00297   84 GPDSEVYKDAKKLEKFFEKKLREL 107
BROMO smart00297
bromo domain;
49-151 1.14e-25

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 102.74  E-value: 1.14e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371      49 VCHELYNTIRDYKDEqgRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYK 128
Cdd:smart00297    7 KLQELLKAVLDKLDS--HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84

                            90       100
                    ....*....|....*....|...
gi 93102371     129 PDSPEYKAACKLWDLYLRTRNEF 151
Cdd:smart00297   85 PDSEVYKDAKKLEKFFEKKLREL 107
BAH smart00439
Bromo adjacent homology domain;
957-1049 1.10e-22

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 94.67  E-value: 1.10e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     957 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSAEK---------------------------EVFKSDYYNKVPVSKILGK 1009
Cdd:smart00439    1 TISVGDFVLVEPDDADEPYYIGRIEEIFETKKNSeskmvrvrwfyrpeetvlekaalfdknEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 93102371    1010 CVVMFVKEYFKLCPENFRD-EDVFVCESRYSAKTKSFKKIK 1049
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSIGePDVFFCESAYDPEKGSFKKLP 121
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 182-273 2.61e-20

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 86.60  E-value: 2.61e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371    182 LKEILEQLLEaivvatnpsgRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKT 261
Cdd:pfam00439    1 CLEILDKLME----------HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNART 70

                           90
                   ....*....|..
gi 93102371    262 YNEPGSQVFKDA 273
Cdd:pfam00439   71 YNGPGSVIYKAA 82
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 54-139 2.93e-20

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 86.60  E-value: 2.93e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     54 YNTIRDYKDEQGRllCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPE 133
Cdd:pfam00439    1 CLEILDKLMEHPI--AAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVI 78


                   ....*.
gi 93102371    134 YKAACK 139
Cdd:pfam00439   79 YKAAEK 84
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 402-471 6.50e-18

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 80.05  E-value: 6.50e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371    402 QLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYK 471
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 189-302 1.32e-16

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 83.70  E-value: 1.32e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  189 LLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQ 268
Cdd:COG5076  150 IAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSS 229

                         90       100       110
                 ....*....|....*....|....*....|....
gi 93102371  269 VFKDANSIKKIFYMKKAEIEHHEMAKSSLRMRTP 302
Cdd:COG5076  230 VYVDAKELEKYFLKLIEEIPEEMLELSIKPGREE 263
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 540-613 1.40e-16

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 76.20  E-value: 1.40e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 93102371    540 RRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHI 613
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAEK 84
BROMO smart00297
bromo domain;
779-879 3.96e-16

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 75.78  E-value: 3.96e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     779 QELIHNLFVSVMSHQDDegRCYSDSLAEIPAVD--PNFPN--KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRM 854
Cdd:smart00297    5 QKKLQELLKAVLDKLDS--HPLSWPFLKPVSRKeaPDYYDiiKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTY 82

                            90       100
                    ....*....|....*....|....*
gi 93102371     855 NRTDSEIYEDAVELQQFFIKIRDEL 879
Cdd:smart00297   83 NGPDSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 678-749 4.39e-14

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 68.88  E-value: 4.39e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371    678 RRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDA 749
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAA 82
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 789-867 2.01e-13

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 66.95  E-value: 2.01e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371    789 VMSHQDDEGRCYSDSLAEIPAVDPNFPN--KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAV 866
Cdd:pfam00439    4 ILDKLMEHPIAAPFLEPVDPDEYPDYYSviKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83


                   .
gi 93102371    867 E 867
Cdd:pfam00439   84 K 84
HMG smart00398
high mobility group;
1326-1379 5.77e-11

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 59.64  E-value: 5.77e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 93102371    1326 KRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGM 1379
Cdd:smart00398    1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEK 54
HMG_box pfam00505
HMG (high mobility group) box;
1328-1379 3.22e-10

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 57.62  E-value: 3.22e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 93102371   1328 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGM 1379
Cdd:pfam00505    2 KRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEK 53
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1311-1377 2.30e-04

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 44.08  E-value: 2.30e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371 1311 STPKSAKGSA-----KKEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYE 1377
Cdd:COG5648   50 TKPRKKTKSKrlvrkKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYY 121
 
Name Accession Description Interval E-value
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 44-156 3.21e-67

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 221.82  E-value: 3.21e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   44 VDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNA 123
Cdd:cd05524    1 LDPIAVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNA 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 93102371  124 KSYYKPDSPEYKAACKLWDLYLRTRNEFVQKGE 156
Cdd:cd05524   81 KAYYKPDSPEHKDACKLWELFLSARNEVLSGGE 113
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 519-622 1.46e-62

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 208.07  E-value: 1.46e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  519 RKQRMKILFNVVLEAREpGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNAR 598
Cdd:cd05518    1 RKKRMLALFLYVLEYRE-GSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNAR 79

                         90       100
                 ....*....|....*....|....
gi 93102371  599 HYNEEGSQVYNDAHILEKLLKEKR 622
Cdd:cd05518   80 HYNEEGSQVYEDANILEKVLKEKR 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 383-484 1.86e-59

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 199.10  E-value: 1.86e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  383 SNPFYQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRY 462
Cdd:cd05520    2 SNPLWQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRY 81

                         90       100
                 ....*....|....*....|..
gi 93102371  463 NVPNSAIYKRVLKLQQVMQAKK 484
Cdd:cd05520   82 NVPNSRIYKDAEKLQKLMQAKK 103
Bromo_polybromo_VI cd05526
Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which ...
 775-882 1.44e-58

Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99956  Cd Length: 110  Bit Score: 196.82  E-value: 1.44e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  775 TLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIP--AVDPNFPNKPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERAR 852
Cdd:cd05526    1 QLLVQELLATLFVSVMNHQDEEGRCYSDSLAELPelAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 93102371  853 RMNRTDSEIYEDAVELQQFFIKIRDELCKN 882
Cdd:cd05526   81 RLSRTDSEIYEDAVELQQFFIKIRDELCKN 110
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 1130-1248 1.60e-58

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 197.04  E-value: 1.60e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371 1130 DMWLKVGDCVFIKSHG-LVRPRVGRIEKVWVR-DGAAYFYGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1207
Cdd:cd04717    1 GLQYRVGDCVYVANPEdPSKPIIFRIERLWKDeDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 93102371 1208 CAVLSFKDFLSCRPTEIPENDILLCESRYNESDKQMKKFKG 1248
Cdd:cd04717   81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIKT 121
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 658-762 2.27e-58

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 195.99  E-value: 2.27e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  658 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 737
Cdd:cd05515    1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                         90       100
                 ....*....|....*....|....*
gi 93102371  738 YNEPESLIYKDALVLHKVLLETRRD 762
Cdd:cd05515   81 YNEPDSQIYKDALTLQKVLLETKRE 105
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 182-284 1.79e-55

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 187.65  E-value: 1.79e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  182 LKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKT 261
Cdd:cd05517    1 LKQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKT 80

                         90       100
                 ....*....|....*....|...
gi 93102371  262 YNEPGSQVFKDANSIKKIFYMKK 284
Cdd:cd05517   81 FNEPGSQVYKDANAIKKIFTAKK 103
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 957-1049 2.91e-39

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 142.34  E-value: 2.91e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  957 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSA-------------------------EKEVFKSDYYNKVPVSKILGKCV 1011
Cdd:cd04717    3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDgekfffgcwfyrpeetfheptrkfyKNEVFKSPLYETVPVEEIVGKCA 82

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 93102371 1012 VMFVKEYFKLCPENFRDEDVFVCESRYSAKTKSFKKIK 1049
Cdd:cd04717   83 VMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIK 120
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 1131-1247 3.48e-32

BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.


Pssm-ID: 460207  Cd Length: 120  Bit Score: 122.03  E-value: 3.48e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   1131 MWLKVGDCVFIKSHG-LVRPRVGRIEKVWVRDGA--AYFYGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1207
Cdd:pfam01426    1 ETYSVGDFVLVEPDDaDEPYYVARIEELFEDTKNgkKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 93102371   1208 CAVLSFKDFLSCRPTEIPENDILLCESRYNESDKQMKKFK 1247
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEPDDFFCELLYDPKTKSFKKLP 120
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 518-621 1.72e-31

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 119.37  E-value: 1.72e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  518 IRKQrMKILFNVVLEArEPGSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNA 597
Cdd:cd05519    1 LKAA-MLEIYDAVLNC-EDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANA 78

                         90       100
                 ....*....|....*....|....
gi 93102371  598 RHYNEEGSQVYNDAHILEKLLKEK 621
Cdd:cd05519   79 RTYNQEGSIVYEDAVEMEKAFKKK 102
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 182-286 4.63e-31

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 118.18  E-value: 4.63e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  182 LKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKT 261
Cdd:cd05515    1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                         90       100
                 ....*....|....*....|....*
gi 93102371  262 YNEPGSQVFKDANSIKKIFYMKKAE 286
Cdd:cd05515   81 YNEPDSQIYKDALTLQKVLLETKRE 105
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 520-624 5.25e-31

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 117.79  E-value: 5.25e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  520 KQRMKILFNVVLEAREPGsGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARH 599
Cdd:cd05515    2 QQKLWELYNAVKNYTDGR-GRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                         90       100
                 ....*....|....*....|....*
gi 93102371  600 YNEEGSQVYNDAHILEKLLKEKRKE 624
Cdd:cd05515   81 YNEPDSQIYKDALTLQKVLLETKRE 105
BROMO smart00297
bromo domain;
651-763 1.95e-30

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 116.22  E-value: 1.95e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     651 KSKYMTPMQQKLNEVYEAVKNYtdkrgrRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVM 730
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSH------PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNL 74

                            90       100       110
                    ....*....|....*....|....*....|...
gi 93102371     731 MFNNACTYNEPESLIYKDALVLHKVLLETRRDL 763
Cdd:smart00297   75 MFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 658-759 1.97e-30

