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Conserved domains on  [gi|47077080|dbj|BAD18469|]
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unnamed protein product, partial [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 428-539 3.84e-63

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: 202.20  E-value: 3.84e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 428 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 507
Cdd:cd05528   1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 47077080 508 DKDPGDKIIRHRACTLKDTAHAIIAAELDPEF 539
Cdd:cd05528  81 DRDPADKLIRSRACELRDEVHAMIEAELDPLF 112
RPT1 super family cl34191
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 1-100 1.05e-35

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


The actual alignment was detected with superfamily member COG1222:

Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 135.90  E-value: 1.05e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGAD 80
Cdd:COG1222 207 LDGFESRGDVLIIAATNRPDLLDPALLRPGRFDRVIEVPLPDEEAREEILKIHLRD-MPLADDVDLDKLAKLTEGFSGAD 285

                        90       100
                ....*....|....*....|
gi 47077080  81 IKALCTEAALIALRRRYPQI 100
Cdd:COG1222 286 LKAIVTEAGMFAIREGRDTV 305
COG5076 super family cl34891
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 320-519 2.60e-09

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


The actual alignment was detected with superfamily member COG5076:

Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 59.05  E-value: 2.60e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 320 LTLLQDIPSFS--PIFLLSTSETMYSELPEEVKcIFRIQYEEV-LYIQRPIEEDRRKFF-QELILNQASMAPPRRKHAAL 395
Cdd:COG5076  42 EEGSKNLFQKQlkRMPKEYITSIVDDREPGSMA-NVNDDLENVgGITYSPFEKNRPESLrFDEIVFLAIESVTPESGLGS 120

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 396 CAMEVLPLalPSPPRQLSESEKSRMEDQEENTLRELR-LFLRDVTKRlatdkrFNIFSKPVDIEEVSDYLEVIKEPMDLS 474
Cdd:COG5076 121 LLMAHLKT--SVKKRKTPKIEDELLYADNKAIAKFKKqLFLRDGRFL------SSIFLGLPSKREYPDYYEIIKSPMDLL 192

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*
gi 47077080 475 TVITKIDKHNYLTAKDFLKDIDLICSNALEYNpdkDPGDKIIRHR 519
Cdd:COG5076 193 TIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVDA 234
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 227-363 8.18e-05

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd19507:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 161  Bit Score: 43.13  E-value: 8.18e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 227 YHQPTsyrPR-LLLSGERGSGQtSHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARRTVPSIVYMPHI- 304
Cdd:cd19507  26 YGLPT---PKgLLLVGIQGTGK-SLTAKAIAGVW-QLPLLRLDMGRLFGGLVGESESRLRQMIQTAEAIAPCVLWIDEIe 100

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47077080 305 ---------GDwwEAVSETVRATFLTLLQDipSFSPIFLLSTSETMYSeLPEEVkcIFRIQYEEVLYI 363
Cdd:cd19507 101 kgfsnadskGD--SGTSSRVLGTFLTWLQE--KKKPVFVVATANNVQS-LPPEL--LRKGRFDEIFFV 161
 
Name Accession Description Interval E-value
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 428-539 3.84e-63

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: 202.20  E-value: 3.84e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 428 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 507
Cdd:cd05528   1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 47077080 508 DKDPGDKIIRHRACTLKDTAHAIIAAELDPEF 539
Cdd:cd05528  81 DRDPADKLIRSRACELRDEVHAMIEAELDPLF 112
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 1-100 1.05e-35

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 135.90  E-value: 1.05e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGAD 80
Cdd:COG1222 207 LDGFESRGDVLIIAATNRPDLLDPALLRPGRFDRVIEVPLPDEEAREEILKIHLRD-MPLADDVDLDKLAKLTEGFSGAD 285

                        90       100
                ....*....|....*....|
gi 47077080  81 IKALCTEAALIALRRRYPQI 100
Cdd:COG1222 286 LKAIVTEAGMFAIREGRDTV 305
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 1-137 5.05e-34

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 136.96  E-value: 5.05e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080     1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGAD 80
Cdd:TIGR01243 306 MDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGAD 384

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 47077080    81 IKALCTEAALIALRRRYPQiyassHKLQLDVSSI---VL-----SAQDFYHAMQNIVPASQRAVM 137
Cdd:TIGR01243 385 LAALAKEAAMAALRRFIRE-----GKINFEAEEIpaeVLkelkvTMKDFMEALKMVEPSAIREVL 444
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 1-100 4.24e-32

