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Conserved domains on  [gi|221330969|ref|NP_001137907|]
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senataxin, isoform B [Drosophila melanogaster]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
1175-1428 2.22e-64

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: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 219.14  E-value: 2.22e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1175 HQENIVLHTYQriiddlQPSLTLIQGPPGTGKSRVISELCLQTL-YGNAAKTLDRKILICAHSNTAVDHIVGLLgsvLRV 1253
Cdd:pfam13086    1 SQREAIRSALS------SSHFTLIQGPPGTGKTTTIVELIRQLLsYPATSAAAGPRILVCAPSNAAVDNILERL---LRK 71
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1254 MNRDQFHLLRFGMHEKMSHYSRPFSLEAHF-----NKAKEQKLQRVSKENAEILKKQHNDLKDEIqqlKEKTNLTSTYLL 1328
Cdd:pfam13086   72 GQKYGPKIVRIGHPAAISEAVLPVSLDYLVesklnNEEDAQIVKDISKELEKLAKALRAFEKEII---VEKLLKSRNKDK 148
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1329 QQLQQKEKKLQLISNQLSPPLTQREEFEISHMcVTRANIICTTLSSC--VKLANYvDFFDICIVDEATQCTEPWTLLPMR 1406
Cdd:pfam13086  149 SKLEQERRKLRSERKELRKELRRREQSLEREI-LDEAQIVCSTLSGAgsRLLSSL-ANFDVVIIDEAAQALEPSTLIPLL 226
                          250       260
                   ....*....|....*....|..
gi 221330969  1407 FGLTHMVLVGDMQQLPAVVLSK 1428
Cdd:pfam13086  227 RGPKKVVLVGDPKQLPPTVISK 248
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
1299-1646 1.26e-53

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


:

Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 203.44  E-value: 1.26e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1299 AEILKKQHNDLKDEIQQLKEKTNLTSTyLLQQLQQKEKKLQLISNQLSppltqreefeishmcvTRANIICTTLSSCVKL 1378
Cdd:COG1112   486 EELIEEHPEELEKLIAELREAARLRRA-LRRELKKRRELRKLLWDALL----------------ELAPVVGMTPASVARL 548
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1379 ANYV-DFFDICIVDEATQCTEPWTLLPMRFGlTHMVLVGDMQQLPAVVLS---KKAIDFGLSNSMFDRIQRSLqtqldkP 1454
Cdd:COG1112   549 LPLGeGSFDLVIIDEASQATLAEALGALARA-KRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLARL------P 621
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1455 GSYHLmhtklfkLSTQYRMHPEICRWPNQYFYEDQLINAECTA--RFASPLIPYCVINLKYTCDSNGaqnKSISNNEEAR 1532
Cdd:COG1112   622 ERGVM-------LREHYRMHPEIIAFSNRLFYDGKLVPLPSPKarRLADPDSPLVFIDVDGVYERRG---GSRTNPEEAE 691
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1533 FVAKLLTEMDKHMPSKRfSYGLISPYQNQCYALSQVIPSHMNITPQ-----TVDSYQGLEKDVIIIS------NARTRGC 1601
Cdd:COG1112   692 AVVELVRELLEDGPDGE-SIGVITPYRAQVALIRELLREALGDGLEpvfvgTVDRFQGDERDVIIFSlvysndEDVPRNF 770
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 221330969 1602 GFLT-NYQRLNVALTRPRRCLVICGNFEDLKSVE---MWRNLLDDARKR 1646
Cdd:COG1112   771 GFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDPstpALKRLLEYLERA 819
FHA cd00060
forkhead associated (FHA) domain superfamily; Forkhead-associated (FHA) domains are small ...
12-94 6.70e-12

forkhead associated (FHA) domain superfamily; Forkhead-associated (FHA) domains are small phosphopeptide recognition modules mostly found in eubacteria and eukaryotes. It is about 95-120 residues long that fold into an 11-stranded beta-sandwich. FHA domains can mediate the recognition of phosphorylated and non-phosphorylated substrates, as well as protein oligomerization. They specifically recognize threonine phosphorylation (pThr) accompanying activation of protein serine/threonine kinases. FHA domains show diverse ligand specificity. They may recognize the pTXXD motif, the pTXXI/L motif, and TQ clusters (singly and multiply phosphorylated). In eukaryotes, FHA superfamily members include forkhead-type transcription factors, as well as other signaling proteins, such as many regulatory proteins, kinases, phosphatases, motor proteins called kinesins, and metabolic enzymes. Many of them localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. FHA domains play important roles in human diseases, particularly in relation to DNA damage responses and cancers. In bacteria, FHA domain-containing proteins may participate in injection of viral proteins into host cells, transmembrane transporters, and cell division. FHA domain-containing proteins rarely include more than one copy of the domain. The only exception in eukaryotes is the checkpoint kinase Rad53 from Saccharomyces cerevisiae, which harbors two FHA domains (FHA1 and FHA2) flanking a central kinase domain. The two FHA domains recognize different phosphorylated targets and function independently from one another. In contrast, Mycobacterium tuberculosis ABC transporter Rv1747 contains two FHA domains but only one of them is essential for protein function.


:

Pssm-ID: 438714 [Multi-domain]  Cd Length: 92  Bit Score: 63.06  E-value: 6.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969   12 TGARLILHNGTNLMGRHSRCRIILGGQYqfVSREHANIIVSEKGVEVESLNPLNGLFINGGKLGDKInrlAVAEGSTISL 91
Cdd:cd00060    10 GGREFPLTKGVVTIGRSPDCDIVLDDPS--VSRRHARIEVDGGGVYLEDLGSTNGTFVNGKRITPPV---PLQDGDVIRL 84

                  ...
gi 221330969   92 GVT 94
Cdd:cd00060    85 GDT 87
 
Name Accession Description Interval E-value
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
1175-1428 2.22e-64

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: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 219.14  E-value: 2.22e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1175 HQENIVLHTYQriiddlQPSLTLIQGPPGTGKSRVISELCLQTL-YGNAAKTLDRKILICAHSNTAVDHIVGLLgsvLRV 1253
Cdd:pfam13086    1 SQREAIRSALS------SSHFTLIQGPPGTGKTTTIVELIRQLLsYPATSAAAGPRILVCAPSNAAVDNILERL---LRK 71
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1254 MNRDQFHLLRFGMHEKMSHYSRPFSLEAHF-----NKAKEQKLQRVSKENAEILKKQHNDLKDEIqqlKEKTNLTSTYLL 1328
Cdd:pfam13086   72 GQKYGPKIVRIGHPAAISEAVLPVSLDYLVesklnNEEDAQIVKDISKELEKLAKALRAFEKEII---VEKLLKSRNKDK 148
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1329 QQLQQKEKKLQLISNQLSPPLTQREEFEISHMcVTRANIICTTLSSC--VKLANYvDFFDICIVDEATQCTEPWTLLPMR 1406
Cdd:pfam13086  149 SKLEQERRKLRSERKELRKELRRREQSLEREI-LDEAQIVCSTLSGAgsRLLSSL-ANFDVVIIDEAAQALEPSTLIPLL 226
                          250       260
                   ....*....|....*....|..
gi 221330969  1407 FGLTHMVLVGDMQQLPAVVLSK 1428
Cdd:pfam13086  227 RGPKKVVLVGDPKQLPPTVISK 248
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
1299-1646 1.26e-53

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 203.44  E-value: 1.26e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1299 AEILKKQHNDLKDEIQQLKEKTNLTSTyLLQQLQQKEKKLQLISNQLSppltqreefeishmcvTRANIICTTLSSCVKL 1378
Cdd:COG1112   486 EELIEEHPEELEKLIAELREAARLRRA-LRRELKKRRELRKLLWDALL----------------ELAPVVGMTPASVARL 548
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1379 ANYV-DFFDICIVDEATQCTEPWTLLPMRFGlTHMVLVGDMQQLPAVVLS---KKAIDFGLSNSMFDRIQRSLqtqldkP 1454
Cdd:COG1112   549 LPLGeGSFDLVIIDEASQATLAEALGALARA-KRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLARL------P 621
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1455 GSYHLmhtklfkLSTQYRMHPEICRWPNQYFYEDQLINAECTA--RFASPLIPYCVINLKYTCDSNGaqnKSISNNEEAR 1532
Cdd:COG1112   622 ERGVM-------LREHYRMHPEIIAFSNRLFYDGKLVPLPSPKarRLADPDSPLVFIDVDGVYERRG---GSRTNPEEAE 691
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1533 FVAKLLTEMDKHMPSKRfSYGLISPYQNQCYALSQVIPSHMNITPQ-----TVDSYQGLEKDVIIIS------NARTRGC 1601
Cdd:COG1112   692 AVVELVRELLEDGPDGE-SIGVITPYRAQVALIRELLREALGDGLEpvfvgTVDRFQGDERDVIIFSlvysndEDVPRNF 770
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 221330969 1602 GFLT-NYQRLNVALTRPRRCLVICGNFEDLKSVE---MWRNLLDDARKR 1646
Cdd:COG1112   771 GFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDPstpALKRLLEYLERA 819
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
1147-1649 4.30e-49

