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Conserved domains on  [gi|767968080|ref|XP_011543296|]
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DNA-binding protein SMUBP-2 isoform X4 [Homo sapiens]

Protein Classification

AN1-type zinc finger protein( domain architecture ID 13510947)

AN1-type zinc finger protein similar to plant zinc finger AN1 domain-containing stress-associated proteins that may be involved in environmental stress response

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TIGR00376 super family cl36628
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 5-230 2.59e-123

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR00376:

Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 377.23  E-value: 2.59e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080    5 AGLSLSLMERLAEEYGARVvRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEE-----TGVPLLL 79
Cdd:TIGR00376 407 EELSLTLFERLIKEYPERS-RTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESeddleTGIPLLF 485

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080   80 VDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQVDLLRQSLVHRHPELEIKSVDGFQGR 159
Cdd:TIGR00376 486 IDTSGCELFELKEADSTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHRHIDIEVSSVDGFQGR 565

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767968080  160 EKEAVILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQHGEVRTAFE 230
Cdd:TIGR00376 566 EKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVREAFK 636
R3H_Smubp-2_like cd02641
R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and ...
 315-373 2.31e-27

R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.


:

Pssm-ID: 100070  Cd Length: 60  Bit Score: 104.74  E-value: 2.31e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080 315 VDHFRAMIVEFMAS-KKMQLEFPPSLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSK 373
Cdd:cd02641    1 VKHLKAMVKAFMKDpKATELEFPPTLSSHDRLLVHELAEELGLRHESTGEGSDRVITVSK 60
ZnF_AN1 smart00154
AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in ...
 491-526 7.08e-09

AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.


:

Pssm-ID: 197545  Cd Length: 39  Bit Score: 51.62  E-value: 7.08e-09
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 767968080   491 CTAGVTTLGQFCQLCSRRYCLSHHLPEIHGCGERAR 526
Cdd:smart00154   4 CRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39
PRK12438 super family cl46960
hypothetical protein; Provisional
 375-434 6.29e-05

hypothetical protein; Provisional


The actual alignment was detected with superfamily member PRK12438:

Pssm-ID: 171499 [Multi-domain]  Cd Length: 991  Bit Score: 46.01  E-value: 6.29e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767968080 375 APRPRAALGPPAGTGGPAPLQPVPPtPAQTEQPPREQRGPDQPDLRTLHLER-LQRVRSAQ 434
Cdd:PRK12438 905 APGGDAASAPPPGAGPPAPPQAVPP-PRTTQPPAAPPRGPDVPPAAVAELREtLADLRSAQ 964
 
Name Accession Description Interval E-value
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 5-230 2.59e-123

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 377.23  E-value: 2.59e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080    5 AGLSLSLMERLAEEYGARVvRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEE-----TGVPLLL 79
Cdd:TIGR00376 407 EELSLTLFERLIKEYPERS-RTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESeddleTGIPLLF 485

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080   80 VDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQVDLLRQSLVHRHPELEIKSVDGFQGR 159
Cdd:TIGR00376 486 IDTSGCELFELKEADSTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHRHIDIEVSSVDGFQGR 565

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767968080  160 EKEAVILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQHGEVRTAFE 230
Cdd:TIGR00376 566 EKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVREAFK 636
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 7-204 3.46e-76

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 240.14  E-value: 3.46e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080    7 LSLSLMERLAEEYGARVVrTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPgvaATEETGVPLLLVDTAGCg 86
Cdd:pfam13087   1 LDRSLFERLQELGPSAVV-MLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPDDF---HLPDPLGPLVFIDVDGS- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080   87 lFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPA-RDIAVVSPYNLQVDLLRQSLVHRH---PELEIKSVDGFQGREKE 162
Cdd:pfam13087  76 -EEEESDGGTSYSNEAEAELVVQLVEKLIKSGPEEpSDIGVITPYRAQVRLIRKLLKRKLggkLEIEVNTVDGFQGREKD 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 767968080  163 AVILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSR 204
Cdd:pfam13087 155 VIIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 33-219 1.73e-61

