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Conserved domains on  [gi|1063534947|ref|WP_069398199|]
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UvrD-helicase domain-containing protein [Mycobacterium shimoidei]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 1006208)

DEAD/DEAH box-containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA; similar to ATP-dependent DNA helicase UvrD, which is a 3'-5' DNA helicase and a single-stranded DNA (ssDNA)-dependent ATPase

EC:  3.6.4.12
Gene Ontology:  GO:0003678|GO:0016887|GO:0043138
PubMed:  25345862|32033386

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
COG3972 super family cl28313
Superfamily I DNA and RNA helicases [Replication, recombination and repair];
245-687 1.10e-43

Superfamily I DNA and RNA helicases [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG3972:

Pssm-ID: 443172 [Multi-domain]  Cd Length: 565  Bit Score: 165.78  E-value: 1.10e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 245 QRAVVEASFNGPARVTGGPGTGKTVVVLHRAHTLAKRNKG-RVLVTTFTSTLSDSLQSGLDM---IVDDDEVRNRIEVSH 320
Cdd:COG3972   164 QERIARSIPDGPQRIRGVAGSGKTVLLAAKAAYLALKHPGwRILVTCFNRSLADHLRDLIPRflrRFSNGEPEDNVKLIV 243

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 321 VDRVAHRVFRRkYGAPnLLRPADEKNlwlgiidklelPFNDVFladewrhivlarcinnageylaakrtgrgrplgpaqr 400
Cdd:COG3972   244 FHAWGGKLLKQ-YGIP-PLTFSQPNE-----------AFDEAC------------------------------------- 273

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 401 aqvwqaiwefeqtltrlgacthetirREATTLLEAETDKP-YRHIVIDEAQDLSPDQWRLLRAAVAEAPDDIFIAGDTHQ 479
Cdd:COG3972   274 --------------------------KALLEAIQGEIIPPiYDAILIDEAQDFEPEFLRLLYQLLKPPKKRLIWAYDEAQ 327

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 480 RIYdGRVSFREVGINI-AGRSARLNLNYRTTAEIL----GWSLGLLRGERIDDMDGGL--DSIAGCRSYVH--------- 543
Cdd:COG3972   328 NIY-GRKIPSAGGIPAgIGRDTILKKNYRNTRPILtfahAFGMGLLRPPGLLQGDAEDyeVERPGDKVTLIrppepagrk 406

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 544 GAMPTLRGFDKYEAETKFIAATVQEWL-AKGIKPSEIGV----AARTKWFGSKIEDALKAEGIKTVDLAKTAKR-----D 613
Cdd:COG3972   407 GPLPEFKKYDDRAEELEAIAEEIKKNLrDEGLRPSDIAViylgNNEAKELGDRLAAALERQGIDSYIAGARSDPnffwkD 486

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063534947 614 DAVRVGTMHRMKGLEFRCVTVAGVgatmvpaanaitpideDKQTHDHDLERERCLLFVACTRAREELHVTWHGE 687
Cdd:COG3972   487 GGVTISTIHRAKGLEAPVVIIVGL----------------DQLAKGESLERLRNLLYVAMTRARGWLVVSGSGE 544
McrB super family cl34253
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 29-298 8.30e-03

5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB [Defense mechanisms];


The actual alignment was detected with superfamily member COG1401:

Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 39.37  E-value: 8.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947  29 FDEFEAATYSGLHLEKINNARNRRFRSIRIDQSWRGIVLAPEhgdvFTLLKVLPHDDAYAWAQRSDISVNAAtgGIEIRD 108
Cdd:COG1401     4 PVLEFKFLIVGLRLKPLESEDAVRELGIRADDLRGAAELATR----LAERLSEELLRADRAARATELVEELS--AALEVV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 109 EEAIDRALPELKKSAENAESLLFAHVSDADLRRLGIDERTLAFARALTNSAQLDAAKSFLPETQWEVLFGLAAGYTPDEV 188
Cdd:COG1401    78 VLLLDLEKVELNEKLALSEAAVAIEELYELEADSEIEAVGLLLELAERSDALEALERARLLLELADLEERAALETEVLEA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 189 WSELGAAILAEPVDTDDLDAAVLRSRDRVVLVNgpdELMGVFAYPFATWRVYLHPTQRAVVEASFNGPARV-TGGPGTGK 267
Cdd:COG1401   158 LEAELEELLAAPEDLSADALAAELSAAEELYSE---DLESEDDYLKDLLREKFEETLEAFLAALKTKKNVIlAGPPGTGK 234

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1063534947 268 TVVVLHRAHTLAKRNKGRVLVTTFTSTLSDS 298
Cdd:COG1401   235 TYLARRLAEALGGEDNGRIEFVQFHPSWSYE 265
 
Name Accession Description Interval E-value
COG3972 COG3972
Superfamily I DNA and RNA helicases [Replication, recombination and repair];
245-687 1.10e-43

