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Conserved domains on  [gi|497074172|ref|WP_009459603|]
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MULTISPECIES: excinuclease ABC subunit UvrB [Proteobacteria]

Protein Classification

excinuclease ABC subunit UvrB( domain architecture ID 11480575)

excinuclease ABC subunit UvrB is part of the UvrABC repair system that catalyzes the recognition and processing of DNA lesions

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
2-658 0e+00

excinuclease ABC subunit UvrB;


:

Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1130.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   2 STGTFILHSSYTPAGDQPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRLKRPTLILAPNKTLTAQLYGEMKHF 81
Cdd:PRK05298   1 MMKPFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEF 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  82 FPENAVEYFVSYYDYFQPEIYMPGTDRFIPKDSAINDHLERLRLSTTKSLIERRDVIVVASVSSIYGLGDPEAYRALQIA 161
Cdd:PRK05298  81 FPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLS 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 162 LSPGVKLNQRELIRRLALLQYDRTERTLKRATFRAQGDVIDIFPADSEHRAVRVELLDDSVASVQWLDPVTGKTLGAIDH 241
Cdd:PRK05298 161 LRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDR 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 242 YLVSPKTLFAPPTNKIDSASKKILADMEERVAELNRNNRLVEANRLYERITHDVEMMREVGYCSGMENYSCYFSERDPAS 321
Cdd:PRK05298 241 VTIYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGE 320
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 322 PPITLLDYLPKDGLLFVDESHVMVPQISAMYRGDQARKETLIDYGFRLPSSKNNRPLNFGEFEKVKPQTIFVSATPGDYE 401
Cdd:PRK05298 321 PPYTLLDYFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYE 400
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 402 LRVSKDRVVEQVIRPTGLLDPKVEVRKADGYIDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDI 481
Cdd:PRK05298 401 LEKSGGVVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDI 480
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 482 KAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADRAGFLRSAHALIQMIGRVARNENGKAILYADAVTPA 561
Cdd:PRK05298 481 DTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDS 560
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 562 MKQAIDETNRRRQLQIAFNEENGISPASSVRKLAGEETNTEEPTVHSEAfcenlsDLCDQITAKEQQLLEFTDTGDEQRV 641
Cdd:PRK05298 561 MQKAIDETERRREIQIAYNEEHGITPKTIKKKIRDILDSVYKKDKLSKK------ELEKLIKELEKQMKEAAKNLEFEEA 634
                        650
                 ....*....|....*..
gi 497074172 642 EDIRRQLDGLYRQFIYI 658
Cdd:PRK05298 635 ARLRDEIKELKEELLGL 651
 
Name Accession Description Interval E-value
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
2-658 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1130.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   2 STGTFILHSSYTPAGDQPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRLKRPTLILAPNKTLTAQLYGEMKHF 81
Cdd:PRK05298   1 MMKPFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEF 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  82 FPENAVEYFVSYYDYFQPEIYMPGTDRFIPKDSAINDHLERLRLSTTKSLIERRDVIVVASVSSIYGLGDPEAYRALQIA 161
Cdd:PRK05298  81 FPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLS 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 162 LSPGVKLNQRELIRRLALLQYDRTERTLKRATFRAQGDVIDIFPADSEHRAVRVELLDDSVASVQWLDPVTGKTLGAIDH 241
Cdd:PRK05298 161 LRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDR 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 242 YLVSPKTLFAPPTNKIDSASKKILADMEERVAELNRNNRLVEANRLYERITHDVEMMREVGYCSGMENYSCYFSERDPAS 321
Cdd:PRK05298 241 VTIYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGE 320
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 322 PPITLLDYLPKDGLLFVDESHVMVPQISAMYRGDQARKETLIDYGFRLPSSKNNRPLNFGEFEKVKPQTIFVSATPGDYE 401
Cdd:PRK05298 321 PPYTLLDYFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYE 400
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 402 LRVSKDRVVEQVIRPTGLLDPKVEVRKADGYIDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDI 481
Cdd:PRK05298 401 LEKSGGVVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDI 480
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 482 KAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADRAGFLRSAHALIQMIGRVARNENGKAILYADAVTPA 561
Cdd:PRK05298 481 DTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDS 560
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 562 MKQAIDETNRRRQLQIAFNEENGISPASSVRKLAGEETNTEEPTVHSEAfcenlsDLCDQITAKEQQLLEFTDTGDEQRV 641
Cdd:PRK05298 561 MQKAIDETERRREIQIAYNEEHGITPKTIKKKIRDILDSVYKKDKLSKK------ELEKLIKELEKQMKEAAKNLEFEEA 634
                        650
                 ....*....|....*..
gi 497074172 642 EDIRRQLDGLYRQFIYI 658
Cdd:PRK05298 635 ARLRDEIKELKEELLGL 651
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
6-654 0e+00

Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1118.17  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   6 FILHSSYTPAGDQPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRLKRPTLILAPNKTLTAQLYGEMKHFFPEN 85
Cdd:COG0556    2 FKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPNN 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  86 AVEYFVSYYDYFQPEIYMPGTDRFIPKDSAINDHLERLRLSTTKSLIERRDVIVVASVSSIYGLGDPEAYRALQIALSPG 165
Cdd:COG0556   82 AVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRVG 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 166 VKLNQRELIRRLALLQYDRTERTLKRATFRAQGDVIDIFPADSEHRAVRVELLDDSVASVQWLDPVTGKTLGAIDHYLVS 245
Cdd:COG0556  162 EEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTIY 241
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 246 PKTLFAPPTNKIDSASKKILADMEERVAELNRNNRLVEANRLYERITHDVEMMREVGYCSGMENYSCYFSERDPASPPIT 325
Cdd:COG0556  242 PASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPPT 321
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 326 LLDYLPKDGLLFVDESHVMVPQISAMYRGDQARKETLIDYGFRLPSSKNNRPLNFGEFEKVKPQTIFVSATPGDYELRVS 405
Cdd:COG0556  322 LLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEKS 401
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 406 KDRVVEQVIRPTGLLDPKVEVRKADGYIDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDIKAED 485
Cdd:COG0556  402 GGQVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLE 481
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 486 RVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADRAGFLRSAHALIQMIGRVARNENGKAILYADAVTPAMKQA 565
Cdd:COG0556  482 RVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQRA 561
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 566 IDETNRRRQLQIAFNEENGISPASSVRKLA-------GEETNTEEPTVHSEAFCENLSDLCDQITAKEQQLLEFTDTGDE 638
Cdd:COG0556  562 IDETNRRREIQEAYNEEHGITPQTIKKSIRdilegtyEADEETEELVAEADAAKLSKEELEKLIKELEKEMKEAAKNLEF 641
                        650
                 ....*....|....*.
gi 497074172 639 QRVEDIRRQLDGLYRQ 654
Cdd:COG0556  642 EEAARLRDEIKELKKE 657
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
5-630 0e+00

excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. 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: 273185 [Multi-domain]  Cd Length: 655  Bit Score: 941.72  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172    5 TFILHSSYTPAGDQPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRLKRPTLILAPNKTLTAQLYGEMKHFFPE 84
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   85 NAVEYFVSYYDYFQPEIYMPGTDRFIPKDSAINDHLERLRLSTTKSLIERRDVIVVASVSSIYGLGDPEAYRALQIALSP 164
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEV 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  165 GVKLNQRELIRRLALLQYDRTERTLKRATFRAQGDVIDIFPADSEHRAVRVELLDDSVASVQWLDPVTGKTLGAIDHYLV 244
Cdd:TIGR00631 161 GKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDEFAVRIEFFGDEIERISRVDPLTGEVLRELDSFTI 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  245 SPKTLFAPPTNKIDSASKKILADMEERVAELNRNNRLVEANRLYERITHDVEMMREVGYCSGMENYSCYFSERDPASPPI 324
Cdd:TIGR00631 241 FPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPPY 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  325 TLLDYLPKDGLLFVDESHVMVPQISAMYRGDQARKETLIDYGFRLPSSKNNRPLNFGEFEKVKPQTIFVSATPGDYELRV 404
Cdd:TIGR00631 321 TLLDYFPDDFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELEQ 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  405 SkDRVVEQVIRPTGLLDPKVEVRKADGYIDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDIKAE 484
Cdd:TIGR00631 401 S-GNVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTL 479
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  485 DRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADRAGFLRSAHALIQMIGRVARNENGKAILYADAVTPAMKQ 564
Cdd:TIGR00631 480 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQK 559
                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 497074172  565 AIDETNRRRQLQIAFNEENGISPaSSVRKLAGEETNTEEPTVHSEAFCENLSDLCDQITAKEQQLL 630
Cdd:TIGR00631 560 AIEETERRRKIQMAYNEEHGITP-QTIRKPIRDILDIELKEKEDAAKKKKKGEDLSDLSKKELKKL 624
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
6-415 2.20e-169

DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II) and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA, but its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a member of the DEAD-like helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350674 [Multi-domain]  Cd Length: 299  Bit Score: 485.56  E-value: 2.20e-169
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   6 FILHSSYTPAGDQPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRLKRPTLILAPNKTLTAQLYGEMKHFFPEN 85
Cdd:cd17916    1 FKLVSPFKPAGDQPQAIAKLVEGLKRGVKFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  86 AVEYFVSYYDYFQPEIYMPGTDRFIPKDSAINDHLERLRLSTTKSLIERRDVIVVASVSSIYglgdpeayralqialspg 165
Cdd:cd17916   81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLERRDVIVVASVSCIY------------------ 142
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 166 vklnqrelirrlallqydrtertlkratfraqgdvidifpadsehravrvellddsvasvqwldpvtgktlgaidhylvs 245
Cdd:cd17916      --------------------------------------------------------------------------------
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 246 pktlfapptnkiDSASKKILADMEERVAELNRNNRLVEANRLYERITHDVEMMREVGYCSGMENYSCYFSERDPASPPIT 325
Cdd:cd17916  143 ------------ERAIKSIEEELEERLKYFRAQGKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 326 LLDYLPKDGLLFVDESHVMVPQISAMYRGDQARKETLIDYGFRLPSSKNNRPLNFGEFEKVKPQTIFVSATPGDYELRVS 405
Cdd:cd17916  211 LLDYFPDDFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEHS 290
                        410
                 ....*....|
gi 497074172 406 kDRVVEQVIR 415
Cdd:cd17916  291 -GQVVEQIIR 299
UvrB_inter pfam17757
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ...
160-250 1.32e-29

UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the UvrA protein.


Pssm-ID: 465486 [Multi-domain]  Cd Length: 91  Bit Score: 112.10  E-value: 1.32e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  160 IALSPGVKLNQRELIRRLALLQYDRTERTLKRATFRAQGDVIDIFPADSEHRAVRVELLDDSVASVQWLDPVTGKTLGAI 239
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
                          90
                  ....*....|.
gi 497074172  240 DHYLVSPKTLF 250
Cdd:pfam17757  81 DEVTIYPASHY 91
HELICc smart00490
helicase superfamily c-terminal domain;
461-545 1.52e-19

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 83.42  E-value: 1.52e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   461 EELTDFLTDNGIRARYMHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADragflRSAHALIQMI 540
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-----WSPASYIQRI 75