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 116.29  E-value: 1.97e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  658 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 737
Cdd:cd05519    1 LKAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANART 80

                         90       100
                 ....*....|....*....|..
gi 93102371  738 YNEPESLIYKDALVLHKVLLET 759
Cdd:cd05519   81 YNQEGSIVYEDAVEMEKAFKKK 102
BAH smart00439
Bromo adjacent homology domain;
1132-1247 1.77e-29

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 114.31  E-value: 1.77e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371    1132 WLKVGDCVFIKSH-GLVRPRVGRIEKVWVRDG---AAYFYGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1207
Cdd:smart00439    1 TISVGDFVLVEPDdADEPYYIGRIEEIFETKKnseSKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 93102371    1208 CAVLSFKDFLSCRPTEIP-ENDILLCESRYNESDKQMKKFK 1247
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSIgEPDVFFCESAYDPEKGSFKKLP 121
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 387-486 8.94e-29

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 111.63  E-value: 8.94e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  387 YQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPN 466
Cdd:cd05515    6 WELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPD 85

                         90       100
                 ....*....|....*....|
gi 93102371  467 SAIYKRVLKLQQVMQAKKKE 486
Cdd:cd05515   86 SQIYKDALTLQKVLLETKRE 105
BROMO smart00297
bromo domain;
519-625 1.35e-28

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 111.22  E-value: 1.35e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     519 RKQRMKILFNVVLEAREpgsGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNAR 598
Cdd:smart00297    4 LQKKLQELLKAVLDKLD---SHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100
                    ....*....|....*....|....*..
gi 93102371     599 HYNEEGSQVYNDAHILEKLLKEKRKEL 625
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEKFFEKKLREL 107
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 411-761 1.95e-28

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 119.14  E-value: 1.95e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  411 LPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLEcDLNLMFENAKRYNVPNSAIYKRV--LKLQQVMQAKKKELa 488
Cdd:COG5076   43 EGSKNLFQKQLKRMPKEYITSIVDDREPGSMANVNDDLE-NVGGITYSPFEKNRPESLRFDEIvfLAIESVTPESGLGS- 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  489 rrddiedgdsmISSATSDTGSAKRKSKKNIRKQRMKILFNVVLEAR--EPGSGRRLCDLFMVKPSKKDYPDYYKIILEPM 566
Cdd:COG5076  121 -----------LLMAHLKTSVKKRKTPKIEDELLYADNKAIAKFKKqlFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPM 189

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  567 DLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKekrKELGPLPDDDDMASPKLKlsrksg 646
Cdd:COG5076  190 DLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFL---KLIEEIPEEMLELSIKPG------ 260

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  647 ispKKSKYMTPmqqklnevyeaVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVE 726
Cdd:COG5076  261 ---REEREERE-----------SVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVR 326

                        330       340       350
                 ....*....|....*....|....*....|....*
gi 93102371  727 DFVMMFNNACTYNEPESLIYKDALVLHKVLLETRR 761
Cdd:COG5076  327 DAKLFFDNCVMYNGEVTDYYKNANVLEDFVIKKTR 361
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 660-760 2.56e-28

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 110.21  E-value: 2.56e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  660 QKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYN 739
Cdd:cd05516    4 KKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83

                         90       100
                 ....*....|....*....|.
gi 93102371  740 EPESLIYKDALVLHKVLLETR 760
Cdd:cd05516   84 LEGSLIYEDSIVLQSVFKSAR 104
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 1328-1383 4.22e-28

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 108.10  E-value: 4.22e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 93102371 1328 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGMMGGY 1383
Cdd:cd21984    1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQ 56
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 182-283 8.14e-28

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 108.61  E-value: 8.14e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  182 LKEILEQLLEAIVVATNPsgrlISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKT 261
Cdd:cd04369    1 LKKKLRSLLDALKKLKRD----LSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKT 76

                         90       100
                 ....*....|....*....|..
gi 93102371  262 YNEPGSQVFKDANSIKKIFYMK 283
Cdd:cd04369   77 YNGPGSPIYKDAKKLEKLFEKL 98
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 50-150 4.57e-27

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 106.62  E-value: 4.57e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   50 CHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKP 129
Cdd:cd05515    5 LWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEP 84

                         90       100
                 ....*....|....*....|.
gi 93102371  130 DSPEYKAACKLWDLYLRTRNE 150
Cdd:cd05515   85 DSQIYKDALTLQKVLLETKRE 105
BROMO smart00297
bromo domain;
181-287 5.77e-27

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 106.59  E-value: 5.77e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     181 YLKEILEQLLEAIVVatnpsgRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAK 260
Cdd:smart00297    7 KLQELLKAVLDKLDS------HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100
                    ....*....|....*....|....*..
gi 93102371     261 TYNEPGSQVFKDANSIKKIFYMKKAEI 287
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEKFFEKKLREL 107
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 956-1049 1.43e-26

BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.


Pssm-ID: 460207  Cd Length: 120  Bit Score: 105.85  E-value: 1.43e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371    956 SMYHVGDYVYVEPAEANLQPHIVCIERLWEDS--------------------------AEKEVFKSDYYNKVPVSKILGK 1009
Cdd:pfam01426    1 ETYSVGDFVLVEPDDADEPYYVARIEELFEDTkngkkmvrvqwfyrpeetvhragkafNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 93102371   1010 CVVMFVKEYFKLCPENFRDEDVFVCESRYSAKTKSFKKIK 1049
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEPDDFFCELLYDPKTKSFKKLP 120
BROMO smart00297
bromo domain;
384-487 4.18e-26

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 103.90  E-value: 4.18e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     384 NPFYQLYDTVRSCRNNQgqLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYN 463
Cdd:smart00297    6 KKLQELLKAVLDKLDSH--PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|....
gi 93102371     464 VPNSAIYKRVLKLQQVMQAKKKEL 487
Cdd:smart00297   84 GPDSEVYKDAKKLEKFFEKKLREL 107
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 520-625 7.59e-26

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 103.28  E-value: 7.59e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  520 KQRMKILFNVVLEAREPGsGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARH 599
Cdd:cd05516    3 TKKMNKIVDVVIKYKDSD-GRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQT 81

                         90       100
                 ....*....|....*....|....*.
gi 93102371  600 YNEEGSQVYNDAHILEKLLKEKRKEL 625
Cdd:cd05516   82 FNLEGSLIYEDSIVLQSVFKSARQKI 107
BROMO smart00297
bromo domain;
49-151 1.14e-25

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 102.74  E-value: 1.14e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371      49 VCHELYNTIRDYKDEqgRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYK 128
Cdd:smart00297    7 KLQELLKAVLDKLDS--HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84

                            90       100
                    ....*....|....*....|...
gi 93102371     129 PDSPEYKAACKLWDLYLRTRNEF 151
Cdd:smart00297   85 PDSEVYKDAKKLEKFFEKKLREL 107
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 407-621 1.18e-25

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 110.67  E-value: 1.18e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  407 PFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKE 486
Cdd:COG5076  168 IFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEE 247

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  487 LARRDDiedgdsmissatsdtGSAKRKSKKNIRKQRMKILFNVVLEAREpgsgrrlcDLFMVKPSKKDYPDYYKIILEPM 566
Cdd:COG5076  248 IPEEML---------------ELSIKPGREEREERESVLITNSQAHVGA--------WPFLRPVSDEEVPDYYKDIRDPM 304

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 93102371  567 DLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEK 621
Cdd:COG5076  305 DLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANVLEDFVIKK 359
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 659-760 1.52e-25

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 102.14  E-value: 1.52e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  659 QQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTY 738
Cdd:cd05518    2 KKRMLALFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHY 81

                         90       100
                 ....*....|....*....|..
gi 93102371  739 NEPESLIYKDALVLHKVLLETR 760
Cdd:cd05518   82 NEEGSQVYEDANILEKVLKEKR 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 657-760 1.72e-25

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 102.03  E-value: 1.72e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  657 PMQQklneVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNAC 736
Cdd:cd05520    4 PLWQ----LYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAK 79

                         90       100
                 ....*....|....*....|....
gi 93102371  737 TYNEPESLIYKDALVLHKVLLETR 760
Cdd:cd05520   80 RYNVPNSRIYKDAEKLQKLMQAKK 103
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 540-621 1.74e-25

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 102.07  E-value: 1.74e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  540 RRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLK 619
Cdd:cd04369   17 RDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFE 96


                 ..
gi 93102371  620 EK 621
Cdd:cd04369   97 KL 98
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 182-280 1.91e-25

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 102.12  E-value: 1.91e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  182 LKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKT 261
Cdd:cd05516    2 LTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQT 81

                         90
                 ....*....|....*....
gi 93102371  262 YNEPGSQVFKDANSIKKIF 280
Cdd:cd05516   82 FNLEGSLIYEDSIVLQSVF 100
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 188-284 2.74e-25

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 101.65  E-value: 2.74e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  188 QLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGS 267
Cdd:cd05520    7 QLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNS 86

                         90
                 ....*....|....*..
gi 93102371  268 QVFKDANSIKKIFYMKK 284
Cdd:cd05520   87 RIYKDAEKLQKLMQAKK 103
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 182-284 6.91e-25

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 100.60  E-value: 6.91e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  182 LKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKT 261
Cdd:cd05518    1 RKKRMLALFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARH 80

                         90       100
                 ....*....|....*....|...
gi 93102371  262 YNEPGSQVFKDANSIKKIFYMKK 284
Cdd:cd05518   81 YNEEGSQVYEDANILEKVLKEKR 103
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 658-758 1.17e-24

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 99.75  E-value: 1.17e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  658 MQQKLNEVYEAVKnytdKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 737
Cdd:cd04369    1 LKKKLRSLLDALK----KLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKT 76