Superfamily I DNA and RNA helicases [Replication, recombination and repair];


Pssm-ID: 443172 [Multi-domain]  Cd Length: 565  Bit Score: 165.78  E-value: 1.10e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 245 QRAVVEASFNGPARVTGGPGTGKTVVVLHRAHTLAKRNKG-RVLVTTFTSTLSDSLQSGLDM---IVDDDEVRNRIEVSH 320
Cdd:COG3972   164 QERIARSIPDGPQRIRGVAGSGKTVLLAAKAAYLALKHPGwRILVTCFNRSLADHLRDLIPRflrRFSNGEPEDNVKLIV 243

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 321 VDRVAHRVFRRkYGAPnLLRPADEKNlwlgiidklelPFNDVFladewrhivlarcinnageylaakrtgrgrplgpaqr 400
Cdd:COG3972   244 FHAWGGKLLKQ-YGIP-PLTFSQPNE-----------AFDEAC------------------------------------- 273

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 401 aqvwqaiwefeqtltrlgacthetirREATTLLEAETDKP-YRHIVIDEAQDLSPDQWRLLRAAVAEAPDDIFIAGDTHQ 479
Cdd:COG3972   274 --------------------------KALLEAIQGEIIPPiYDAILIDEAQDFEPEFLRLLYQLLKPPKKRLIWAYDEAQ 327

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 480 RIYdGRVSFREVGINI-AGRSARLNLNYRTTAEIL----GWSLGLLRGERIDDMDGGL--DSIAGCRSYVH--------- 543
Cdd:COG3972   328 NIY-GRKIPSAGGIPAgIGRDTILKKNYRNTRPILtfahAFGMGLLRPPGLLQGDAEDyeVERPGDKVTLIrppepagrk 406

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 544 GAMPTLRGFDKYEAETKFIAATVQEWL-AKGIKPSEIGV----AARTKWFGSKIEDALKAEGIKTVDLAKTAKR-----D 613
Cdd:COG3972   407 GPLPEFKKYDDRAEELEAIAEEIKKNLrDEGLRPSDIAViylgNNEAKELGDRLAAALERQGIDSYIAGARSDPnffwkD 486

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063534947 614 DAVRVGTMHRMKGLEFRCVTVAGVgatmvpaanaitpideDKQTHDHDLERERCLLFVACTRAREELHVTWHGE 687
Cdd:COG3972   487 GGVTISTIHRAKGLEAPVVIIVGL----------------DQLAKGESLERLRNLLYVAMTRARGWLVVSGSGE 544
UvrD-helicase pfam00580
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ...
 241-489 5.69e-17

UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.


Pssm-ID: 395462 [Multi-domain]  Cd Length: 267  Bit Score: 81.52  E-value: 5.69e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 241 LHPTQRAVVeASFNGPARVTGGPGTGKTVVVLHR-AHTLAKRN--KGRVLVTTFTSTLSDSLQSGLDMIVDDDEVRNrIE 317
Cdd:pfam00580   1 LNPEQRKAV-THLGGPLLVLAGAGSGKTRVLTERiAYLILEGGidPEEILAVTFTNKAAREMKERILKLLGKAELSE-LN 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 318 VSHVDRVAHRVFRR---KYGAPNLLRPADEKNlWLGIIDKLELPFNDVFLADEWRHIVLARCINNAGEYL--AAKRTGRG 392
Cdd:pfam00580  79 ISTFHSFCLRILRKyanRIGLLPNFSILDELD-QLALLKELLEKDRLNLDPKLLRKLELKELISKAKNRLlsPEELQQGA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 393 RPLGPAQRAQVWQaiwEFEQTLTRLGA-------CTHETIRREATTLLEAETDKpYRHIVIDEAQDLSPDQWRLLRaAVA 465
Cdd:pfam00580 158 ADPRDKLAAEFYQ---EYQERLKENNAldfddllLLTLELLRSDPELLEAYRER-FKYILVDEFQDTNPIQYRLLK-LLA 232

                         250       260
                  ....*....|....*....|....
gi 1063534947 466 EAPDDIFIAGDTHQRIYdgrvSFR 489
Cdd:pfam00580 233 GGHENLFLVGDPDQSIY----GFR 252
SF1_C_UvrD cd18807
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ...
 547-684 1.53e-13