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350195 [Multi-domain]  Cd Length: 184  Bit Score: 201.31  E-value: 1.73e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080  33 MHQAIMRWASDTMYLGQLTAHSSVARHLLRDlpgvaATEETGVPLLLVDTAGCglfELEEEDEQSKGNPGEVRLVSLHIQ 112
Cdd:cd18808    1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPP-----PLPGPSKPLVFVDVSGG---EEREESGTSKSNEAEAELVVELVK 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080 113 ALVDAGVPARDIAVVSPYNLQVDLLRQSLVHRH---PELEIKSVDGFQGREKEAVILSFVRSNRKGE-VGFLAEDRRINV 188
Cdd:cd18808   73 YLLKSGVKPSSIGVITPYRAQVALIRELLRKRGgllEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNV 152

                        170       180       190
                 ....*....|....*....|....*....|.
gi 767968080 189 AVTRARRHVAVICDSRTVNNHAFLKTLVEYF 219
Cdd:cd18808  153 ALTRAKRGLIIVGNPDTLSKDPLWKKLLEYL 183
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
5-219 2.40e-44

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 168.77  E-value: 2.40e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080   5 AGLSLSLMERLAEEYGARVVrTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGvaateetgvPLLLVDTAG 84
Cdd:COG1112  606 EGLDESLLDRLLARLPERGV-MLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRLADPDS---------PLVFIDVDG 675

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080  85 CGlfeleEEDEQSKGNPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQVDLLRQSL----VHRHPELEIKSVDGFQGRE 160
Cdd:COG1112  676 VY-----ERRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLrealGDGLEPVFVGTVDRFQGDE 750

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767968080 161 KEAVILSFVRSNRK---GEVGFLAED-RRINVAVTRARRHVAVICDSRTV---NNHAFLKTLVEYF 219
Cdd:COG1112  751 RDVIIFSLVYSNDEdvpRNFGFLNGGpRRLNVAVSRARRKLIVVGSRELLdsdPSTPALKRLLEYL 816
R3H_Smubp-2_like cd02641
R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and ...
 315-373 2.31e-27

R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.


Pssm-ID: 100070  Cd Length: 60  Bit Score: 104.74  E-value: 2.31e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080 315 VDHFRAMIVEFMAS-KKMQLEFPPSLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSK 373
Cdd:cd02641    1 VKHLKAMVKAFMKDpKATELEFPPTLSSHDRLLVHELAEELGLRHESTGEGSDRVITVSK 60
R3H smart00393
Putative single-stranded nucleic acids-binding domain;
295-374 1.26e-18

Putative single-stranded nucleic acids-binding domain;


Pssm-ID: 214647  Cd Length: 79  Bit Score: 80.42  E-value: 1.26e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080   295 APSQPSLNGGSPEGVESQDGVDHFRAMIVEFMASKKMQLEFPPsLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSKR 374
Cdd:smart00393   1 ADFLPVTLDALSYRPRRREELIELELEIARFVKSTKESVELPP-MNSYERKIVHELAEKYGLESESFGEGPKRRVVISKK 79
R3H pfam01424
R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most ...
 322-373 1.13e-11

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.


Pssm-ID: 460206  Cd Length: 60  Bit Score: 60.20  E-value: 1.13e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767968080  322 IVEFMASKKMQLEFPPsLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSK 373
Cdd:pfam01424  10 LAEFVKDTGKSLELPP-MSSYERRIIHELAQKYGLESESEGEEPNRRVVVYK 60
ZnF_AN1 smart00154
AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in ...
 491-526 7.08e-09

AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.