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 127.26  E-value: 4.24e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080    1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDWNPKlSDAFLGELAEKCVGYCGAD 80
Cdd:PRK03992 262 MDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLA-DDVDLEELAELTEGASGAD 340

                         90       100
                 ....*....|....*....|
gi 47077080   81 IKALCTEAALIALRRRYPQI 100
Cdd:PRK03992 341 LKAICTEAGMFAIRDDRTEV 360
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 1-38 1.35e-19

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 86.02  E-value: 1.35e-19
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 38
Cdd:cd19517 133 MDGLDNRGQVVVIGATNRPDALDPALRRPGRFDREFYF 170
BROMO smart00297
bromo domain;
428-526 1.95e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 80.79  E-value: 1.95e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080    428 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 507
Cdd:smart00297   5 QKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84

                           90
                   ....*....|....*....
gi 47077080    508 DkdpgDKIIRHRACTLKDT 526
Cdd:smart00297  85 P----DSEVYKDAKKLEKF 99
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 450-507 6.79e-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: 72.73  E-value: 6.79e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 47077080   450 IFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 507
Cdd:pfam00439  16 PFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNG 73
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 63-103 1.64e-10

AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.


Pssm-ID: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 56.39  E-value: 1.64e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 47077080    63 DAFLGELAEKCVGYCGADIKALCTEAALIALRRRYPQIYAS 103
Cdd:pfam17862   1 DVDLEELAERTEGFSGADLEALCREAALAALRRGLEAVTQE 41
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 320-519 2.60e-09

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 59.05  E-value: 2.60e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 320 LTLLQDIPSFS--PIFLLSTSETMYSELPEEVKcIFRIQYEEV-LYIQRPIEEDRRKFF-QELILNQASMAPPRRKHAAL 395
Cdd:COG5076  42 EEGSKNLFQKQlkRMPKEYITSIVDDREPGSMA-NVNDDLENVgGITYSPFEKNRPESLrFDEIVFLAIESVTPESGLGS 120

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 396 CAMEVLPLalPSPPRQLSESEKSRMEDQEENTLRELR-LFLRDVTKRlatdkrFNIFSKPVDIEEVSDYLEVIKEPMDLS 474
Cdd:COG5076 121 LLMAHLKT--SVKKRKTPKIEDELLYADNKAIAKFKKqLFLRDGRFL------SSIFLGLPSKREYPDYYEIIKSPMDLL 192

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*
gi 47077080 475 TVITKIDKHNYLTAKDFLKDIDLICSNALEYNpdkDPGDKIIRHR 519
Cdd:COG5076 193 TIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVDA 234
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 227-363 8.18e-05

ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of photosynthesis in cyanobacteria, especially in CO2 uptake and utilization. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410915 [Multi-domain]  Cd Length: 161  Bit Score: 43.13  E-value: 8.18e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 227 YHQPTsyrPR-LLLSGERGSGQtSHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARRTVPSIVYMPHI- 304
Cdd:cd19507  26 YGLPT---PKgLLLVGIQGTGK-SLTAKAIAGVW-QLPLLRLDMGRLFGGLVGESESRLRQMIQTAEAIAPCVLWIDEIe 100

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47077080 305 ---------GDwwEAVSETVRATFLTLLQDipSFSPIFLLSTSETMYSeLPEEVkcIFRIQYEEVLYI 363
Cdd:cd19507 101 kgfsnadskGD--SGTSSRVLGTFLTWLQE--KKKPVFVVATANNVQS-LPPEL--LRKGRFDEIFFV 161
 
Name Accession Description Interval E-value
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 428-539 3.84e-63

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: 202.20  E-value: 3.84e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 428 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 507
Cdd:cd05528   1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 47077080 508 DKDPGDKIIRHRACTLKDTAHAIIAAELDPEF 539
Cdd:cd05528  81 DRDPADKLIRSRACELRDEVHAMIEAELDPLF 112
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 1-100 1.05e-35

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 135.90  E-value: 1.05e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGAD 80
Cdd:COG1222 207 LDGFESRGDVLIIAATNRPDLLDPALLRPGRFDRVIEVPLPDEEAREEILKIHLRD-MPLADDVDLDKLAKLTEGFSGAD 285

                        90       100
                ....*....|....*....|
gi 47077080  81 IKALCTEAALIALRRRYPQI 100
Cdd:COG1222 286 LKAIVTEAGMFAIREGRDTV 305
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 1-137 5.05e-34

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 136.96  E-value: 5.05e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080     1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGAD 80
Cdd:TIGR01243 306 MDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGAD 384