C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. This family also includes ATP-dependent helicase/nuclease AddA and helicase/nuclease RecBCD subunit RecB, among others. UvrD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350194 [Multi-domain]  Cd Length: 150  Bit Score: 68.41  E-value: 1.53e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 547 PTLRGFDKYEAETKFIAATVQEWLAKG-IKPSEIGVAARTKWFGSKIEDALKaegiktvdlaktakrddaVRVGTMHRMK 625
Cdd:cd18807    34 VELLLAKDEADEAKAIADEIKRLIESGpVQYSDIAILVRTNRQARVIEEALR------------------VTLMTIHASK 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063534947 626 GLEFRCVTVAGVGATMVPAANAITPIDEDKqthdHDLERERCLLFVACTRAREELHVTW 684
Cdd:cd18807    96 GLEFPVVFIVGLGEGFIPSDASYHAAKEDE----ERLEEERRLLYVALTRAKKELYLVG 150
addA_alphas TIGR02784
double-strand break repair helicase AddA, alphaproteobacterial type; AddAB, also called RexAB, ...
 443-514 1.39e-06

double-strand break repair helicase AddA, alphaproteobacterial type; AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274298 [Multi-domain]  Cd Length: 1135  Bit Score: 52.00  E-value: 1.39e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947  443 HIVIDEAQDLSPDQWRLLRAAVAE----------APDDIFIAGDTHQRIYdgrvSF-----------------REVGINI 495
Cdd:TIGR02784  393 HILVDEAQDTSPEQWDIIQALAEEffsgegarsgVERTIFAVGDEKQSIY----SFqgadperfaeerrefsrKVRAVGR 468

                           90
                   ....*....|....*....
gi 1063534947  496 AGRSARLNLNYRTTAEILG 514
Cdd:TIGR02784  469 KFEDLSLNYSFRSTPDVLA 487
PRK13909 PRK13909
RecB-like helicase;
438-604 3.09e-05

RecB-like helicase;


Pssm-ID: 237554 [Multi-domain]  Cd Length: 910  Bit Score: 47.27  E-value: 3.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 438 DKPYRHIVIDEAQDLSPDQWRLLRAAVAEAPDDI--------FIAGDTHQRIYDGRVSFREVGINIAGR----SARLNLN 505
Cdd:PRK13909  326 DSKISHILIDEFQDTSVLQYKILLPLIDEIKSGEgqkkfrsfFYVGDVKQSIYRFRGGKKELFDKVSKDfkqkVDNLDTN 405

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 506 YRTTAEIL------------GWSLGLLRgeriDDMDGGldsiagcrsYVHgampTLRGFDKYEAETKFIAATVQEWLAKG 573
Cdd:PRK13909  406 YRSAPLIVdfvnevfkkkykNYKTQYAE----QHKSGG---------YVE----VVEVADESEELLEQLLQEIQFLLEKG 468

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1063534947 574 IKPSEIGVAARTKWFGSKIEDALKAE-GIKTV 604
Cdd:PRK13909  469 IDPDDIAILCWTNDDALEIKEFLQEQfGIKAV 500
McrB COG1401
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 29-298 8.30e-03

5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB [Defense mechanisms];


Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 39.37  E-value: 8.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947  29 FDEFEAATYSGLHLEKINNARNRRFRSIRIDQSWRGIVLAPEhgdvFTLLKVLPHDDAYAWAQRSDISVNAAtgGIEIRD 108
Cdd:COG1401     4 PVLEFKFLIVGLRLKPLESEDAVRELGIRADDLRGAAELATR----LAERLSEELLRADRAARATELVEELS--AALEVV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 109 EEAIDRALPELKKSAENAESLLFAHVSDADLRRLGIDERTLAFARALTNSAQLDAAKSFLPETQWEVLFGLAAGYTPDEV 188
Cdd:COG1401    78 VLLLDLEKVELNEKLALSEAAVAIEELYELEADSEIEAVGLLLELAERSDALEALERARLLLELADLEERAALETEVLEA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 189 WSELGAAILAEPVDTDDLDAAVLRSRDRVVLVNgpdELMGVFAYPFATWRVYLHPTQRAVVEASFNGPARV-TGGPGTGK 267
Cdd:COG1401   158 LEAELEELLAAPEDLSADALAAELSAAEELYSE---DLESEDDYLKDLLREKFEETLEAFLAALKTKKNVIlAGPPGTGK 234

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1063534947 268 TVVVLHRAHTLAKRNKGRVLVTTFTSTLSDS 298
Cdd:COG1401   235 TYLARRLAEALGGEDNGRIEFVQFHPSWSYE 265
 
Name Accession Description Interval E-value
COG3972 COG3972
Superfamily I DNA and RNA helicases [Replication, recombination and repair];
245-687 1.10e-43

Superfamily I DNA and RNA helicases [Replication, recombination and repair];


Pssm-ID: 443172 [Multi-domain]  Cd Length: 565  Bit Score: 165.78  E-value: 1.10e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 245 QRAVVEASFNGPARVTGGPGTGKTVVVLHRAHTLAKRNKG-RVLVTTFTSTLSDSLQSGLDM---IVDDDEVRNRIEVSH 320
Cdd:COG3972   164 QERIARSIPDGPQRIRGVAGSGKTVLLAAKAAYLALKHPGwRILVTCFNRSLADHLRDLIPRflrRFSNGEPEDNVKLIV 243

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 321 VDRVAHRVFRRkYGAPnLLRPADEKNlwlgiidklelPFNDVFladewrhivlarcinnageylaakrtgrgrplgpaqr 400
Cdd:COG3972   244 FHAWGGKLLKQ-YGIP-PLTFSQPNE-----------AFDEAC------------------------------------- 273