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: 186.56  E-value: 4.30e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1147 ILKPTQTVNEVSLpkQPFTfkgcHKLNEHQENIVLHTYqriiddLQPSLTLIQGPPGTGKSRVISELCLQTLYGNaaktl 1226
Cdd:TIGR00376  139 REAPSKASEIHDF--QFFD----PNLNESQKEAVLFAL------SSKDLFLIHGPPGTGKTRTVVELIRQLVKRG----- 201
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1227 dRKILICAHSNTAVDHIV-GLLGSVLRVmnrdqfhlLRFGMHEKMSHYSRPFSLEAHF-NKAKEQKLQRVSKENAEILKK 1304
Cdd:TIGR00376  202 -LRVLVTAPSNIAVDNLLeRLALCDQKI--------VRLGHPARLLKSNKQHSLDYLIeNHPKYQIVADIREKIDELIEE 272
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1305 QHNDLKD---------EIQQLKEKTNLTSTYLLQQLQQKEKKLQLISNQ-LSPPLT--QREEFEISHMCVTRANIICTTL 1372
Cdd:TIGR00376  273 RNKKTKPspqkrrglsDIKILRKALKKREARGIESLKIASMAEWIETNKsIDRLLKllPESEERIMNEILAESDATNSMA 352
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1373 SSCVKLANYvdfFDICIVDEATQCTEPWTLLPMRFGlTHMVLVGDMQQLPAVVLSKKAidFGLSNSMFDRIQRSLqtqld 1452
Cdd:TIGR00376  353 GSEILNGQY---FDVAVIDEASQAMEPSCLIPLLKA-RKLILAGDHKQLPPTILSHDA--EELSLTLFERLIKEY----- 421
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1453 kPGSYHLmhtklfkLSTQYRMHPEICRWPNQYFYEDQLINAECTARFA-------------------SPLIPYCVINLKY 1513
Cdd:TIGR00376  422 -PERSRT-------LNVQYRMNQKIMEFPSREFYNGKLTAHESVANILlrdlpkveateseddletgIPLLFIDTSGCEL 493
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1514 tCDSNGAQNKSISNNEEARFVAKLLTEMDKhMPSKRFSYGLISPYQNQCYALSQVIPSHM-NITPQTVDSYQGLEKDVII 1592
Cdd:TIGR00376  494 -FELKEADSTSKYNPGEAELVSEIIQALVK-MGVPANDIGVITPYDAQVDLLRQLLEHRHiDIEVSSVDGFQGREKEVII 571
                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1593 ISNART---RGCGFLTNYQRLNVALTRPRRCLVICGNFEDLKSVEMWRNLLDDARKRKVY 1649
Cdd:TIGR00376  572 ISFVRSnrkGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEV 631
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
1435-1626 5.53e-47

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: 167.34  E-value: 5.53e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1435 LSNSMFDRIQRSLqtqldkpgsyhlmHTKLFKLSTQYRMHPEICRWPNQYFYEDQLINAECTA--------RFASPLIPY 1506
Cdd:pfam13087    1 LDRSLFERLQELG-------------PSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAerplpddfHLPDPLGPL 67
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1507 CVINLKYTCDSNGAQNKSISNNEEARFVAKLLTEMDKHMPSKRFSYGLISPYQNQCYALSQVIPSHMNITPQ----TVDS 1582
Cdd:pfam13087   68 VFIDVDGSEEEESDGGTSYSNEAEAELVVQLVEKLIKSGPEEPSDIGVITPYRAQVRLIRKLLKRKLGGKLEievnTVDG 147
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 221330969  1583 YQGLEKDVIIISNARTRGC---GFLTNYQRLNVALTRPRRCLVICGN 1626
Cdd:pfam13087  148 FQGREKDVIIFSCVRSNEKggiGFLSDPRRLNVALTRAKRGLIIVGN 194
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
1172-1472 9.42e-44

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX 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: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 158.92  E-value: 9.42e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1172 LNEHQENIVLHTYQRiiddlQPSLTLIQGPPGTGKSRVISELCLQTLYGNAAKTLD-------------------RKILI 1232
Cdd:cd18042     1 LNESQLEAIASALQN-----SPGITLIQGPPGTGKTKTIVGILSVLLAGKYRKYYEkvkkklrklqrnlnnkkkkNRILV 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1233 CAHSNTAVDHIVgllgsvLRVMNrdqfhllrfgmhekmshySRPFSLEAHFNKAKeqkLQRVSKENA--EILKKqhndlk 1310
Cdd:cd18042    76 CAPSNAAVDEIV------LRLLS------------------EGFLDGDGRSYKPN---VVRVGRQELraSILNE------ 122
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1311 deiqqlkektnltstyllqqlqqkekklqlisnqlsppltqreefeishmcvtrANIICTTLSSC--VKLANYVDFFDIC 1388
Cdd:cd18042   123 ------------------------------------------------------ADIVCTTLSSSgsDLLESLPRGFDTV 148
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1389 IVDEATQCTEPWTLLPMRFGLTHMVLVGDMQQLPAVVLSKKAIDFGLSNSMFDRIQRSLQTqldkpgsyHLMhtklfkLS 1468
Cdd:cd18042   149 IIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQLAGYP--------VLM------LT 214

                  ....
gi 221330969 1469 TQYR 1472
Cdd:cd18042   215 TQYR 218
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
1473-1644 8.49e-43

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: 154.70  E-value: 8.49e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1473 MHPEICRWPNQYFYEDQLINAECTARFAS------PLIPYCVINLKYtCDSNGAQNKSISNNEEARFVAKLLTEMDKHmP 1546
Cdd:cd18808     1 MHPEISEFPSKLFYEGKLKAGVSVAARLNppplpgPSKPLVFVDVSG-GEEREESGTSKSNEAEAELVVELVKYLLKS-G 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1547 SKRFSYGLISPYQNQCYALSQVIPSHMNITPQ----TVDSYQGLEKDVIIISNARTR----GCGFLTNYQRLNVALTRPR 1618
Cdd:cd18808    79 VKPSSIGVITPYRAQVALIRELLRKRGGLLEDvevgTVDNFQGREKDVIILSLVRSNesggSIGFLSDPRRLNVALTRAK 158
                         170       180
                  ....*....|....*....|....*.
gi 221330969 1619 RCLVICGNFEDLKSVEMWRNLLDDAR 1644
Cdd:cd18808   159 RGLIIVGNPDTLSKDPLWKKLLEYLE 184
FHA cd00060
forkhead associated (FHA) domain superfamily; Forkhead-associated (FHA) domains are small ...
12-94 6.70e-12

forkhead associated (FHA) domain superfamily; Forkhead-associated (FHA) domains are small phosphopeptide recognition modules mostly found in eubacteria and eukaryotes. It is about 95-120 residues long that fold into an 11-stranded beta-sandwich. FHA domains can mediate the recognition of phosphorylated and non-phosphorylated substrates, as well as protein oligomerization. They specifically recognize threonine phosphorylation (pThr) accompanying activation of protein serine/threonine kinases. FHA domains show diverse ligand specificity. They may recognize the pTXXD motif, the pTXXI/L motif, and TQ clusters (singly and multiply phosphorylated). In eukaryotes, FHA superfamily members include forkhead-type transcription factors, as well as other signaling proteins, such as many regulatory proteins, kinases, phosphatases, motor proteins called kinesins, and metabolic enzymes. Many of them localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. FHA domains play important roles in human diseases, particularly in relation to DNA damage responses and cancers. In bacteria, FHA domain-containing proteins may participate in injection of viral proteins into host cells, transmembrane transporters, and cell division. FHA domain-containing proteins rarely include more than one copy of the domain. The only exception in eukaryotes is the checkpoint kinase Rad53 from Saccharomyces cerevisiae, which harbors two FHA domains (FHA1 and FHA2) flanking a central kinase domain. The two FHA domains recognize different phosphorylated targets and function independently from one another. In contrast, Mycobacterium tuberculosis ABC transporter Rv1747 contains two FHA domains but only one of them is essential for protein function.