                         90       100
                 ....*....|....*....|.
gi 93102371  738 YNEPESLIYKDALVLHKVLLE 758
Cdd:cd04369   77 YNGPGSPIYKDAKKLEKLFEK 97
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 51-143 1.67e-24

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 99.34  E-value: 1.67e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   51 HELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPD 130
Cdd:cd05520    6 WQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPN 85

                         90
                 ....*....|...
gi 93102371  131 SPEYKAACKLWDL 143
Cdd:cd05520   86 SRIYKDAEKLQKL 98
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 182-280 1.91e-24

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 99.34  E-value: 1.91e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  182 LKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKT 261
Cdd:cd05519    1 LKAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANART 80

                         90
                 ....*....|....*....
gi 93102371  262 YNEPGSQVFKDANSIKKIF 280
Cdd:cd05519   81 YNQEGSIVYEDAVEMEKAF 99
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 388-487 4.81e-24

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 98.56  E-value: 4.81e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  388 QLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNS 467
Cdd:cd05524    9 ELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDS 88

                         90       100
                 ....*....|....*....|
gi 93102371  468 AIYKRVLKLQQVMQAKKKEL 487
Cdd:cd05524   89 PEHKDACKLWELFLSARNEV 108
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 520-622 6.49e-24

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 97.51  E-value: 6.49e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  520 KQRMKILFNVVLEAREPgSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARH 599
Cdd:cd05517    2 KQILEQLLEAVMTATDP-SGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKT 80

                         90       100
                 ....*....|....*....|...
gi 93102371  600 YNEEGSQVYNDAHILEKLLKEKR 622
Cdd:cd05517   81 FNEPGSQVYKDANAIKKIFTAKK 103
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 386-483 9.34e-24

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 97.06  E-value: 9.34e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  386 FYQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVP 465
Cdd:cd04369    1 LKKKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGP 80

                         90
                 ....*....|....*...
gi 93102371  466 NSAIYKRVLKLQQVMQAK 483
Cdd:cd04369   81 GSPIYKDAKKLEKLFEKL 98
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 10-280 1.34e-23

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 104.50  E-value: 1.34e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   10 SPSSSVSGDFDDGHHSVSTPGPSRKRRRLSNLPTVDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVS 89
Cdd:COG5076  107 LAIESVTPESGLGSLLMAHLKTSVKKRKTPKIEDELLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIK 186

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   90 QPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQKgeaddedddedgqdn 169
Cdd:COG5076  187 SPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEE--------------- 251

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  170 qgtvTEGSSPAYLKEILEQLLEAIVvaTNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMA 249
Cdd:COG5076  252 ----MLELSIKPGREEREERESVLI--TNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFV 325

                        250       260       270
                 ....*....|....*....|....*....|.
gi 93102371  250 KDIDLLAKNAKTYNEPGSQVFKDANSIKKIF 280
Cdd:COG5076  326 RDAKLFFDNCVMYNGEVTDYYKNANVLEDFV 356
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 393-478 1.95e-23

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 96.16  E-value: 1.95e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  393 VRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKR 472
Cdd:cd05522   13 LRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKD 92


                 ....*.
gi 93102371  473 VLKLQQ 478
Cdd:cd05522   93 AVLLEK 98
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 661-768 3.42e-23

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 95.86  E-value: 3.42e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  661 KLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNE 740
Cdd:cd05524    6 VCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYK 85

                         90       100
                 ....*....|....*....|....*...
gi 93102371  741 PESLIYKDALVLHKVLLETRRDLEGDED 768
Cdd:cd05524   86 PDSPEHKDACKLWELFLSARNEVLSGGE 113
BAH smart00439
Bromo adjacent homology domain;
957-1049 1.10e-22

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 94.67  E-value: 1.10e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     957 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSAEK---------------------------EVFKSDYYNKVPVSKILGK 1009
Cdd:smart00439    1 TISVGDFVLVEPDDADEPYYIGRIEEIFETKKNSeskmvrvrwfyrpeetvlekaalfdknEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 93102371    1010 CVVMFVKEYFKLCPENFRD-EDVFVCESRYSAKTKSFKKIK 1049
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSIGePDVFFCESAYDPEKGSFKKLP 121
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 388-483 1.21e-22

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 93.94  E-value: 1.21e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  388 QLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNS 467
Cdd:cd05519    7 EIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGS 86

                         90
                 ....*....|....*.
gi 93102371  468 AIYKRVLKLQQVMQAK 483
Cdd:cd05519   87 IVYEDAVEMEKAFKKK 102
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 523-622 1.56e-21

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 90.86  E-value: 1.56e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  523 MKILFNVVLEAREPgSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNE 602
Cdd:cd05520    5 LWQLYDTIRNARNN-QGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNV 83

                         90       100
                 ....*....|....*....|
gi 93102371  603 EGSQVYNDAHILEKLLKEKR 622
Cdd:cd05520   84 PNSRIYKDAEKLQKLMQAKK 103
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 384-484 1.70e-21

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 90.96  E-value: 1.70e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  384 NPFYQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYN 463
Cdd:cd05517    3 QILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82

                         90       100
                 ....*....|....*....|.
gi 93102371  464 VPNSAIYKRVLKLQQVMQAKK 484
Cdd:cd05517   83 EPGSQVYKDANAIKKIFTAKK 103
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 47-146 1.28e-20

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 88.20  E-value: 1.28e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   47 IAVCHELYNTIRDYKdeqgRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSY 126
Cdd:cd04369    2 KKKLRSLLDALKKLK----RDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTY 77

                         90       100
                 ....*....|....*....|
gi 93102371  127 YKPDSPEYKAACKLWDLYLR 146
Cdd:cd04369   78 NGPGSPIYKDAKKLEKLFEK 97
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 544-773 1.53e-20

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 95.64  E-value: 1.53e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  544 DLFMVKPSKKDYPDYYkiiLEPMDLKIIEHNIRNDKYagEEGMIEDMKLMF-----RNARHYNEEGSQVYNDA--HILEK 616
Cdd:COG5076   37 PNAPEEEGSKNLFQKQ---LKRMPKEYITSIVDDREP--GSMANVNDDLENvggitYSPFEKNRPESLRFDEIvfLAIES 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  617 LLKEKRKElGPLPDDDDMASPKLKlsrksgiSPKKSKYMTPMQQKLneVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDY 696
Cdd:COG5076  112 VTPESGLG-SLLMAHLKTSVKKRK-------TPKIEDELLYADNKA--IAKFKKQLFLRDGRFLSSIFLGLPSKREYPDY 181

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 93102371  697 YLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDLEGDEDSHVPN 773
Cdd:COG5076  182 YEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEMLELSIK 258
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 657-754 2.17e-20

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 87.68  E-value: 2.17e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  657 PMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNAC 736
Cdd:cd05522    1 PYEARIKNILKGLRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAK 80

                         90
                 ....*....|....*...
gi 93102371  737 TYNEPESLIYKDALVLHK 754
Cdd:cd05522   81 LYNENDSQEYKDAVLLEK 98
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 182-273 2.61e-20

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 86.60  E-value: 2.61e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371    182 LKEILEQLLEaivvatnpsgRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKT 261
Cdd:pfam00439    1 CLEILDKLME----------HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNART 70

                           90
                   ....*....|..
gi 93102371    262 YNEPGSQVFKDA 273
Cdd:pfam00439   71 YNGPGSVIYKAA 82
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 54-139 2.93e-20

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 86.60  E-value: 2.93e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     54 YNTIRDYKDEQGRllCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPE 133
Cdd:pfam00439    1 CLEILDKLMEHPI--AAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVI 78


                   ....*.
gi 93102371    134 YKAACK 139
Cdd:pfam00439   79 YKAAEK 84
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 388-479 7.97e-20

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 86.33  E-value: 7.97e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  388 QLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNS 467
Cdd:cd05516    8 KIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGS 87

                         90
                 ....*....|..
gi 93102371  468 AIYKRVLKLQQV 479
Cdd:cd05516   88 LIYEDSIVLQSV 99
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 659-755 1.17e-19

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 85.57  E-value: 1.17e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  659 QQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTY 738
Cdd:cd05517    2 KQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTF 81

                         90
                 ....*....|....*..
gi 93102371  739 NEPESLIYKDALVLHKV 755
Cdd:cd05517   82 NEPGSQVYKDANAIKKI 98
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 48-148 6.68e-19

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 83.59  E-value: 6.68e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   48 AVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYY 127
Cdd:cd05525    5 QVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYY 84

                         90       100
                 ....*....|....*....|.
gi 93102371  128 KPDSPEYKAACKLWDLYLRTR 148
Cdd:cd05525   85 GRKSPIGRDVCRLRKAYYQAK 105
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 546-625 9.10e-19

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 82.99  E-value: 9.10e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  546 FMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKEL 625
Cdd:cd05509   22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKEL 101
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 57-140 1.11e-18

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 82.67  E-value: 1.11e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   57 IRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKA 136
Cdd:cd05522   13 LRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKD 92


                 ....
gi 93102371  137 ACKL 140
Cdd:cd05522   93 AVLL 96
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 197-280 1.16e-18

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 82.67  E-value: 1.16e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  197 TNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSI 276
Cdd:cd05522   17 RDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLL 96


                 ....
gi 93102371  277 KKIF 280
Cdd:cd05522   97 EKEA 100
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 521-616 1.19e-18

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 82.67  E-value: 1.19e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  521 QRMKILFNVVLEAREPgSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHY 600
Cdd:cd05522    4 ARIKNILKGLRKERDE-NGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLY 82

                         90
                 ....*....|....*.
gi 93102371  601 NEEGSQVYNDAHILEK 616
Cdd:cd05522   83 NENDSQEYKDAVLLEK 98
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 48-147 2.50e-18

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 81.62  E-value: 2.50e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   48 AVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYY 127
Cdd:cd05519    3 AAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYN 82

                         90       100
                 ....*....|....*....|
gi 93102371  128 KPDSPEYKAACKLWDLYLRT 147
Cdd:cd05519   83 QEGSIVYEDAVEMEKAFKKK 102
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 53-140 3.05e-18

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 81.34  E-value: 3.05e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   53 LYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSP 132
Cdd:cd05518    8 LFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQ 87


                 ....*...
gi 93102371  133 EYKAACKL 140
Cdd:cd05518   88 VYEDANIL 95
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 402-471 6.50e-18

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 80.05  E-value: 6.50e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371    402 QLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYK 471
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 182-287 7.57e-18

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 80.44  E-value: 7.57e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  182 LKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNgsYKSIHAMAKDIDLLAKNAKT 261
Cdd:cd05521    2 LSKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARL 79

                         90       100
                 ....*....|....*....|....*.
gi 93102371  262 YNEPGSQVFKDANSIKKifYMKKAEI 287
Cdd:cd05521   80 YNTKGSVIYKYALILEK--YINDVII 103
BAH cd04370
BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). ...
 955-1049 8.84e-18

BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.