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 401 aqvwqaiwefeqtltrlgacthetirREATTLLEAETDKP-YRHIVIDEAQDLSPDQWRLLRAAVAEAPDDIFIAGDTHQ 479
Cdd:COG3972   274 --------------------------KALLEAIQGEIIPPiYDAILIDEAQDFEPEFLRLLYQLLKPPKKRLIWAYDEAQ 327

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 480 RIYdGRVSFREVGINI-AGRSARLNLNYRTTAEIL----GWSLGLLRGERIDDMDGGL--DSIAGCRSYVH--------- 543
Cdd:COG3972   328 NIY-GRKIPSAGGIPAgIGRDTILKKNYRNTRPILtfahAFGMGLLRPPGLLQGDAEDyeVERPGDKVTLIrppepagrk 406

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 544 GAMPTLRGFDKYEAETKFIAATVQEWL-AKGIKPSEIGV----AARTKWFGSKIEDALKAEGIKTVDLAKTAKR-----D 613
Cdd:COG3972   407 GPLPEFKKYDDRAEELEAIAEEIKKNLrDEGLRPSDIAViylgNNEAKELGDRLAAALERQGIDSYIAGARSDPnffwkD 486

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063534947 614 DAVRVGTMHRMKGLEFRCVTVAGVgatmvpaanaitpideDKQTHDHDLERERCLLFVACTRAREELHVTWHGE 687
Cdd:COG3972   487 GGVTISTIHRAKGLEAPVVIIVGL----------------DQLAKGESLERLRNLLYVAMTRARGWLVVSGSGE 544
HelD COG3973
DNA helicase IV [Replication, recombination and repair];
245-694 1.86e-29

DNA helicase IV [Replication, recombination and repair];


Pssm-ID: 443173 [Multi-domain]  Cd Length: 699  Bit Score: 124.59  E-value: 1.86e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 245 QRAVVEASFNGPARVTGGPGTGKTVVVLHRA----HTLAKR-NKGRVLV----TTFTSTLSD---SL------QSGLDMI 306
Cdd:COG3973   196 QDRIIRADLRGVLVVQGGAGSGKTAVALHRAayllYTHRERlERGGVLIvgpnRLFLDYISQvlpSLgeegvvQTTFGDL 275

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 307 VDDdevRNRIEVSHVDRVAhrVFRRKyGAPnllrpadeknLWLGIIDKL------ELPFNDVFL--------ADEWRHIV 372
Cdd:COG3973   276 VPE---LLGVEATAEEDPE--VARLK-GSL----------RMAEVLDRAvrdlerEVPFEDIRVeggevilsAEEIAEAF 339

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 373 LARCIN---NAG---------EYLAAKRTGRGRPLGPAQRAQVWQAIWEFEQ-----------------------TLTRL 417
Cdd:COG3973   340 YRARRSlphNKRrerlrerllDALKDQLAAELGKLWDEERDELRRELRRSKPvraalnrlwpfldpaelyrdlfsDPELL 419

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 418 GACTH-------ETIRRE-------------ATTLLEA-------ETDKPYRHIVIDEAQDLSPDQWRLLRAAVaeaPDD 470
Cdd:COG3973   420 ARAAGwlspeerALLLRPtrelkkgrwtvadVALLDELaellggpDRTWTYGHVVVDEAQDLSPMQWRVLKRRF---PSA 496

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 471 IF-IAGDTHQRI--YDGRVSFREVGINIAGRSAR---LNLNYRTTAEILGWSLGLLRgeridDMDGGLDSIagcRSYV-H 543
Cdd:COG3973   497 SFtIVGDLAQAIhpYRGAESWEEVLEPLGGDRARlveLTKSYRSTAEIMEFANRVLR-----AAGPDLPPP---ESVRrH 568

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 544 GAMPTLRGFDKYEAETKFIAATVQEWLAKGikPSEIGVAARTKWFGSKIEDALKAEGIKTVDLAKTAKRDDAVRVGTMHR 623
Cdd:COG3973   569 GEPPRVVRVPSEAELAAAVVEAVRELLAEG--EGTIAVICKTAREAEALYAALKAGLPVTLIDDESEELEAGVVVLPAYL 646

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063534947 624 MKGLEFRCVtvagvgatMVPAANAITPidedkqthdhDLERERCLLFVACTRAREELHVTWHGEPSPFLTA 694
Cdd:COG3973   647 AKGLEFDAV--------VVVDPDEIVY----------ESPRGRRLLYVALTRATHRLTVLHTGELPPLLAG 699
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
241-699 3.37e-24