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 47077080    81 IKALCTEAALIALRRRYPQiyassHKLQLDVSSI---VL-----SAQDFYHAMQNIVPASQRAVM 137
Cdd:TIGR01243 385 LAALAKEAAMAALRRFIRE-----GKINFEAEEIpaeVLkelkvTMKDFMEALKMVEPSAIREVL 444
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 1-100 4.24e-32

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 127.26  E-value: 4.24e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080    1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDWNPKlSDAFLGELAEKCVGYCGAD 80
Cdd:PRK03992 262 MDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLA-DDVDLEELAELTEGASGAD 340

                         90       100
                 ....*....|....*....|
gi 47077080   81 IKALCTEAALIALRRRYPQI 100
Cdd:PRK03992 341 LKAICTEAGMFAIRDDRTEV 360
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 1-137 7.61e-28

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 118.09  E-value: 7.61e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080     1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDWnPKLSDAFLGELAEKCVGYCGAD 80
Cdd:TIGR01243 582 MDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSM-PLAEDVDLEELAEMTEGYTGAD 660

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 47077080    81 IKALCTEAALIALRRrypqIYASSHKLQLDVSS------IVLSAQDFYHAMQNIVPASQRAVM 137
Cdd:TIGR01243 661 IEAVCREAAMAALRE----SIGSPAKEKLEVGEeeflkdLKVEMRHFLEALKKVKPSVSKEDM 719
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
 1-100 8.72e-27

ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH. [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273520 [Multi-domain]  Cd Length: 495  Bit Score: 113.53  E-value: 8.72e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080     1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRdwNPKLS-DAFLGELAEKCVGYCGA 79
Cdd:TIGR01241 185 MDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAK--NKKLApDVDLKAVARRTPGFSGA 262

                          90       100
                  ....*....|....*....|.
gi 47077080    80 DIKALCTEAALIALRRRYPQI 100
Cdd:TIGR01241 263 DLANLLNEAALLAARKNKTEI 283
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
1-96 2.06e-26

ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 113.21  E-value: 2.06e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRdwNPKLS-DAFLGELAEKCVGYCGA 79
Cdd:COG0465 272 MDGFEGNEGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDVKGREAILKVHAR--KKPLApDVDLEVIARRTPGFSGA 349

                        90
                ....*....|....*..
gi 47077080  80 DIKALCTEAALIALRRR 96
Cdd:COG0465 350 DLANLVNEAALLAARRN 366
26Sp45 TIGR01242
26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an ...
 1-96 1.60e-25

26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an internal


Pssm-ID: 130309 [Multi-domain]  Cd Length: 364  Bit Score: 107.96  E-value: 1.60e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080     1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDWNPKlSDAFLGELAEKCVGYCGAD 80
Cdd:TIGR01242 253 LDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLA-EDVDLEAIAKMTEGASGAD 331

                          90
                  ....*....|....*.
gi 47077080    81 IKALCTEAALIALRRR 96
Cdd:TIGR01242 332 LKAICTEAGMFAIREE 347
ftsH CHL00176
cell division protein; Validated
 1-100 3.18e-25

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 109.75  E-value: 3.18e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080    1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRdwNPKL-SDAFLGELAEKCVGYCGA 79
Cdd:CHL00176 313 MDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHAR--NKKLsPDVSLELIARRTPGFSGA 390

                         90       100
                 ....*....|....*....|.
gi 47077080   80 DIKALCTEAALIALRRRYPQI 100
Cdd:CHL00176 391 DLANLLNEAAILTARRKKATI 411
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 1-100 4.52e-24

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 104.85  E-value: 4.52e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080    1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDWNPKlSDAFLGELAEKCVGYCGAD 80
Cdd:PTZ00361 314 LDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLA-EDVDLEEFIMAKDELSGAD 392

                         90       100
                 ....*....|....*....|
gi 47077080   81 IKALCTEAALIALRRRYPQI 100
Cdd:PTZ00361 393 IKAICTEAGLLALRERRMKV 412
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 1-100 1.67e-23

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 102.68  E-value: 1.67e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080   1 MDGLdnRGEIVVIGATNRLDSIDPALRRpgRFDREFLFNLPDQKARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGAD 80
Cdd:COG0464 285 MEEL--RSDVVVIAATNRPDLLDPALLR--RFDEIIFFPLPDAEERLEIFRIHLRK-RPLDEDVDLEELAEATEGLSGAD 359

                        90       100
                ....*....|....*....|
gi 47077080  81 IKALCTEAALIALRRRYPQI 100
Cdd:COG0464 360 IRNVVRRAALQALRLGREPV 379
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 428-531 1.61e-21