Pssm-ID: 239835 [Multi-domain]  Cd Length: 123  Bit Score: 80.90  E-value: 8.84e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  955 NSMYHVGDYVYVEPAE--ANLQPHIVCIERLWEDSA-------------------------EKEVFKSDYYNKVPVSKIL 1007
Cdd:cd04370    1 GITYEVGDSVYVEPDDsiKSDPPYIARIEELWEDTNgskqvkvrwfyrpeetpkglspfalRRELFLSDHLDEIPVESII 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 93102371 1008 GKCVVMFVKEYFKLC-PENFRDEDVFVCESRYSAKTKSFKKIK 1049
Cdd:cd04370   81 GKCKVLFVSEFEGLKqRPNKIDTDDFFCRLAYDPTTKEFKALE 123
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 51-151 1.99e-17

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 79.39  E-value: 1.99e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   51 HELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPD 130
Cdd:cd05516    7 NKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEG 86

                         90       100
                 ....*....|....*....|.
gi 93102371  131 SPEYKAACKLWDLYLRTRNEF 151
Cdd:cd05516   87 SLIYEDSIVLQSVFKSARQKI 107
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 402-488 8.37e-17

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 77.82  E-value: 8.37e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  402 QLIAE--------PFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRV 473
Cdd:cd05504   19 QLLVEivkhkdswPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAG 98

                         90
                 ....*....|....*
gi 93102371  474 LKLQQVMQAKKKELA 488
Cdd:cd05504   99 TRLQRFFIKRCRKLG 113
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 657-759 8.61e-17

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 77.36  E-value: 8.61e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  657 PMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMmaNKYQDIDSMVEDFVMMFNNAC 736
Cdd:cd05521    1 KLSKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRL--PHYTNAQEFVNDLAQIPWNAR 78

                         90       100
                 ....*....|....*....|...
gi 93102371  737 TYNEPESLIYKDALVLHKVLLET 759
Cdd:cd05521   79 LYNTKGSVIYKYALILEKYINDV 101
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 189-302 1.32e-16

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 83.70  E-value: 1.32e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  189 LLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQ 268
Cdd:COG5076  150 IAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSS 229

                         90       100       110
                 ....*....|....*....|....*....|....
gi 93102371  269 VFKDANSIKKIFYMKKAEIEHHEMAKSSLRMRTP 302
Cdd:COG5076  230 VYVDAKELEKYFLKLIEEIPEEMLELSIKPGREE 263
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 540-613 1.40e-16

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 76.20  E-value: 1.40e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 93102371    540 RRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHI 613
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAEK 84
BROMO smart00297
bromo domain;
779-879 3.96e-16

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 75.78  E-value: 3.96e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371     779 QELIHNLFVSVMSHQDDegRCYSDSLAEIPAVD--PNFPN--KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRM 854
Cdd:smart00297    5 QKKLQELLKAVLDKLDS--HPLSWPFLKPVSRKeaPDYYDiiKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTY 82

                            90       100
                    ....*....|....*....|....*
gi 93102371     855 NRTDSEIYEDAVELQQFFIKIRDEL 879
Cdd:smart00297   83 NGPDSEVYKDAKKLEKFFEKKLREL 107
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 389-478 9.78e-16

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 74.28  E-value: 9.78e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  389 LYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNqeYETLDHLECDLNLMFENAKRYNVPNSA 468
Cdd:cd05521    9 LYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLYNTKGSV 86

                         90
                 ....*....|
gi 93102371  469 IYKRVLKLQQ 478
Cdd:cd05521   87 IYKYALILEK 96
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 218-283 1.57e-15

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 73.74  E-value: 1.57e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 93102371  218 PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMK 283
Cdd:cd05509   32 PDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKK 97
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 386-487 1.60e-15

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 73.74  E-value: 1.60e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  386 FYQLYDTVRSCRNNQGqliAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVP 465
Cdd:cd05509    3 YTQLKKVLDSLKNHKS---AWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGP 79

                         90       100
                 ....*....|....*....|..
gi 93102371  466 NSAIYKRVLKLQQVMQAKKKEL 487
Cdd:cd05509   80 DTEYYKCANKLEKFFWKKLKEL 101
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 546-627 2.84e-15

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 73.58  E-value: 2.84e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  546 FMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKEL 625
Cdd:cd05504   33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRKL 112


                 ..
gi 93102371  626 GP 627
Cdd:cd05504  113 GL 114
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 386-479 3.24e-15

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 72.81  E-value: 3.24e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  386 FYQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVP 465
Cdd:cd05525    7 LKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGR 86

                         90
                 ....*....|....
gi 93102371  466 NSAIYKRVLKLQQV 479
Cdd:cd05525   87 KSPIGRDVCRLRKA 100
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 212-280 4.51e-15

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 72.36  E-value: 4.51e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371  212 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIF 280
Cdd:cd05506   27 VVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELLKIF 95
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 539-626 1.74e-14

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 71.21  E-value: 1.74e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  539 GRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLL 618
Cdd:cd05524   22 GRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWELF 101


                 ....*...
gi 93102371  619 KEKRKELG 626
Cdd:cd05524  102 LSARNEVL 109
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 678-749 4.39e-14

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 68.88  E-value: 4.39e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371    678 RRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDA 749
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAA 82
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 82-140 5.30e-14

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 69.12  E-value: 5.30e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371   82 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKL 140
Cdd:cd05509   32 PDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKL 90
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 202-280 5.85e-14

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 70.06  E-value: 5.85e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  202 RLISELFQ---------------KLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPG 266
Cdd:cd05529   28 RLISGLDKlllslqleiaeyfeyPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPN 107

                         90
                 ....*....|....
gi 93102371  267 SQVFKDANSIKKIF 280
Cdd:cd05529  108 SEIAKKAKRLSDWL 121
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 525-628 6.17e-14

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 69.60  E-value: 6.17e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  525 ILFNVVLEAR-EPGSgrrlcDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEE 603
Cdd:cd05511    4 ILDEIVNELKnLPDS-----WPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGP 78

                         90       100
                 ....*....|....*....|....*....
gi 93102371  604 GSQVYNDA-HIL---EKLLKEKRKELGPL 628
Cdd:cd05511   79 DSVYTKKAkEMLelaEELLAEREEKLTQL 107
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 180-285 7.28e-14

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 68.96  E-value: 7.28e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  180 AYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNA 259
Cdd:cd05525    1 ARLAQVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNA 80

                         90       100
                 ....*....|....*....|....*.
gi 93102371  260 KTYNEPGSQVFKDANSIKKIFYMKKA 285
Cdd:cd05525   81 EKYYGRKSPIGRDVCRLRKAYYQAKH 106
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 684-763 9.39e-14

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 68.96  E-value: 9.39e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  684 FLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 763
Cdd:cd05504   33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRKL 112
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 405-492 1.85e-13

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 68.06  E-value: 1.85e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  405 AEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKrvlKLQQVMQAKK 484
Cdd:cd05511   18 SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTK---KAKEMLELAE 94


                 ....*...
gi 93102371  485 KELARRDD 492
Cdd:cd05511   95 ELLAEREE 102
BAH cd04370
BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). ...
 1135-1247 1.92e-13

BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.


Pssm-ID: 239835 [Multi-domain]  Cd Length: 123  Bit Score: 68.57  E-value: 1.92e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371 1135 VGDCVFIK---SHGLVRPRVGRIEKVWVR-DGAAYFYGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGKCAV 1210
Cdd:cd04370    6 VGDSVYVEpddSIKSDPPYIARIEELWEDtNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESIIGKCKV 85

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 93102371 1211 LSFKDFLS-CRPTEIPENDILLCESRYNESDKQMKKFK 1247
Cdd:cd04370   86 LFVSEFEGlKQRPNKIDTDDFFCRLAYDPTTKEFKALE 123
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 789-867 2.01e-13

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 66.95  E-value: 2.01e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371    789 VMSHQDDEGRCYSDSLAEIPAVDPNFPN--KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAV 866
Cdd:pfam00439    4 ILDKLMEHPIAAPFLEPVDPDEYPDYYSviKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83


                   .
gi 93102371    867 E 867
Cdd:pfam00439   84 K 84
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 399-483 3.00e-13

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 67.30  E-value: 3.00e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  399 NQGQLIAEPFYHL--PSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKL 476
Cdd:cd05498   15 KKHKAYAWPFYKPvdPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKL 94


                 ....*..
gi 93102371  477 QQVMQAK 483
Cdd:cd05498   95 QDVFEDR 101
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 550-630 3.24e-13

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 67.32  E-value: 3.24e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  550 PSKKDYPDYYKIILEPMDLKIIEHNIR---NDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKELg 626
Cdd:cd05502   28 PVSPSVPNYYKIIKTPMDLSLIRKKLQpksPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQLKEI- 106