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


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 108.10  E-value: 3.37e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 241 LHPTQRAVVEAsFNGPARVTGGPGTGKTVVVLHR-AHTLAKRN--KGRVLVTTFT----STLSDSLQSGLDMIVdddevr 313
Cdd:COG0210     7 LNPEQRAAVEH-PEGPLLVLAGAGSGKTRVLTHRiAYLIAEGGvdPEQILAVTFTnkaaREMRERIEALLGRLA------ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 314 NRIEVSHVDRVAHRVFRRKYGA------PNLLRPADEKNLWLGIIDKLELPfNDVFLADEWRHIvlarcINNAGEYLAAK 387
Cdd:COG0210    80 RGLWVGTFHSLALRILRRHAELlglppnFTILDGDDQLRLIKELLKELGLD-EKRFPPRELLSL-----ISRAKNEGLTP 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 388 RTGRGRPLGPAQRAQVWQAIWEFEQTLTRLGACT-----HETIR--REATTLLEAETDKpYRHIVIDEAQDLSPDQWRLL 460
Cdd:COG0210   154 EELAELLAADPEWRAAAELYEAYQERLRANNALDfddllLLAVRllEENPEVLEKYQNR-FRYILVDEYQDTNPAQYELL 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 461 RAaVAEAPDDIFIAGDTHQRIYdgrvSFR--EVGiNIA--------GRSARLNLNYRTTAEILGWSLGLLR--GERIDDM 528
Cdd:COG0210   233 RL-LAGDGRNLCVVGDDDQSIY----GFRgaDPE-NILrfekdfpdAKVIKLEQNYRSTQNILDAANAVIAnnPGRLGKN 306

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 529 dggLDSIAGcrsyvHGAMPTLRGFDKYEAETKFIAATVQEWLAKGIKPSEIGVAARTKWFGSKIEDALKAEGI------- 601
Cdd:COG0210   307 ---LWTDNG-----EGEKVRLYVAPDEEEEARFVADEIRELHEEGVPLSDIAVLYRTNAQSRALEEALRRAGIpyrvvgg 378

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 602 -----------------------------------------KTV------------------------------------ 604
Cdd:COG0210   379 lrfyeraeikdllaylrllanpdddvallrilnvprrgigaATLerlreaareegisllealrdlgelaglsgraakalr 458

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947     --------------------------------------------------------------------------------
Cdd:COG0210   459 rfaellealraaaerlpleellealldesgyeeelreeageeaerrlenleelvdaaarfeernpgasleafleelalls 538

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 605 DLAKTAKRDDAVRVGTMHRMKGLEFRCVTVAGVGATMVPAANAITpiDEDkqthdhDLERERCLLFVACTRAREELHVTW 684
Cdd:COG0210   539 DLDAADEDEDAVTLMTLHAAKGLEFPVVFLVGLEEGLFPHQRSLD--DEE------ELEEERRLFYVAITRARERLYLTY 610

                         650       660
                  ....*....|....*....|....*.
gi 1063534947 685 HG-----------EPSPFLTAISGDC 699
Cdd:COG0210   611 AAsrrlwgetqdnEPSRFLDELPEEL 636
UvrD-helicase pfam00580
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ...
 241-489 5.69e-17

UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.


Pssm-ID: 395462 [Multi-domain]  Cd Length: 267  Bit Score: 81.52  E-value: 5.69e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 241 LHPTQRAVVeASFNGPARVTGGPGTGKTVVVLHR-AHTLAKRN--KGRVLVTTFTSTLSDSLQSGLDMIVDDDEVRNrIE 317
Cdd:pfam00580   1 LNPEQRKAV-THLGGPLLVLAGAGSGKTRVLTERiAYLILEGGidPEEILAVTFTNKAAREMKERILKLLGKAELSE-LN 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 318 VSHVDRVAHRVFRR---KYGAPNLLRPADEKNlWLGIIDKLELPFNDVFLADEWRHIVLARCINNAGEYL--AAKRTGRG 392
Cdd:pfam00580  79 ISTFHSFCLRILRKyanRIGLLPNFSILDELD-QLALLKELLEKDRLNLDPKLLRKLELKELISKAKNRLlsPEELQQGA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 393 RPLGPAQRAQVWQaiwEFEQTLTRLGA-------CTHETIRREATTLLEAETDKpYRHIVIDEAQDLSPDQWRLLRaAVA 465
Cdd:pfam00580 158 ADPRDKLAAEFYQ---EYQERLKENNAldfddllLLTLELLRSDPELLEAYRER-FKYILVDEFQDTNPIQYRLLK-LLA 232

                         250       260
                  ....*....|....*....|....
gi 1063534947 466 EAPDDIFIAGDTHQRIYdgrvSFR 489
Cdd:pfam00580 233 GGHENLFLVGDPDQSIY----GFR 252
RecB COG1074
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 441-601 2.82e-15

3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440692 [Multi-domain]  Cd Length: 866  Bit Score: 80.01  E-value: 2.82e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 441 YRHIVIDEAQDLSPDQWRLLRAAVAEAPDD---IFIAGDTHQRIYdgrvSFR------------EVGINIAGRSARLNLN 505
Cdd:COG1074   285 YRHILVDEFQDTSPLQWEILRRLAGEALADgrtLFLVGDPKQSIY----RFRgadpelflearrALEGRVDGERLTLTTN 360

