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Conserved domains on  [gi|1802993127|ref|WP_161609382|]
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excinuclease ABC subunit UvrB [Mycoplasmoides pneumoniae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
 10-648 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: 1119.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  10 LFHLKSNFAPTGDQPAAIAKLAEFQTN---EQVLLGATGTGKTFTIANVIQKVQLPTVVIAHNKTLAGQLYQELKELFPN 86
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDgekHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  87 NAVEYFISYFDFYQPEAYLPAKGVYIEKSATVNEEIKRLRVSTLHSLSTRKDVIVVGSVASIYPTSSPADFAQYSLWLVV 166
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 167 GKEYGLSELKTQLIHLNYVVNKQQLTPGKFRFQGDVVEVFPGYAQDYVLRLSFFDQQLEQIARIDPLTNKVLETLNSFKL 246
Cdd:TIGR00631 161 GKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDEFAVRIEFFGDEIERISRVDPLTGEVLRELDSFTI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 247 GPADEYIVNQNDLGVALDTIKAELKDRLKYFERLNFPERAQRLQTITEHDLADLKAWGVCSGVENYARHLEHRPPHSKPY 326
Cdd:TIGR00631 241 FPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPPY 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 327 NIFDYFTKgEWLLVVDESHQTLPQIKGMYNTDISRKQSLIEYGFRLPSALDNRPLSYEEFRQGINKVIYVSATPREEEIQ 406
Cdd:TIGR00631 321 TLLDYFPD-DFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELE 399

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 407 LSHnNVVEQLVRPTYLLDPEVIVKPKDNQVEDLVIEIINQRKHNGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKDIKA 486
Cdd:TIGR00631 400 QSG-NVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDT 478

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 487 LERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDADIPGLPRDERSLIQIIGRAARNVHGRVIMYANTISEQMD 566
Cdd:TIGR00631 479 LERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQ 558

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 567 KAIKETQRRRTIQMAYNEQHHKTPMTVQKPITLNQPIKLKTKSSEQQKA---------------ALIKQLTKEMKQAAAN 631
Cdd:TIGR00631 559 KAIEETERRRKIQMAYNEEHGITPQTIRKPIRDILDIELKEKEDAAKKKkkgedlsdlskkelkKLIKQLEKEMKQAARN 638

                         650
                  ....*....|....*..
gi 1802993127 632 QNYELAIEIRDSIFELE 648
Cdd:TIGR00631 639 LEFEEAARLRDEILELK 655
 
Name Accession Description Interval E-value
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
 10-648 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: 1119.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  10 LFHLKSNFAPTGDQPAAIAKLAEFQTN---EQVLLGATGTGKTFTIANVIQKVQLPTVVIAHNKTLAGQLYQELKELFPN 86
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDgekHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  87 NAVEYFISYFDFYQPEAYLPAKGVYIEKSATVNEEIKRLRVSTLHSLSTRKDVIVVGSVASIYPTSSPADFAQYSLWLVV 166
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 167 GKEYGLSELKTQLIHLNYVVNKQQLTPGKFRFQGDVVEVFPGYAQDYVLRLSFFDQQLEQIARIDPLTNKVLETLNSFKL 246
Cdd:TIGR00631 161 GKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDEFAVRIEFFGDEIERISRVDPLTGEVLRELDSFTI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 247 GPADEYIVNQNDLGVALDTIKAELKDRLKYFERLNFPERAQRLQTITEHDLADLKAWGVCSGVENYARHLEHRPPHSKPY 326
Cdd:TIGR00631 241 FPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPPY 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 327 NIFDYFTKgEWLLVVDESHQTLPQIKGMYNTDISRKQSLIEYGFRLPSALDNRPLSYEEFRQGINKVIYVSATPREEEIQ 406
Cdd:TIGR00631 321 TLLDYFPD-DFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELE 399

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 407 LSHnNVVEQLVRPTYLLDPEVIVKPKDNQVEDLVIEIINQRKHNGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKDIKA 486
Cdd:TIGR00631 400 QSG-NVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDT 478