                 ....
gi 93102371  627 pLPD 630
Cdd:cd05502  107 -LPD 109
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 202-287 4.09e-13

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 66.93  E-value: 4.09e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  202 RLISELF-QKL------PSKVQYPDYYAIIKEPIDLKTIAQRIQNGS---YKSIHAMAKDIDLLAKNAKTYNEPGSQVFK 271
Cdd:cd05502   11 RLLLELYcHELslpfhePVSPSVPNYYKIIKTPMDLSLIRKKLQPKSpqhYSSPEEFVADVRLMFKNCYKFNEEDSEVAQ 90

                         90
                 ....*....|....*.
gi 93102371  272 DANSIKKIFYMKKAEI 287
Cdd:cd05502   91 AGKELELFFEEQLKEI 106
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 218-283 5.57e-13

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 66.54  E-value: 5.57e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 93102371  218 PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMK 283
Cdd:cd05499   36 PNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDK 101
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 520-621 7.36e-13

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 66.19  E-value: 7.36e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  520 KQRMKILFNVVLEAREPgSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNdkYAGEEGMIEDMKLMFRNARH 599
Cdd:cd05521    3 SKKLKPLYDGIYTLKEE-NGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARL 79

                         90       100
                 ....*....|....*....|..
gi 93102371  600 YNEEGSQVYNDAHILEKLLKEK 621
Cdd:cd05521   80 YNTKGSVIYKYALILEKYINDV 101
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 548-625 1.10e-12

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 65.91  E-value: 1.10e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 93102371  548 VKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEKRKEL 625
Cdd:cd05497   30 VDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLAQM 107
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 688-755 1.13e-12

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 65.76  E-value: 1.13e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 93102371  688 PSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKV 755
Cdd:cd05498   30 PEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDV 97
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 186-271 1.16e-12

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 65.88  E-value: 1.16e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  186 LEQLLEAIVVATNpsgrliSELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEP 265
Cdd:cd05504   17 LEQLLVEIVKHKD------SWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPE 90


                 ....*.
gi 93102371  266 GSQVFK 271
Cdd:cd05504   91 HTSVYK 96
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 655-755 1.44e-12

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 65.41  E-value: 1.44e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  655 MTPMQQKLneVYEAVKNYtdKRGRrlSAIFLRLPS---RSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMM 731
Cdd:cd05500    1 MTKHQHKF--LLSSIRSL--KRLK--DARPFLVPVdpvKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLM 74

                         90       100
                 ....*....|....*....|....
gi 93102371  732 FNNACTYNEPESLIYKDALVLHKV 755
Cdd:cd05500   75 VDNCLTFNGPEHPVSQMGKRLQAA 98
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 1314-1379 2.45e-12

high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal proteins NHP6A, NHP6B and similar proteins; This subfamily includes Saccharomyces cerevisiae high-mobility-group proteins NHP6A and its closely related paralog NHP6B. NHP6A and NHP6B seem to be functionally redundant. They are DNA-binding proteins that induce severe bending of DNA and are required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. They augment the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex. They may also play essential roles in transcriptional initiation fidelity of some but not all tRNA genes.


Pssm-ID: 438792 [Multi-domain]  Cd Length: 81  Bit Score: 63.93  E-value: 2.45e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 93102371 1314 KSAKGSAKKEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGM 1379
Cdd:cd01390    1 KKKKGRKKKDPNAPKRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEK 66
BAH_BAHCC1 cd04714
BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. ...
 1133-1237 5.43e-12

BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240065  Cd Length: 121  Bit Score: 64.35  E-value: 5.43e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371 1133 LKVGDCVFIKSHGLVR-PRVGRIEKVWVRDGAA------YFYgpifiHPEETEHEPTKMFYKKEVFLSNLEETCPMTCIL 1205
Cdd:cd04714    4 IRVGDCVLFKSPGRPSlPYVARIESLWEDPEGNmvvrvkWYY-----RPEETKGGRKPNHGEKELFASDHQDENSVQTIE 78

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 93102371 1206 GKCAVLSFKDF---LSCRPTEIPENDILLCESRYN 1237
Cdd:cd04714   79 HKCYVLTFAEYerlARVKKKPQDGVDFYYCAGTYN 113
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 205-290 6.18e-12

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 63.82  E-value: 6.18e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  205 SELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKK 284
Cdd:cd05511   18 SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLELAEELL 97


                 ....*.
gi 93102371  285 AEIEHH 290
Cdd:cd05511   98 AEREEK 103
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 556-621 7.63e-12

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 63.07  E-value: 7.63e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 93102371  556 PDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEK 621
Cdd:cd05499   36 PNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDK 101
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 214-286 9.11e-12

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 63.21  E-value: 9.11e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 93102371  214 KVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAE 286
Cdd:cd05497   34 KLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLAQ 106
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 692-758 9.38e-12

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 63.21  E-value: 9.38e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 93102371  692 ELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLE 758
Cdd:cd05497   36 NLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQ 102
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 546-622 9.98e-12

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 62.78  E-value: 9.98e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 93102371  546 FMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLkEKR 622
Cdd:cd05503   21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFF-EKR 96
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 205-278 1.32e-11

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 62.84  E-value: 1.32e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 93102371  205 SELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKD-ANSIKK 278
Cdd:cd05510   26 STPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPLRRhANFMKK 100
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 684-755 1.56e-11

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 62.19  E-value: 1.56e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371  684 FLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKV 755
Cdd:cd05509   22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKF 93
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 688-758 1.73e-11

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 62.46  E-value: 1.73e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 93102371  688 PSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLE 758
Cdd:cd05495   31 PKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQ 101
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 212-280 2.00e-11

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 61.95  E-value: 2.00e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371  212 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIF 280
Cdd:cd05500   31 PVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAAF 99
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 548-621 2.61e-11

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 61.58  E-value: 2.61e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 93102371  548 VKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEK 621
Cdd:cd05506   25 VDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELLKIFETR 98
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 412-479 3.83e-11

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 61.18  E-value: 3.83e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 93102371  412 PSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQV 479
Cdd:cd05500   31 PVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAA 98
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 548-621 4.29e-11

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 61.14  E-value: 4.29e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 93102371  548 VKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLKEK 621
Cdd:cd05498   28 VDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101
HMG smart00398
high mobility group;
1326-1379 5.77e-11

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 59.64  E-value: 5.77e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 93102371    1326 KRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGM 1379
Cdd:smart00398    1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEK 54
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 212-283 6.92e-11

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 60.37  E-value: 6.92e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371  212 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMK 283
Cdd:cd05498   30 PEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1331-1377 8.17e-11

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 58.68  E-value: 8.17e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 93102371 1331 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYE 1377
Cdd:cd00084    3 LSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYE 49
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 404-476 9.49e-11

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 60.81  E-value: 9.49e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 93102371  404 IAEPF-YHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKL 476
Cdd:cd05529   44 IAEYFeYPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRL 117
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 216-263 1.06e-10

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 60.45  E-value: 1.06e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 93102371  216 QYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYN 263
Cdd:cd05528   32 EVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 418-483 1.67e-10

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 59.22  E-value: 1.67e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 93102371  418 PDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAK 483
Cdd:cd05499   36 PNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDK 101
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 548-616 2.19e-10

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 59.25  E-value: 2.19e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371  548 VKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEK 616
Cdd:cd05500   29 VDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQA 97
HMG_box pfam00505
HMG (high mobility group) box;
1328-1379 3.22e-10

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 57.62  E-value: 3.22e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 93102371   1328 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGM 1379
Cdd:pfam00505    2 KRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEK 53
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 76-140 3.63e-10

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 58.48  E-value: 3.63e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 93102371   76 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKL 140
Cdd:cd05500   31 PVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRL 95
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 694-749 5.65e-10

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 57.81  E-value: 5.65e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 93102371  694 PDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDA 749
Cdd:cd05513   32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAA 87
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 216-284 5.86e-10

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 57.77  E-value: 5.86e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371  216 QYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKiFYMKK 284
Cdd:cd05503   29 LVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRK-FFEKR 96
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 212-280 6.65e-10

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 57.84  E-value: 6.65e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371  212 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIF 280
Cdd:cd05495   31 PKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVF 99
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 82-143 6.78e-10

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 57.41  E-value: 6.78e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371   82 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDL 143
Cdd:cd05512   32 PDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLRDQ 93
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 693-749 6.95e-10

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 58.04  E-value: 6.95e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 93102371  693 LPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDA 749
Cdd:cd05511   30 VPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKA 86
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 399-477 1.17e-09

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 57.02  E-value: 1.17e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371  399 NQGQLIAEPFyhlpSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQ 477
Cdd:cd05512   17 DTAEIFSEPV----DLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLR 91
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 658-760 1.22e-09

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 57.01  E-value: 1.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  658 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 737
Cdd:cd05525    3 LAQVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEK 82

                         90       100
                 ....*....|....*....|...
gi 93102371  738 YNEPESLIYKDALVLHKVLLETR 760
Cdd:cd05525   83 YYGRKSPIGRDVCRLRKAYYQAK 105
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 76-146 1.25e-09

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 57.07  E-value: 1.25e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 93102371   76 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLR 146
Cdd:cd05495   31 PKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQ 101
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 72-140 1.48e-09

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 57.02  E-value: 1.48e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371   72 FIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKL 140
Cdd:cd05504   33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRL 101
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 405-482 2.35e-09

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 56.30  E-value: 2.35e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  405 AEPFYHL--PSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQA 482
Cdd:cd05495   22 SLPFRQPvdPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQ 101
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 680-754 2.44e-09

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 56.15  E-value: 2.44e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 93102371  680 LSAIFLRlPSRSELPDYYLTIKKPMDMEKIRSHM---MANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHK 754
Cdd:cd05502   21 LSLPFHE-PVSPSVPNYYKIIKTPMDLSLIRKKLqpkSPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELEL 97
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 521-617 2.66e-09

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 56.24  E-value: 2.66e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  521 QRMKILFNVVLEAREPgSGRRLCDLFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHY 600
Cdd:cd05525    5 QVLKEICDAIITYKDS-NGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKY 83

                         90
                 ....*....|....*..
gi 93102371  601 NEEGSQVYNDAHILEKL 617
Cdd:cd05525   84 YGRKSPIGRDVCRLRKA 100
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 691-752 2.87e-09

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 55.87  E-value: 2.87e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371  691 SELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVL 752
Cdd:cd05512   29 SEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRL 90
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 688-755 3.38e-09

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 55.75  E-value: 3.38e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 93102371  688 PSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKV 755
Cdd:cd05499   30 PVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEV 97
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 688-741 3.72e-09

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 55.41  E-value: 3.72e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 93102371  688 PSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEP 741
Cdd:cd05506   27 VVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPP 80
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 692-754 3.77e-09

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 55.46  E-value: 3.77e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 93102371  692 ELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHK 754
Cdd:cd05503   29 LVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRK 91
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 1331-1376 4.49e-09

high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; The HMG20 subfamily includes HMG20A and HMG20B. HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1, HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B. HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2, HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex. Both HMG20A and HMG20B contain one HMG-box.