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 506 YRTTAEILGWSLGLLRGEriddMDGGLDSIA--GCRSYVHGAMPTLR----------GFDKYEAETKFIAATVQEWLAKG 573
Cdd:COG1074   361 FRSTPEVVDAVNALFAQL----MGAGFGEIPyePVEALRPGAYPAVElwplepddvsEEDAREREARAVAARIRRLLAEG 436

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1063534947 574 ---------IKPSEIGVAARTKWFGSKIEDALKAEGI 601
Cdd:COG1074   437 ttvegggrpVRPGDIAVLVRTRSEAAAIARALKAAGI 473
SF1_C_UvrD cd18807
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ...
 547-684 1.53e-13

C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. This family also includes ATP-dependent helicase/nuclease AddA and helicase/nuclease RecBCD subunit RecB, among others. UvrD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350194 [Multi-domain]  Cd Length: 150  Bit Score: 68.41  E-value: 1.53e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 547 PTLRGFDKYEAETKFIAATVQEWLAKG-IKPSEIGVAARTKWFGSKIEDALKaegiktvdlaktakrddaVRVGTMHRMK 625
Cdd:cd18807    34 VELLLAKDEADEAKAIADEIKRLIESGpVQYSDIAILVRTNRQARVIEEALR------------------VTLMTIHASK 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063534947 626 GLEFRCVTVAGVGATMVPAANAITPIDEDKqthdHDLERERCLLFVACTRAREELHVTW 684
Cdd:cd18807    96 GLEFPVVFIVGLGEGFIPSDASYHAAKEDE----ERLEEERRLLYVALTRAKKELYLVG 150
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
 243-489 7.48e-12

DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD 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: 350690 [Multi-domain]  Cd Length: 189  Bit Score: 64.84  E-value: 7.48e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 243 PTQRAVVEAsFNGPARVTGGPGTGKTVVVLHR-AHTLAKRN--KGRVLVTTFTSTLSDSLQSGLDMIVDDDEVrNRIEVS 319
Cdd:cd17932     2 PEQREAVTH-PDGPLLVLAGAGSGKTRVLTHRiAYLILEGGvpPERILAVTFTNKAAKEMRERLRKLLGEQLA-SGVWIG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 320 HVDRVAHRVFRRKYGAPNLLRPAdeknlwlgiidkLELPFNDVFLADEWRhivlarcinnageylaakrtgrgrplgpaq 399
Cdd:cd17932    80 TFHSFALRILRRYGDFDDLLLYA------------LELLEENPDVREKLQ------------------------------ 117

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 400 raqvwqaiwefeqtltrlgacthetirreattlleaetdKPYRHIVIDEAQDLSPDQWRLLRaAVAEAPDDIFIAGDTHQ 479
Cdd:cd17932   118 ---------------------------------------SRFRYILVDEYQDTNPLQYELLK-LLAGDGKNLFVVGDDDQ 157

                         250
                  ....*....|
gi 1063534947 480 RIYdgrvSFR 489
Cdd:cd17932   158 SIY----GFR 163
UvrD_C pfam13361
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 501-605 1.34e-07

UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.


Pssm-ID: 433145 [Multi-domain]  Cd Length: 377  Bit Score: 54.33  E-value: 1.34e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 501 RLNLNYRTTAEILGWSLGLLRGERIDDMDGGLDSIAgcRSYVHGAMPTLRGFDKYEAETKFIAATVQEWLAKGIKPSEIG 580
Cdd:pfam13361   2 HLEINYRSTKNLLKAANEFINNNFGRATIYPKKILA--ETVEDGEKIKIIEAETEEEEAEWIALEIKKLVARDEKYNDIA 79

                          90       100
                  ....*....|....*....|....*..
gi 1063534947 581 VAARTKWFGSKIEDALKAEGI--KTVD 605
Cdd:pfam13361  80 VLTRSNSDADLIEEALKKLGIpyFVVG 106
UvrD_C pfam13361
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 613-685 5.33e-07

UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.