Pssm-ID: 197545  Cd Length: 39  Bit Score: 51.62  E-value: 7.08e-09
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 767968080   491 CTAGVTTLGQFCQLCSRRYCLSHHLPEIHGCGERAR 526
Cdd:smart00154   4 CRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39
zf-AN1 pfam01428
AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in ...
 486-523 1.19e-08

AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues.


Pssm-ID: 460208  Cd Length: 37  Bit Score: 50.77  E-value: 1.19e-08
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 767968080  486 CGFAKCTAGVTTLGQfCQLCSRRYCLSHHLPEIHGCGE 523
Cdd:pfam01428   1 CSFKGCKKKDFLPFK-CRFCGKNFCLKHRLPEDHDCSG 37
PRK12438 PRK12438
hypothetical protein; Provisional
 375-434 6.29e-05

hypothetical protein; Provisional


Pssm-ID: 171499 [Multi-domain]  Cd Length: 991  Bit Score: 46.01  E-value: 6.29e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767968080 375 APRPRAALGPPAGTGGPAPLQPVPPtPAQTEQPPREQRGPDQPDLRTLHLER-LQRVRSAQ 434
Cdd:PRK12438 905 APGGDAASAPPPGAGPPAPPQAVPP-PRTTQPPAAPPRGPDVPPAAVAELREtLADLRSAQ 964
PHA03247 PHA03247
large tegument protein UL36; Provisional
 251-467 5.35e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.92  E-value: 5.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080  251 AATKPQGPATSTRTGSQRQEGGQEAAAPARQgrkKPAGKSLASEAPSQPSLNGGSPEGVESQDGVDHFRAMIVEFMASKK 330
Cdd:PHA03247 2744 VPAGPATPGGPARPARPPTTAGPPAPAPPAA---PAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPP 2820

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080  331 MQLEFPPSLNSHDRLRVH-QIAEEHGLRHDSSGEGKRRFITVSKRAPRPRAALGPPAGTGGPAPLQPVPPTPAQTE---Q 406
Cdd:PHA03247 2821 AASPAGPLPPPTSAQPTApPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTEsfaL 2900

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767968080  407 PPREQRGPDQPDLRTLHLERLQRVRSAQGQPAsKEQQASGQQKLPEKKKKKAKGHPATDLP 467
Cdd:PHA03247 2901 PPDQPERPPQPQAPPPPQPQPQPPPPPQPQPP-PPPPPRPQPPLAPTTDPAGAGEPSGAVP 2960
 
Name Accession Description Interval E-value
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 5-230 2.59e-123

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 377.23  E-value: 2.59e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080    5 AGLSLSLMERLAEEYGARVvRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEE-----TGVPLLL 79
Cdd:TIGR00376 407 EELSLTLFERLIKEYPERS-RTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESeddleTGIPLLF 485

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080   80 VDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQVDLLRQSLVHRHPELEIKSVDGFQGR 159
Cdd:TIGR00376 486 IDTSGCELFELKEADSTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHRHIDIEVSSVDGFQGR 565

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767968080  160 EKEAVILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQHGEVRTAFE 230
Cdd:TIGR00376 566 EKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVREAFK 636
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 7-204 3.46e-76

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 240.14  E-value: 3.46e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080    7 LSLSLMERLAEEYGARVVrTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPgvaATEETGVPLLLVDTAGCg 86
Cdd:pfam13087   1 LDRSLFERLQELGPSAVV-MLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPDDF---HLPDPLGPLVFIDVDGS- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080   87 lFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPA-RDIAVVSPYNLQVDLLRQSLVHRH---PELEIKSVDGFQGREKE 162
Cdd:pfam13087  76 -EEEESDGGTSYSNEAEAELVVQLVEKLIKSGPEEpSDIGVITPYRAQVRLIRKLLKRKLggkLEIEVNTVDGFQGREKD 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 767968080  163 AVILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSR 204
Cdd:pfam13087 155 VIIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 33-219 1.73e-61