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 487 LERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDADIPGLPRDERSLIQIIGRAARNVHGRVIMYANTISEQMD 566
Cdd:TIGR00631 479 LERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQ 558

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 567 KAIKETQRRRTIQMAYNEQHHKTPMTVQKPITLNQPIKLKTKSSEQQKA---------------ALIKQLTKEMKQAAAN 631
Cdd:TIGR00631 559 KAIEETERRRKIQMAYNEEHGITPQTIRKPIRDILDIELKEKEDAAKKKkkgedlsdlskkelkKLIKQLEKEMKQAARN 638

                         650
                  ....*....|....*..
gi 1802993127 632 QNYELAIEIRDSIFELE 648
Cdd:TIGR00631 639 LEFEEAARLRDEILELK 655
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
7-654 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1055.80  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127   7 DSKLFHLKSNFAPTGDQPAAIAKLAE-FQTNE--QVLLGATGTGKTFTIANVIQKVQLPTVVIAHNKTLAGQLYQELKEL 83
Cdd:PRK05298    1 MMKPFKLVSPYKPAGDQPQAIEELVEgIEAGEkhQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  84 FPNNAVEYFISYFDFYQPEAYLPAKGVYIEKSATVNEEIKRLRVSTLHSLSTRKDVIVVGSVASIYPTSSPADFAQYSLW 163
Cdd:PRK05298   81 FPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 164 LVVGKEYGLSELKTQLIHLNYVVNKQQLTPGKFRFQGDVVEVFPGYAQDYVLRLSFFDQQLEQIARIDPLTNKVLETLNS 243
Cdd:PRK05298  161 LRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDR 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 244 FKLGPADEYIVNQNDLGVALDTIKAELKDRLKYFERLNFPERAQRLQTITEHDLADLKAWGVCSGVENYARHLEHRPPHS 323
Cdd:PRK05298  241 VTIYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGE 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 324 KPYNIFDYFTKgEWLLVVDESHQTLPQIKGMYNTDISRKQSLIEYGFRLPSALDNRPLSYEEFRQGINKVIYVSATPREE 403
Cdd:PRK05298  321 PPYTLLDYFPD-DFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDY 399

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 404 EIQLSHNNVVEQLVRPTYLLDPEVIVKPKDNQVEDLVIEIINQRKHNGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKD 483
Cdd:PRK05298  400 ELEKSGGVVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSD 479

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 484 IKALERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDADIPGLPRDERSLIQIIGRAARNVHGRVIMYANTISE 563
Cdd:PRK05298  480 IDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITD 559

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 564 QMDKAIKETQRRRTIQMAYNEQHHKTPMTVQKPIT-LNQPIKLKTKSSEQQKAALIKQLTKEMKQAAANQNYELAIEIRD 642
Cdd:PRK05298  560 SMQKAIDETERRREIQIAYNEEHGITPKTIKKKIRdILDSVYKKDKLSKKELEKLIKELEKQMKEAAKNLEFEEAARLRD 639

                         650
                  ....*....|..
gi 1802993127 643 SIFELEKQFRGK 654
Cdd:PRK05298  640 EIKELKEELLGL 651
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
11-650 0e+00