Pssm-ID: 433145 [Multi-domain]  Cd Length: 377  Bit Score: 52.41  E-value: 5.33e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1063534947 613 DDAVRVGTMHRMKGLEFRCVTVAGVgatmvpaANAITPIDEDKQThDHDLERERCLLFVACTRAREELHVTWH 685
Cdd:pfam13361 311 KERIPIMTIHQAKGLEFDTVFLAGL-------EEGIFPSYRSIKD-EGNLEEERRLFYVAITRAKKRLYISYS 375
addA_alphas TIGR02784
double-strand break repair helicase AddA, alphaproteobacterial type; AddAB, also called RexAB, ...
 443-514 1.39e-06

double-strand break repair helicase AddA, alphaproteobacterial type; AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274298 [Multi-domain]  Cd Length: 1135  Bit Score: 52.00  E-value: 1.39e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947  443 HIVIDEAQDLSPDQWRLLRAAVAE----------APDDIFIAGDTHQRIYdgrvSF-----------------REVGINI 495
Cdd:TIGR02784  393 HILVDEAQDTSPEQWDIIQALAEEffsgegarsgVERTIFAVGDEKQSIY----SFqgadperfaeerrefsrKVRAVGR 468

                           90
                   ....*....|....*....
gi 1063534947  496 AGRSARLNLNYRTTAEILG 514
Cdd:TIGR02784  469 KFEDLSLNYSFRSTPDVLA 487
AAA_19 pfam13245
AAA domain;
245-292 3.07e-06

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 47.21  E-value: 3.07e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063534947 245 QRAVVEASFNGPARVTGGPGTGKTVVVLHRAHTLAKRN--KGRVLVTTFT 292
Cdd:pfam13245   2 REAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvSFPILLAAPT 51
PRK13909 PRK13909
RecB-like helicase;
438-604 3.09e-05

RecB-like helicase;


Pssm-ID: 237554 [Multi-domain]  Cd Length: 910  Bit Score: 47.27  E-value: 3.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 438 DKPYRHIVIDEAQDLSPDQWRLLRAAVAEAPDDI--------FIAGDTHQRIYDGRVSFREVGINIAGR----SARLNLN 505
Cdd:PRK13909  326 DSKISHILIDEFQDTSVLQYKILLPLIDEIKSGEgqkkfrsfFYVGDVKQSIYRFRGGKKELFDKVSKDfkqkVDNLDTN 405

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 506 YRTTAEIL------------GWSLGLLRgeriDDMDGGldsiagcrsYVHgampTLRGFDKYEAETKFIAATVQEWLAKG 573
Cdd:PRK13909  406 YRSAPLIVdfvnevfkkkykNYKTQYAE----QHKSGG---------YVE----VVEVADESEELLEQLLQEIQFLLEKG 468

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1063534947 574 IKPSEIGVAARTKWFGSKIEDALKAE-GIKTV 604
Cdd:PRK13909  469 IDPDDIAILCWTNDDALEIKEFLQEQfGIKAV 500
recB TIGR00609
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ...
 409-604 4.36e-05

exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273172 [Multi-domain]  Cd Length: 1087  Bit Score: 47.04  E-value: 4.36e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947  409 EFEQTLTRLGACTHETIRREATTLLEAETDKP--------YRHIVIDEAQDLSPDQWRLL-RAAVAEAPDDIFIAGDTHQ 479
Cdd:TIGR00609  257 ELKKEKKRRREIGFDDLLSRLETALKSAEGEKlaqaireqYPIALIDEFQDTDPQQYRIFsKLFIAQKETSLFLIGDPKQ 336

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947  480 RIYdgrvSFREVGI----NIAGR-SARLNL--NYRTTAEILGwSLGLLRGERIDDmdgGLDSIAGCRSYVHGAMPTLR-- 550
Cdd:TIGR00609  337 AIY----SFRGADIftylQAKSKaDARYTLgtNWRSTPALVG-SLNKLFSLISNP---FLEKPIFIPVLAHQKNSKGSfv 408

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947  551 ---------GFDKYEAETKFI-----------AATVQEWLAKG---------------IKPSEIGVAARTKWFGSKIEDA 595
Cdd:TIGR00609  409 ingqeqppiHFFTTEVESEGVddyrqtiaqkcAREIALWLASAalglanfiatfggrpLRAGDIAVLVRGRKEANQIRKA 488


                   ....*....
gi 1063534947  596 LKAEGIKTV 604
Cdd:TIGR00609  489 LKKAQIPSV 497
uvrD PRK11773
DNA-dependent helicase II; Provisional
 614-699 6.31e-05

DNA-dependent helicase II; Provisional


Pssm-ID: 236976 [Multi-domain]  Cd Length: 721  Bit Score: 46.40  E-value: 6.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 614 DAVRVGTMHRMKGLEFRCVTVAGVGATMVPAANAitpIDEDKQthdhdLERERCLLFVACTRAREELHVTW------HGE 687
Cdd:PRK11773  552 DAVQLMTLHSAKGLEFPLVFIVGMEEGLFPSQMS---LEEGGR-----LEEERRLAYVGITRAMQKLTLTYaesrrlYGK 623

                          90
                  ....*....|....*..
gi 1063534947 688 -----PSPFLTAISGDC 699
Cdd:PRK11773  624 evyhrPSRFIREIPEEC 640
PRK10919 PRK10919
ATP-dependent DNA helicase Rep; Provisional
 614-698 9.89e-05