                   ....*
gi 497074172   541 GRVAR 545
Cdd:smart00490  76 GRAGR 80
 
Name Accession Description Interval E-value
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
2-658 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1130.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   2 STGTFILHSSYTPAGDQPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRLKRPTLILAPNKTLTAQLYGEMKHF 81
Cdd:PRK05298   1 MMKPFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEF 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  82 FPENAVEYFVSYYDYFQPEIYMPGTDRFIPKDSAINDHLERLRLSTTKSLIERRDVIVVASVSSIYGLGDPEAYRALQIA 161
Cdd:PRK05298  81 FPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLS 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 162 LSPGVKLNQRELIRRLALLQYDRTERTLKRATFRAQGDVIDIFPADSEHRAVRVELLDDSVASVQWLDPVTGKTLGAIDH 241
Cdd:PRK05298 161 LRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDR 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 242 YLVSPKTLFAPPTNKIDSASKKILADMEERVAELNRNNRLVEANRLYERITHDVEMMREVGYCSGMENYSCYFSERDPAS 321
Cdd:PRK05298 241 VTIYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGE 320
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 322 PPITLLDYLPKDGLLFVDESHVMVPQISAMYRGDQARKETLIDYGFRLPSSKNNRPLNFGEFEKVKPQTIFVSATPGDYE 401
Cdd:PRK05298 321 PPYTLLDYFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYE 400
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 402 LRVSKDRVVEQVIRPTGLLDPKVEVRKADGYIDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDI 481
Cdd:PRK05298 401 LEKSGGVVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDI 480
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 482 KAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADRAGFLRSAHALIQMIGRVARNENGKAILYADAVTPA 561
Cdd:PRK05298 481 DTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDS 560
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 562 MKQAIDETNRRRQLQIAFNEENGISPASSVRKLAGEETNTEEPTVHSEAfcenlsDLCDQITAKEQQLLEFTDTGDEQRV 641
Cdd:PRK05298 561 MQKAIDETERRREIQIAYNEEHGITPKTIKKKIRDILDSVYKKDKLSKK------ELEKLIKELEKQMKEAAKNLEFEEA 634
                        650
                 ....*....|....*..
gi 497074172 642 EDIRRQLDGLYRQFIYI 658
Cdd:PRK05298 635 ARLRDEIKELKEELLGL 651
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
6-654 0e+00

Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1118.17  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   6 FILHSSYTPAGDQPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRLKRPTLILAPNKTLTAQLYGEMKHFFPEN 85
Cdd:COG0556    2 FKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPNN 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  86 AVEYFVSYYDYFQPEIYMPGTDRFIPKDSAINDHLERLRLSTTKSLIERRDVIVVASVSSIYGLGDPEAYRALQIALSPG 165
Cdd:COG0556   82 AVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRVG 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 166 VKLNQRELIRRLALLQYDRTERTLKRATFRAQGDVIDIFPADSEHRAVRVELLDDSVASVQWLDPVTGKTLGAIDHYLVS 245
Cdd:COG0556  162 EEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTIY 241
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 246 PKTLFAPPTNKIDSASKKILADMEERVAELNRNNRLVEANRLYERITHDVEMMREVGYCSGMENYSCYFSERDPASPPIT 325
Cdd:COG0556  242 PASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPPT 321
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 326 LLDYLPKDGLLFVDESHVMVPQISAMYRGDQARKETLIDYGFRLPSSKNNRPLNFGEFEKVKPQTIFVSATPGDYELRVS 405
Cdd:COG0556  322 LLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEKS 401
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 406 KDRVVEQVIRPTGLLDPKVEVRKADGYIDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDIKAED 485
Cdd:COG0556  402 GGQVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLE 481
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 486 RVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADRAGFLRSAHALIQMIGRVARNENGKAILYADAVTPAMKQA 565
Cdd:COG0556  482 RVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQRA 561
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 566 IDETNRRRQLQIAFNEENGISPASSVRKLA-------GEETNTEEPTVHSEAFCENLSDLCDQITAKEQQLLEFTDTGDE 638
Cdd:COG0556  562 IDETNRRREIQEAYNEEHGITPQTIKKSIRdilegtyEADEETEELVAEADAAKLSKEELEKLIKELEKEMKEAAKNLEF 641
                        650
                 ....*....|....*.
gi 497074172 639 QRVEDIRRQLDGLYRQ 654
Cdd:COG0556  642 EEAARLRDEIKELKKE 657
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
5-630 0e+00

excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. 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: 273185 [Multi-domain]  Cd Length: 655  Bit Score: 941.72  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172    5 TFILHSSYTPAGDQPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRLKRPTLILAPNKTLTAQLYGEMKHFFPE 84
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   85 NAVEYFVSYYDYFQPEIYMPGTDRFIPKDSAINDHLERLRLSTTKSLIERRDVIVVASVSSIYGLGDPEAYRALQIALSP 164
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEV 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  165 GVKLNQRELIRRLALLQYDRTERTLKRATFRAQGDVIDIFPADSEHRAVRVELLDDSVASVQWLDPVTGKTLGAIDHYLV 244
Cdd:TIGR00631 161 GKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDEFAVRIEFFGDEIERISRVDPLTGEVLRELDSFTI 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  245 SPKTLFAPPTNKIDSASKKILADMEERVAELNRNNRLVEANRLYERITHDVEMMREVGYCSGMENYSCYFSERDPASPPI 324
Cdd:TIGR00631 241 FPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPPY 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  325 TLLDYLPKDGLLFVDESHVMVPQISAMYRGDQARKETLIDYGFRLPSSKNNRPLNFGEFEKVKPQTIFVSATPGDYELRV 404
Cdd:TIGR00631 321 TLLDYFPDDFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELEQ 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  405 SkDRVVEQVIRPTGLLDPKVEVRKADGYIDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDIKAE 484
Cdd:TIGR00631 401 S-GNVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTL 479
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  485 DRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADRAGFLRSAHALIQMIGRVARNENGKAILYADAVTPAMKQ 564
Cdd:TIGR00631 480 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQK 559
                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 497074172  565 AIDETNRRRQLQIAFNEENGISPaSSVRKLAGEETNTEEPTVHSEAFCENLSDLCDQITAKEQQLL 630
Cdd:TIGR00631 560 AIEETERRRKIQMAYNEEHGITP-QTIRKPIRDILDIELKEKEDAAKKKKKGEDLSDLSKKELKKL 624
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
6-415 2.20e-169

DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II) and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA, but its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a member of the DEAD-like helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350674 [Multi-domain]  Cd Length: 299  Bit Score: 485.56  E-value: 2.20e-169
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   6 FILHSSYTPAGDQPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRLKRPTLILAPNKTLTAQLYGEMKHFFPEN 85
Cdd:cd17916    1 FKLVSPFKPAGDQPQAIAKLVEGLKRGVKFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  86 AVEYFVSYYDYFQPEIYMPGTDRFIPKDSAINDHLERLRLSTTKSLIERRDVIVVASVSSIYglgdpeayralqialspg 165
Cdd:cd17916   81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLERRDVIVVASVSCIY------------------ 142
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 166 vklnqrelirrlallqydrtertlkratfraqgdvidifpadsehravrvellddsvasvqwldpvtgktlgaidhylvs 245
Cdd:cd17916      --------------------------------------------------------------------------------
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 246 pktlfapptnkiDSASKKILADMEERVAELNRNNRLVEANRLYERITHDVEMMREVGYCSGMENYSCYFSERDPASPPIT 325
Cdd:cd17916  143 ------------ERAIKSIEEELEERLKYFRAQGKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 326 LLDYLPKDGLLFVDESHVMVPQISAMYRGDQARKETLIDYGFRLPSSKNNRPLNFGEFEKVKPQTIFVSATPGDYELRVS 405
Cdd:cd17916  211 LLDYFPDDFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEHS 290
                        410
                 ....*....|
gi 497074172 406 kDRVVEQVIR 415
Cdd:cd17916  291 -GQVVEQIIR 299
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
421-589 6.80e-92

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 281.83  E-value: 6.80e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 421 DPKVEVRKADGYIDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDIKAEDRVEIINGLRAGEFDV 500
Cdd:cd18790    1 DPEIEVRPTEGQVDDLLGEIRKRVARGERVLVTTLTKRMAEDLTEYLQELGVKVRYLHSEIDTLERVEIIRDLRLGEFDV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 501 LIGISLLREGLDIPEASLVAILDADRAGFLRSAHALIQMIGRVARNENGKAILYADAVTPAMKQAIDETNRRRQLQIAFN 580
Cdd:cd18790   81 LVGINLLREGLDLPEVSLVAILDADKEGFLRSETSLIQTIGRAARNVNGKVILYADKITDSMQKAIEETERRREIQMEYN 160

                 ....*....
gi 497074172 581 EENGISPAS 589
Cdd:cd18790  161 EEHGITPKT 169
UvrB_inter pfam17757
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ...
160-250 1.32e-29

UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the UvrA protein.


Pssm-ID: 465486 [Multi-domain]  Cd Length: 91  Bit Score: 112.10  E-value: 1.32e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  160 IALSPGVKLNQRELIRRLALLQYDRTERTLKRATFRAQGDVIDIFPADSEHRAVRVELLDDSVASVQWLDPVTGKTLGAI 239
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
                          90
                  ....*....|.
gi 497074172  240 DHYLVSPKTLF 250
Cdd:pfam17757  81 DEVTIYPASHY 91
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
433-545 5.10e-20

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


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 85.73  E-value: 5.10e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  433 IDDLLAEISKcvKKKNRVLVTTLTKVSAEElTDFLTDNGIRARYMHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLD 512
Cdd:pfam00271   3 LEALLELLKK--ERGGKVLIFSQTKKTLEA-ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLD 79
                          90       100       110
                  ....*....|....*....|....*....|...
gi 497074172  513 IPEASLVAILDADragflRSAHALIQMIGRVAR 545
Cdd:pfam00271  80 LPDVDLVINYDLP-----WNPASYIQRIGRAGR 107
HELICc smart00490
helicase superfamily c-terminal domain;
461-545 1.52e-19

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 83.42  E-value: 1.52e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   461 EELTDFLTDNGIRARYMHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADragflRSAHALIQMI 540
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-----WSPASYIQRI 75

                   ....*
gi 497074172   541 GRVAR 545
Cdd:smart00490  76 GRAGR 80
UvrB pfam12344
Ultra-violet resistance protein B; This domain family is found in bacteria, archaea and ...
553-595 3.14e-17

Ultra-violet resistance protein B; This domain family is found in bacteria, archaea and eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00271, pfam02151, pfam04851. There are two conserved sequence motifs: YAD and RRR. This family is the C terminal region of the UvrB protein which conveys mutational resistance against UV light to various different species.


Pssm-ID: 463540 [Multi-domain]  Cd Length: 43  Bit Score: 75.50  E-value: 3.14e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 497074172  553 LYADAVTPAMKQAIDETNRRRQLQIAFNEENGISPASSVRKLA 595
Cdd:pfam12344   1 LYADKITDSMQRAIDETERRREIQEAYNEEHGITPKTIKKKIR 43
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
434-653 7.39e-15

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 77.76  E-value: 7.39e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 434 DDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLDI 513
Cdd:COG1061  292 DKILRELLREHPDDRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDV 371
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 514 PEASLVAILDAdragfLRSAHALIQMIGRVARNENGK--AILYaDAVTPAMKQAIDETNRRR-----QLQIAFNEENGIS 586
Cdd:COG1061  372 PRLDVAILLRP-----TGSPREFIQRLGRGLRPAPGKedALVY-DFVGNDVPVLEELAKDLRdlagyRVEFLDEEESEEL 445
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 497074172 587 PASSVRKLAGEETNTEEPTVHSEAFCENLSDLCDQITAKEQQLLEFTDTGDEQRVEDIRRQLDGLYR 653
Cdd:COG1061  446 ALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEK 512
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
434-553 1.16e-13

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 68.30  E-value: 1.16e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 434 DDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLDI 513
Cdd:cd18787   14 KLLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDI 93
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 497074172 514 PEASLVAILDadragFLRSAHALIQMIGRVAR-NENGKAIL 553
Cdd:cd18787   94 PGVDHVINYD-----LPRDAEDYVHRIGRTGRaGRKGTAIT 129
ResIII pfam04851
Type III restriction enzyme, res subunit;
18-140 4.31e-13

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 67.31  E-value: 4.31e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   18 QPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRL-----KRPTLILAPNKTLTAQLYGEMKHFFPEnaveyfvs 92
Cdd:pfam04851   8 QIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLfkkgpIKKVLFLVPRKDLLEQALEEFKKFLPN-------- 79
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 497074172   93 yyDYFQPEIYMPGTDRFIPKDSAIN----DHL-ERLRLSTTKSLIERRDVIVV 140
Cdd:pfam04851  80 --YVEIGEIISGDKKDESVDDNKIVvttiQSLyKALELASLELLPDFFDVIII 130
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
433-571 2.51e-12

Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];


Pssm-ID: 443274 [Multi-domain]  Cd Length: 451  Bit Score: 69.52  E-value: 2.51e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 433 IDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFL--TDNGIRARYMHSdiKAEDRVEIINGLRAGEFDVLIGISLLREG 510
Cdd:COG4098  305 PRKLLKWLKKRLKEGRQLLIFVPTIELLEQLVALLqkLFPEERIAGVHA--EDPERKEKVQAFRDGEIPILVTTTILERG 382
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497074172 511 LDIPEASlVAILDADRAGFlrSAHALIQMIGRVARNE---NGKAILYADAVTPAMKQAIDETNR 571
Cdd:COG4098  383 VTFPNVD-VAVLGADHPVF--TEAALVQIAGRVGRSAdypTGEVIFFHHGKTRAMKRAIREIKR 443
PRK13766 PRK13766
Hef nuclease; Provisional
403-552 1.88e-11

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 67.21  E-value: 1.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 403 RVSKDRVVEQVIR---PTGLLDPKVEVRKadgyidDLLAEISKcVKKKNRVLVTTLTKVSAEELTDFLTDNGIRA-RYMH 478
Cdd:PRK13766 325 RLVEDPRFRKAVRkakELDIEHPKLEKLR------EIVKEQLG-KNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAvRFVG 397
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 479 SDIKAEDR-------VEIINGLRAGEFDVLIGISLLREGLDIPEASLV--------AIldadragflRSahalIQMIGRV 543
Cdd:PRK13766 398 QASKDGDKgmsqkeqIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVifyepvpsEI---------RS----IQRKGRT 464

                 ....*....
gi 497074172 544 ARNENGKAI 552
Cdd:PRK13766 465 GRQEEGRVV 473
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
383-554 2.12e-10

ERCC4-related helicase [Replication, recombination and repair];


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 63.98  E-value: 2.12e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 383 FEKVKPQTIFVSATPGDYELRvsKDRVVEQVIRPTGLLD---PKVEvrkadgYIDDLLAEISKcVKKKNRVLVTTLTKVS 459
Cdd:COG1111  295 LERLEEEARSSGGSKASKRLV--SDPRFRKAMRLAEEADiehPKLS------KLREILKEQLG-TNPDSRIIVFTQYRDT 365
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 460 AEELTDFLTDNGIRAR--YMHSDIKAED------RVEIINGLRAGEFDVLIGISLLREGLDIPEASLV--------AIld 523
Cdd:COG1111  366 AEMIVEFLSEPGIKAGrfVGQASKEGDKgltqkeQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVifyepvpsEI-- 443
                        170       180       190
                 ....*....|....*....|....*....|.
gi 497074172 524 adragflRSahalIQMIGRVARNENGKAILY 554
Cdd:COG1111  444 -------RS----IQRKGRTGRKREGRVVVL 463
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
419-553 1.11e-09

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 56.98  E-value: 1.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 419 LLDPKVEvrkadgYIDDLLAEI--SKCVKKKNRVLVTTLTKVSAEELTDFLTDN--GIRA-RYMHSDIKAEDR------- 486
Cdd:cd18801    6 KIHPKLE------KLEEIVKEHfkKKQEGSDTRVIIFSEFRDSAEEIVNFLSKIrpGIRAtRFIGQASGKSSKgmsqkeq 79
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 497074172 487 VEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADragflRSAHALIQMIGRVARNENGKAIL 553
Cdd:cd18801   80 KEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDAS-----PSPIRMIQRMGRTGRKRQGRVVV 141
DEXDc smart00487
DEAD-like helicases superfamily;
6-93 1.89e-09

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 57.89  E-value: 1.89e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172     6 FILHSSYTPAGDQPEAIARLLSDIEEGAthqtLKGITGSGKTFTMANVIHRL-----KRPTLILAPNKTLTAQLYGEMKH 80
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGLRDVI----LAAPTGSGKTLAALLPALEAlkrgkGGRVLVLVPTRELAEQWAEELKK 76
                           90
                   ....*....|...
gi 497074172    81 FFPENAVEYFVSY 93
Cdd:smart00487  77 LGPSLGLKVVGLY 89
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
389-557 2.89e-09

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 59.78  E-value: 2.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 389 QTIFVSAT-PGD------------YELRVSKDRV----VEQVIrptglldpkVEVRKADGYidDLLAEISKcVKKKNRVL 451
Cdd:COG0513  178 QTLLFSATmPPEirklakrylknpVRIEVAPENAtaetIEQRY---------YLVDKRDKL--ELLRRLLR-DEDPERAI 245
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 452 VTTLTKVSAEELTDFLTDNGIRARYMHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVaI-----LDAD- 525
Cdd:COG0513  246 VFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHV-InydlpEDPEd 324
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 497074172 526 ---RagflrsahaliqmIGRVAR-NENGKAILYADA 557
Cdd:COG0513  325 yvhR-------------IGRTGRaGAEGTAISLVTP 347
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
434-547 1.50e-08

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 54.27  E-value: 1.50e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 434 DDLLAEISKCVKKKNRVLVT--------TLTKVSAEELTDFLTDNgIRARY----MHSDIKAEDRVEIINGLRAGEFDVL 501
Cdd:cd18811   13 DKVYEFVREEIAKGRQAYVIyplieeseKLDLKAAVAMYEYLKER-FRPELnvglLHGRLKSDEKDAVMAEFREGEVDIL 91
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 497074172 502 IGISLLREGLDIPEASLVAILDADRAGFlrsaHALIQMIGRVARNE 547
Cdd:cd18811   92 VSTTVIEVGVDVPNATVMVIEDAERFGL----SQLHQLRGRVGRGD 133
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
33-168 1.93e-08

