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Conserved domains on  [gi|799320925|ref|XP_012047964|]
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DNA repair protein Rad8 [Cryptococcus neoformans var. grubii H99]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 2149-2281 4.59e-24

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


:

Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 99.86  E-value: 4.59e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 2149 YGAKLEHLVNLIHSIPK-NERVLVFLQWEDLAGKVSEALSAGRIPHVTLSGS--AKSRANTLDRFQstNADSARVLLLkM 2225
Cdd:cd18793     9 VSGKLEALLELLEELREpGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGStsSKERQKLVDRFN--EDPDIRVFLL-S 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 799320925 2226 NDASAAGSNLTTANHAVFLGPLFtNSlfnyrAVETQAIGRVRRYGQQKKVHIHRLL 2281
Cdd:cd18793    86 TKAGGVGLNLTAANRVILYDPWW-NP-----AVEEQAIDRAHRIGQKKPVVVYRLI 135
Dcm super family cl43082
DNA-cytosine methylase [Replication, recombination and repair];
375-545 1.86e-23

DNA-cytosine methylase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0270:

Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 102.58  E-value: 1.86e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  375 GLTLAFE-----HVFSCEIEPFKQAYIERNF-TPPILFRDVTELGKKrahtaygsmvDVPGDVDILIAGTSCVDYSNLNN 448
Cdd:COG0270    15 GLSLGFEkagfeVVFAVEIDPDACETYRANFpEAKVIEGDIRDIDPE----------ELIPDVDLLIGGPPCQPFSVAGK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  449 vQQDIDanGESGRTFRGMLQWVKKHQPPIVILENVCN-------APWDKVVEYFGQIDYDAQYTRLDTKEFYIPHTRTRV 521
Cdd:COG0270    85 -RKGLE--DPRGTLFFEFIRIVEELRPKAFVLENVPGllssdkgKTFEEILKELEELGYRVDYKVLNAADYGVPQNRERV 161

                         170       180
                  ....*....|....*....|....*...
gi 799320925  522 YLFATPSSSESDDLPEKW----AQTVKD 545
Cdd:COG0270   162 FIVGFRKDLDLFEFPEPThlkpYVTVGD 189
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 1455-1558 3.29e-17

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd18008:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 241  Bit Score: 83.49  E-value: 3.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1455 MVRGGVIADQVGYGKTVISIALVAQTLS--------LPAPEPATPGLIDLKATLIVVPGHLSKQWPNEIARFTGSM-FKV 1525
Cdd:cd18008    13 LPRGGILADEMGLGKTIQALALILATRPqdpkipeeLEENSSDPKKLYLSKTTLIVVPLSLLSQWKDEIEKHTKPGsLKV 92

                          90       100       110
                  ....*....|....*....|....*....|...
gi 799320925 1526 IVIQGMKDLqeKTIAELGKADIIVMASEIFESD 1558
Cdd:cd18008    93 YVYHGSKRI--KSIEELSDYDIVITTYGTLASE 123
HepA super family cl33945
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 1346-1571 2.18e-10

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


The actual alignment was detected with superfamily member COG0553:

Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 66.02  E-value: 2.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1346 LAHRALSRLPPTTSEHKISLSWRLTPGHVTESPQPRRVFILPSNKQDPEnSQPEAFKLPLRKEQLRSLWWMLEQEKATGk 1425
Cdd:COG0553   184 LALLALLELALLAAEAELLLLLELLLELELLAEAAVDAFRLRRLREALE-SLPAGLKATLRPYQLEGAAWLLFLRRLGL- 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1426 thtfveeeisesllpavgwraegkaerpvmvrGGVIADQVGYGKTVISIALVAQTLSLPAPEPAtpglidlkatLIVVPG 1505
Cdd:COG0553   262 --------------------------------GGLLADDMGLGKTIQALALLLELKERGLARPV----------LIVAPT 299

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 799320925 1506 HLSKQWPNEIARFTGSMfKVIVIQGMKDlQEKTIAELGKADIIVMASEIFesdvyWSRLEYLSAQP 1571
Cdd:COG0553   300 SLVGNWQRELAKFAPGL-RVLVLDGTRE-RAKGANPFEDADLVITSYGLL-----RRDIELLAAVD 358
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
 62-116 1.21e-08

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.


:

Pssm-ID: 349274 [Multi-domain]  Cd Length: 50  Bit Score: 52.86  E-value: 1.21e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 799320925   62 YEIDYIADSRVIRRKgrqiLQYLIHWAGYAVHERTWEDEDGIGGeDCALVQEFYR 116
Cdd:cd00024     1 YEVEKILDHRVRKGK----LEYLVKWKGYPPEENTWEPEENLTN-APELIKEYEK 50
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 1705-1770 6.74e-04

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd18071:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 239  Bit Score: 43.61  E-value: 6.74e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 799320925 1705 DYKLLPNPVLHMFRFRRVIADE---FTYLQKKSLAAVLRLSSSYRWILSGTPPVSDFAAIRSIATFMGI 1770
Cdd:cd18071   132 DFGAKGDSPLHTINWLRVVLDEghqIRNPNAQQTKAVLNLSSERRWVLTGTPIQNSPKDLGSLLSFLHL 200
 
Name Accession Description Interval E-value
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 2149-2281 4.59e-24

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 99.86  E-value: 4.59e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 2149 YGAKLEHLVNLIHSIPK-NERVLVFLQWEDLAGKVSEALSAGRIPHVTLSGS--AKSRANTLDRFQstNADSARVLLLkM 2225
Cdd:cd18793     9 VSGKLEALLELLEELREpGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGStsSKERQKLVDRFN--EDPDIRVFLL-S 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 799320925 2226 NDASAAGSNLTTANHAVFLGPLFtNSlfnyrAVETQAIGRVRRYGQQKKVHIHRLL 2281
Cdd:cd18793    86 TKAGGVGLNLTAANRVILYDPWW-NP-----AVEEQAIDRAHRIGQKKPVVVYRLI 135
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
375-545 1.86e-23

DNA-cytosine methylase [Replication, recombination and repair];


Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 102.58  E-value: 1.86e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  375 GLTLAFE-----HVFSCEIEPFKQAYIERNF-TPPILFRDVTELGKKrahtaygsmvDVPGDVDILIAGTSCVDYSNLNN 448
Cdd:COG0270    15 GLSLGFEkagfeVVFAVEIDPDACETYRANFpEAKVIEGDIRDIDPE----------ELIPDVDLLIGGPPCQPFSVAGK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  449 vQQDIDanGESGRTFRGMLQWVKKHQPPIVILENVCN-------APWDKVVEYFGQIDYDAQYTRLDTKEFYIPHTRTRV 521
Cdd:COG0270    85 -RKGLE--DPRGTLFFEFIRIVEELRPKAFVLENVPGllssdkgKTFEEILKELEELGYRVDYKVLNAADYGVPQNRERV 161

                         170       180
                  ....*....|....*....|....*...
gi 799320925  522 YLFATPSSSESDDLPEKW----AQTVKD 545
Cdd:COG0270   162 FIVGFRKDLDLFEFPEPThlkpYVTVGD 189
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 2151-2291 2.09e-22

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 104.92  E-value: 2.09e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 2151 AKLEHLVNLIHSIP-KNERVLVFLQWEDLAGKVSEALSAGRIPHVTLSG--SAKSRANTLDRFQstNADSARVLLLkmnd 2227
Cdd:COG0553   533 AKLEALLELLEELLaEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGgtSAEERDELVDRFQ--EGPEAPVFLI---- 606

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 799320925 2228 ASAAGS---NLTTANHAVFLGPLFTNslfnyrAVETQAIGRVRRYGQQKKVHIHRLLALDTIDMTIF 2291
Cdd:COG0553   607 SLKAGGeglNLTAADHVIHYDLWWNP------AVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKIL 667
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
 1455-1558 3.29e-17

DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350766 [Multi-domain]  Cd Length: 241  Bit Score: 83.49  E-value: 3.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1455 MVRGGVIADQVGYGKTVISIALVAQTLS--------LPAPEPATPGLIDLKATLIVVPGHLSKQWPNEIARFTGSM-FKV 1525
Cdd:cd18008    13 LPRGGILADEMGLGKTIQALALILATRPqdpkipeeLEENSSDPKKLYLSKTTLIVVPLSLLSQWKDEIEKHTKPGsLKV 92

                          90       100       110
                  ....*....|....*....|....*....|...
gi 799320925 1526 IVIQGMKDLqeKTIAELGKADIIVMASEIFESD 1558
Cdd:cd18008    93 YVYHGSKRI--KSIEELSDYDIVITTYGTLASE 123
Cyt_C5_DNA_methylase cd00315
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
 374-553 5.00e-17

Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.


Pssm-ID: 238192 [Multi-domain]  Cd Length: 275  Bit Score: 83.82  E-value: 5.00e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  374 HGLTLA-FEHVFSCEIEPFKQAYIERNFTPPILFRDVTELGKKrahtaygsmvDVPGDVDILIAGTSCVDYSNLNNvQQD 452
Cdd:cd00315    15 LGLEKAgFEIVAANEIDKSAAETYEANFPNKLIEGDITKIDEK----------DFIPDIDLLTGGFPCQPFSIAGK-RKG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  453 IDANgesgrtfRGMLQW-----VKKHQPPIVILENVCNA-------PWDKVVEYFGQIDYDAQYTRLDTKEFYIPHTRTR 520
Cdd:cd00315    84 FEDT-------RGTLFFeiiriLKEKKPKYFLLENVKGLlthdngnTLKVILNTLEELGYNVYWKLLNASDYGVPQNRER 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 799320925  521 VYLFAT---------PSSSESDDLPekwaQTVKDL--RRPWSSP 553
Cdd:cd00315   157 VFIIGIrkdlilnffSPFPKPSEKK----KTLKDIlrIRDPDEP 196
DNA_methylase pfam00145
C-5 cytosine-specific DNA methylase;
374-526 1.98e-13

C-5 cytosine-specific DNA methylase;


Pssm-ID: 395093 [Multi-domain]  Cd Length: 324  Bit Score: 73.89  E-value: 1.98e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   374 HGLTLA-FEHVFSCEIEPFKQAYIERNFTPPILFrDVTELGKKrahtaygsmvDVPgDVDILIAGTSCVDYSnLNNVQQD 452
Cdd:pfam00145   15 LGLEQAgFECVAANEIDKSAAKTYEANFPKVPIG-DITLIDIK----------DIP-DIDILTGGFPCQDFS-IAGKQKG 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   453 IDANgesgrtfRGMLQW-----VKKHQPPIVILENVCNA-------PWDKVVEYFGQIDYDAQYTRLDTKEFYIPHTRTR 520
Cdd:pfam00145   82 FEDT-------RGTLFFeiiriIKEKKPKAFLLENVKGLlshdngnTLNVILETLEELGYHVSWKVLNASDYGVPQNRER 154


                   ....*.
gi 799320925   521 VYLFAT 526
Cdd:pfam00145  155 VFIVGI 160
dcm TIGR00675
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
 375-525 5.20e-12

DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273211 [Multi-domain]  Cd Length: 315  Bit Score: 69.28  E-value: 5.20e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   375 GLTLAFEH-----VFSCEIEPFKQAYIERNFTPPILFRDVTELGKKrahtaygsmvDVPgDVDILIAGTSCVDYSnLNNV 449
Cdd:TIGR00675   10 GIRLGFEQagfkcVFASEIDKYAQKTYEANFGNKVPFGDITKISPS----------DIP-DFDILLGGFPCQPFS-IAGK 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   450 QQDIdaNGESGRTFRGMLQWVKKHQPPIVILENVCN-APWDK------VVEYFGQIDYDAQYTRLDTKEFYIPHTRTRVY 522
Cdd:TIGR00675   78 RKGF--EDTRGTLFFEIVRILKEKKPKFFLLENVKGlVSHDKgrtfkvIIETLEELGYKVYYKVLNAKDFGVPQNRERIY 155


                   ...
gi 799320925   523 LFA 525
Cdd:TIGR00675  156 IVG 158
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 1346-1571 2.18e-10

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 66.02  E-value: 2.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1346 LAHRALSRLPPTTSEHKISLSWRLTPGHVTESPQPRRVFILPSNKQDPEnSQPEAFKLPLRKEQLRSLWWMLEQEKATGk 1425
Cdd:COG0553   184 LALLALLELALLAAEAELLLLLELLLELELLAEAAVDAFRLRRLREALE-SLPAGLKATLRPYQLEGAAWLLFLRRLGL- 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1426 thtfveeeisesllpavgwraegkaerpvmvrGGVIADQVGYGKTVISIALVAQTLSLPAPEPAtpglidlkatLIVVPG 1505
Cdd:COG0553   262 --------------------------------GGLLADDMGLGKTIQALALLLELKERGLARPV----------LIVAPT 299

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 799320925 1506 HLSKQWPNEIARFTGSMfKVIVIQGMKDlQEKTIAELGKADIIVMASEIFesdvyWSRLEYLSAQP 1571
Cdd:COG0553   300 SLVGNWQRELAKFAPGL-RVLVLDGTRE-RAKGANPFEDADLVITSYGLL-----RRDIELLAAVD 358
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
 62-116 1.21e-08

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.