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


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 972.18  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  11 FHLKSNFAPTGDQPAAIAKLAE-FQTNE--QVLLGATGTGKTFTIANVIQKVQLPTVVIAHNKTLAGQLYQELKELFPNN 87
Cdd:COG0556     2 FKLVSPYKPAGDQPQAIEKLVEgIEAGEkhQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPNN 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  88 AVEYFISYFDFYQPEAYLPAKGVYIEKSATVNEEIKRLRVSTLHSLSTRKDVIVVGSVASIYPTSSPADFAQYSLWLVVG 167
Cdd:COG0556    82 AVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRVG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 168 KEYGLSELKTQLIHLNYVVNKQQLTPGKFRFQGDVVEVFPGYAQDYVLRLSFFDQQLEQIARIDPLTNKVLETLNSFKLG 247
Cdd:COG0556   162 EEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTIY 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 248 PADEYIVNQNDLGVALDTIKAELKDRLKYFERLNFPERAQRLQTITEHDLADLKAWGVCSGVENYARHLEHRPPHSKPYN 327
Cdd:COG0556   242 PASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPPT 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 328 IFDYFTKgEWLLVVDESHQTLPQIKGMYNTDISRKQSLIEYGFRLPSALDNRPLSYEEFRQGINKVIYVSATPREEEIQL 407
Cdd:COG0556   322 LLDYFPD-DFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEK 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 408 SHNNVVEQLVRPTYLLDPEVIVKPKDNQVEDLVIEIINQRKHNGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKDIKAL 487
Cdd:COG0556   401 SGGQVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTL 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 488 ERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDADIPGLPRDERSLIQIIGRAARNVHGRVIMYANTISEQMDK 567
Cdd:COG0556   481 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQR 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 568 AIKETQRRRTIQMAYNEQHHKTPMTVQKPI--TLNQPIKLKTKS------------SEQQKAALIKQLTKEMKQAAANQN 633
Cdd:COG0556   561 AIDETNRRREIQEAYNEEHGITPQTIKKSIrdILEGTYEADEETeelvaeadaaklSKEELEKLIKELEKEMKEAAKNLE 640

                         650
                  ....*....|....*..
gi 1802993127 634 YELAIEIRDSIFELEKQ 650
Cdd:COG0556   641 FEEAARLRDEIKELKKE 657
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
 11-418 7.20e-159

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: 458.60  E-value: 7.20e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  11 FHLKSNFAPTGDQPAAIAKLAEFQTN---EQVLLGATGTGKTFTIANVIQKVQLPTVVIAHNKTLAGQLYQELKELFPNN 87
Cdd:cd17916     1 FKLVSPFKPAGDQPQAIAKLVEGLKRgvkFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  88 AVEYFISYFDFYQPEAYLPAKGVYIEKSATVNEEIKRLRVSTLHSLSTRKDVIVVGSVASIYPtsspadfaqyslwlvvg 167
Cdd:cd17916    81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLERRDVIVVASVSCIYE----------------- 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 168 keyglselktqlihlnyvvnkqqltpgkfrfqgdvvevfpgyaqdyvlrlsffdqqleqiaridpltnkvletlnsfklg 247
Cdd:cd17916       --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 248 padeyivnqndlgVALDTIKAELKDRLKYFERLNFPERAQRLQTITEHDLADLKAWGVCSGVENYARHLEHRPPHSKPYN 327
Cdd:cd17916   144 -------------RAIKSIEEELEERLKYFRAQGKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 328 IFDYFTKgEWLLVVDESHQTLPQIKGMYNTDISRKQSLIEYGFRLPSALDNRPLSYEEFRQGINKVIYVSATPREEEIQL 407
Cdd:cd17916   211 LLDYFPD-DFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEH 289

                         410
                  ....*....|.
gi 1802993127 408 ShNNVVEQLVR 418
Cdd:cd17916   290 S-GQVVEQIIR 299
UvrB_inter pfam17757
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ...
 162-252 1.46e-28

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: 109.41  E-value: 1.46e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 162 LWLVVGKEYGLSELKTQLIHLNYVVNKQQLTPGKFRFQGDVVEVFPGYAQDYVLRLSFFDQQLEQIARIDPLTNKVLETL 241
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80

                          90
                  ....*....|.
gi 1802993127 242 NSFKLGPADEY 252
Cdd:pfam17757  81 DEVTIYPASHY 91
HELICc smart00490
helicase superfamily c-terminal domain;
464-548 5.64e-20

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 84.57  E-value: 5.64e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  464 ENLTDFLKERNIKVAYIHKDIKALERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDadipgLPRDERSLIQII 543
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYD-----LPWSPASYIQRI 75