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 53.56  E-value: 1.93e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  33 ATHQTLKGITGSGKTFTMANVIHRL----KRPTLILAPNKTLTAQLYGEMKHFFPENA-VEYFVSYYDyfqpeiymPGTD 107
Cdd:cd00046    1 GENVLITAPTGSGKTLAALLAALLLllkkGKKVLVLVPTKALALQTAERLRELFGPGIrVAVLVGGSS--------AEER 72
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 497074172 108 RFIPKDSAI-----NDHLERLRLSTTKSLIERRDVIVV--ASVSSIYGLGDPEAYRALQIALSPGVKL 168
Cdd:cd00046   73 EKNKLGDADiiiatPDMLLNLLLREDRLFLKDLKLIIVdeAHALLIDSRGALILDLAVRKAGLKNAQV 140
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
460-553 2.30e-08

C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350191 [Multi-domain]  Cd Length: 238  Bit Score: 55.33  E-value: 2.30e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 460 AEELTDFLTDNGIrARyMHSDI--KAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDAD--------RAGf 529
Cdd:cd18804  107 EEELKTLFPEARI-AR-IDRDTtrKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNADsglnspdfRAS- 183
                         90       100
                 ....*....|....*....|....*
gi 497074172 530 LRSAHALIQMIGRVAR-NENGKAIL 553
Cdd:cd18804  184 ERAFQLLTQVSGRAGRgDKPGKVII 208
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1-83 5.56e-08

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 55.80  E-value: 5.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   1 MSTGTFILHSSYTPAGDQPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRL--KRPTLILAPNKTLTAQLYGEM 78
Cdd:COG1061   68 LEAGDEASGTSFELRPYQQEALEALLAALERGGGRGLVVAPTGTGKTVLALALAAELlrGKRVLVLVPRRELLEQWAEEL 147

                 ....*
gi 497074172  79 KHFFP 83
Cdd:COG1061  148 RRFLG 152
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
455-545 1.33e-06

C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 48.80  E-value: 1.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 455 LTKVSAEELTDFLTDNGIRARY--MHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADRAGFlrs 532
Cdd:cd18792   42 LDLKSIEALAEELKELVPEARValLHGKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGL--- 118
                         90
                 ....*....|...
gi 497074172 533 aHALIQMIGRVAR 545
Cdd:cd18792  119 -SQLHQLRGRVGR 130
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
460-542 2.75e-06

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 46.78  E-value: 2.75e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 460 AEELTDFLTDNGIRARYMHSD-IKAEDRVEIINGLRAGE--FDVLIGISLLREGLDIPEASLVAildadragFLR---SA 533
Cdd:cd18799   19 AEFMAEAFNEAGIDAVALNSDySDRERGDEALILLFFGElkPPILVTVDLLTTGVDIPEVDNVV--------FLRpteSR 90

                 ....*....
gi 497074172 534 HALIQMIGR 542
Cdd:cd18799   91 TLFLQMLGR 99
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
473-578 7.59e-06

C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 46.18  E-value: 7.59e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 473 RARYMHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADRAGFLRsahaLIQMIGRVARnenGKAI 552
Cdd:cd18810   53 RIAIAHGQMTENELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIIERADKFGLAQ----LYQLRGRVGR---SKER 125
                         90       100
                 ....*....|....*....|....*.
gi 497074172 553 LYADAVTPAMKqAIDETNRRRQLQIA 578
Cdd:cd18810  126 AYAYFLYPDQK-KLTEDALKRLEAIQ 150
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
18-90 8.14e-06

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


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 46.14  E-value: 8.14e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497074172  18 QPEAIARLLsdIEEGATHQTLKGITGSGKTFTMANVI-HRLKRPTLILAPNKTLTAQLYGEMKHFFPENAVEYF 90
Cdd:cd17926    5 QEEALEAWL--AHKNNRRGILVLPTGSGKTLTALALIaYLKELRTLIVVPTDALLDQWKERFEDFLGDSSIGLI 76
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
447-553 8.83e-06

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 45.66  E-value: 8.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 447 KNRVLVTTLTKVSAEEL-------TDFLTDNGIRARYMHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLV 519
Cdd:cd18802   33 ERRATAVVLSRLLKEHPstlafirCGFLIGRGNSSQRKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLV 112
                         90       100       110
                 ....*....|....*....|....*....|....
gi 497074172 520 AILdaDRAGFLRSahaLIQMIGRvARNENGKAIL 553
Cdd:cd18802  113 IRF--DLPKTLRS---YIQSRGR-ARAPNSKYIL 140
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
497-554 2.18e-05

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 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: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 43.08  E-value: 2.18e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 497 EFDVLIGISLLREGLDIPEASLVAILDADRagFLRSAhalIQMIGRVARN--ENGKAILY 554
Cdd:cd18785   22 SLEILVATNVLGEGIDVPSLDTVIFFDPPS--SAASY---IQRVGRAGRGgkDEGEVILF 76
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
391-554 2.80e-05

CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 47.00  E-value: 2.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 391 IFVSAT-PGDYELRVSK------DRVVEQVIRPTGLLDPKVEVRKADGYIDDLLAEISKCVKKKNRVLVTTLTKVSAEEL 463
Cdd:COG1203  303 ILMTATlPPLLREELLEayelipDEPEELPEYFRAFVRKRVELKEGPLSDEELAELILEALHKGKSVLVIVNTVKDAQEL 382
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 464 TDFLTDNG--IRARYMHSDIKAEDRVEIINGLRA----GEFDVLIGISLLREGLDIpeaslvailDADR-----AGfLRS 532
Cdd:COG1203  383 YEALKEKLpdEEVYLLHSRFCPADRSEIEKEIKErlerGKPCILVSTQVVEAGVDI---------DFDVvirdlAP-LDS 452
                        170       180
                 ....*....|....*....|....
gi 497074172 533 ahaLIQMIGRVARN--ENGKAILY 554
Cdd:COG1203  453 ---LIQRAGRCNRHgrKEEEGNVY 473
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
488-576 5.89e-05

Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 46.26  E-value: 5.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 488 EIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADRAGFL-------RSAHALIQMIGRVARNEN-GKAIL---YAD 556
Cdd:COG1198  522 KLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVLDADLGLNSpdfraaeRTFQLLTQVAGRAGRAEKpGEVLIqtyNPE 601
                         90       100
                 ....*....|....*....|....*....
gi 497074172 557 AvtPAMKQAID---------ETNRRRQLQ 576
Cdd:COG1198  602 H--PVIQALLNhdyeafyeeELAERKAAG 628
PRK05580 PRK05580
primosome assembly protein PriA; Validated
488-553 8.53e-05

primosome assembly protein PriA; Validated


Pssm-ID: 235514 [Multi-domain]  Cd Length: 679  Bit Score: 45.92  E-value: 8.53e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 497074172 488 EIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDAD--------RAGfLRSAHALIQMIGRVAR-NENGKAIL 553
Cdd:PRK05580 471 QLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADlglfspdfRAS-ERTFQLLTQVAGRAGRaEKPGEVLI 544
DEAD-like_helicase_C cd09300
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ...
500-546 1.18e-04

C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases is composed of two superfamilies, SF1 and SF2, that share almost identical folds and extensive structural similarity in their catalytic core. Helicases are involved in ATP-dependent RNA or DNA unwinding. Two distinct types of helicases exist, those forming toroidal, predominantly hexameric structures, and those that do not. SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Their conserved 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: 350171 [Multi-domain]  Cd Length: 59  Bit Score: 40.22  E-value: 1.18e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 497074172 500 VLIGISLLREGLDIPEASLVAILDADragflRSAHALIQMIGRVARN 546
Cdd:cd09300    8 VLIAVN*ALTGFDAPELNTIIVDKNL-----RSYRGLNQAFGRANRI 49
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
422-545 3.57e-04

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


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 40.92  E-value: 3.57e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 422 PKVEVRKADGYIDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDIKAEDRVEIINGLRA--GEFD 499
Cdd:cd18793    2 PPKIEEVVSGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEdpDIRV 81
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 497074172 500 VLIGISLLREGLDIPEASLVAILDADragflRSAHALIQMIGRVAR 545
Cdd:cd18793   82 FLLSTKAGGVGLNLTAANRVILYDPW-----WNPAVEEQAIDRAHR 122
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
18-86 4.92e-04

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs 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: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 41.01  E-value: 4.92e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497074172  18 QPEAIARLLSDIEEGATHQTLKGITGSGKTFTMANVIHRLKRPT-----LILAPNKTLTAQLYGEMKHFFPENA 86
Cdd:cd18032    5 QQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANrkkriLFLAHREELLEQAERSFKEVLPDGS 78
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
418-550 5.12e-04

C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350183 [Multi-domain]  Cd Length: 150  Bit Score: 41.10  E-value: 5.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 418 GLLDPKVEVRKAD-------GYIDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFL----TDNGIRARYM--HSDIKAE 484
Cdd:cd18796    2 KKLDIKVILPVAPeifpwagESGADAYAEVIFLLERHKSTLVFTNTRSQAERLAQRLrelcPDRVPPDFIAlhHGSLSRE 81
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 497074172 485 DRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDADragflRSAHALIQMIGRVARNENGK 550
Cdd:cd18796   82 LREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIQIGSP-----KSVARLLQRLGRSGHRPGAA 142
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
12-88 6.95e-04

DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350676 [Multi-domain]  Cd Length: 180  Bit Score: 41.25  E-value: 6.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  12 YTPAGDQPEAIARLLSD-IEEGATHQTLKGITGSGKT----FTMANVIHRLKRpTLILAPNKTLTAQLYGEMKHFFPENA 86
Cdd:cd17918   14 FSLTKDQAQAIKDIEKDlHSPEPMDRLLSGDVGSGKTlvalGAALLAYKNGKQ-VAILVPTEILAHQHYEEARKFLPFIN 92

                 ..
gi 497074172  87 VE 88
Cdd:cd17918   93 VE 94
PTZ00110 PTZ00110
helicase; Provisional
384-545 1.05e-03

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 42.07  E-value: 1.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 384 EKVKP--QTIFVSATPGDYELRVSKDRVVEQVIR-PTGLLDPK-----------VEVRKADGYIDDLLAEIskcVKKKNR 449
Cdd:PTZ00110 303 SQIRPdrQTLMWSATWPKEVQSLARDLCKEEPVHvNVGSLDLTachnikqevfvVEEHEKRGKLKMLLQRI---MRDGDK 379
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 450 VLVTTLTKVSAEELTDFLTDNGIRARYMHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDadragF 529
Cdd:PTZ00110 380 ILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFD-----F 454
                        170
                 ....*....|....*.
gi 497074172 530 LRSAHALIQMIGRVAR 545
Cdd:PTZ00110 455 PNQIEDYVHRIGRTGR 470
PTZ00424 PTZ00424
helicase 45; Provisional
456-577 1.07e-03

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 41.74  E-value: 1.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 456 TKVSAEELTDFLTDNGIRARYMHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILDadragFLRSAHA 535
Cdd:PTZ00424 276 TRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYD-----LPASPEN 350
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 497074172 536 LIQMIGRVAR-NENGKAILYadaVTPAMKQAIDETNRRRQLQI 577
Cdd:PTZ00424 351 YIHRIGRSGRfGRKGVAINF---VTPDDIEQLKEIERHYNTQI 390
DEAD-like_helicase_N cd17912
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
35-75 1.13e-03

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


Pssm-ID: 350670 [Multi-domain]  Cd Length: 81  Bit Score: 38.27  E-value: 1.13e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 497074172  35 HQTLKGITGSGKTFTMANVIHRL---KRPTLILAPNKTLTAQLY 75
Cdd:cd17912    1 NILHLGPTGSGKTLVAIQKIASAmssGKSVLVVTPTKLLAHEIL 44
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
483-554 2.64e-03

C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 38.77  E-value: 2.64e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 497074172 483 AEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLVAILdadrAGFLRSAHALIQMIGRVAR---NENGKAILY 554
Cdd:cd18789   80 QSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQI----SGHGGSRRQEAQRLGRILRpkkGGGKNAFFY 150
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
435-545 3.24e-03

ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];