Pssm-ID: 438714 [Multi-domain]  Cd Length: 92  Bit Score: 63.06  E-value: 6.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969   12 TGARLILHNGTNLMGRHSRCRIILGGQYqfVSREHANIIVSEKGVEVESLNPLNGLFINGGKLGDKInrlAVAEGSTISL 91
Cdd:cd00060    10 GGREFPLTKGVVTIGRSPDCDIVLDDPS--VSRRHARIEVDGGGVYLEDLGSTNGTFVNGKRITPPV---PLQDGDVIRL 84

                  ...
gi 221330969   92 GVT 94
Cdd:cd00060    85 GDT 87
FHA COG1716
Forkhead associated (FHA) domain, binds pSer, pThr, pTyr [Signal transduction mechanisms];
7-92 1.02e-11

Forkhead associated (FHA) domain, binds pSer, pThr, pTyr [Signal transduction mechanisms];


Pssm-ID: 441322 [Multi-domain]  Cd Length: 96  Bit Score: 62.67  E-value: 1.02e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969    7 LEHVTTGARLILHNGTNLMGRHSRCRIILGGQYqfVSREHANIIVSEKGVEVESLNPLNGLFINGGKLGDKInrlAVAEG 86
Cdd:COG1716     7 LEGPLAGRRFPLDGGPLTIGRAPDNDIVLDDPT--VSRRHARIRRDGGGWVLEDLGSTNGTFVNGQRVTEPA---PLRDG 81

                  ....*.
gi 221330969   87 STISLG 92
Cdd:COG1716    82 DVIRLG 87
FHA pfam00498
FHA domain; The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
24-91 5.26e-08

FHA domain; The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.


Pssm-ID: 459831 [Multi-domain]  Cd Length: 66  Bit Score: 51.04  E-value: 5.26e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 221330969    24 LMGRHSRCRIILggQYQFVSREHANIIVSEKG-VEVESLNPLNGLFINGGKLGDKINRLavAEGSTISL 91
Cdd:pfam00498    2 TIGRSPDCDIVL--DDPSVSRRHAEIRYDGGGrFYLEDLGSTNGTFVNGQRLGPEPVRL--KDGDVIRL 66
FHA smart00240
Forkhead associated domain; Found in eukaryotic and prokaryotic proteins. Putative nuclear ...
26-74 5.16e-04

Forkhead associated domain; Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.


Pssm-ID: 214578 [Multi-domain]  Cd Length: 52  Bit Score: 39.47  E-value: 5.16e-04
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|..
gi 221330969     26 GRHS-RCRIILGGQyqFVSREHAnIIVSEKG--VEVESLNPLNGLFINGGKL 74
Cdd:smart00240    4 GRSSeDCDIQLDGP--SISRRHA-VIVYDGGgrFYLIDLGSTNGTFVNGKRI 52
 
Name Accession Description Interval E-value
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
1175-1428 2.22e-64

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: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 219.14  E-value: 2.22e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1175 HQENIVLHTYQriiddlQPSLTLIQGPPGTGKSRVISELCLQTL-YGNAAKTLDRKILICAHSNTAVDHIVGLLgsvLRV 1253
Cdd:pfam13086    1 SQREAIRSALS------SSHFTLIQGPPGTGKTTTIVELIRQLLsYPATSAAAGPRILVCAPSNAAVDNILERL---LRK 71
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1254 MNRDQFHLLRFGMHEKMSHYSRPFSLEAHF-----NKAKEQKLQRVSKENAEILKKQHNDLKDEIqqlKEKTNLTSTYLL 1328
Cdd:pfam13086   72 GQKYGPKIVRIGHPAAISEAVLPVSLDYLVesklnNEEDAQIVKDISKELEKLAKALRAFEKEII---VEKLLKSRNKDK 148
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1329 QQLQQKEKKLQLISNQLSPPLTQREEFEISHMcVTRANIICTTLSSC--VKLANYvDFFDICIVDEATQCTEPWTLLPMR 1406
Cdd:pfam13086  149 SKLEQERRKLRSERKELRKELRRREQSLEREI-LDEAQIVCSTLSGAgsRLLSSL-ANFDVVIIDEAAQALEPSTLIPLL 226
                          250       260
                   ....*....|....*....|..
gi 221330969  1407 FGLTHMVLVGDMQQLPAVVLSK 1428
Cdd:pfam13086  227 RGPKKVVLVGDPKQLPPTVISK 248
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
1299-1646 1.26e-53

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 203.44  E-value: 1.26e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1299 AEILKKQHNDLKDEIQQLKEKTNLTSTyLLQQLQQKEKKLQLISNQLSppltqreefeishmcvTRANIICTTLSSCVKL 1378
Cdd:COG1112   486 EELIEEHPEELEKLIAELREAARLRRA-LRRELKKRRELRKLLWDALL----------------ELAPVVGMTPASVARL 548
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1379 ANYV-DFFDICIVDEATQCTEPWTLLPMRFGlTHMVLVGDMQQLPAVVLS---KKAIDFGLSNSMFDRIQRSLqtqldkP 1454
Cdd:COG1112   549 LPLGeGSFDLVIIDEASQATLAEALGALARA-KRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLARL------P 621
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1455 GSYHLmhtklfkLSTQYRMHPEICRWPNQYFYEDQLINAECTA--RFASPLIPYCVINLKYTCDSNGaqnKSISNNEEAR 1532
Cdd:COG1112   622 ERGVM-------LREHYRMHPEIIAFSNRLFYDGKLVPLPSPKarRLADPDSPLVFIDVDGVYERRG---GSRTNPEEAE 691
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1533 FVAKLLTEMDKHMPSKRfSYGLISPYQNQCYALSQVIPSHMNITPQ-----TVDSYQGLEKDVIIIS------NARTRGC 1601
Cdd:COG1112   692 AVVELVRELLEDGPDGE-SIGVITPYRAQVALIRELLREALGDGLEpvfvgTVDRFQGDERDVIIFSlvysndEDVPRNF 770
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 221330969 1602 GFLT-NYQRLNVALTRPRRCLVICGNFEDLKSVE---MWRNLLDDARKR 1646
Cdd:COG1112   771 GFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDPstpALKRLLEYLERA 819
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
1147-1649 4.30e-49

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: 186.56  E-value: 4.30e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1147 ILKPTQTVNEVSLpkQPFTfkgcHKLNEHQENIVLHTYqriiddLQPSLTLIQGPPGTGKSRVISELCLQTLYGNaaktl 1226
Cdd:TIGR00376  139 REAPSKASEIHDF--QFFD----PNLNESQKEAVLFAL------SSKDLFLIHGPPGTGKTRTVVELIRQLVKRG----- 201
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1227 dRKILICAHSNTAVDHIV-GLLGSVLRVmnrdqfhlLRFGMHEKMSHYSRPFSLEAHF-NKAKEQKLQRVSKENAEILKK 1304
Cdd:TIGR00376  202 -LRVLVTAPSNIAVDNLLeRLALCDQKI--------VRLGHPARLLKSNKQHSLDYLIeNHPKYQIVADIREKIDELIEE 272
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1305 QHNDLKD---------EIQQLKEKTNLTSTYLLQQLQQKEKKLQLISNQ-LSPPLT--QREEFEISHMCVTRANIICTTL 1372
Cdd:TIGR00376  273 RNKKTKPspqkrrglsDIKILRKALKKREARGIESLKIASMAEWIETNKsIDRLLKllPESEERIMNEILAESDATNSMA 352
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1373 SSCVKLANYvdfFDICIVDEATQCTEPWTLLPMRFGlTHMVLVGDMQQLPAVVLSKKAidFGLSNSMFDRIQRSLqtqld 1452
Cdd:TIGR00376  353 GSEILNGQY---FDVAVIDEASQAMEPSCLIPLLKA-RKLILAGDHKQLPPTILSHDA--EELSLTLFERLIKEY----- 421
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1453 kPGSYHLmhtklfkLSTQYRMHPEICRWPNQYFYEDQLINAECTARFA-------------------SPLIPYCVINLKY 1513
Cdd:TIGR00376  422 -PERSRT-------LNVQYRMNQKIMEFPSREFYNGKLTAHESVANILlrdlpkveateseddletgIPLLFIDTSGCEL 493
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1514 tCDSNGAQNKSISNNEEARFVAKLLTEMDKhMPSKRFSYGLISPYQNQCYALSQVIPSHM-NITPQTVDSYQGLEKDVII 1592
Cdd:TIGR00376  494 -FELKEADSTSKYNPGEAELVSEIIQALVK-MGVPANDIGVITPYDAQVDLLRQLLEHRHiDIEVSSVDGFQGREKEVII 571
                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1593 ISNART---RGCGFLTNYQRLNVALTRPRRCLVICGNFEDLKSVEMWRNLLDDARKRKVY 1649
Cdd:TIGR00376  572 ISFVRSnrkGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEV 631
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
1435-1626 5.53e-47