Pssm-ID: 438796 [Multi-domain]  Cd Length: 81  Bit Score: 54.48  E-value: 4.49e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 93102371 1331 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEY 1376
Cdd:cd21980    6 LTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKY 51
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 548-608 4.65e-09

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 55.53  E-value: 4.65e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 93102371  548 VKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVY 608
Cdd:cd05495   29 VDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVY 89
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 53-137 6.24e-09

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 55.02  E-value: 6.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   53 LYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKmeEYDDVNLLTADFQLLFNNAKSYYKPDSP 132
Cdd:cd05521    9 LYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYNTKGSV 86


                 ....*
gi 93102371  133 EYKAA 137
Cdd:cd05521   87 IYKYA 91
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 405-489 7.98e-09

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 55.14  E-value: 7.98e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  405 AEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLklqQVMQAKK 484
Cdd:cd05510   26 STPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPLRRHA---NFMKKKA 102


                 ....*
gi 93102371  485 KELAR 489
Cdd:cd05510  103 EHLLK 107
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 82-144 8.24e-09

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 54.59  E-value: 8.24e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 93102371   82 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLY 144
Cdd:cd05498   36 HDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVF 98
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 82-140 8.64e-09

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 54.34  E-value: 8.64e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371   82 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKL 140
Cdd:cd05513   32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 90
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 546-608 1.39e-08

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 54.37  E-value: 1.39e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 93102371  546 FMVKPSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVY 608
Cdd:cd05510   29 FLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPL 91
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 555-618 1.51e-08

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 54.65  E-value: 1.51e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 93102371  555 YPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLL 618
Cdd:cd05529   58 YPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWL 121
HMG-box_AtSSRP1 cd22013
high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and ...
 1320-1379 1.81e-08

high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and similar proteins; SSRP1, also called facilitates chromatin transcription complex subunit SSRP1, high mobility group B protein 8, nucleosome/chromatin assembly factor group D 08 (or D 8), protein NUCLEAR FUSION DEFECTIVE 8, or recombination signal sequence recognition protein 1, is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair. SSRP1 may bind specifically to double-stranded DNA. It is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. SSRP1 contains only one HMG-box domain.


Pssm-ID: 438829 [Multi-domain]  Cd Length: 80  Bit Score: 52.94  E-value: 1.81e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371 1320 AKKEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGM 1379
Cdd:cd22013    2 KKKDPNAPKRALSGFMFFSLMERENLKKEKPGISFGEVGKVLGEKWKNMSADDKAPYEAK 61
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 183-263 2.48e-08

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 53.62  E-value: 2.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  183 KEILEQLLEAIVVATNpsgrliSELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTY 262
Cdd:cd05496    7 KKQCKELVNLMWDCED------SEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSY 80


                 .
gi 93102371  263 N 263
Cdd:cd05496   81 T 81
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 550-607 3.46e-08

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 52.54  E-value: 3.46e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 93102371  550 PSKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQV 607
Cdd:cd05505   25 VTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYV 82
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 66-140 5.21e-08

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 52.68  E-value: 5.21e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   66 RLLCELFIRAPKRRNQ-------PDYYEVVSQPIDLMKIQQKLKMEE---YDDVNLLTADFQLLFNNAKSYYKPDSPEYK 135
Cdd:cd05502   11 RLLLELYCHELSLPFHepvspsvPNYYKIIKTPMDLSLIRKKLQPKSpqhYSSPEEFVADVRLMFKNCYKFNEEDSEVAQ 90


                 ....*
gi 93102371  136 AACKL 140
Cdd:cd05502   91 AGKEL 95
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 407-487 5.52e-08

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 52.29  E-value: 5.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  407 PFyHLPSKKKYPDYYQQIKMPISLQQIRTKLK---NQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAK 483
Cdd:cd05502   24 PF-HEPVSPSVPNYYKIIKTPMDLSLIRKKLQpksPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQ 102


                 ....
gi 93102371  484 KKEL 487
Cdd:cd05502  103 LKEI 106
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 407-478 1.14e-07

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 51.38  E-value: 1.14e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371  407 PFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQ 478
Cdd:cd05505   20 PFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYVLSCMRKTEQ 91
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 1331-1379 1.32e-07

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.


Pssm-ID: 438810 [Multi-domain]  Cd Length: 67  Bit Score: 49.99  E-value: 1.32e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 93102371 1331 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGM 1379
Cdd:cd21994    3 MSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQK 51
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 218-273 1.42e-07

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 50.87  E-value: 1.42e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 93102371  218 PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDA 273
Cdd:cd05513   32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAA 87
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 657-743 1.80e-07

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 50.90  E-value: 1.80e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  657 PMQQKLNEVYEAVKNYTDKrgrrlSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNAC 736
Cdd:cd05510    7 EFYESLDKVLNELKTYTEH-----STPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCL 81


                 ....*..
gi 93102371  737 TYNEPES 743
Cdd:cd05510   82 LYNSDPS 88
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 76-144 1.87e-07

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 50.75  E-value: 1.87e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371   76 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLY 144
Cdd:cd05499   30 PVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVF 98
HMG-box_HMG20B cd22018
high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar ...
 1328-1376 2.47e-07

high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar proteins; HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2 (HMGXB2), HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex.


Pssm-ID: 438834 [Multi-domain]  Cd Length: 85  Bit Score: 49.97  E-value: 2.47e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 93102371 1328 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEY 1376
Cdd:cd22018    3 KAPVTGYVRFLNERREQIRTQHPDLPFPEITKMLGAEWSKLQPHEKQRY 51
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 208-269 2.50e-07

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 50.23  E-value: 2.50e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371  208 FQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQV 269
Cdd:cd05505   21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYV 82
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 418-479 2.86e-07

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 50.10  E-value: 2.86e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371  418 PDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQV 479
Cdd:cd05513   32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKLLHS 93
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
 1103-1245 3.53e-07

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 51.43  E-value: 3.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371 1103 EKEKEDVPVEMSNGEPGCHYFEQLHYNDMWLkvgdcvfikshglvrprvGRIEKVWVRDGAAYFYGPIFIHPEETEHEPT 1182
Cdd:cd04718   25 EVEKSGQSAMPQLPPTSRSACEKLLSGDLWL------------------ARIEKLWEENGTYWYAARWYTLPEETHMGRQ 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 93102371 1183 KMFYKKEVFLSNLEETCPMTCILGKCAVLSFKDFlscRPTEIPENDILLCESRYNESDKQMKK 1245
Cdd:cd04718   87 PHNLRRELYLTNDFADIEMECILRHCSVKCPKEF---RDASNDGDDVFLCEYEYDVHWQSFKR 146
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 418-483 3.70e-07

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 50.05  E-value: 3.70e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  418 PDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPN----SAIYKRVLKLQQVMQAK 483
Cdd:cd05528   34 PDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRdpadKLIRSRACELRDEVHAM 103
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 405-469 4.09e-07

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 49.68  E-value: 4.09e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 93102371  405 AEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAI 469
Cdd:cd05503   18 AWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEV 82
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 404-487 4.11e-07

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 49.73  E-value: 4.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  404 IAEPFYHL--PSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDhlEC--DLNLMFENAKRYNVPNSAIYKRVLKLQQV 479
Cdd:cd05497   22 FAWPFQQPvdAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSAS--ECiqDFNTMFTNCYIYNKPGDDVVLMAQTLEKL 99


                 ....*...
gi 93102371  480 MQAKKKEL 487
Cdd:cd05497  100 FLQKLAQM 107
HMG-box_ROX1-like cd01389
high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar ...
 1334-1377 4.90e-07

high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar proteins; This family includes class I members of the HMG-box superfamily of DNA-binding proteins, including Saccharomyces cerevisiae repressor ROX1, Schizosaccharomyces pombe mating-type M-specific polypeptide Mc (mat-Mc), Schizosaccharomyces pombe transcription factor ste11, Podospora anserina MAT+ sexual cell fertilization-promoting factor (FPR1), Podospora anserina sporulation minus regulator 2 (SMR2) and Candida albicans repressor of filamentous growth 1 (RFG1). These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. ROX1, also called heme-dependent repression factor, or hypoxic function repressor, is a transcription factor that represses the expression of HEM13, COX5B, ANB1, CYC7 or AAC3. It binds to the DNA sequence 5'-RRRTAACAAGAG-3'. mat-Mc belongs to the mating type protein family, which contains sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. mat-Mc is a positive regulator of MFM genes and is required for conjugation and efficient meiosis. Its HMG box recognizes the DNA sequence 5'-AACAAAG-3'. Ste11 is a key transcription factor for sexual development. It activates the transcription of the matp, matm, mei2, mfm, ste6 and rgs1 genes. It binds specifically to a DNA fragment carrying a 10-base motif 5'-TTCTTTGTTY-3'. FPR1 controls fertilization, probably by determining the mating type. SMR2 is a transcription factor that is required for post-fertilization events. It is required for the developmental events that occur in the female organ after fertilization. RFG1 is a transcription regulator that functions in both the positive and negative regulation of filamentous growth, depending upon environmental conditions.