Pssm-ID: 349274 [Multi-domain]  Cd Length: 50  Bit Score: 52.86  E-value: 1.21e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 799320925   62 YEIDYIADSRVIRRKgrqiLQYLIHWAGYAVHERTWEDEDGIGGeDCALVQEFYR 116
Cdd:cd00024     1 YEVEKILDHRVRKGK----LEYLVKWKGYPPEENTWEPEENLTN-APELIKEYEK 50
CHROMO smart00298
Chromatin organization modifier domain;
62-119 3.79e-07

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 48.75  E-value: 3.79e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 799320925     62 YEIDYIADSRVIRRKGrqiLQYLIHWAGYAVHERTWEDEDGIgGEDCALVQEFYRKNP 119
Cdd:smart00298    2 YEVEKILDHRWKKKGE---LEYLVKWKGYSYSEDTWEPEENL-LNCSKKLDNYKKKER 55
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
62-117 3.85e-07

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 48.73  E-value: 3.85e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 799320925    62 YEIDYIADSRVirRKGRQiLQYLIHWAGYAVHERTWEDEDGIggEDC-ALVQEFYRK 117
Cdd:pfam00385    1 YEVERILDHRK--DKGGK-EEYLVKWKGYPYDENTWEPEENL--SKCpELIEEFKDR 52
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 1456-1537 6.21e-07

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 53.46  E-value: 6.21e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  1456 VRGGVIADQVGYGKTVISIALVAqTLSLPAPepatpglIDLKATLIVVPGHLSKQWPNEIARFTG-SMFKVIVIQGMKDL 1534
Cdd:pfam00176   17 GRGGILADEMGLGKTLQTISLLL-YLKHVDK-------NWGGPTLIVVPLSLLHNWMNEFERWVSpPALRVVVLHGNKRP 88


                   ...
gi 799320925  1535 QEK 1537
Cdd:pfam00176   89 QER 91
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 2151-2270 2.56e-06

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 48.36  E-value: 2.56e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  2151 AKLEHLVNLIHSIpKNERVLVFLQWEDLAgKVSEALSAGRIPHVTLSG--SAKSRANTLDRFqstNADSARVLLlkmndA 2228
Cdd:pfam00271    1 EKLEALLELLKKE-RGGKVLIFSQTKKTL-EAELLLEKEGIKVARLHGdlSQEEREEILEDF---RKGKIDVLV-----A 70

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 799320925  2229 SAAGS---NLTTANHAVFLGPLFTNSLFNyravetQAIGRVRRYG 2270
Cdd:pfam00271   71 TDVAErglDLPDVDLVINYDLPWNPASYI------QRIGRAGRAG 109
DEXDc smart00487
DEAD-like helicases superfamily;
1457-1565 3.03e-04

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 44.41  E-value: 3.03e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   1457 RGGVIADQVGYGKTVISIALVAQTLslpAPEPATPglidlkaTLIVVPG-HLSKQWPNEIARFTGSMF--KVIVIQGMKD 1533
Cdd:smart00487   25 RDVILAAPTGSGKTLAALLPALEAL---KRGKGGR-------VLVLVPTrELAEQWAEELKKLGPSLGlkVVGLYGGDSK 94

                            90       100       110
                    ....*....|....*....|....*....|..
gi 799320925   1534 LQEKTIAELGKADIIVMASEIFESDVYWSRLE 1565
Cdd:smart00487   95 REQLRKLESGKTDILVTTPGRLLDLLENDKLS 126
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
 1705-1770 6.74e-04

DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350829 [Multi-domain]  Cd Length: 239  Bit Score: 43.61  E-value: 6.74e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 799320925 1705 DYKLLPNPVLHMFRFRRVIADE---FTYLQKKSLAAVLRLSSSYRWILSGTPPVSDFAAIRSIATFMGI 1770
Cdd:cd18071   132 DFGAKGDSPLHTINWLRVVLDEghqIRNPNAQQTKAVLNLSSERRWVLTGTPIQNSPKDLGSLLSFLHL 200
HELICc smart00490
helicase superfamily c-terminal domain;
2181-2270 3.14e-03

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 38.73  E-value: 3.14e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   2181 KVSEALSAGRIPHVTLSG--SAKSRANTLDRFqstNADSARVLLlkmndASAAGS---NLTTANHAVFLGPLFTnslfny 2255
Cdd:smart00490    2 ELAELLKELGIKVARLHGglSQEEREEILDKF---NNGKIKVLV-----ATDVAErglDLPGVDLVIIYDLPWS------ 67

                            90
                    ....*....|....*
gi 799320925   2256 RAVETQAIGRVRRYG 2270
Cdd:smart00490   68 PASYIQRIGRAGRAG 82
 
Name Accession Description Interval E-value
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 2149-2281 4.59e-24

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 99.86  E-value: 4.59e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 2149 YGAKLEHLVNLIHSIPK-NERVLVFLQWEDLAGKVSEALSAGRIPHVTLSGS--AKSRANTLDRFQstNADSARVLLLkM 2225
Cdd:cd18793     9 VSGKLEALLELLEELREpGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGStsSKERQKLVDRFN--EDPDIRVFLL-S 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 799320925 2226 NDASAAGSNLTTANHAVFLGPLFtNSlfnyrAVETQAIGRVRRYGQQKKVHIHRLL 2281
Cdd:cd18793    86 TKAGGVGLNLTAANRVILYDPWW-NP-----AVEEQAIDRAHRIGQKKPVVVYRLI 135
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
375-545 1.86e-23