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350195 [Multi-domain]  Cd Length: 184  Bit Score: 201.31  E-value: 1.73e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080  33 MHQAIMRWASDTMYLGQLTAHSSVARHLLRDlpgvaATEETGVPLLLVDTAGCglfELEEEDEQSKGNPGEVRLVSLHIQ 112
Cdd:cd18808    1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPP-----PLPGPSKPLVFVDVSGG---EEREESGTSKSNEAEAELVVELVK 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080 113 ALVDAGVPARDIAVVSPYNLQVDLLRQSLVHRH---PELEIKSVDGFQGREKEAVILSFVRSNRKGE-VGFLAEDRRINV 188
Cdd:cd18808   73 YLLKSGVKPSSIGVITPYRAQVALIRELLRKRGgllEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNV 152

                        170       180       190
                 ....*....|....*....|....*....|.
gi 767968080 189 AVTRARRHVAVICDSRTVNNHAFLKTLVEYF 219
Cdd:cd18808  153 ALTRAKRGLIIVGNPDTLSKDPLWKKLLEYL 183
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
5-219 2.40e-44

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 168.77  E-value: 2.40e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080   5 AGLSLSLMERLAEEYGARVVrTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGvaateetgvPLLLVDTAG 84
Cdd:COG1112  606 EGLDESLLDRLLARLPERGV-MLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRLADPDS---------PLVFIDVDG 675

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080  85 CGlfeleEEDEQSKGNPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQVDLLRQSL----VHRHPELEIKSVDGFQGRE 160
Cdd:COG1112  676 VY-----ERRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLrealGDGLEPVFVGTVDRFQGDE 750

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767968080 161 KEAVILSFVRSNRK---GEVGFLAED-RRINVAVTRARRHVAVICDSRTV---NNHAFLKTLVEYF 219
Cdd:COG1112  751 RDVIIFSLVYSNDEdvpRNFGFLNGGpRRLNVAVSRARRKLIVVGSRELLdsdPSTPALKRLLEYL 816
R3H_Smubp-2_like cd02641
R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and ...
 315-373 2.31e-27

R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.


Pssm-ID: 100070  Cd Length: 60  Bit Score: 104.74  E-value: 2.31e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080 315 VDHFRAMIVEFMAS-KKMQLEFPPSLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSK 373
Cdd:cd02641    1 VKHLKAMVKAFMKDpKATELEFPPTLSSHDRLLVHELAEELGLRHESTGEGSDRVITVSK 60
R3H smart00393
Putative single-stranded nucleic acids-binding domain;
295-374 1.26e-18

Putative single-stranded nucleic acids-binding domain;


Pssm-ID: 214647  Cd Length: 79  Bit Score: 80.42  E-value: 1.26e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080   295 APSQPSLNGGSPEGVESQDGVDHFRAMIVEFMASKKMQLEFPPsLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSKR 374
Cdd:smart00393   1 ADFLPVTLDALSYRPRRREELIELELEIARFVKSTKESVELPP-MNSYERKIVHELAEKYGLESESFGEGPKRRVVISKK 79
R3H cd02325
R3H domain. The name of the R3H domain comes from the characteristic spacing of the most ...
 315-373 6.41e-12

R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100064  Cd Length: 59  Bit Score: 60.71  E-value: 6.41e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080 315 VDHFRAMIVEFMASK-KMQLEFPPsLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSK 373
Cdd:cd02325    1 REEREEELEAFAKDAaGKSLELPP-MNSYERKLIHDLAEYYGLKSESEGEGPNRRVVITK 59
R3H pfam01424
R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most ...
 322-373 1.13e-11

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.