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: 167.34  E-value: 5.53e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1435 LSNSMFDRIQRSLqtqldkpgsyhlmHTKLFKLSTQYRMHPEICRWPNQYFYEDQLINAECTA--------RFASPLIPY 1506
Cdd:pfam13087    1 LDRSLFERLQELG-------------PSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAerplpddfHLPDPLGPL 67
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969  1507 CVINLKYTCDSNGAQNKSISNNEEARFVAKLLTEMDKHMPSKRFSYGLISPYQNQCYALSQVIPSHMNITPQ----TVDS 1582
Cdd:pfam13087   68 VFIDVDGSEEEESDGGTSYSNEAEAELVVQLVEKLIKSGPEEPSDIGVITPYRAQVRLIRKLLKRKLGGKLEievnTVDG 147
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 221330969  1583 YQGLEKDVIIISNARTRGC---GFLTNYQRLNVALTRPRRCLVICGN 1626
Cdd:pfam13087  148 FQGREKDVIIFSCVRSNEKggiGFLSDPRRLNVALTRAKRGLIIVGN 194
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
1172-1472 9.42e-44

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX 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: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 158.92  E-value: 9.42e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1172 LNEHQENIVLHTYQRiiddlQPSLTLIQGPPGTGKSRVISELCLQTLYGNAAKTLD-------------------RKILI 1232
Cdd:cd18042     1 LNESQLEAIASALQN-----SPGITLIQGPPGTGKTKTIVGILSVLLAGKYRKYYEkvkkklrklqrnlnnkkkkNRILV 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1233 CAHSNTAVDHIVgllgsvLRVMNrdqfhllrfgmhekmshySRPFSLEAHFNKAKeqkLQRVSKENA--EILKKqhndlk 1310
Cdd:cd18042    76 CAPSNAAVDEIV------LRLLS------------------EGFLDGDGRSYKPN---VVRVGRQELraSILNE------ 122
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1311 deiqqlkektnltstyllqqlqqkekklqlisnqlsppltqreefeishmcvtrANIICTTLSSC--VKLANYVDFFDIC 1388
Cdd:cd18042   123 ------------------------------------------------------ADIVCTTLSSSgsDLLESLPRGFDTV 148
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1389 IVDEATQCTEPWTLLPMRFGLTHMVLVGDMQQLPAVVLSKKAIDFGLSNSMFDRIQRSLQTqldkpgsyHLMhtklfkLS 1468
Cdd:cd18042   149 IIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQLAGYP--------VLM------LT 214

                  ....
gi 221330969 1469 TQYR 1472
Cdd:cd18042   215 TQYR 218
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
1473-1644 8.49e-43

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: 154.70  E-value: 8.49e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1473 MHPEICRWPNQYFYEDQLINAECTARFAS------PLIPYCVINLKYtCDSNGAQNKSISNNEEARFVAKLLTEMDKHmP 1546
Cdd:cd18808     1 MHPEISEFPSKLFYEGKLKAGVSVAARLNppplpgPSKPLVFVDVSG-GEEREESGTSKSNEAEAELVVELVKYLLKS-G 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1547 SKRFSYGLISPYQNQCYALSQVIPSHMNITPQ----TVDSYQGLEKDVIIISNARTR----GCGFLTNYQRLNVALTRPR 1618
Cdd:cd18808    79 VKPSSIGVITPYRAQVALIRELLRKRGGLLEDvevgTVDNFQGREKDVIILSLVRSNesggSIGFLSDPRRLNVALTRAK 158
                         170       180
                  ....*....|....*....|....*.
gi 221330969 1619 RCLVICGNFEDLKSVEMWRNLLDDAR 1644
Cdd:cd18808   159 RGLIIVGNPDTLSKDPLWKKLLEYLE 184
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
1171-1472 1.26e-33

DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 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: 350797 [Multi-domain]  Cd Length: 234  Bit Score: 130.44  E-value: 1.26e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1171 KLNEHQENIVLHTyqriiddLQPSLTLIQGPPGTGKSRVISELCLQTLYGNAAKtldrkILICAHSNTAVDHI------V 1244
Cdd:cd18039     1 ELNHSQVDAVKTA-------LQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGP-----VLVCAPSNVAVDQLtekihqT 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1245 GLlgSVLRVMNRdqfhlLRFGMHEKMSHYSrpfsleahfnkAKEQKLQRVSKENAEILKKQHNDLkDEIQQLKEKTNLTS 1324
Cdd:cd18039    69 GL--KVVRLCAK-----SREAVESPVSFLA-----------LHNQVRNLDSAEKLELLKLLKLET-GELSSADEKRYRKL 129
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1325 TyllqqlqqKEKKLQLISNqlsppltqreefeishmcvtrANIICTTLSSC--VKLANYVdfFDICIVDEATQCTEPWTL 1402
Cdd:cd18039   130 K--------RKAERELLRN---------------------ADVICCTCVGAgdPRLSKMK--FRTVLIDEATQATEPECL 178
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 221330969 1403 LPMRFGLTHMVLVGDMQQLPAVVLSKKAIDFGLSNSMFDRIqrslqTQLD-KPgsyhlmhtklFKLSTQYR 1472
Cdd:cd18039   179 IPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERL-----VQLGiRP----------IRLQVQYR 234
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
1171-1472 2.59e-22

DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 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: 350799 [Multi-domain]  Cd Length: 203  Bit Score: 96.54  E-value: 2.59e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1171 KLNEHQENIVLHTYqriiddLQPSLTLIQGPPGTGKSRVISELcLQTLYgnaakTLDRKILICAHSNTAVDHIVgllgsv 1250
Cdd:cd18041     1 GLNKDQRQAIKKVL------NAKDYALILGMPGTGKTTTIAAL-VRILV-----ALGKSVLLTSYTHSAVDNIL------ 62
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1251 LRVMNRDqFHLLRFGMhekmshysrpfsleahfnkakeqklqrvskenaeiLKKQHNDlkdeIQQLKEKTNLTSTYLLQQ 1330
Cdd:cd18041    63 LKLKKFG-VNFLRLGR-----------------------------------LKKIHPD----VQEFTLEAILKSCKSVEE 102
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1331 LQQKEKKLQLISNQ----LSPPLTQReefeishmcvtraniicttlsscvklanyvdFFDICIVDEATQCTEPWTLLPMR 1406
Cdd:cd18041   103 LESKYESVSVVATTclgiNHPIFRRR-------------------------------TFDYCIVDEASQITLPICLGPLR 151
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 221330969 1407 FGLThMVLVGDMQQLPAVVLSKKAIDFGLSNSMFDRIQRSlqtqldKPGSyhlmhtkLFKLSTQYR 1472
Cdd:cd18041   152 LAKK-FVLVGDHYQLPPLVKSREARELGMDESLFKRLSEA------HPDA-------VVQLTIQYR 203
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
1192-1472 4.02e-22

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: 95.75  E-value: 4.02e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1192 QPSLTLIQGPPGTGKSRVISELCLQTLygnaakTLDRKILICAHSNTAVDHIVGLLgsVLRVMNrdqfhLLRFGMHEKMS 1271
Cdd:cd18044    16 QKDVALIHGPPGTGKTTTVVEIILQAV------KRGEKVLACAPSNIAVDNLVERL--VALKVK-----VVRIGHPARLL 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1272 HYSRPFSLEAHFnkakeqklqrvskenaeilkkqhndlkdeiqqlkektnltstyllqqlqqkekklqlisnqlsppltq 1351
Cdd:cd18044    83 ESVLDHSLDALV-------------------------------------------------------------------- 94
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1352 reefeishmcvtRANIICTTL-SSCVKLANYVDFFDICIVDEATQCTEP--WT-LLPMRfgltHMVLVGDMQQLPAVVLS 1427
Cdd:cd18044    95 ------------AAQVVLATNtGAGSRQLLPNELFDVVVIDEAAQALEAscWIpLLKAR----RCILAGDHKQLPPTILS 158
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 221330969 1428 KKAIDFGLSNSMFDRIqrsLQTQLDKPGSyhlmhtklfKLSTQYR 1472
Cdd:cd18044   159 DKAARGGLGVTLFERL---VNLYGESVVR---------MLTVQYR 191
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
1172-1472 3.64e-21

DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All 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: 350796 [Multi-domain]  Cd Length: 229  Bit Score: 94.22  E-value: 3.64e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1172 LNEHQ----ENIVLHTYQRIiddlqPSLtlIQGPPGTGKSRVISELCLQtLYGNAAKTldrKILICAHSNTAVDHIVGLL 1247
Cdd:cd18038     2 LNDEQklavRNIVTGTSRPP-----PYI--IFGPPGTGKTVTLVEAILQ-VLRQPPEA---RILVCAPSNSAADLLAERL 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1248 gsvLRVMNRDQfHLLRFgmhekmshYSRpfsleahfnkakeqklQRVSKENAEILKKQHNDLKDEIQQLKEKTNLtstyl 1327
Cdd:cd18038    71 ---LNALVTKR-EILRL--------NAP----------------SRDRASVPPELLPYCNSKAEGTFRLPSLEEL----- 117
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1328 lqqlqqkekklqlisnqlsppltqrEEFEIshmcvtranIICTTLSSCVKLANYVD--FFDICIVDEATQCTEPWTLLPM 1405
Cdd:cd18038   118 -------------------------KKYRI---------VVCTLMTAGRLVQAGVPngHFTHIFIDEAGQATEPEALIPL 163
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 221330969 1406 RFGL---THMVLVGDMQQLPAVVLSKKAIDFGLSNSMFDRIqrSLQTQLDKPGSYH-LMHTKLFKlstQYR 1472
Cdd:cd18038   164 SELAsknTQIVLAGDPKQLGPVVRSPLARKYGLGKSLLERL--MERPLYYKDGEYNpSYITKLLK---NYR 229
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
1171-1472 2.27e-18

C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It 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: 350798 [Multi-domain]  Cd Length: 271  Bit Score: 87.20  E-value: 2.27e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1171 KLNEHQENIVLHTyqriiddLQPSLTLIQGPPGTGKSRVISELCLQTLYGNAAKTLDRK-------ILICAHSNTAVDHI 1243
Cdd:cd18040     1 KLNPSQNHAVRTA-------LTKPFTLIQGPPGTGKTVTGVHIAYWFAKQNREIQSVSGegdggpcVLYCGPSNKSVDVV 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1244 VGLLgsvlrvMNRDQFHLLRfgMHEKMSH--------YSRPFSLEAHFNKAKEQKLQRVSKENaeILKKQHNDLKDEIQQ 1315
Cdd:cd18040    74 AELL------LKVPGLKILR--VYSEQIEtteypipnEPRHPNKKSERESKPNSELSSITLHH--RIRQPSNPHSQQIKA 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1316 LKEKTNLTSTYLLQQLQQKEKKLqlisnqlsppLTQREEFEISHMCVtranIICT-TLSSCVKLANYVDFFDiCIVDEAT 1394
Cdd:cd18040   144 FEARFERTQEKITEEDIKTYKIL----------IWEARFEELETVDV----ILCTcSEAASQKMRTHANVKQ-CIVDECG 208
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1395 QCTEPWTLLPM--RFGLTHMVLVGDMQQLPAVVLSKKAIDFGLSNSMFDRiqrslqtqldkpgsyhlMHTKLFKLSTQYR 1472
Cdd:cd18040   209 MCTEPESLIPIvsAPRAEQVVLIGDHKQLRPVVQNKEAQKLGLGRSLFER-----------------YAEKACMLDTQYR 271
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
1195-1472 2.92e-15

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong 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: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 73.81  E-value: 2.92e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1195 LTLIQGPPGTGKSRVISELCLQTLYGNaaktLDRKILICAHSNTAVDHIvgllgsvlrvmnrdqfhllrfgmhekmshys 1274
Cdd:cd17934     1 ISLIQGPPGTGKTTTIAAIVLQLLKGL----RGKRVLVTAQSNVAVDNV------------------------------- 45
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1275 rpfsleahfnkakeqklqrvskenaeilkkqhndlkdeiqqlkektnltstyllqqlqqkekklqlisnqlsppltqree 1354
Cdd:cd17934       --------------------------------------------------------------------------------
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1355 feishmcvtraniicttlsscvklanyvdffDICIVDEATQCTEPwTLLPMRFGLTHMVLVGDMQQLPAVVLS----KKA 1430
Cdd:cd17934    46 -------------------------------DVVIIDEASQITEP-ELLIALIRAKKVVLVGDPKQLPPVVQEdhaaLLG 93
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 221330969 1431 IDFGLSNSMFDRIQrslqtqldkpgsyHLMHTKLFkLSTQYR 1472
Cdd:cd17934    94 LSFILSLLLLFRLL-------------LPGSPKVM-LDTQYR 121
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
1171-1472 1.94e-14

DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. Mov10L1 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: 350836 [Multi-domain]  Cd Length: 230  Bit Score: 74.71  E-value: 1.94e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1171 KLNEHQENIVLhtyqRIID-DLQPSLTLIQGPPGTGKSRVISELCLQTLYgnaaKTLDRKILICAHSNTAVDHIVgllgs 1249
Cdd:cd18078     1 DLNELQKEAVK----RILGgECRPLPYILFGPPGTGKTVTIIEAILQVVY----NLPRSRILVCAPSNSAADLVT----- 67
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1250 vLRVMNRDQFhllrfgmhekmshysRPFSLeAHFNKAkeqkLQRVSkenaeilkkqhnDLKDEIQqlkektnltstyllq 1329
Cdd:cd18078    68 -SRLHESKVL---------------KPGDM-VRLNAV----NRFES------------TVIDARK--------------- 99
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1330 qlqqkekklqlisnqlsPPLTQREEFEIShmcvTRANII---CTTLSSCVKLANYVDFFDICIVDEATQCTEPWTLLPMr 1406
Cdd:cd18078   100 -----------------LYCRLGEDLSKA----SRHRIVistCSTAGLLYQMGLPVGHFTHVFVDEAGQATEPESLIPL- 157
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 221330969 1407 fGLTH-----MVLVGDMQQLPAVVLSKKAIDFGLSNSMFDRI------QRSLQTQLDKPGSYHLMHTKLFKlstQYR 1472
Cdd:cd18078   158 -GLISsrdgqIILAGDPMQLGPVIKSRLASAYGLGVSFLERLmnrplyLRDPNRFGESGGYNPLLVTKLVD---NYR 230
FHA cd00060
forkhead associated (FHA) domain superfamily; Forkhead-associated (FHA) domains are small ...
12-94 6.70e-12

forkhead associated (FHA) domain superfamily; Forkhead-associated (FHA) domains are small phosphopeptide recognition modules mostly found in eubacteria and eukaryotes. It is about 95-120 residues long that fold into an 11-stranded beta-sandwich. FHA domains can mediate the recognition of phosphorylated and non-phosphorylated substrates, as well as protein oligomerization. They specifically recognize threonine phosphorylation (pThr) accompanying activation of protein serine/threonine kinases. FHA domains show diverse ligand specificity. They may recognize the pTXXD motif, the pTXXI/L motif, and TQ clusters (singly and multiply phosphorylated). In eukaryotes, FHA superfamily members include forkhead-type transcription factors, as well as other signaling proteins, such as many regulatory proteins, kinases, phosphatases, motor proteins called kinesins, and metabolic enzymes. Many of them localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. FHA domains play important roles in human diseases, particularly in relation to DNA damage responses and cancers. In bacteria, FHA domain-containing proteins may participate in injection of viral proteins into host cells, transmembrane transporters, and cell division. FHA domain-containing proteins rarely include more than one copy of the domain. The only exception in eukaryotes is the checkpoint kinase Rad53 from Saccharomyces cerevisiae, which harbors two FHA domains (FHA1 and FHA2) flanking a central kinase domain. The two FHA domains recognize different phosphorylated targets and function independently from one another. In contrast, Mycobacterium tuberculosis ABC transporter Rv1747 contains two FHA domains but only one of them is essential for protein function.


Pssm-ID: 438714 [Multi-domain]  Cd Length: 92  Bit Score: 63.06  E-value: 6.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969   12 TGARLILHNGTNLMGRHSRCRIILGGQYqfVSREHANIIVSEKGVEVESLNPLNGLFINGGKLGDKInrlAVAEGSTISL 91
Cdd:cd00060    10 GGREFPLTKGVVTIGRSPDCDIVLDDPS--VSRRHARIEVDGGGVYLEDLGSTNGTFVNGKRITPPV---PLQDGDVIRL 84

                  ...
gi 221330969   92 GVT 94
Cdd:cd00060    85 GDT 87
FHA COG1716
Forkhead associated (FHA) domain, binds pSer, pThr, pTyr [Signal transduction mechanisms];
7-92 1.02e-11

Forkhead associated (FHA) domain, binds pSer, pThr, pTyr [Signal transduction mechanisms];


Pssm-ID: 441322 [Multi-domain]  Cd Length: 96  Bit Score: 62.67  E-value: 1.02e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969    7 LEHVTTGARLILHNGTNLMGRHSRCRIILGGQYqfVSREHANIIVSEKGVEVESLNPLNGLFINGGKLGDKInrlAVAEG 86
Cdd:COG1716     7 LEGPLAGRRFPLDGGPLTIGRAPDNDIVLDDPT--VSRRHARIRRDGGGWVLEDLGSTNGTFVNGQRVTEPA---PLRDG 81