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: 89.35  E-value: 1.61e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 428 LRELRLFLRDVTKRLATDkRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 507
Cdd:cd04369   1 LKKKLRSLLDALKKLKRD-LSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNG 79

                        90       100
                ....*....|....*....|....
gi 47077080 508 DkdpgDKIIRHRACTLKDTAHAII 531
Cdd:cd04369  80 P----GSPIYKDAKKLEKLFEKLL 99
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 431-531 2.42e-20

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: 85.91  E-value: 2.42e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 431 LRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNpDKD 510
Cdd:cd05512   2 LEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN-AKD 80

                        90       100
                ....*....|....*....|..
gi 47077080 511 pgdkIIRHRACT-LKDTAHAII 531
Cdd:cd05512  81 ----TIFYRAAVrLRDQGGAIL 98
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 1-38 1.35e-19

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 86.02  E-value: 1.35e-19
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 38
Cdd:cd19517 133 MDGLDNRGQVVVIGATNRPDALDPALRRPGRFDREFYF 170
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 451-511 1.72e-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: 83.37  E-value: 1.72e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 47077080 451 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDP 511
Cdd:cd05509  22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTE 82
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
1-94 1.24e-18

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 89.32  E-value: 1.24e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080    1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDWnPKLSDAFLGELAEKCVGYCGAD 80
Cdd:PRK10733 282 MDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRV-PLAPDIDAAIIARGTPGFSGAD 360

                         90
                 ....*....|....
gi 47077080   81 IKALCTEAALIALR 94
Cdd:PRK10733 361 LANLVNEAALFAAR 374
BROMO smart00297
bromo domain;
428-526 1.95e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 80.79  E-value: 1.95e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080    428 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 507
Cdd:smart00297   5 QKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84

                           90
                   ....*....|....*....
gi 47077080    508 DkdpgDKIIRHRACTLKDT 526
Cdd:smart00297  85 P----DSEVYKDAKKLEKF 99
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 434-511 3.93e-18

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: 79.63  E-value: 3.93e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 434 FLRDVTKRLATDKRFNI---FSKPVDIE--EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPD 508
Cdd:cd05498   4 FCSGILKELFSKKHKAYawpFYKPVDPEalGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPP 83


                ...
gi 47077080 509 KDP 511
Cdd:cd05498  84 DHP 86
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 1-38 9.78e-18

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 80.80  E-value: 9.78e-18
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 38
Cdd:cd19503 128 MDGMSSRGKVVVIAATNRPDAIDPALRRPGRFDREVEI 165
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 1-97 9.41e-17

26S protease regulatory subunit 6B-like protein; Provisional


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 82.12  E-value: 9.41e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080    1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDWNpkLSDAF-LGELAEKCVGYCGA 79
Cdd:PTZ00454 276 MDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMN--LSEEVdLEDFVSRPEKISAA 353

                         90
                 ....*....|....*....
gi 47077080   80 DIKALCTEAALIALRR-RY 97
Cdd:PTZ00454 354 DIAAICQEAGMQAVRKnRY 372
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 450-507 6.79e-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: 72.73  E-value: 6.79e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 47077080   450 IFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 507
Cdd:pfam00439  16 PFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNG 73
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 451-506 2.46e-15

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: 71.91  E-value: 2.46e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 47077080 451 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 506
Cdd:cd05511  21 FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYN 76
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 440-511 5.04e-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: 70.82  E-value: 5.04e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 47077080 440 KRLATDKRFNIFSKPVDIE--EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDP 511
Cdd:cd05506  10 RKLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGND 83
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
1-94 8.48e-15

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 74.15  E-value: 8.48e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080   1 MDGLdnRGEIVVIGATNRLDSIDPALRRpgRFDREFLFNLPDQKARKHILQIHTRDWNPKLSDAfLGELAEKCVGYCGAD 80
Cdd:COG1223 129 LDGL--PSGSVVIAATNHPELLDSALWR--RFDEVIEFPLPDKEERKEILELNLKKFPLPFELD-LKKLAKKLEGLSGAD 203

                        90
                ....*....|....
gi 47077080  81 IKALCTEAALIALR 94
Cdd:COG1223 204 IEKVLKTALKKAIL 217
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 1-35 1.98e-14

first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r1-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410927 [Multi-domain]  Cd Length: 166  Bit Score: 71.31  E-value: 1.98e-14
                        10        20        30
                ....*....|....*....|....*....|....*
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDRE 35
Cdd:cd19519 128 MDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDRE 162
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 420-510 8.18e-14