ATP-dependent DNA helicase Rep; Provisional


Pssm-ID: 182838 [Multi-domain]  Cd Length: 672  Bit Score: 45.60  E-value: 9.89e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 614 DAVRVGTMHRMKGLEFRCVTVAGVGATMVPAAnaiTPIDEDkqthdhDLERERCLLFVACTRAREELHVTW------HG- 686
Cdd:PRK10919  550 DQVQLMTLHASKGLEFPYVYLVGMEEGLLPHQ---SSIDED------NIDEERRLAYVGITRAQKELTFTLckerrqYGe 620

                          90
                  ....*....|....*.
gi 1063534947 687 ----EPSPFLTAISGD 698
Cdd:PRK10919  621 lvrpEPSRFLLELPQD 636
uvrD PRK11773
DNA-dependent helicase II; Provisional
 441-601 1.42e-04

DNA-dependent helicase II; Provisional


Pssm-ID: 236976 [Multi-domain]  Cd Length: 721  Bit Score: 45.25  E-value: 1.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 441 YRHIVIDEAQDLSPDQWRLLRaAVAEAPDDIFIAGDTHQRIYDGRVSFREvgiNI--------AGRSARLNLNYRTTAEI 512
Cdd:PRK11773  214 FTHILVDEFQDTNAIQYAWIR-LLAGDTGKVMIVGDDDQSIYGWRGAQVE---NIqrflndfpGAETIRLEQNYRSTANI 289

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 513 LGWSLGLL--RGERI------DDMDGGLDSIagcrsyvhgamptlrgfdkYEA-----ETKFIAATVQEWLAKGIKPSEI 579
Cdd:PRK11773  290 LKAANALIanNNGRLgkelwtDGGDGEPISL-------------------YCAfneldEARFVVERIKTWQDNGGALSDC 350

                         170       180
                  ....*....|....*....|..
gi 1063534947 580 GVAARTKWFGSKIEDALKAEGI 601
Cdd:PRK11773  351 AILYRSNAQSRVLEEALLQAGI 372
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 256-341 2.63e-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: 41.32  E-value: 2.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 256 PARVTGGPGTGKTVVVLHR-AHTLAKRN--KGRVLVTTFTSTLSDSLQSgldMIVDDDEVRNRIEVSHVDRVAHRVFRRK 332
Cdd:cd17914     1 LSLIQGPPGTGKTRVLVKIvAALMQNKNgePGRILLVTPTNKAAAQLDN---ILVDEAAQILEPETSRLIDLALDQGRVI 77

                          90
                  ....*....|
gi 1063534947 333 -YGAPNLLRP 341
Cdd:cd17914    78 lVGDHDQLGP 87
helD PRK11054
DNA helicase IV; Provisional
 440-482 2.29e-03

DNA helicase IV; Provisional


Pssm-ID: 182930 [Multi-domain]  Cd Length: 684  Bit Score: 41.09  E-value: 2.29e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063534947 440 PYRHIVIDEAQDLSPDQWRLLRAAVAEAPD-DIFIAGDTHQRIY 482
Cdd:PRK11054  430 PWKHILVDEFQDISPQRAALLAALRKQNSQtTLFAVGDDWQAIY 473
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 241-283 5.94e-03

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: 39.05  E-value: 5.94e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063534947 241 LHPTQRAVVEASFNGP-ARVTGGPGTGKTVVVLHRAHTLAKRNK 283
Cdd:cd18040     2 LNPSQNHAVRTALTKPfTLIQGPPGTGKTVTGVHIAYWFAKQNR 45
McrB COG1401
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 29-298 8.30e-03

5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB [Defense mechanisms];


Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 39.37  E-value: 8.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947  29 FDEFEAATYSGLHLEKINNARNRRFRSIRIDQSWRGIVLAPEhgdvFTLLKVLPHDDAYAWAQRSDISVNAAtgGIEIRD 108
Cdd:COG1401     4 PVLEFKFLIVGLRLKPLESEDAVRELGIRADDLRGAAELATR----LAERLSEELLRADRAARATELVEELS--AALEVV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 109 EEAIDRALPELKKSAENAESLLFAHVSDADLRRLGIDERTLAFARALTNSAQLDAAKSFLPETQWEVLFGLAAGYTPDEV 188
Cdd:COG1401    78 VLLLDLEKVELNEKLALSEAAVAIEELYELEADSEIEAVGLLLELAERSDALEALERARLLLELADLEERAALETEVLEA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063534947 189 WSELGAAILAEPVDTDDLDAAVLRSRDRVVLVNgpdELMGVFAYPFATWRVYLHPTQRAVVEASFNGPARV-TGGPGTGK 267
Cdd:COG1401   158 LEAELEELLAAPEDLSADALAAELSAAEELYSE---DLESEDDYLKDLLREKFEETLEAFLAALKTKKNVIlAGPPGTGK 234

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1063534947 268 TVVVLHRAHTLAKRNKGRVLVTTFTSTLSDS 298
Cdd:COG1401   235 TYLARRLAEALGGEDNGRIEFVQFHPSWSYE 265
 
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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