Pssm-ID: 438791 [Multi-domain]  Cd Length: 72  Bit Score: 48.73  E-value: 4.90e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 93102371 1334 YILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYE 1377
Cdd:cd01389    8 FILFRKEKHKQLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYK 51
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 782-872 7.61e-07

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 49.16  E-value: 7.61e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  782 IHNLFVSVMSHQDDEGRCYSDSLAEIPavDPN-FPN-----KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRMN 855
Cdd:cd05522    6 IKNILKGLRKERDENGRLLTLHFEKLP--DKArEPEyyqeiSNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYN 83

                         90
                 ....*....|....*..
gi 93102371  856 RTDSEIYEDAVELQQFF 872
Cdd:cd05522   84 ENDSQEYKDAVLLEKEA 100
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 82-142 9.87e-07

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 48.89  E-value: 9.87e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 93102371   82 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKA----ACKLWD 142
Cdd:cd05528   34 PDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDPADKLirsrACELRD 98
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 679-745 1.08e-06

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 48.30  E-value: 1.08e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 93102371  679 RLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLI 745
Cdd:cd05505   16 RFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYV 82
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 72-131 1.14e-06

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 48.30  E-value: 1.14e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   72 FIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDS 131
Cdd:cd05505   21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 405-516 1.44e-06

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 48.61  E-value: 1.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  405 AEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNvPN--SAIYKRVLKLQQVMQA 482
Cdd:cd05496   23 SEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT-PNkrSRIYSMTLRLSALFEE 101

                         90       100       110
                 ....*....|....*....|....*....|....
gi 93102371  483 KkkelarrddiedgdsmISSATSDTGSAKRKSKK 516
Cdd:cd05496  102 H----------------IKKIISDWKSALKRNEK 119
HMG-box_TOX-like cd21995
high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family ...
 1332-1376 1.45e-06

high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family includes four members: TOX, TOX2, TOX3 and TOX4. TOX, also called thymus high mobility group box protein TOX, is a transcriptional regulator with a major role in neural stem cell commitment and corticogenesis as well as in lymphoid cell development and lymphoid tissue organogenesis. It binds to GC-rich DNA sequences in the proximity of transcription start sites and may alter chromatin structure, modifying access of transcription factors to DNA. TOX2, also called granulosa cell HMG box protein 1 (GCX-1), is a putative transcriptional activator involved in the hypothalamic-pituitary-gonadal system. TOX3, also called CAG trinucleotide repeat-containing gene F9 protein (CAGF9), or trinucleotide repeat-containing gene 9 protein (TNRC9), is a transcriptional coactivator of the p300/CBP-mediated transcription complex. It activates transactivation through cAMP response element (CRE) sites. It protects against cell death by inducing anti-apoptotic and repressing pro-apoptotic transcripts. TOX4, also called epidermal Langerhans cell protein LCP1, is a component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. All family members contain one HMG-box domain.


Pssm-ID: 438811 [Multi-domain]  Cd Length: 70  Bit Score: 47.09  E-value: 1.45e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 93102371 1332 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEY 1376
Cdd:cd21995    5 SAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLDEEQKQVY 49
BAH_Orc1p_like cd04715
BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of ...
 1122-1223 1.64e-06

BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240066  Cd Length: 159  Bit Score: 49.43  E-value: 1.64e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371 1122 YFEQLHYNDMWLKVGDCVFIKsHGLVRPRVGRIEKVW---VRDGAAYFYGPIFIHPEET--EHEPTKMFYKKEVFLS--- 1193
Cdd:cd04715   19 FYRSFTYDGVEYRLYDDVYVH-NGDSEPYIGKIIKIYetaIDSGKKKVKVIWFFRPSEIrmELKGEPKRHINEVFLAcgr 97

                         90       100       110
                 ....*....|....*....|....*....|...
gi 93102371 1194 --NLEETCPMTCILGKCAVLSF-KDFLSCRPTE 1223
Cdd:cd04715   98 geGLANINLLESIIGKCNVVCIsEDFRNPQPSD 130
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 205-276 1.83e-06

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 48.13  E-value: 1.83e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371  205 SELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSI 276
Cdd:cd05507   21 ASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAVEM 92
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 76-140 2.72e-06

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 47.32  E-value: 2.72e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 93102371   76 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKL 140
Cdd:cd05506   27 VVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKEL 91
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 556-611 2.89e-06

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 47.36  E-value: 2.89e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 93102371  556 PDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDA 611
Cdd:cd05507   34 PGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMA 89
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 662-874 3.03e-06

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 51.34  E-value: 3.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  662 LNEVYEAVKNYTDKRGRrlsaiFLRLPSRSELPDYYLtikKPMDMEKIRS-------HMMANKYQDidsmVEDFVMMFNN 734
Cdd:COG5076   22 GNELLRLVDNDSSPFPN-----APEEEGSKNLFQKQL---KRMPKEYITSivddrepGSMANVNDD----LENVGGITYS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  735 ACTYNEPESL-----------------IYKDALVLHKVLLETRRDLEGDEDSHVPNVTLLIQELIHNLFvsvmshqDDEG 797
Cdd:COG5076   90 PFEKNRPESLrfdeivflaiesvtpesGLGSLLMAHLKTSVKKRKTPKIEDELLYADNKAIAKFKKQLF-------LRDG 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  798 RCYSDsLAEIPAVDPNFPN-----KPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFF 872
Cdd:COG5076  163 RFLSS-IFLGLPSKREYPDyyeiiKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYF 241


                 ..
gi 93102371  873 IK 874
Cdd:COG5076  242 LK 243
HMG-box_HMG20A cd22017
high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar ...
 1322-1376 3.11e-06

high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar proteins; HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1 (HMGXB1), HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B.


Pssm-ID: 438833 [Multi-domain]  Cd Length: 104  Bit Score: 47.25  E-value: 3.11e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 93102371 1322 KEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEY 1376
Cdd:cd22017   16 RDSNAPKAPLTGYVRFMNERREQLRAERPDVPFPEITRMLGNEWSKLPAEEKQRY 70
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 520-625 3.12e-06

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 47.84  E-value: 3.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  520 KQRMKILFNVVLEAREPGSGRRLCDLFmvkpskkDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARH 599
Cdd:cd05496    7 KKQCKELVNLMWDCEDSEPFRQPVDLL-------KYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKS 79

                         90       100
                 ....*....|....*....|....*..
gi 93102371  600 YN-EEGSQVYNDAHILEKLLKEKRKEL 625
Cdd:cd05496   80 YTpNKRSRIYSMTLRLSALFEEHIKKI 106
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 218-263 3.32e-06

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 47.01  E-value: 3.32e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 93102371  218 PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYN 263
Cdd:cd05512   32 PDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN 77
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 551-619 3.45e-06

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 46.99  E-value: 3.45e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371  551 SKKDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAHILEKLLK 619
Cdd:cd05508   28 DLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAIVKICE 96
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 1332-1377 3.73e-06

second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of HMGB family and functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory response. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. The family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa. It is a tumor suppressor that is a major constituent of the promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomeres lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, is a Drosophila HMG1 protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438795 [Multi-domain]  Cd Length: 71  Bit Score: 45.87  E-value: 3.73e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 93102371 1332 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYE 1377
Cdd:cd21979    8 SAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYE 53
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 205-279 4.71e-06

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 46.61  E-value: 4.71e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 93102371  205 SELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKI 279
Cdd:cd05508   20 AEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAIVKI 94
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 1331-1376 5.74e-06

second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2), intrastrand cross-link recognition protein (Ixr1) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Both ABF2 and Ixr1 contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438828 [Multi-domain]  Cd Length: 64  Bit Score: 45.35  E-value: 5.74e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 93102371 1331 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEY 1376
Cdd:cd22012    6 ASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPY 51
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 390-481 7.22e-06

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 46.20  E-value: 7.22e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  390 YDTVRSCRNnqgqliAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAI 469
Cdd:cd05507   12 YRTLASHRY------ASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDV 85

                         90
                 ....*....|...
gi 93102371  470 YKRVLKLQQ-VMQ 481
Cdd:cd05507   86 YLMAVEMQReVMS 98
HMG-box_AtHMGB6-like_rpt2 cd22007
second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1331-1379 7.46e-06

second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438823 [Multi-domain]  Cd Length: 68  Bit Score: 45.32  E-value: 7.46e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 93102371 1331 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGM 1379
Cdd:cd22007    5 QSAYFLYANDRRAALKEENKNVKITEIAKMLGAEWKNLSDAKKKPYEEK 53
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 82-143 8.82e-06

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 46.10  E-value: 8.82e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371   82 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDL 143
Cdd:cd05511   31 PDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLEL 92
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 556-625 9.73e-06

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 45.86  E-value: 9.73e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  556 PDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEEGSQVYNDAhilEKLLKEKRKEL 625
Cdd:cd05513   32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAA---KKLLHSGMKIL 98
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 76-145 1.42e-05

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 45.49  E-value: 1.42e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   76 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYL 145
Cdd:cd05497   32 AVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFL 101
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 418-470 1.70e-05

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 45.01  E-value: 1.70e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 93102371  418 PDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIY 470
Cdd:cd05506   33 PDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVH 85
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 50-126 1.80e-05

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 45.51  E-value: 1.80e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 93102371   50 CHELYNTIRDYKDEQgrllcELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSY 126
Cdd:cd05510   12 LDKVLNELKTYTEHS-----TPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLY 83
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 50-126 2.76e-05

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 45.14  E-value: 2.76e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 93102371   50 CHELYNTIRDYKDEqgrllcELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSY 126
Cdd:cd05496   10 CKELVNLMWDCEDS------EPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSY 80
HMG-box_HMGXB4 cd21982
high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar ...
 1327-1373 3.00e-05

high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar proteins; HMGXB4, also called HMG box-containing protein 4, high mobility group protein 2-like 1 (HMG2L1), or protein HMGBCG, is a non-histone chromosomal protein that negatively regulates Wnt/beta-catenin signaling during development. It plays a role in the hematopoietic system.