                  ....*.
gi 221330969   87 STISLG 92
Cdd:COG1716    82 DVIRLG 87
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
1386-1630 3.58e-11

helicase domain of coronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409652 [Multi-domain]  Cd Length: 341  Bit Score: 66.78  E-value: 3.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1386 DICIVDEATQCTE-PWTLLPMRFGLTHMVLVGDMQQLPA--VVLSKKAidfgLSNSMFDRIQRSLQTQldKPGSYhlmht 1462
Cdd:cd21718   119 DIVVVDEVSMCTNyDLSVVNARLKYKHIVYVGDPAQLPAprTLLTEGS----LEPKDYNVVTRLMVGS--GPDVF----- 187
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1463 klfkLSTQYRMHPEICRWPNQYFYEDQLINAECTARfasplipYCvinLKYTCDSN-GAQNKSISNNEEARFVAKLLTEm 1541
Cdd:cd21718   188 ----LSKCYRCPKEIVDTVSKLVYDNKLKAIKPKSR-------QC---FKTFGKGDvRHDNGSAINRPQLEFVKRFLDR- 252
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1542 dkhmpSKRFSYG-LISPYQNQCYALSQVipshMNITPQTVDSYQGLEKDVIIIsnARTRGCGFLTNYQRLNVALTRPRR- 1619
Cdd:cd21718   253 -----NPRWRKAvFISPYNAMNNRASRL----LGLSTQTVDSSQGSEYDYVIF--CQTTDTAHALNINRFNVAITRAKHg 321
                         250
                  ....*....|.
gi 221330969 1620 CLVICGNFEDL 1630
Cdd:cd21718   322 ILVIMRDENDL 332
alphaCoV_Nsp13-helicase cd21723
helicase domain of alphacoronavirus non-structural protein 13; This model represents the ...
1386-1635 4.79e-10

helicase domain of alphacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alphacoronavirus, including Porcine epidemic diarrhea virus and Human coronavirus (CoV) NL63. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409656 [Multi-domain]  Cd Length: 340  Bit Score: 63.21  E-value: 4.79e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1386 DICIVDEATQCTE-PWTLLPMRFGLTHMVLVGDMQQLPA--VVLSKKAIdfglsnsmfdriqrslqtqldKPGSYHLMHT 1462
Cdd:cd21723   119 DIVVVDEVSMCTNyDLSVINQRVSYKHIVYVGDPQQLPAprTMITRGVL---------------------EPKDYNVVTQ 177
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1463 KLFK------LSTQYRMHPEICRWPNQYFYEDQLInaectarfasPLIPYCVINLKYTCDSN-GAQNKSISNNEEARFVA 1535
Cdd:cd21723   178 RMCAlgpdvfLHKCYRCPAEIVNTVSELVYENKFK----------PVHPESKQCFKIFCKGNvQVDNGSSINRRQLDVVK 247
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1536 KLLTEmdkhmpSKRFSYG-LISPYQNQCYALSQVipshMNITPQTVDSYQGLEKDVIIIsnARTRGCGFLTNYQRLNVAL 1614
Cdd:cd21723   248 MFLAK------NPKWSKAvFISPYNSQNYVASRV----LGLQIQTVDSSQGSEYDYVIY--TQTSDTAHACNVNRFNVAI 315
                         250       260
                  ....*....|....*....|....*
gi 221330969 1615 TRPRRCL--VICGN--FEDLKSVEM 1635
Cdd:cd21723   316 TRAKKGIlcVMCDKelFDALKFFEL 340
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
1172-1253 7.56e-10

EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 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: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 59.87  E-value: 7.56e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1172 LNEHQENIVLHTyqriiddLQPSLTLIQGPPGTGKSRVISELClQTLYGNAAKTLDRKILICAHSNTAVDHI-VGLL--- 1247
Cdd:cd17936     2 LDPSQLEALKHA-------LTSELALIQGPPGTGKTFLGVKLV-RALLQNQDLSITGPILVVCYTNHALDQFlEGLLdfg 73

                  ....*..
gi 221330969 1248 -GSVLRV 1253
Cdd:cd17936    74 pTKIVRL 80
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
1187-1265 2.78e-08

EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds precursor-mRNA introns at a defined position and is part of a pentameric intron-binding complex (IBC). It 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: 350693 [Multi-domain]  Cd Length: 207  Bit Score: 55.90  E-value: 2.78e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 221330969 1187 IIDDLQPSLTLIQGPPGTGKSRVISELcLQTLYGNAAktlDRKILICAHSNTAVDHIVGLLgSVLRVmnrDQFHLLRFG 1265
Cdd:cd17935    14 IRSGMQPGLTMVVGPPGTGKTDVAVQI-ISNLYHNFP---NQRTLIVTHSNQALNQLFEKI-MALDI---DERHLLRLG 84
betaCoV_Nsp13-helicase cd21722
helicase domain of betacoronavirus non-structural protein 13; This model represents the ...
1386-1619 2.94e-08

helicase domain of betacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from betacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409655 [Multi-domain]  Cd Length: 340  Bit Score: 57.50  E-value: 2.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1386 DICIVDEATQCTE-PWTLLPMRFGLTHMVLVGDMQQLPA--VVLSKKAidfgLSNSMFDRIQRSLQTqldkpgsyhlMHT 1462
Cdd:cd21722   119 DILVVDEVSMCTNyDLSVINARVRAKHIVYIGDPAQLPAprTLLTKGT----LEPEYFNSVTRLMCC----------LGP 184
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1463 KLFkLSTQYRMHPEICRWPNQYFYEDQLInaecTARFASPLIPYCVINLKYTCDSNGAQNKsisnnEEARFVAKLLTEMd 1542
Cdd:cd21722   185 DIF-LGTCYRCPKEIVDTVSALVYDNKLK----AKKDNSGQCFKVYYKGSVTHDSSSAINR-----PQIYLVKKFLKAN- 253
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 221330969 1543 khmPSKRFSYgLISPYQNQCYALSQVipshMNITPQTVDSYQGLEKDVIIISnaRTRGCGFLTNYQRLNVALTRPRR 1619
Cdd:cd21722   254 ---PAWSKAV-FISPYNSQNAVARRV----LGLQTQTVDSSQGSEYDYVIYC--QTAETAHSVNVNRFNVAITRAKK 320
FHA pfam00498
FHA domain; The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
24-91 5.26e-08

FHA domain; The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.


Pssm-ID: 459831 [Multi-domain]  Cd Length: 66  Bit Score: 51.04  E-value: 5.26e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 221330969    24 LMGRHSRCRIILggQYQFVSREHANIIVSEKG-VEVESLNPLNGLFINGGKLGDKINRLavAEGSTISL 91
Cdd:pfam00498    2 TIGRSPDCDIVL--DDPSVSRRHAEIRYDGGGrFYLEDLGSTNGTFVNGQRLGPEPVRL--KDGDVIRL 66
FHA_DgcB-like cd22682
forkhead associated (FHA) domain found in Bdellovibrio bacteriovorus GGDEF domain protein DgcB ...
13-94 1.46e-06

forkhead associated (FHA) domain found in Bdellovibrio bacteriovorus GGDEF domain protein DgcB and similar proteins; DgcB is a GGDEF enzyme that produces cyclic-di-GMP in response to an unknown stimulus. It appends the C-terminal GGDEF enzymatic domain with an N-terminal forkhead-associated (FHA) domain that acts as a consensus phosphopeptide sensor. The GGDEF and sensory FHA domains form an asymmetrical dimer.


Pssm-ID: 438734 [Multi-domain]  Cd Length: 96  Bit Score: 47.91  E-value: 1.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969   13 GARLILHNGTNLMGRHSRCRIILggQYQFVSREHANIIVSEKGVEVESLNPLNGLFINGGKLgDKINRLAVAEGSTISLG 92
Cdd:cd22682    12 GKQFPITESTIVIGRSVESQVQI--DDDSVSRYHAKLAVNPSAVSIIDLGSTNGTIVNGKKI-PKLASCDLQNGDQIKIG 88

                  ..
gi 221330969   93 VT 94
Cdd:cd22682    89 NT 90
Yop-YscD_cpl pfam16697
Inner membrane component of T3SS, cytoplasmic domain; Yop-YscD-cpl is the cytoplasmic domain ...
13-94 6.25e-06

Inner membrane component of T3SS, cytoplasmic domain; Yop-YscD-cpl is the cytoplasmic domain of Yop proteins like YscD from Proteobacteria. YscD forms part of the inner membrane component of the bacterial type III secretion injectosome apparatus.