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: 67.85  E-value: 8.18e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 420 MEDQEENTLRELRLFLRDVTKrlatdkrfniFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLIC 499
Cdd:cd05510   8 FYESLDKVLNELKTYTEHSTP----------FLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIW 77

                        90
                ....*....|.
gi 47077080 500 SNALEYNPDKD 510
Cdd:cd05510  78 KNCLLYNSDPS 88
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 430-511 8.88e-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: 64.61  E-value: 8.88e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 430 ELRlFLRDVTKRLATDKRFNI---FSKPVDieEVSD----YLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNA 502
Cdd:cd05499   1 ELK-FCEEVLKELMKPKHSAYnwpFLDPVD--PVALnipnYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNC 77


                ....*....
gi 47077080 503 LEYNPDKDP 511
Cdd:cd05499  78 YTFNPEGTD 86
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 451-509 1.02e-12

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: 64.79  E-value: 1.02e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 47077080 451 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDK 509
Cdd:cd05496  26 FRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNK 84
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 451-510 1.03e-11

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: 62.03  E-value: 1.03e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 451 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKD 510
Cdd:cd05504  33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHT 92
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 1-35 1.23e-11

ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. It is anchored to the cytoplasmic membrane such that the amino- and carboxy-termini are exposed to the cytoplasm. It presents a membrane-bound hexameric structure that is able to unfold and degrade protein substrates. It is comprised of an N-terminal transmembrane region and the larger C-terminal cytoplasmic region, which consists of an ATPase domain and a protease domain. This RecA-Like FTsH subfamily represents the ATPase domain, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410909 [Multi-domain]  Cd Length: 171  Bit Score: 63.41  E-value: 1.23e-11
                        10        20        30
                ....*....|....*....|....*....|....*
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDRE 35
Cdd:cd19501 134 MDGFESNTGVIVIAATNRPDVLDPALLRPGRFDRQ 168
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 1-34 1.47e-11

proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410910 [Multi-domain]  Cd Length: 171  Bit Score: 63.13  E-value: 1.47e-11
                        10        20        30
                ....*....|....*....|....*....|....
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19502 134 LDGFDPRGNIKVIMATNRPDILDPALLRPGRFDR 167
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 1-38 6.07e-11

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 60.76  E-value: 6.07e-11
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 38
Cdd:cd19481 121 LDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEVIEF 158
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 451-506 6.99e-11

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: 58.96  E-value: 6.99e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 47077080 451 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 506
Cdd:cd05513  22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYN 77
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 451-506 7.73e-11

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: 58.70  E-value: 7.73e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 47077080 451 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 506
Cdd:cd05505  21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY 76
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 1-34 1.10e-10

second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase domains; This subfamily includes the second of two ATPase domains of the molecular chaperone CDC48 in yeast and p97 or VCP in metazoans, Peroxisomal biogenesis factor 1 (PEX1) and -6 (PEX6), Valosin-containing protein-like ATPase (VAT), and nuclear VCP-like protein (NVL). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 59.99  E-value: 1.10e-10
                        10        20        30
                ....*....|....*....|....*....|....
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19511 122 LDGIESLKGVVVIAATNRPDMIDPALLRPGRLDK 155
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 63-103 1.64e-10

AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.


Pssm-ID: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 56.39  E-value: 1.64e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 47077080    63 DAFLGELAEKCVGYCGADIKALCTEAALIALRRRYPQIYAS 103
Cdd:pfam17862   1 DVDLEELAERTEGFSGADLEALCREAALAALRRGLEAVTQE 41
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 439-506 1.83e-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: 58.09  E-value: 1.83e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 439 TKRLaTDKRFniFSKPVDIEE--VSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 506
Cdd:cd05500  16 LKRL-KDARP--FLVPVDPVKlnIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFN 82
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 430-507 3.51e-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: 57.45  E-value: 3.51e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 430 ELRLFLRDVTKRLATDKRFNI-FSKPVD--IEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 506
Cdd:cd05495   3 ELRQALMPTLEKLYKQDPESLpFRQPVDpkLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYN 82


                .
gi 47077080 507 P 507
Cdd:cd05495  83 R 83
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 1-34 4.59e-10

second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ATPase domains; The Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), is an archaeal homolog of the ubiquitous Cdc48/p97. It is a protein unfoldase that functions in concert with the 20S proteasome by unfolding proteasome substrates and passing them on for degradation. VAT forms a homohexamer, each monomer contains two tandem ATPase domains, referred to as D1 and D2, and an N-terminal domain. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410937 [Multi-domain]  Cd Length: 159  Bit Score: 58.28  E-value: 4.59e-10
                        10        20        30
                ....*....|....*....|....*....|....
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19529 122 LDGLEEMNGVVVIAATNRPDIIDPALLRAGRFDR 155
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 1-35 7.21e-10

first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 58.18  E-value: 7.21e-10
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 47077080   1 MDGL----DNRGEIVVIGATNRLDSIDPALRRPGRFDRE 35
Cdd:cd19518 128 MDELnnekTAGGPVLVIGATNRPDSLDPALRRAGRFDRE 166
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 430-516 8.41e-10