Pssm-ID: 438798 [Multi-domain]  Cd Length: 61  Bit Score: 43.04  E-value: 3.00e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 93102371 1327 RKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKK 1373
Cdd:cd21982    1 KKKNMSAYQVFCKEYRVSIVAEHPGIDFGELSKKLAEVWKQLPEKDK 47
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 687-763 3.15e-05

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 45.02  E-value: 3.15e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 93102371  687 LPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDL 763
Cdd:cd05529   52 VDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLRILSSL 128
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 692-739 5.38e-05

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 43.89  E-value: 5.38e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 93102371  692 ELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYN 739
Cdd:cd05528   32 EVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 1326-1379 8.60e-05

HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail.


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 42.39  E-value: 8.60e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 93102371   1326 KRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGM 1379
Cdd:pfam09011    3 KPKRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEM 56
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 409-463 9.38e-05

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 43.19  E-value: 9.38e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 93102371  409 YHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYN 463
Cdd:cd05501   22 FFISKPYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFY 76
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 557-620 1.11e-04

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 42.80  E-value: 1.11e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 93102371  557 DYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYNEE---GSQVYNDAHILEKLLKE 620
Cdd:cd05501   32 DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDddfGQVGITLEKKFEKNFKE 98
BAH_BAHCC1 cd04714
BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. ...
 960-1043 1.17e-04

BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240065  Cd Length: 121  Bit Score: 43.16  E-value: 1.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  960 VGDYVYVEPAEANLQPHIVCIERLWEDSA-------------------------EKEVFKSDYYNKVPVSKILGKCVVMF 1014
Cdd:cd04714    6 VGDCVLFKSPGRPSLPYVARIESLWEDPEgnmvvrvkwyyrpeetkggrkpnhgEKELFASDHQDENSVQTIEHKCYVLT 85

                         90       100
                 ....*....|....*....|....*....
gi 93102371 1015 VKEYFKLCPENFRDEDVFVCesRYSAKTK 1043
Cdd:cd04714   86 FAEYERLARVKKKPQDGVDF--YYCAGTY 112
HMG-box_SOX cd22004
high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family ...
 1331-1376 1.91e-04

high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family transcription factors; The SOX gene family of transcription factors are characterized by the evolutionarily conserved SRY-type HMG box, which is a DNA binding domain that binds the minor groove of DNA on a common consensus site, (A/T)(A/T)CAA(A/T)G but with different levels of efficiency. Members include SRY and its homologs identified in mammals that can be subdivided into 8 groups (A, B1, B2, C, D, E, F, G, H). They are involved in embryonic development, regulating processes such as cell differentiation, maintenance of stemness, sex determination, and development of the central nervous, haematopoietic and other organ systems. The SOX gene family has a crucial role in carcinogenesis and cancer progression.


Pssm-ID: 438820 [Multi-domain]  Cd Length: 75  Bit Score: 41.38  E-value: 1.91e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 93102371 1331 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEY 1376
Cdd:cd22004    6 MNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPY 51
HMG-box_SMARCE1 cd21983
high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent ...
 1334-1376 2.09e-04

high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (SMARCE1) and similar proteins; SMARCE1, also called BRG1-associated factor 57 (BAF57), is a ubiquitously expressed protein involved in transcriptional activation and repression of select genes by chromatin remodeling. It is a component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. SMARCE1 has a single HMG domain that displays non-specific DNA-binding characteristics. It also contains a kinesin-like coiled-coil (KLCC) domain.


Pssm-ID: 438799 [Multi-domain]  Cd Length: 73  Bit Score: 41.13  E-value: 2.09e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 93102371 1334 YILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEY 1376
Cdd:cd21983   12 YMRYSRKVWDQVKASNPDLKLWEIGKIIGQMWRELSDEEKQEY 54
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1311-1377 2.30e-04

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 44.08  E-value: 2.30e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 93102371 1311 STPKSAKGSA-----KKEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYE 1377
Cdd:COG5648   50 TKPRKKTKSKrlvrkKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYY 121
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 554-601 2.37e-04

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 42.34  E-value: 2.37e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 93102371  554 DYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYN 601
Cdd:cd05528   32 EVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
HMG-box_AtHMGB9-like cd22009
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 ...
 1328-1378 3.63e-04

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 (HMGB9) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB9, 10, 11, and 15. They are DNA-binding proteins containing both HMG-box and AT-rich interaction domains. They bind preferentially to DNA with A/T-rich content. HMGB9 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily have only one HMG-box domain.


Pssm-ID: 438825 [Multi-domain]  Cd Length: 67  Bit Score: 40.14  E-value: 3.63e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 93102371 1328 KINMSGYILFSSEMRAVIKAQHPDYSfGELSRLVGTEWRNLETAKKAEYEG 1378
Cdd:cd22009    2 KPNRSGYNFFFAEQHARLKALYPGKD-REISKMIGEMWSNLTEEEKEVYQD 51
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 761-875 5.82e-04

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 41.55  E-value: 5.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  761 RDLEGDEDSHVPNVTLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVDPNFPNkpPLTFDIIRKNVENNRYRRLDLF 840
Cdd:cd05529   12 FDPGWEQPHIRDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRAWYPDYWNRVPV--PMDLETIRSRLENRYYRSLEAL 89

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 93102371  841 QeHMFEVLER-ARRMNRTDSEIYEDAVELQQFFIKI 875
Cdd:cd05529   90 R-HDVRLILSnAETFNEPNSEIAKKAKRLSDWLLRI 124
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 72-130 6.26e-04

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 40.87  E-value: 6.26e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 93102371   72 FIRAPKRRNqpDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPD 130
Cdd:cd05501   23 FISKPYYIR--DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD 79
HMG-box_AtHMGB6-like_rpt3 cd22008
third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1322-1382 8.95e-04

third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the third one.


Pssm-ID: 438824 [Multi-domain]  Cd Length: 78  Bit Score: 39.55  E-value: 8.95e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 93102371 1322 KEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGMMGG 1382
Cdd:cd22008    5 VDPNKPKKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAV 65
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 1331-1379 1.09e-03

fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins; UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the fourth one.


Pssm-ID: 438817 [Multi-domain]  Cd Length: 66  Bit Score: 38.82  E-value: 1.09e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 93102371 1331 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGM 1379
Cdd:cd22001    7 ISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKK 55
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 82-151 1.13e-03

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 40.78  E-value: 1.13e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371   82 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEF 151
Cdd:cd05529   59 PDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLRILSSL 128
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 1332-1376 1.58e-03

first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438827 [Multi-domain]  Cd Length: 75  Bit Score: 38.67  E-value: 1.58e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 93102371 1332 SGYILFSSEMRAVIKAQ-HPDYSFGELSRLVGTEWRNLETAKKAEY 1376
Cdd:cd22011    6 SAYFLFSQEIRKNLKSQgSPEEKVPELSKRAAEQWRSLTLAEKQPY 51
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
 980-1048 2.96e-03

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 39.88  E-value: 2.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 93102371  980 IERLWEDSA--------EKEVFKSDYYNKVPVSKILGKCVVMfvkeyfklCPENFRDE-----DVFVCESRYSAKTKSFK 1046
Cdd:cd04718   74 WYTLPEETHmgrqphnlRRELYLTNDFADIEMECILRHCSVK--------CPKEFRDAsndgdDVFLCEYEYDVHWQSFK 145


                 ..
gi 93102371 1047 KI 1048
Cdd:cd04718  146 RL 147
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 82-136 3.80e-03

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 38.51  E-value: 3.80e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 93102371   82 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKA 136
Cdd:cd05503   31 PGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRA 85
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 553-601 3.97e-03

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 38.15  E-value: 3.97e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 93102371  553 KDYPDYYKIILEPMDLKIIEHNIRNDKYAGEEGMIEDMKLMFRNARHYN 601
Cdd:cd05512   29 SEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN 77
HMG-box_AtHMGB1-like cd22005
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 ...
 1332-1379 6.59e-03

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 (HMGB1) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB1, 2, 3, 4, 5, 7, 12 and 14. They bind preferentially to double-stranded DNA. HMGB1 modulates general plant growth and stress tolerance and confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. HMGB2 and HMGB5 confer sensitivity to salt and drought stresses. HMGB7 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily contain only one HMG-box domain.


Pssm-ID: 438821 [Multi-domain]  Cd Length: 60  Bit Score: 36.52  E-value: 6.59e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 93102371 1332 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEYEGM 1379
Cdd:cd22005    5 TAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEK 52
HMG-box_BHMG1 cd21977
high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing ...
 1327-1376 8.60e-03

high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing protein 1 (BHMG1) and similar proteins; BHMG1 is an uncharacterized HMG-box containing protein that contains a degenerate basic motif not likely to bind DNA.


Pssm-ID: 438793 [Multi-domain]  Cd Length: 66  Bit Score: 36.53  E-value: 8.60e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 93102371 1327 RKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLETAKKAEY 1376
Cdd:cd21977    1 KKKWVNGFIMFCRLNRKNYIDKHPGLASTELTKELGQLWRELSAEEKKPY 50
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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