Pssm-ID: 465238 [Multi-domain]  Cd Length: 94  Bit Score: 46.10  E-value: 6.25e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969    13 GARLILHNGTNLMGRHSRCRIILGGQYqfVSREHANIIVSEKGVEVESLNPLNGLFINGGKLGDKINRLAVaeGSTISLG 92
Cdd:pfam16697    9 GAEFPLEGGRYRIGSDPDCDIVLSDKE--VSRVHLKLEVDDEGWRLDDLGSGNGTLVNGQRVTELGIALRP--GDRIELG 84

                   ..
gi 221330969    93 VT 94
Cdd:pfam16697   85 QT 86
FHA_Ki67 cd22673
forkhead associated (FHA) domain found in proliferation marker protein Ki-67 and similar ...
9-92 1.04e-05

forkhead associated (FHA) domain found in proliferation marker protein Ki-67 and similar proteins; Ki-67, also called antigen identified by monoclonal antibody Ki-67, antigen KI-67, or antigen Ki67, acts as a biological surfactant to disperse mitotic chromosomes. It is required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly. Ki-67 binds DNA with a preference for supercoiled DNA and AT-rich DNA. It may also play a role in chromatin organization. Ki-67 contains an FHA domain at its N-terminus. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438725 [Multi-domain]  Cd Length: 95  Bit Score: 45.67  E-value: 1.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969    9 HVTTGARLILHNGTNLMGRHSRC--RIILGGqyqfVSREHANIIVSEKG-VEVESLNPLNGLFINGGKLGDKInrlAVAE 85
Cdd:cd22673     9 DGTDGSRFPLTKKSCTFGRDLSCdiRIQLPG----VSREHCRIEVDENGkAYLENLSTTNPTLVNGKAIEKSA---ELKD 81

                  ....*..
gi 221330969   86 GSTISLG 92
Cdd:cd22673    82 GDVITIG 88
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
1546-1623 1.06e-05

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: 45.51  E-value: 1.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1546 PSKRFSYGLISPYQNQCYALSQVIPSHMNITPQ-------TVDSYQGLEKDVIIISNARTrgcgFLTNYQRLNVALTRPR 1618
Cdd:cd18786     7 ANGLYKGVVLTPYHRDRAYLNQYLQGLSLDEFDlqlvgaiTIDSSQGLTFDVVTLYLPTA----NSLTPRRLYVALTRAR 82

                  ....*
gi 221330969 1619 RCLVI 1623
Cdd:cd18786    83 KRLVI 87
FHA_MDC1 cd22665
forkhead associated (FHA) domain found in mediator of DNA damage checkpoint protein 1 (MDC1) ...
18-74 2.35e-05

forkhead associated (FHA) domain found in mediator of DNA damage checkpoint protein 1 (MDC1) and similar proteins; MDC1, also called nuclear factor with BRCT domains 1 (NFBD1), is a nuclear chromatin-associated protein that is required for checkpoint mediated cell cycle arrest in response to DNA damage within both the S and G2/M phases of the cell cycle. It directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. MDC1 contains a forkhead-associated (FHA) domain and two BRCT domains, as well as an internal 41-amino acid repeat sequence. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438717 [Multi-domain]  Cd Length: 97  Bit Score: 44.53  E-value: 2.35e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 221330969   18 LHNGTNLMGRHSRCRIILGGQYqfVSREHANIIVSEKGVEVESLNPLNGLFINGGKL 74
Cdd:cd22665    18 LYEGENVIGRDPSCSVVLPDKS--VSKQHACIEVDGGTHLIEDLGSTNGTRIGNKVR 72
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
1171-1443 3.28e-05

DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases 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: 350835 [Multi-domain]  Cd Length: 226  Bit Score: 47.09  E-value: 3.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1171 KLNEHQENIVLHTYQRIIDDLQPslTLIQGPPGTGKSRVISELCLQtlygnAAKTLDRKILICAHSNTAVDHIVgllgsv 1250
Cdd:cd18077     1 RLNAKQKEAVLAITTPLSIQLPP--VLLIGPFGTGKTFTLAQAVKH-----ILQQPETRILICTHSNSAADLYI------ 67
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1251 lrvmnRDQFHllrfgmhekmshysrPFSLEAHfnkaKEQKLQRVSKENAEiLKKQHNDLkdeiqqlkEKTNLTSTYLLQQ 1330
Cdd:cd18077    68 -----KEYLH---------------PYVETGN----PRARPLRVYYRNRW-VKTVHPVV--------QKYCLIDEHGTFR 114
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1331 LQQKEKklqlisnqlsppltqreefeishmcVTRANIICTTLSSCVKLANYV---DFFDICIVDEATQCTEPWTLLPMRF 1407
Cdd:cd18077   115 MPTRED-------------------------VMRHRVVVVTLSTSQYLCQLDlepGFFTHILLDEAAQAMECEAIMPLAL 169
                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 221330969 1408 GL--THMVLVGDMQQLPAVVLSKKAIDFGLSNSMFDRI 1443
Cdd:cd18077   170 ATksTRIVLAGDHMQLSPEVYSEFARERNLHISLLERL 207
FHA_GarA_OdhI-like cd22684
forkhead associated (FHA) domain found in Mycobacterium tuberculosis GarA, Corynebacterium ...
13-92 6.46e-05

forkhead associated (FHA) domain found in Mycobacterium tuberculosis GarA, Corynebacterium glutamicum OdhI and similar proteins; This family includes Mycobacterium tuberculosis glycogen accumulation regulator GarA and Corynebacterium glutamicum oxoglutarate dehydrogenase inhibitor (OdhI). GarA is involved in the regulation of glutamate metabolism. It acts as a phosphorylation-dependent molecular switch that modulates the activities of Kgd, Gdh and GltB. GarA binds to Kgd, Gdh, GltB, PknB, and the N-terminal region of PknG via its FHA domain. OdhI is an essential component of the PknG signaling pathway. It can inhibit the activity of 2-oxoglutarate dehydrogenase only when it is unphosphorylated. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438736 [Multi-domain]  Cd Length: 94  Bit Score: 43.52  E-value: 6.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969   13 GARLILHNGTNLMGRHSRCRIILGGQYqfVSREHANIIVSEKGVEVESLNPLNGLFINggklGDKINRLAVAEGSTISLG 92
Cdd:cd22684    13 GARFLLDQDVTTAGRHPESDIFLDDVT--VSRRHAEFRRAEGGFVVRDVGSLNGTYVN----RERIDSAVLRNGDEVQIG 86
FHA_FhaB-like cd22693
forkhead associated (FHA) domain found in Mycobacterium tuberculosis FHA domain-containing ...
12-94 1.38e-04

forkhead associated (FHA) domain found in Mycobacterium tuberculosis FHA domain-containing protein FhaB and similar proteins; FhaB, also called FtsZ-interacting protein A (FipA), is a putative virulence factor involved in regulating cell shape. It can interact with polyketide-associated protein PapA5, a putative membrane protein involved in the biosynthesis of virulence enhancing lipids. FhaB regulates growth and cell division. It is probably required for divisomal protein assembly under oxidative stress. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438745 [Multi-domain]  Cd Length: 91  Bit Score: 42.29  E-value: 1.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969   12 TGARLILHNGTNLMGRHSRCRIILGGQyqFVSREHANIIVSEKGVEVESLNPLNGLFINGGKLGdkiNRLAVAEGSTISL 91
Cdd:cd22693     9 QGQTFPIDKSGITIGRADDNDLVLSDD--FVSSRHARIYLQGSSWYLEDLGSTNGTFVNGNRVT---QPVVVQPGDTIRI 83

                  ...
gi 221330969   92 GVT 94
Cdd:cd22693    84 GAT 86
gammaCoV_Nsp13-helicase cd21720
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ...
1386-1623 1.84e-04

helicase domain of gammacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from gammacoronavirus, including Avian infectious bronchitis virus. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Coronavirus (CoV) Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409653 [Multi-domain]  Cd Length: 343  Bit Score: 45.68  E-value: 1.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1386 DICIVDEATQCTE-PWTLLPMRFGLTHMVLVGDMQQLPAvvlskkaidfglsnsmfdriQRSLQTQLDKPGSYHLMhTKL 1464
Cdd:cd21720   119 DILLVDEVSMLTNyELSFINGKINYQYVVYVGDPAQLPA--------------------PRTLLNGSLSPKDYNVV-TNL 177
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1465 FK-------LSTQYRMHPEICRWPNQYFYEDQLI--NAECTARFAsplipyCVINlkyTCDSN-GAQNKSISNNEEARFV 1534
Cdd:cd21720   178 MVcvkpdifLAKCYRCPKEIVDTVSTLVYDGKFIanNPESRQCFK------VIVN---NGNSDvGHESGSAYNTTQLEFV 248
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969 1535 AKLLTemdKHMPSKRFSYglISPYQnqcyALSQVIPSHMNITPQTVDSYQGLEKDVIIIsnARTRGCGFLTNYQRLNVAL 1614
Cdd:cd21720   249 KDFVC---RNKEWREATF--ISPYN----AMNQRAYRMLGLNVQTVDSSQGSEYDYVIF--CVTADSQHALNINRFNVAL 317