Pssm-ID: 440818 [Multi-domain]  Cd Length: 758  Bit Score: 40.59  E-value: 3.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 435 DLLAEiskCVKKKNRVLVTT----LTKVSAEELTDFLTDNGIRAR---YmHSDIKAEDRVEIINGLRAGEFDVLIGISLL 507
Cdd:COG1205  279 RLLAD---LVREGLRTLVFTrsrrGAELLARYARRALREPDLADRvaaY-RAGYLPEERREIERGLRSGELLGVVSTNAL 354
                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 497074172 508 REGLDIPEASLVaILdadrAGFLRSAHALIQMIGRVAR 545
Cdd:COG1205  355 ELGIDIGGLDAV-VL----AGYPGTRASFWQQAGRAGR 387
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
323-519 4.55e-03

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 39.90  E-value: 4.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 323 PITLLDYLPKdGLLFVDESHVMVPqisamyrgDQARKetLIDYGFrLPSSKN---NRPlnfgefEKVKPQTIFVSATPGD 399
Cdd:PRK01297 221 PGRLLDFNQR-GEVHLDMVEVMVL--------DEADR--MLDMGF-IPQVRQiirQTP------RKEERQTLLFSATFTD 282
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 400 YELRVSKDRVVEQV---IRPTGLLDPKVE-----VRKADGY--IDDLLAEiskcvKKKNRVLVTTLTKVSAEELTDFLTD 469
Cdd:PRK01297 283 DVMNLAKQWTTDPAiveIEPENVASDTVEqhvyaVAGSDKYklLYNLVTQ-----NPWERVMVFANRKDEVRRIEERLVK 357
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 497074172 470 NGIRARYMHSDIKAEDRVEIINGLRAGEFDVLIGISLLREGLDIPEASLV 519
Cdd:PRK01297 358 DGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHV 407
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
416-523 5.02e-03

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 40.21  E-value: 5.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 416 PTGLLDPKVEVRKADGYIDDLLAEISKCVKKKNRVLVTTLTKVSAEELTDFLTDNGIRARYMHSDIKAEDRVEIINGLRA 495
Cdd:COG0553  518 PALLLEEGAELSGRSAKLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQE 597
                         90       100       110
                 ....*....|....*....|....*....|.
gi 497074172 496 G-EFDVLIgISL--LREGLDIPEASLVAILD 523
Cdd:COG0553  598 GpEAPVFL-ISLkaGGEGLNLTAADHVIHYD 627
PRK10689 PRK10689
transcription-repair coupling factor; Provisional
38-336 6.37e-03

transcription-repair coupling factor; Provisional


Pssm-ID: 182649 [Multi-domain]  Cd Length: 1147  Bit Score: 39.73  E-value: 6.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172   38 LKGITGSGKTFTMANVIHRLKRPTLILAPNKTLTAQLYGEMKHFfpenaVEYFVSYYDYFQPEIYmpgtDRFIPKDSAIN 117
Cdd:PRK10689   19 LGELTGAACATEVAEIAERHAGPVVLIAPDMQNALRLHDEIQQF-----TDQMVMNLADWETLPY----DSFSPHQDIIS 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  118 DhlerlRLSTTKSLIERRDVIVVASVSSIYGLGDPEAY-RALQIALSPGVKLNQRELIRRLALLQYDRTERTLKRATFRA 196
Cdd:PRK10689   90 S-----RLSTLYQLPTMQRGVLILPVNTLMQRVCPHSFlHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYAT 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172  197 QGDVIDIFPADSEHrAVRVELLDDSVASVQWLDPVTGKTLGAIDHYLVSPKTLFapPTNKidSASKKILADMEERVaELN 276
Cdd:PRK10689  165 RGALLDLFPMGSEE-PYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEF--PTDK--AAIELFRSQWRDTF-EVK 238
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 497074172  277 RnnrlvEANRLYERITHDVemmrevgYCSGMENYS-CYFSErdpasPPITLLDYLPKDGLL 336
Cdd:PRK10689  239 R-----DAEHIYQQVSKGT-------LPAGIEYWQpLFFSE-----PLPPLFSYFPANTLL 282
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
454-502 7.51e-03

Superfamily II DNA helicase RecQ [Replication, recombination and repair];


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 39.35  E-value: 7.51e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 497074172 454 TLTKVSAEELTDFLTDNGIRARYMHSDIKAEDRVEIINGLRAGEFDVLI 502
Cdd:COG0514  237 CLSRKKVEELAEWLREAGIRAAAYHAGLDAEEREANQDRFLRDEVDVIV 285
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
18-89 7.69e-03

DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA 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: 350687 [Multi-domain]  Cd Length: 178  Bit Score: 37.96  E-value: 7.69e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 497074172  18 QPEAIARLLSDIEEGATHqTLKGITGSGKT----FTMANVIHRLKRpTLILAPNKTLTAQLYGEMKHFFPENAVEY 89
Cdd:cd17929    1 QRKAYEAIVSSLGGFKTF-LLHGVTGSGKTevyiELIEKVLAKGKQ-VLVLVPEISLTPQLIKRFKKRFGDKVAVL 74
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
15-66 8.36e-03

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. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 37.93  E-value: 8.36e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 497074172   15 AGDQPEAIARLLSDieeGATHQTLKGITGSGKTFTM---ANVIHRLKRPTLILAP 66
Cdd:pfam13604   3 NAEQAAAVRALLTS---GDRVAVLVGPAGTGKTTALkalREAWEAAGYRVIGLAP 54
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
459-545 9.92e-03

RecG-like helicase [Replication, recombination and repair];


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 38.88  E-value: 9.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497074172 459 SAEELTDFLTDN--GIRARYMHSDIKAEDRVEIINGLRAGEFDVLIG---IsllrE-GLDIPEASLVAILDADRagF--- 529
Cdd:COG1200  489 AAEETYEELREAfpGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVAttvI----EvGVDVPNATVMVIENAER--Fgls 562
                         90       100
                 ....*....|....*....|
gi 497074172 530 ----LRsahaliqmiGRVAR 545
Cdd:COG1200  563 qlhqLR---------GRVGR 573
 
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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