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: 56.28  E-value: 8.41e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 430 ELRLFLRDVTKRLATDKRFNIFSKPVDIE--EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 507
Cdd:cd05497   5 QLQYLLKVVLKALWKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK 84


                ....*....
gi 47077080 508 dkdPGDKII 516
Cdd:cd05497  85 ---PGDDVV 90
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 451-511 1.35e-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: 1.35e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 47077080 451 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDP 511
Cdd:cd05503  21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSE 81
pup_AAA TIGR03689
proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some ...
 1-136 2.15e-09

proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 200312 [Multi-domain]  Cd Length: 512  Bit Score: 59.72  E-value: 2.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080     1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDWNPklsdaFLGELAEKcVGYCGAD 80
Cdd:TIGR03689 325 IDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKYLTDDLP-----LPEDLAAH-DGDREAT 398

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 47077080    81 IKALcteaaliaLRRRYPQIYASS---HKLQL---DVSSIVLSAQDFYH-AM-QNIVP-ASQRAV 136
Cdd:TIGR03689 399 AAAL--------IQRVVDALYARSeanRYVEVtyaNGSTEVLYFADFVSgAMlANIVDrAKKRAI 455
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 320-519 2.60e-09

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 59.05  E-value: 2.60e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 320 LTLLQDIPSFS--PIFLLSTSETMYSELPEEVKcIFRIQYEEV-LYIQRPIEEDRRKFF-QELILNQASMAPPRRKHAAL 395
Cdd:COG5076  42 EEGSKNLFQKQlkRMPKEYITSIVDDREPGSMA-NVNDDLENVgGITYSPFEKNRPESLrFDEIVFLAIESVTPESGLGS 120

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 396 CAMEVLPLalPSPPRQLSESEKSRMEDQEENTLRELR-LFLRDVTKRlatdkrFNIFSKPVDIEEVSDYLEVIKEPMDLS 474
Cdd:COG5076 121 LLMAHLKT--SVKKRKTPKIEDELLYADNKAIAKFKKqLFLRDGRFL------SSIFLGLPSKREYPDYYEIIKSPMDLL 192

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*
gi 47077080 475 TVITKIDKHNYLTAKDFLKDIDLICSNALEYNpdkDPGDKIIRHR 519
Cdd:COG5076 193 TIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVDA 234
ycf46 CHL00195
Ycf46; Provisional
 12-133 3.45e-09

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 59.26  E-value: 3.45e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080   12 VIGATNRLDSIDPALRRPGRFDREFLFNLPDQKARKHILQIHTRDWNPKLSDAF-LGELAEKCVGYCGADIKALCTEAAL 90
Cdd:CHL00195 363 VVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYdIKKLSKLSNKFSGAEIEQSIIEAMY 442

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 47077080   91 IAL--RRRYpqiyasshklqldvssivlSAQDFYHAMQNIVPASQ 133
Cdd:CHL00195 443 IAFyeKREF-------------------TTDDILLALKQFIPLAQ 468
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 1-34 8.35e-09

second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410938 [Multi-domain]  Cd Length: 161  Bit Score: 54.80  E-value: 8.35e-09
                        10        20        30
                ....*....|....*....|....*....|....
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19530 124 MDGLEERSNVFVIAATNRPDIIDPAMLRPGRLDK 157
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 438-510 1.38e-08

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: 52.75  E-value: 1.38e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 47077080 438 VTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN-PDKD 510
Cdd:cd05507  11 VYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNsSDHD 84
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 428-508 1.67e-08

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: 52.31  E-value: 1.67e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 428 LRELRLFLRDVT----KRLATdkrfnIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNAL 503
Cdd:cd05515   5 LWELYNAVKNYTdgrgRRLSL-----IFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNAC 79


                ....*.
gi 47077080 504 EYN-PD 508
Cdd:cd05515  80 KYNePD 85
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 1-34 2.38e-08

second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP in metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the second of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r2-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410936 [Multi-domain]  Cd Length: 161  Bit Score: 53.67  E-value: 2.38e-08
                        10        20        30
                ....*....|....*....|....*....|....
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19528 124 MDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQ 157
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 1-40 2.60e-08