Pssm-ID: 460206  Cd Length: 60  Bit Score: 60.20  E-value: 1.13e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767968080  322 IVEFMASKKMQLEFPPsLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSK 373
Cdd:pfam01424  10 LAEFVKDTGKSLELPP-MSSYERRIIHELAQKYGLESESEGEEPNRRVVVYK 60
R3H_G-patch cd02646
R3H domain of a group of fungal and plant proteins with unknown function, who also contain a ...
 315-373 1.84e-09

R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100075  Cd Length: 58  Bit Score: 53.73  E-value: 1.84e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 767968080 315 VDHFRAMIVEFMASKKMQLEFPPsLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSK 373
Cdd:cd02646    1 IEDIKDEIEAFLLDSRDSLSFPP-MDKHGRKTIHKLANCYNLKSKSRGKGKKRFVTVTK 58
ZnF_AN1 smart00154
AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in ...
 491-526 7.08e-09

AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.


Pssm-ID: 197545  Cd Length: 39  Bit Score: 51.62  E-value: 7.08e-09
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 767968080   491 CTAGVTTLGQFCQLCSRRYCLSHHLPEIHGCGERAR 526
Cdd:smart00154   4 CRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 122-197 8.21e-09

C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The 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: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 52.82  E-value: 8.21e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080 122 RDIAVVSPYNLQVDLLRQSLVHRH------PELEIKSVDGFQGREKEAVILSFVRSNrkgevgfLAEDRRINVAVTRARR 195
Cdd:cd18786   11 YKGVVLTPYHRDRAYLNQYLQGLSldefdlQLVGAITIDSSQGLTFDVVTLYLPTAN-------SLTPRRLYVALTRARK 83


                 ..
gi 767968080 196 HV 197
Cdd:cd18786   84 RL 85
zf-AN1 pfam01428
AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in ...
 486-523 1.19e-08

AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues.


Pssm-ID: 460208  Cd Length: 37  Bit Score: 50.77  E-value: 1.19e-08
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 767968080  486 CGFAKCTAGVTTLGQfCQLCSRRYCLSHHLPEIHGCGE 523
Cdd:pfam01428   1 CSFKGCKKKDFLPFK-CRFCGKNFCLKHRLPEDHDCSG 37
R3H_DEXH_helicase cd06007
R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may ...
 321-373 1.59e-08

R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100077  Cd Length: 59  Bit Score: 51.16  E-value: 1.59e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 767968080 321 MIVEFMASKKMQLEFPPSLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSK 373
Cdd:cd06007    7 ALEDFRASDNEEYEFPSSLTNHERAVIHRLCRKLGLKSKSKGKGSNRRLSVYK 59
R3H_NRF cd02640
R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB ...
 319-373 1.25e-07

R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100069  Cd Length: 60  Bit Score: 48.55  E-value: 1.25e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 767968080 319 RAMIVEFMASKKMQ-LEFPPSLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSK 373
Cdd:cd02640    5 RQIIQNYAHSDDIRdMVFSPEFSKEERALIHQIAQKYGLKSRSYGSGNDRYLVISK 60
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 2-32 5.23e-07

DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 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: 350802 [Multi-domain]  Cd Length: 191  Bit Score: 50.30  E-value: 5.23e-07
                         10        20        30
                 ....*....|....*....|....*....|.
gi 767968080   2 AALAGLSLSLMERLAEEYGARVVRTLTVQYR 32
Cdd:cd18044  161 AARGGLGVTLFERLVNLYGESVVRMLTVQYR 191
R3H_encore_like cd02642
R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the ...
 322-374 2.00e-05

R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100071  Cd Length: 63  Bit Score: 42.59  E-value: 2.00e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 767968080 322 IVEFMASKK-MQLEFPPSlNSHDRLRVHQIAEEHGLRHDSSGEGKRRfITVSKR 374
Cdd:cd02642   12 LLAFIKDSTrQSLELPPM-NSYYRLLAHRVAQYYGLDHNVDNSGGKC-VIVNKT 63
SF1_C_UvrD cd18807
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ...
 90-201 5.19e-05