DNA-cytosine methylase [Replication, recombination and repair];


Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 102.58  E-value: 1.86e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  375 GLTLAFE-----HVFSCEIEPFKQAYIERNF-TPPILFRDVTELGKKrahtaygsmvDVPGDVDILIAGTSCVDYSNLNN 448
Cdd:COG0270    15 GLSLGFEkagfeVVFAVEIDPDACETYRANFpEAKVIEGDIRDIDPE----------ELIPDVDLLIGGPPCQPFSVAGK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  449 vQQDIDanGESGRTFRGMLQWVKKHQPPIVILENVCN-------APWDKVVEYFGQIDYDAQYTRLDTKEFYIPHTRTRV 521
Cdd:COG0270    85 -RKGLE--DPRGTLFFEFIRIVEELRPKAFVLENVPGllssdkgKTFEEILKELEELGYRVDYKVLNAADYGVPQNRERV 161

                         170       180
                  ....*....|....*....|....*...
gi 799320925  522 YLFATPSSSESDDLPEKW----AQTVKD 545
Cdd:COG0270   162 FIVGFRKDLDLFEFPEPThlkpYVTVGD 189
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 2151-2291 2.09e-22

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 104.92  E-value: 2.09e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 2151 AKLEHLVNLIHSIP-KNERVLVFLQWEDLAGKVSEALSAGRIPHVTLSG--SAKSRANTLDRFQstNADSARVLLLkmnd 2227
Cdd:COG0553   533 AKLEALLELLEELLaEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGgtSAEERDELVDRFQ--EGPEAPVFLI---- 606

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 799320925 2228 ASAAGS---NLTTANHAVFLGPLFTNslfnyrAVETQAIGRVRRYGQQKKVHIHRLLALDTIDMTIF 2291
Cdd:COG0553   607 SLKAGGeglNLTAADHVIHYDLWWNP------AVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKIL 667
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
 1455-1558 3.29e-17

DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350766 [Multi-domain]  Cd Length: 241  Bit Score: 83.49  E-value: 3.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1455 MVRGGVIADQVGYGKTVISIALVAQTLS--------LPAPEPATPGLIDLKATLIVVPGHLSKQWPNEIARFTGSM-FKV 1525
Cdd:cd18008    13 LPRGGILADEMGLGKTIQALALILATRPqdpkipeeLEENSSDPKKLYLSKTTLIVVPLSLLSQWKDEIEKHTKPGsLKV 92

                          90       100       110
                  ....*....|....*....|....*....|...
gi 799320925 1526 IVIQGMKDLqeKTIAELGKADIIVMASEIFESD 1558
Cdd:cd18008    93 YVYHGSKRI--KSIEELSDYDIVITTYGTLASE 123
Cyt_C5_DNA_methylase cd00315
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
 374-553 5.00e-17

Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.


Pssm-ID: 238192 [Multi-domain]  Cd Length: 275  Bit Score: 83.82  E-value: 5.00e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  374 HGLTLA-FEHVFSCEIEPFKQAYIERNFTPPILFRDVTELGKKrahtaygsmvDVPGDVDILIAGTSCVDYSNLNNvQQD 452
Cdd:cd00315    15 LGLEKAgFEIVAANEIDKSAAETYEANFPNKLIEGDITKIDEK----------DFIPDIDLLTGGFPCQPFSIAGK-RKG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  453 IDANgesgrtfRGMLQW-----VKKHQPPIVILENVCNA-------PWDKVVEYFGQIDYDAQYTRLDTKEFYIPHTRTR 520
Cdd:cd00315    84 FEDT-------RGTLFFeiiriLKEKKPKYFLLENVKGLlthdngnTLKVILNTLEELGYNVYWKLLNASDYGVPQNRER 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 799320925  521 VYLFAT---------PSSSESDDLPekwaQTVKDL--RRPWSSP 553
Cdd:cd00315   157 VFIIGIrkdlilnffSPFPKPSEKK----KTLKDIlrIRDPDEP 196
DNA_methylase pfam00145
C-5 cytosine-specific DNA methylase;
374-526 1.98e-13

C-5 cytosine-specific DNA methylase;


Pssm-ID: 395093 [Multi-domain]  Cd Length: 324  Bit Score: 73.89  E-value: 1.98e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   374 HGLTLA-FEHVFSCEIEPFKQAYIERNFTPPILFrDVTELGKKrahtaygsmvDVPgDVDILIAGTSCVDYSnLNNVQQD 452
Cdd:pfam00145   15 LGLEQAgFECVAANEIDKSAAKTYEANFPKVPIG-DITLIDIK----------DIP-DIDILTGGFPCQDFS-IAGKQKG 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   453 IDANgesgrtfRGMLQW-----VKKHQPPIVILENVCNA-------PWDKVVEYFGQIDYDAQYTRLDTKEFYIPHTRTR 520
Cdd:pfam00145   82 FEDT-------RGTLFFeiiriIKEKKPKAFLLENVKGLlshdngnTLNVILETLEELGYHVSWKVLNASDYGVPQNRER 154


                   ....*.
gi 799320925   521 VYLFAT 526
Cdd:pfam00145  155 VFIVGI 160
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 1405-1560 1.79e-12

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 69.68  E-value: 1.79e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1405 LRKEQLRSLWWMLeqekatgkthtfveeeisesllpavgwraegkaerpvmVRGGVIADQVGYGKTVISIALVaqtLSLP 1484
Cdd:cd18070     1 LLPYQRRAVNWML--------------------------------------VPGGILADEMGLGKTVEVLALI---LLHP 39

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1485 APEPATPGLID-------------------LKATLIVVPGHLSKQWPNEIARFTGSMFKVIVIQGMKD---LQEKTIAEL 1542
Cdd:cd18070    40 RPDNDLDAADDdsdemvccpdclvaetpvsSKATLIVCPSAILAQWLDEINRHVPSSLKVLTYQGVKKdgaLASPAPEIL 119

                         170
                  ....*....|....*...
gi 799320925 1543 GKADIIVMASEIFESDVY 1560
Cdd:cd18070   120 AEYDIVVTTYDVLRTELH 137
dcm TIGR00675
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
 375-525 5.20e-12

DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273211 [Multi-domain]  Cd Length: 315  Bit Score: 69.28  E-value: 5.20e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   375 GLTLAFEH-----VFSCEIEPFKQAYIERNFTPPILFRDVTELGKKrahtaygsmvDVPgDVDILIAGTSCVDYSnLNNV 449
Cdd:TIGR00675   10 GIRLGFEQagfkcVFASEIDKYAQKTYEANFGNKVPFGDITKISPS----------DIP-DFDILLGGFPCQPFS-IAGK 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   450 QQDIdaNGESGRTFRGMLQWVKKHQPPIVILENVCN-APWDK------VVEYFGQIDYDAQYTRLDTKEFYIPHTRTRVY 522
Cdd:TIGR00675   78 RKGF--EDTRGTLFFEIVRILKEKKPKFFLLENVKGlVSHDKgrtfkvIIETLEELGYKVYYKVLNAKDFGVPQNRERIY 155


                   ...
gi 799320925   523 LFA 525
Cdd:TIGR00675  156 IVG 158
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 1346-1571 2.18e-10

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 66.02  E-value: 2.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1346 LAHRALSRLPPTTSEHKISLSWRLTPGHVTESPQPRRVFILPSNKQDPEnSQPEAFKLPLRKEQLRSLWWMLEQEKATGk 1425
Cdd:COG0553   184 LALLALLELALLAAEAELLLLLELLLELELLAEAAVDAFRLRRLREALE-SLPAGLKATLRPYQLEGAAWLLFLRRLGL- 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1426 thtfveeeisesllpavgwraegkaerpvmvrGGVIADQVGYGKTVISIALVAQTLSLPAPEPAtpglidlkatLIVVPG 1505
Cdd:COG0553   262 --------------------------------GGLLADDMGLGKTIQALALLLELKERGLARPV----------LIVAPT 299

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 799320925 1506 HLSKQWPNEIARFTGSMfKVIVIQGMKDlQEKTIAELGKADIIVMASEIFesdvyWSRLEYLSAQP 1571
Cdd:COG0553   300 SLVGNWQRELAKFAPGL-RVLVLDGTRE-RAKGANPFEDADLVITSYGLL-----RRDIELLAAVD 358
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 1457-1563 2.85e-09

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 58.73  E-value: 2.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1457 RGGVIADQVGYGKTVISIALVAQtLSLPAPEPatpglidlKATLIVVPGHLSKQWPNEIARFTGSMfKVIVIQGMKDLQE 1536
Cdd:cd17919    20 PGGILADEMGLGKTLQAIAFLAY-LLKEGKER--------GPVLVVCPLSVLENWEREFEKWTPDL-RVVVYHGSQRERA 89

                          90       100
                  ....*....|....*....|....*....
gi 799320925 1537 K--TIAELGKADIIVMASEIFESDVYWSR 1563
Cdd:cd17919    90 QirAKEKLDKFDVVLTTYETLRRDKASLR 118
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
 62-116 1.21e-08

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.


Pssm-ID: 349274 [Multi-domain]  Cd Length: 50  Bit Score: 52.86  E-value: 1.21e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 799320925   62 YEIDYIADSRVIRRKgrqiLQYLIHWAGYAVHERTWEDEDGIGGeDCALVQEFYR 116
Cdd:cd00024     1 YEVEKILDHRVRKGK----LEYLVKWKGYPPEENTWEPEENLTN-APELIKEYEK 50
CD_MarY1_POL_like cd18975
chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes ...
 62-116 2.91e-07

chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in the polyprotein from the MarY1 Ty3/Gypsy long terminal repeat (LTR) retroelement from the from the Ectomycorrhizal Basidiomycete Tricholoma matsutake. The pol gene in TY3/gypsy elements generally encodes domains in the following order: prt-reverse transcriptase-RNase H-integrase, in marY1 POL the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349331  Cd Length: 49  Bit Score: 49.08  E-value: 2.91e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 799320925   62 YEIDYIADSRVIRRKgrqiLQYLIHWAGYAVHERTWEDEDGIGGEDcaLVQEFYR 116
Cdd:cd18975     1 YEVESILNSRLHRGK----LQYLIQWKGYPLEEASWELEDNIKNPR--LIEEFHK 49
CHROMO smart00298
Chromatin organization modifier domain;
62-119 3.79e-07

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 48.75  E-value: 3.79e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 799320925     62 YEIDYIADSRVIRRKGrqiLQYLIHWAGYAVHERTWEDEDGIgGEDCALVQEFYRKNP 119
Cdd:smart00298    2 YEVEKILDHRWKKKGE---LEYLVKWKGYSYSEDTWEPEENL-LNCSKKLDNYKKKER 55
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
62-117 3.85e-07

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 48.73  E-value: 3.85e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 799320925    62 YEIDYIADSRVirRKGRQiLQYLIHWAGYAVHERTWEDEDGIggEDC-ALVQEFYRK 117
Cdd:pfam00385    1 YEVERILDHRK--DKGGK-EEYLVKWKGYPYDENTWEPEENL--SKCpELIEEFKDR 52
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 1456-1537 6.21e-07

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 53.46  E-value: 6.21e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  1456 VRGGVIADQVGYGKTVISIALVAqTLSLPAPepatpglIDLKATLIVVPGHLSKQWPNEIARFTG-SMFKVIVIQGMKDL 1534
Cdd:pfam00176   17 GRGGILADEMGLGKTLQTISLLL-YLKHVDK-------NWGGPTLIVVPLSLLHNWMNEFERWVSpPALRVVVLHGNKRP 88


                   ...
gi 799320925  1535 QEK 1537
Cdd:pfam00176   89 QER 91
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 2151-2270 2.56e-06

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 48.36  E-value: 2.56e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925  2151 AKLEHLVNLIHSIpKNERVLVFLQWEDLAgKVSEALSAGRIPHVTLSG--SAKSRANTLDRFqstNADSARVLLlkmndA 2228
Cdd:pfam00271    1 EKLEALLELLKKE-RGGKVLIFSQTKKTL-EAELLLEKEGIKVARLHGdlSQEEREEILEDF---RKGKIDVLV-----A 70

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 799320925  2229 SAAGS---NLTTANHAVFLGPLFTNSLFNyravetQAIGRVRRYG 2270
Cdd:pfam00271   71 TDVAErglDLPDVDLVINYDLPWNPASYI------QRIGRAGRAG 109
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
 1409-1562 2.71e-06

DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350829 [Multi-domain]  Cd Length: 239  Bit Score: 50.93  E-value: 2.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1409 QLRSLWWMLEQEKaTGKTHTFVEEEISESLLPAVGWRAEgkaERPVMVRGGVIADQVGYGKTVISIALVAqtlslpapep 1488
Cdd:cd18071     5 QKQALAWMVSREN-SQDLPPFWEEAVGLFLNTITNFSQK---KRPELVRGGILADDMGLGKTLTTISLIL---------- 70

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 799320925 1489 ATPglidlkaTLIVVPGHLSKQWPNEIARFTG-SMFKVIVIQGMKDLQekTIAELGKADIIVMASEIFESDVYWS 1562
Cdd:cd18071    71 ANF-------TLIVCPLSVLSNWETQFEEHVKpGQLKVYTYHGGERNR--DPKLLSKYDIVLTTYNTLASDFGAK 136
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
 1458-1550 4.64e-06

DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350770 [Multi-domain]  Cd Length: 218  Bit Score: 49.87  E-value: 4.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1458 GGVIADQVGYGKTVISIALVAQTLSLPAPEPAtpglidlkatLIVVPGHLSKQWPNEIARFTGSMfKVIVIQGmKDLQEK 1537
Cdd:cd18012    25 GGILADDMGLGKTLQTLALLLSRKEEGRKGPS----------LVVAPTSLIYNWEEEAAKFAPEL-KVLVIHG-TKRKRE 92

                          90
                  ....*....|...
gi 799320925 1538 TIAELGKADIIVM 1550
Cdd:cd18012    93 KLRALEDYDLVIT 105
CD_HP1a_insect cd18653
chromodomain of insect HP1a; CHRomatin Organization Modifier (chromo) domain of insect HP1a. ...
 62-114 2.22e-05

chromodomain of insect HP1a; CHRomatin Organization Modifier (chromo) domain of insect HP1a. HP1a is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. In Drosophila, there are at least five HP1 family proteins, this subgroup includes the CD of Drosophila melanogaster HP1a.


Pssm-ID: 349300  Cd Length: 50  Bit Score: 43.87  E-value: 2.22e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 799320925   62 YEIDYIADSRVirRKGRqiLQYLIHWAGYAVHERTWEDEDGIGGEDcaLVQEF 114
Cdd:cd18653     2 YAVEKICDRRV--RKGK--VEYYLKWKGYPETENTWEPEENLDCQD--LIQQY 48
chromodomain cd18968
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
 62-116 1.26e-04

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349324  Cd Length: 57  Bit Score: 41.95  E-value: 1.26e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 799320925   62 YEIDYIADSRVIRRKGRQIL--QYLIHWAGYAVHERTWEDEDGIGGEDcALVQEFYR 116
Cdd:cd18968     2 YEVEVILAARVVKDAESRKKgwKYLVKWAGYPDEENTWEPEESFDGCD-DLLERFWE 57
DEXDc smart00487
DEAD-like helicases superfamily;
1457-1565 3.03e-04

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 44.41  E-value: 3.03e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   1457 RGGVIADQVGYGKTVISIALVAQTLslpAPEPATPglidlkaTLIVVPG-HLSKQWPNEIARFTGSMF--KVIVIQGMKD 1533
Cdd:smart00487   25 RDVILAAPTGSGKTLAALLPALEAL---KRGKGGR-------VLVLVPTrELAEQWAEELKKLGPSLGlkVVGLYGGDSK 94

                            90       100       110
                    ....*....|....*....|....*....|..
gi 799320925   1534 LQEKTIAELGKADIIVMASEIFESDVYWSRLE 1565
Cdd:smart00487   95 REQLRKLESGKTDILVTTPGRLLDLLENDKLS 126
CD_HP1beta_Cbx1 cd18650
chromodomain of heterochromatin protein 1 homolog beta; CHRomatin Organization Modifier ...
 62-114 5.43e-04

chromodomain of heterochromatin protein 1 homolog beta; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog beta (also known as HP1beta, CBX1, and chromobox 1), and related proteins. HP1beta is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3).


Pssm-ID: 349297  Cd Length: 50  Bit Score: 39.93  E-value: 5.43e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 799320925   62 YEIDYIADSRVIrrKGRqiLQYLIHWAGYAVHERTWEDEDGIggeDCA-LVQEF 114
Cdd:cd18650     2 YVVEKVLDRRVV--KGK--VEYLLKWKGFSDEDNTWEPEENL---DCPdLIAEF 48
CD_POL_like cd18976
chromodomain of uncharacterized putative retroelement polyprotein proteins; This subgroup ...
 66-98 5.46e-04

chromodomain of uncharacterized putative retroelement polyprotein proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in uncharacterized putative retrotransposon proteins, and similar proteins. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349332  Cd Length: 51  Bit Score: 39.86  E-value: 5.46e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 799320925   66 YIADSRVIRRKGRQILQYLIHWAGYAVHERTWE 98
Cdd:cd18976     1 YIVESLLDRRKVRGQVQYLVKWRGFPRSEATWE 33
chromodomain cd18966
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
 62-107 6.26e-04

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349322  Cd Length: 49  Bit Score: 39.57  E-value: 6.26e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 799320925   62 YEIDYIADSRVIRRKgrqiLQYLIHWAGYAVHERTWEDEDGIGGED 107
Cdd:cd18966     1 YEVERILAERRDDGG----KRYLVKWEGYPLEEATWEPEENIGDEE 42
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
 1705-1770 6.74e-04

DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350829 [Multi-domain]  Cd Length: 239  Bit Score: 43.61  E-value: 6.74e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 799320925 1705 DYKLLPNPVLHMFRFRRVIADE---FTYLQKKSLAAVLRLSSSYRWILSGTPPVSDFAAIRSIATFMGI 1770
Cdd:cd18071   132 DFGAKGDSPLHTINWLRVVLDEghqIRNPNAQQTKAVLNLSSERRWVLTGTPIQNSPKDLGSLLSFLHL 200
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
 1457-1562 9.23e-04

DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350763 [Multi-domain]  Cd Length: 245  Bit Score: 43.52  E-value: 9.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1457 RGGVIADQVGYGKTVISIALVAQTL-----------SLPAPEPATPGLIDLKATLIVVPGHLSKQWPNEIARFtGSmFKV 1525
Cdd:cd18005    20 RGGILGDDMGLGKTVQVIAFLAAVLgktgtrrdrenNRPRFKKKPPASSAKKPVLIVAPLSVLYNWKDELDTW-GH-FEV 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 799320925 1526 IVIQGMK---DLQEKTIAelGKADIIVMASEIFE------SDVYWS 1562
Cdd:cd18005    98 GVYHGSRkddELEGRLKA--GRLEVVVTTYDTLRrcidslNSINWS 141
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
 1459-1564 1.17e-03

DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or SMARCA6) is a major epigenetic regulator crucial for normal heterochromatin structure and function. HELLS is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350767 [Multi-domain]  Cd Length: 236  Bit Score: 42.76  E-value: 1.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1459 GVIADQVGYGKTVISIALVAQTLslpapEPATPGlidlkATLIVVPGHLSKQWPNEIARFTGSMfKVIVIQGMKDLQEKT 1538
Cdd:cd18009    25 GILADEMGLGKTIQTIALLAHLR-----ERGVWG-----PFLVIAPLSTLPNWVNEFARFTPSV-PVLLYHGTKEERERL 93

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 799320925 1539 IAE-------LGKADIIVMASEIFESD------VYWSRL 1564
Cdd:cd18009    94 RKKimkregtLQDFPVVVTSYEIAMRDrkalqhYAWKYL 132
DEXHc_RAD54B cd18066
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
 1458-1536 1.22e-03

DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as RDH54, binds to double-stranded DNA, displays ATPase activity in the presence of DNA, and may have a role in meiotic and mitotic recombination. RAD54B is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350824 [Multi-domain]  Cd Length: 235  Bit Score: 42.91  E-value: 1.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1458 GGVIADQVGYGKTVISIALVaQTLSLPAPEPATPGLidlKATLIVVPGHLSKQWPNEIARFTGS-MFKVIVIQGMKDLQE 1536
Cdd:cd18066    26 GAILADEMGLGKTLQCISLI-WTLLRQGPYGGKPVI---KRALIVTPGSLVKNWKKEFQKWLGSeRIKVFTVDQDHKVEE 101
CD_HP1_like cd18631
chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; ...
 62-114 1.27e-03

chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; CHRomatin Organization Modifier (chromo) domain of mammalian HP1alpha (Cbx5), HP1beta (Cbx1), HP1gamma (Cbx5), and similar proteins. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).


Pssm-ID: 349281  Cd Length: 50  Bit Score: 38.57  E-value: 1.27e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 799320925   62 YEIDYIADSRVirRKGRqiLQYLIHWAGYAVHERTWEDEDGIggeDCA-LVQEF 114
Cdd:cd18631     2 YVVEKVLDRRV--VKGK--VEYLLKWKGYPDEDNTWEPEENL---DCPdLIAEF 48
CD_POL_like cd18977
chromodomain of a Rhizoctonia solani AG-3 Rhs1AP polyprotein, and similar proteins; This ...
 62-100 1.32e-03

chromodomain of a Rhizoctonia solani AG-3 Rhs1AP polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Rhizoctonia solani AG-3 Rhs1AP, a putative Ty3/Gypsy polyprotein/retrotransposon which includes a protease, a reverse transcriptase, a ribonuclease H, and an integrase domain, in that order, with a chromodomain at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349333  Cd Length: 57  Bit Score: 39.00  E-value: 1.32e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 799320925   62 YEIDYIADSRVIRRKGRQILQYLIHWAGYAVHERTWEDE 100
Cdd:cd18977     4 YEVEKIVGEKWKKRKNRRVKLYKVRFKGYGPEEDEWLTK 42
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 1460-1511 1.58e-03

DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350769 [Multi-domain]  Cd Length: 207  Bit Score: 42.28  E-value: 1.58e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 799320925 1460 VIADQVGYGKTvISIALVAQTLSLPApepatpgliDLKATLIVVPGHLSKQW 1511
Cdd:cd18011    21 LLADEVGLGKT-IEAGLIIKELLLRG---------DAKRVLILCPASLVEQW 62
chromodomain cd18964
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
 62-115 1.62e-03

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349320  Cd Length: 54  Bit Score: 38.47  E-value: 1.62e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 799320925   62 YEIDYIADSRVIRRKGRQILQYLIHWAGYAVHERTWEDEDGIgGEDCALVQEFY 115
Cdd:cd18964     1 FFVERIIGRRPSARDGPGKFLWLVKWDGYPIEDATWEPPENL-GEHAKLIEDFE 53
chromodomain cd18965
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
 66-103 1.64e-03

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349321  Cd Length: 53  Bit Score: 38.61  E-value: 1.64e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 799320925   66 YIADSRVIRRKGRQILQYLIHWAGYAVHERTWEDEDGI 103
Cdd:cd18965     1 YIIEALLKKRQFNRKLEYLVKWHGLPESENTWEREKDI 38
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
2151-2319 1.67e-03

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 43.47  E-value: 1.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 2151 AKLEHLVNLIHSIPKNERVLVFLQWEDLAGKVSEALSAGRIPHVTLSG--SAKSRANTLDRFQSTNAD---SARVLllkm 2225
Cdd:COG1061   290 RKDKILRELLREHPDDRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGdtPKKEREEILEAFRDGELRilvTVDVL---- 365

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 2226 ndasAAGSNLTTANHAVFLGPlfTNSlfnyRAVETQAIGRVRRYGQQKKvhihRLLALDTIDMTIFNARrtELKEKTDWE 2305
Cdd:COG1061   366 ----NEGVDVPRLDVAILLRP--TGS----PREFIQRLGRGLRPAPGKE----DALVYDFVGNDVPVLE--ELAKDLRDL 429

                         170
                  ....*....|....
gi 799320925 2306 EIPQEEYKGRGSSI 2319
Cdd:COG1061   430 AGYRVEFLDEEESE 443
HELICc smart00490
helicase superfamily c-terminal domain;
2181-2270 3.14e-03

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 38.73  E-value: 3.14e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925   2181 KVSEALSAGRIPHVTLSG--SAKSRANTLDRFqstNADSARVLLlkmndASAAGS---NLTTANHAVFLGPLFTnslfny 2255
Cdd:smart00490    2 ELAELLKELGIKVARLHGglSQEEREEILDKF---NNGKIKVLV-----ATDVAErglDLPGVDLVIIYDLPWS------ 67