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 52.60  E-value: 2.60e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 47077080     1 MDGLDNR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFNL 40
Cdd:pfam00004  92 LDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 451-509 3.97e-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: 51.52  E-value: 3.97e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 47077080 451 FSKPVDiEEVSDYLEVIKEPMDLSTVITKIDKHN---YLTAKDFLKDIDLICSNALEYNPDK 509
Cdd:cd05502  25 FHEPVS-PSVPNYYKIIKTPMDLSLIRKKLQPKSpqhYSSPEEFVADVRLMFKNCYKFNEED 85
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 462-529 2.05e-07

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: 49.36  E-value: 2.05e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47077080 462 DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNpdkDPGDKiIRHRACTLKDTAHA 529
Cdd:cd05517  38 DYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN---EPGSQ-VYKDANAIKKIFTA 101
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 451-506 3.18e-07

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: 48.53  E-value: 3.18e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 47077080 451 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 506
Cdd:cd05508  23 FLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYN 78
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 459-506 3.99e-07

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: 48.58  E-value: 3.99e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 47077080 459 EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 506
Cdd:cd05516  36 ELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 420-531 5.29e-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: 48.01  E-value: 5.29e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 420 MEDQEENTLRELRLFlRDVTKRLatdkRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLIC 499
Cdd:cd05522   2 YEARIKNILKGLRKE-RDENGRL----LTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMF 76

                        90       100       110
                ....*....|....*....|....*....|..
gi 47077080 500 SNALEYNpdkDPGDKIIRhRACTLKDTAHAII 531
Cdd:cd05522  77 ENAKLYN---ENDSQEYK-DAVLLEKEARLLA 104
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 1-33 5.72e-07

first of two ATPase domains of NSF and SEC18, and similar ATPase domains; N-ethylmaleimide-sensitive factor (NSF) and Saccharomyces cerevisiae Vesicular-fusion protein Sec18, key factors for eukaryotic trafficking, are ATPases and SNARE disassembly chaperones. NSF/Sec18 activate or prime SNAREs, the terminal catalysts of membrane fusion. Sec18/NSF associates with SNARE complexes through binding Sec17/alpha-SNAP. Sec18 has an N-terminal cap domain and two nucleotide-binding domains (D1 and D2) which form the two rings of the hexameric complex. The hydrolysis of ATP by D1 generates most of the energy necessary to disassemble inactive SNARE bundles, while the D2 ring binds ATP to stabilize the homohexamer. This subfamily includes the first (D1) ATPase domain of NSF/Sec18, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410912 [Multi-domain]  Cd Length: 177  Bit Score: 49.80  E-value: 5.72e-07
                        10        20        30
                ....*....|....*....|....*....|...
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFD 33
Cdd:cd19504 140 IDGVEQLNNILVIGMTNRKDLIDEALLRPGRLE 172
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 1-34 1.07e-06

second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as Peroxin61)/PEX1 is a protein unfoldase; PEX6 and PEX1 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. This subfamily represents the second ATPase domain of PEX6. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 48.66  E-value: 1.07e-06
                        10        20        30
                ....*....|....*....|....*....|....*
gi 47077080   1 MDGLDNRGE-IVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19527 122 LDGMSSSGQdVFVIGATNRPDLLDPALLRPGRFDK 156
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 450-526 2.66e-06

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: 46.56  E-value: 2.66e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47077080 450 IFSKPVDI-EEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDT 526
Cdd:cd05529  47 YFEYPVDLrAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLRI 124
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 429-506 2.77e-06

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: 45.90  E-value: 2.77e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 47077080 429 RELRLFLRDVTKRLATDKRF-NIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYN 506
Cdd:cd05518   4 RMLALFLYVLEYREGSGRRLcDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 462-507 7.02e-06

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: 45.02  E-value: 7.02e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 47077080 462 DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNP 507
Cdd:cd05520  38 DYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNV 83
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 1-34 8.92e-06

second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as Peroxin-1)/PEX6 is a protein unfoldase; PEX1 and PEX6 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. PEX-1 is required for stability of PEX5. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410934 [Multi-domain]  Cd Length: 158  Bit Score: 45.88  E-value: 8.92e-06
                        10        20        30
                ....*....|....*....|....*....|....
gi 47077080   1 MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 34
Cdd:cd19526 121 LDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDK 154
Bromodomain_1 cd05494
Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated ...
 430-543 1.83e-05