                  ....*....
gi 221330969 1615 TRPRRCLVI 1623
Cdd:cd21720   318 TRAKRGILV 326
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
1195-1241 2.39e-04

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 42.47  E-value: 2.39e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 221330969 1195 LTLIQGPPGTGKSRVISELcLQTLYGNaAKTLDRKILICAHSNTAVD 1241
Cdd:cd17914     1 LSLIQGPPGTGKTRVLVKI-VAALMQN-KNGEPGRILLVTPTNKAAA 45
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
1173-1241 3.68e-04

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases 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: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 42.18  E-value: 3.68e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 221330969 1173 NEHQENIvlhtyqrIIDDLQPSLTLIQGPPGTGKSRVISelclqTLYGNAAKTlDRKILICAHSNTAVD 1241
Cdd:cd18043     1 DSSQEAA-------IISARNGKNVVIQGPPGTGKSQTIA-----NIIANALAR-GKRVLFVSEKKAALD 56
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
1377-1426 4.21e-04

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases 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: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 41.80  E-value: 4.21e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 221330969 1377 KLANYVDF----FDICIVDEATQCtEPWTLLPMRFGLTHMVLVGDMQQLPAVVL 1426
Cdd:cd18043    69 SVSQYLPLnrnlFDLVIFDEASQI-PIEEALPALFRGKQVVVVGDDKQLPPSIL 121
FHA smart00240
Forkhead associated domain; Found in eukaryotic and prokaryotic proteins. Putative nuclear ...
26-74 5.16e-04

Forkhead associated domain; Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.


Pssm-ID: 214578 [Multi-domain]  Cd Length: 52  Bit Score: 39.47  E-value: 5.16e-04
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|..
gi 221330969     26 GRHS-RCRIILGGQyqFVSREHAnIIVSEKG--VEVESLNPLNGLFINGGKL 74
Cdd:smart00240    4 GRSSeDCDIQLDGP--SISRRHA-VIVYDGGgrFYLIDLGSTNGTFVNGKRI 52
FHA_ArnA-like cd22680
forkhead associated (FHA) domain found in Sulfolobus Acidocaldarius FHA domain-containing ...
24-73 8.23e-04

forkhead associated (FHA) domain found in Sulfolobus Acidocaldarius FHA domain-containing protein ArnA and similar proteins; ArnA is an FHA domain-containing protein from Sulfolobus acidocaldarius that was shown to strongly interact with ArnB, a von Willebrand domain-containing protein. They act synergistically and negatively to modulate motility. ArnA is involved in regulating archaella expression in S. acidocaldarius. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438732 [Multi-domain]  Cd Length: 96  Bit Score: 40.40  E-value: 8.23e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 221330969   24 LMGRHSRCRIILggQYQFVSREHANIIVSEKGVEVESLNPLNGLFINGGK 73
Cdd:cd22680    24 SIGRDPENVIVI--PDPFVSRNHARITVDSNEIYIEDLGSTNGTFVNDFK 71
FHA_NBN cd22667
forkhead associated (FHA) domain found in nibrin and similar proteins; Nibrin (NBN), also ...
5-96 8.47e-04

forkhead associated (FHA) domain found in nibrin and similar proteins; Nibrin (NBN), also called cell cycle regulatory protein p95, or Nijmegen breakage syndrome protein 1 (NBS1), is a novel DNA double-strand break repair protein that is mutated in Nijmegen breakage syndrome. It is a component of the MRE11-RAD50-NBN (MRN complex) which plays a critical role in the cellular response to DNA damage and the maintenance of chromosome integrity. Nibrin modulates the DNA damage signal sensing by recruiting PI3/PI4-kinase family members ATM, ATR, and probably DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to the DNA damage sites and activating their functions. It can also recruit MRE11 and RAD50 to the proximity of DSBs by an interaction with the histone H2AX. Nibrin also functions in telomere length maintenance by generating the 3' overhang which serves as a primer for telomerase dependent telomere elongation. Nibrin is a major player in the control of intra-S-phase checkpoint. This subfamily also includes Schizosaccharomyces pombe DNA repair and telomere maintenance protein Nbs1 and Arabidopsis thaliana AtNbs1. SpNbs1 is an FHA domain-containing protein required for DNA damage repair and S-phase DNA damage checkpoint. It is involved in telomere length maintenance and maintenance of chromatin structure. AtNbs1 is a component of MRN complex. It also functions in the very early stages of meiosis. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438719 [Multi-domain]  Cd Length: 108  Bit Score: 40.39  E-value: 8.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969    5 WYLEHVTTGA---RLILHNGTNLMGRHSRCRIILGGQyqFVSREHANIIVSEKGVEVESLNPLNGL----------FING 71
Cdd:cd22667     1 WWLLSEQDGAgtsYYLLPGGEYTVGRKDCDIIIVDDS--SISRKHATLTVLHPEANLSDPDTRPELtlkdlskygtFVNG 78
                          90       100
                  ....*....|....*....|....*
gi 221330969   72 GKLgDKINRLAVAEGSTISLGVTGV 96
Cdd:cd22667    79 EKL-KGGSEVTLKDGDVITFGVLGS 102
FHA_RNF8 cd22663
forkhead associated (FHA) domain found in RING finger protein 8 (RNF8) and similar proteins; ...
5-93 1.03e-03

forkhead associated (FHA) domain found in RING finger protein 8 (RNF8) and similar proteins; RNF8 is a telomere-associated E3 ubiquitin-protein ligase that plays an important role in DNA double-strand break (DSB) repair via histone ubiquitination. It is localized in the nucleus and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3), but not with other E2s (UbcH5, UbcH7, UbcH10, hCdc34, and hBendless). It recruits UBC13 for lysine 63-based self polyubiquitylation. Its deficiency causes neuronal pathology and cognitive decline, and its loss results in neuron degeneration. RNF8, together with RNF168, catalyzes a series of ubiquitylation events on substrates such as H2A and H2AX, with the H2AK13/15 ubiquitylation being particularly important for recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of DSBs. Specially, RNF8 mediates the ubiquitination of gammaH2AX, and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DNA damage response (DDR) and inhibits chromosomal instability. Moreover, RNF8 interacts with retinoid X receptor alpha (RXR alpha) and enhances its transcription-stimulating activity. It also regulates the rate of exit from mitosis and cytokinesis. RNF8 contains an N-terminal FHA domain, which is a small phosphopeptide recognition module.


Pssm-ID: 438715 [Multi-domain]  Cd Length: 110  Bit Score: 40.42  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 221330969    5 WYL---EHVTTGARLILHNGTNL-MGRHsrcriiLGGQYQ-------FVSREHANIIVSEKGV-EVESLNPLNGLFINGG 72
Cdd:cd22663     1 WCLrrvGHGIDPLVLLLEDGKEVtVGRG------LGVTYQlvstcplMISRNHCVLKKNDEGQwTIKDNKSLNGVWVNGE 74
                          90       100
                  ....*....|....*....|.
gi 221330969   73 KLgDKINRLAVAEGSTISLGV 93
Cdd:cd22663    75 RI-EPLKPYPLNEGDLIQLGV 94
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
1382-1442 1.13e-03

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 40.55  E-value: 1.13e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 221330969 1382 VDFFDICIVDEATQCTEPWTLLPMRFGLTH--MVLVGDMQQLPAVVLSKKAIDFGLSNSMFDR 1442
Cdd:cd17914    44 AAQLDNILVDEAAQILEPETSRLIDLALDQgrVILVGDHDQLGPVWRGAVLAKICNEQSLFTR 106
FHA_EmbR-like cd22669
forkhead associated (FHA) domain found in Mycobacterium tuberculosis transcriptional ...
7-74 4.14e-03

forkhead associated (FHA) domain found in Mycobacterium tuberculosis transcriptional regulatory protein EmbR and similar proteins; EmbR is a transcriptional regulator of the embCAB operon encoding cell wall arabinosyltransferases (EmbC, -A, and -B), and is phosphorylated by the cognate mycobacterial serine/threonine protein kinase PknH. It interacts with RNA polymerase and possesses a phosphorylation-dependent ATPase activity. EmbR contains a regulatory C-terminal forkhead-associated (FHA) domain, which mediates binding to a threonine-phosphorylated site in PknH. The FHA domain is a small phosphopeptide recognition module.


Pssm-ID: 438721 [Multi-domain]  Cd Length: 89  Bit Score: 38.17  E-value: 4.14e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 221330969    7 LEHVTTGARLILHNGTNLMGRHSRCRI-ILGGQyqfVSREHANIIVSEKGVEVESLNPLNGLFINGGKL 74
Cdd:cd22669     2 LHDIASGRGYPLQAAATRIGRLHDNDIvLDSAN---VSRHHAVIVDTGTNYVINDLRSSNGVHVQHERI 67
 
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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