                            90
                    ....*....|....*
gi 799320925   2256 RAVETQAIGRVRRYG 2270
Cdd:smart00490   68 PASYIQRIGRAGRAG 82
CD_Chp1_like cd18636
chromodomain of chromodomain-containing protein 1, and similar proteins; CHRomatin ...
 62-110 3.14e-03

chromodomain of chromodomain-containing protein 1, and similar proteins; CHRomatin Organization Modifier (chromo) domain of chromodomain-containing protein 1 (CHp1), and similar proteins. Chp1 is needed for RNA interference-dependent heterochromatin formation in fission yeast. Chp1 is a member of the RNA-induced transcriptional silencing (RITS) complex which maintains the heterochromatin regions. The chromodomain of the Chp1 component binds the histone H3 lysine 9 methylated tail (H3K9me) and the core of the nucleosome. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349286  Cd Length: 52  Bit Score: 37.81  E-value: 3.14e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 799320925   62 YEIDYIADSRViRRKGRQilQYLIHWAGYAVHERTWEDEDGIGGEDCAL 110
Cdd:cd18636     2 YEVEDILADRV-NKNGIN--EYYIKWAGYDWYDNTWEPEQNLFGAEKVL 47
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
 1457-1530 3.24e-03

DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350759 [Multi-domain]  Cd Length: 232  Bit Score: 41.59  E-value: 3.24e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 799320925 1457 RGGVIADQVGYGKTVISIALVAqtlslpapepatpGLID---LKATLIVVPGHLSKQWPNEIARFTGSMfKVIVIQG 1530
Cdd:cd18001    20 KGGILADDMGLGKTVQICAFLS-------------GMFDsglIKSVLVVMPTSLIPHWVKEFAKWTPGL-RVKVFHG 82
CD_polycomb_like cd18627
chromodomain of polycomb and chromobox family proteins; CHRomatin Organization Modifier ...
 62-103 3.35e-03

chromodomain of polycomb and chromobox family proteins; CHRomatin Organization Modifier (chromo) domain of Polycomb and Polycomb-group (PcG) chromobox (CBX) family proteins such as CBX2, CBX4, CBX6, CBX7, and CBX8. These CBX proteins are components of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.


Pssm-ID: 349277  Cd Length: 49  Bit Score: 37.37  E-value: 3.35e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 799320925   62 YEIDYIADSRVirRKGRqiLQYLIHWAGYAVHERTWEDEDGI 103
Cdd:cd18627     1 FAAECILKKRI--RKGK--VEYLVKWKGWSQKYNTWEPEENI 38
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
 60-116 3.48e-03

repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349306 [Multi-domain]  Cd Length: 54  Bit Score: 37.56  E-value: 3.48e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 799320925   60 DWYEIDYIADSRVIRRKGRQilqYLIHWAGYAVHERTWEDEDGIGGEDCALVQEFYR 116
Cdd:cd18659     1 EYTIVERIIAHREDDEGVTE---YLVKWKGLPYDECTWESEEDISDIFQEAIDEYKK 54
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
 1457-1555 3.84e-03

DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350762 [Multi-domain]  Cd Length: 240  Bit Score: 41.50  E-value: 3.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1457 RGGVI-ADQVGYGKTVISIALVaQTLsLPAPEPATPgliDLKATLIVVPGHLSKQWPNEIARFTGSMF-KVIVIQGMKDL 1534
Cdd:cd18004    24 GGGAIlADEMGLGKTLQAIALV-WTL-LKQGPYGKP---TAKKALIVCPSSLVGNWKAEFDKWLGLRRiKVVTADGNAKD 98

                          90       100
                  ....*....|....*....|....
gi 799320925 1535 QEKTIAELGKA---DIIVMASEIF 1555
Cdd:cd18004    99 VKASLDFFSSAstyPVLIISYETL 122
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 1457-1521 4.31e-03

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 39.98  E-value: 4.31e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 799320925 1457 RGGVIADQVGYGKTVISIALVAQTLSLPapepatpglidlkaTLIVVPG-HLSKQWPNEIARFTGS 1521
Cdd:cd17926    19 RRGILVLPTGSGKTLTALALIAYLKELR--------------TLIVVPTdALLDQWKERFEDFLGD 70
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
 1459-1555 4.37e-03

DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350755 [Multi-domain]  Cd Length: 222  Bit Score: 41.15  E-value: 4.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1459 GVIADQVGYGKTVISIALVA---QTLSLPAPEpatpglidlkatLIVVPGHLSKQWPNEIARFTGSMfKVIVIQGMKDLQ 1535
Cdd:cd17997    25 GILADEMGLGKTLQTISLLGylkHYKNINGPH------------LIIVPKSTLDNWMREFKRWCPSL-RVVVLIGDKEER 91

                          90       100
                  ....*....|....*....|...
gi 799320925 1536 EKTIAEL---GKADIIVMASEIF 1555
Cdd:cd17997    92 ADIIRDVllpGKFDVCITSYEMV 114
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
 1458-1517 8.19e-03

DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350758 [Multi-domain]  Cd Length: 193  Bit Score: 40.00  E-value: 8.19e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 799320925 1458 GGVIADQVGYGKTVISIALVAqtlSLPAPEpatpglIDLKATLIVVPGHLSKQWPNEIAR 1517
Cdd:cd18000    21 GGILGDEMGLGKTIQIIAFLA---ALHHSK------LGLGPSLIVCPATVLKQWVKEFHR 71
CD_EhHp1_like cd18638
chromodomain of Entamoeba histolytica heterochromatin protein 1, and similar proteins; This ...
 62-116 9.91e-03

chromodomain of Entamoeba histolytica heterochromatin protein 1, and similar proteins; This subgroup includes the N-terminal CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 (HP1)-like protein from Entamoeba histolytica, and similar proteins. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349288  Cd Length: 52  Bit Score: 36.47  E-value: 9.91e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 799320925   62 YEIDYIADSRVIRRKGrqilQYLIHWAGYAVHERTWEDEDGIGGEDCALVQEFYR 116
Cdd:cd18638     2 FEVEKIVKKKTVKGGT----EYFVKWKGYSAKENTWETEDNLEKSYKEMIDEFEK 52
 
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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