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


Pssm-ID: 99926 [Multi-domain]  Cd Length: 114  Bit Score: 43.97  E-value: 1.83e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 430 ELRLFLRdVTKRLATDKRFNIFSKPVD--IEEVSDYLEVIKEPMDLST---VITKIDKHNYLTAkdflkdidlicsnale 504
Cdd:cd05494   4 ALERVLR-ELKRHRRNEDAWPFLEPVNppRRGAPDYRDVIKRPMSFGTkvnNIVETGARDLEDL---------------- 66

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 47077080 505 YNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLC 543
Cdd:cd05494  67 QIVQEDPADKQIDDEGRRSPSNIYAVEALEQLIVFQCKQ 105
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 452-517 2.40e-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: 2.40e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 47077080 452 SKPVDIEevsDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIR 517
Cdd:cd05501  25 SKPYYIR---DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDDDFGQVGIT 87
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 462-505 4.45e-05

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: 42.71  E-value: 4.45e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 47077080 462 DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEY 505
Cdd:cd05524  40 EYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAY 83
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 227-363 8.18e-05

ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of photosynthesis in cyanobacteria, especially in CO2 uptake and utilization. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410915 [Multi-domain]  Cd Length: 161  Bit Score: 43.13  E-value: 8.18e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 227 YHQPTsyrPR-LLLSGERGSGQtSHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARRTVPSIVYMPHI- 304
Cdd:cd19507  26 YGLPT---PKgLLLVGIQGTGK-SLTAKAIAGVW-QLPLLRLDMGRLFGGLVGESESRLRQMIQTAEAIAPCVLWIDEIe 100

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47077080 305 ---------GDwwEAVSETVRATFLTLLQDipSFSPIFLLSTSETMYSeLPEEVkcIFRIQYEEVLYI 363
Cdd:cd19507 101 kgfsnadskGD--SGTSSRVLGTFLTWLQE--KKKPVFVVATANNVQS-LPPEL--LRKGRFDEIFFV 161
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 214-338 2.13e-03

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 38.80  E-value: 2.13e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 214 AIHKPYLHFTMSPYHQPtsYRPRLLLSGERGSGQTsHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARR 293
Cdd:cd19481   8 AVEAPRRGSRLRRYGLG--LPKGILLYGPPGTGKT-LLAKALAGEL-GLPLIVVKLSSLLSKYVGESEKNLRKIFERARR 83

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 47077080 294 TVPSIV-------------YMPHIGDWWEAVSEtvratFLTLLQDIPSFSPIFLLSTS 338
Cdd:cd19481  84 LAPCILfideidaigrkrdSSGESGELRRVLNQ-----LLTELDGVNSRSKVLVIAAT 136
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 462-525 2.20e-03

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: 37.69  E-value: 2.20e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 47077080 462 DYLEVIKEPMDLSTVITKIDkhNYLTAKDFLKDIDLICSNALEYNPdkdPGDKIIRHrACTLKD 525
Cdd:cd05521  39 DYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYNT---KGSVIYKY-ALILEK 96
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 225-323 3.41e-03

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 38.43  E-value: 3.41e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077080 225 SPYHQPTSYR------PR-LLLSGERGSGQTsHLAPALLHTLERFsVHRLDLPALYSVSAKTPEESCAQIFREARRTVPS 297
Cdd:cd19503  18 LPLKYPELFRalglkpPRgVLLHGPPGTGKT-LLARAVANEAGAN-FLSISGPSIVSKYLGESEKNLREIFEEARSHAPS 95

                        90       100       110
                ....*....|....*....|....*....|...
gi 47077080 298 IVYM-------PHIGDWWEAVSETVRATFLTLL 323
Cdd:cd19503  96 IIFIdeidalaPKREEDQREVERRVVAQLLTLM 128
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 460-525 4.78e-03

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: 36.98  E-value: 4.78e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 47077080 460 VSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPgdkiIRHRACTLKD 525
Cdd:cd05525  38 NPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSP----IGRDVCRLRK 99
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 1-37 7.79e-03

ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This subfamily includes the ATPase domains of vacuolar protein sorting-associated protein 4 (VPS4), ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase), Katanin p60 ATPase-containing subunit A1 (KTNA1), Spastin, and Fidgetin-Like 1 (FIGL-1). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410917 [Multi-domain]  Cd Length: 163  Bit Score: 37.33  E-value: 7.79e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 47077080   1 MDGLDNRGE--IVVIGATNRLDSIDPALRRpgRFDREFL 37
Cdd:cd19509 126 MDGVLNKPEdrVLVLGATNRPWELDEAFLR--RFEKRIY 162
 
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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