C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. This family also includes ATP-dependent helicase/nuclease AddA and helicase/nuclease RecBCD subunit RecB, among others. UvrD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350194 [Multi-domain]  Cd Length: 150  Bit Score: 43.76  E-value: 5.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080  90 LEEEDEQSkgnpgEVRLVSLHIQALVDAG-VPARDIAVVSPYNLQVDLLRQSL------VHrhpeleiKSvdgfQGREKE 162
Cdd:cd18807   37 LLAKDEAD-----EAKAIADEIKRLIESGpVQYSDIAILVRTNRQARVIEEALrvtlmtIH-------AS----KGLEFP 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 767968080 163 AVILSFVRSNRKGEVGF----------LAEDRRI-NVAVTRARRHVAVIC 201
Cdd:cd18807  101 VVFIVGLGEGFIPSDASyhaakedeerLEEERRLlYVALTRAKKELYLVG 150
PRK12438 PRK12438
hypothetical protein; Provisional
 375-434 6.29e-05

hypothetical protein; Provisional


Pssm-ID: 171499 [Multi-domain]  Cd Length: 991  Bit Score: 46.01  E-value: 6.29e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767968080 375 APRPRAALGPPAGTGGPAPLQPVPPtPAQTEQPPREQRGPDQPDLRTLHLER-LQRVRSAQ 434
Cdd:PRK12438 905 APGGDAASAPPPGAGPPAPPQAVPP-PRTTQPPAAPPRGPDVPPAAVAELREtLADLRSAQ 964
PHA03247 PHA03247
large tegument protein UL36; Provisional
 251-467 5.35e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.92  E-value: 5.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080  251 AATKPQGPATSTRTGSQRQEGGQEAAAPARQgrkKPAGKSLASEAPSQPSLNGGSPEGVESQDGVDHFRAMIVEFMASKK 330
Cdd:PHA03247 2744 VPAGPATPGGPARPARPPTTAGPPAPAPPAA---PAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPP 2820

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080  331 MQLEFPPSLNSHDRLRVH-QIAEEHGLRHDSSGEGKRRFITVSKRAPRPRAALGPPAGTGGPAPLQPVPPTPAQTE---Q 406
Cdd:PHA03247 2821 AASPAGPLPPPTSAQPTApPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTEsfaL 2900

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767968080  407 PPREQRGPDQPDLRTLHLERLQRVRSAQGQPAsKEQQASGQQKLPEKKKKKAKGHPATDLP 467
Cdd:PHA03247 2901 PPDQPERPPQPQAPPPPQPQPQPPPPPQPQPP-PPPPPRPQPPLAPTTDPAGAGEPSGAVP 2960
PHA03378 PHA03378
EBNA-3B; Provisional
 250-445 5.92e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 39.67  E-value: 5.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080 250 HAATKPQGPATSTR---TGSQRQEGGQEAAAPARQGRKKPAG-KSLASEAPSQP--------SLNGGSPEGVESQDGVDH 317
Cdd:PHA03378 601 HPSQTPEPPTTQSHipeTSAPRQWPMPLRPIPMRPLRMQPITfNVLVFPTPHQPpqveitpyKPTWTQIGHIPYQPSPTG 680

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080 318 FRAMIVEFMASKKMQ------LEFPPSLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSKRAPRPRAALG-------- 383
Cdd:PHA03378 681 ANTMLPIQWAPGTMQppprapTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGrarppaaa 760

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767968080 384 -----PPAGTGG-PAPLQP--VPPTPAQ------TEQPPRE---------------QRGPDQPDLRTLHLERLQRVRSAQ 434
Cdd:PHA03378 761 pgrarPPAAAPGaPTPQPPpqAPPAPQQrprgapTPQPPPQagptsmqlmpraapgQQGPTKQILRQLLTGGVKRGRPSL 840

                        250
                 ....*....|.
gi 767968080 435 GQPASKEQQAS 445
Cdd:PHA03378 841 KKPAALERQAA 851
 
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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