                   ....*
gi 1802993127  544 GRAAR 548
Cdd:smart00490  76 GRAGR 80
 
Name Accession Description Interval E-value
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
 10-648 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: 1119.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  10 LFHLKSNFAPTGDQPAAIAKLAEFQTN---EQVLLGATGTGKTFTIANVIQKVQLPTVVIAHNKTLAGQLYQELKELFPN 86
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDgekHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  87 NAVEYFISYFDFYQPEAYLPAKGVYIEKSATVNEEIKRLRVSTLHSLSTRKDVIVVGSVASIYPTSSPADFAQYSLWLVV 166
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 167 GKEYGLSELKTQLIHLNYVVNKQQLTPGKFRFQGDVVEVFPGYAQDYVLRLSFFDQQLEQIARIDPLTNKVLETLNSFKL 246
Cdd:TIGR00631 161 GKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDEFAVRIEFFGDEIERISRVDPLTGEVLRELDSFTI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 247 GPADEYIVNQNDLGVALDTIKAELKDRLKYFERLNFPERAQRLQTITEHDLADLKAWGVCSGVENYARHLEHRPPHSKPY 326
Cdd:TIGR00631 241 FPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPPY 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 327 NIFDYFTKgEWLLVVDESHQTLPQIKGMYNTDISRKQSLIEYGFRLPSALDNRPLSYEEFRQGINKVIYVSATPREEEIQ 406
Cdd:TIGR00631 321 TLLDYFPD-DFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELE 399

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 407 LSHnNVVEQLVRPTYLLDPEVIVKPKDNQVEDLVIEIINQRKHNGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKDIKA 486
Cdd:TIGR00631 400 QSG-NVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDT 478

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 487 LERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDADIPGLPRDERSLIQIIGRAARNVHGRVIMYANTISEQMD 566
Cdd:TIGR00631 479 LERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQ 558

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 567 KAIKETQRRRTIQMAYNEQHHKTPMTVQKPITLNQPIKLKTKSSEQQKA---------------ALIKQLTKEMKQAAAN 631
Cdd:TIGR00631 559 KAIEETERRRKIQMAYNEEHGITPQTIRKPIRDILDIELKEKEDAAKKKkkgedlsdlskkelkKLIKQLEKEMKQAARN 638

                         650
                  ....*....|....*..
gi 1802993127 632 QNYELAIEIRDSIFELE 648
Cdd:TIGR00631 639 LEFEEAARLRDEILELK 655
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
7-654 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1055.80  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127   7 DSKLFHLKSNFAPTGDQPAAIAKLAE-FQTNE--QVLLGATGTGKTFTIANVIQKVQLPTVVIAHNKTLAGQLYQELKEL 83
Cdd:PRK05298    1 MMKPFKLVSPYKPAGDQPQAIEELVEgIEAGEkhQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  84 FPNNAVEYFISYFDFYQPEAYLPAKGVYIEKSATVNEEIKRLRVSTLHSLSTRKDVIVVGSVASIYPTSSPADFAQYSLW 163
Cdd:PRK05298   81 FPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 164 LVVGKEYGLSELKTQLIHLNYVVNKQQLTPGKFRFQGDVVEVFPGYAQDYVLRLSFFDQQLEQIARIDPLTNKVLETLNS 243
Cdd:PRK05298  161 LRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDR 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 244 FKLGPADEYIVNQNDLGVALDTIKAELKDRLKYFERLNFPERAQRLQTITEHDLADLKAWGVCSGVENYARHLEHRPPHS 323
Cdd:PRK05298  241 VTIYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGE 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 324 KPYNIFDYFTKgEWLLVVDESHQTLPQIKGMYNTDISRKQSLIEYGFRLPSALDNRPLSYEEFRQGINKVIYVSATPREE 403
Cdd:PRK05298  321 PPYTLLDYFPD-DFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDY 399

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 404 EIQLSHNNVVEQLVRPTYLLDPEVIVKPKDNQVEDLVIEIINQRKHNGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKD 483
Cdd:PRK05298  400 ELEKSGGVVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSD 479

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 484 IKALERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDADIPGLPRDERSLIQIIGRAARNVHGRVIMYANTISE 563
Cdd:PRK05298  480 IDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITD 559

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 564 QMDKAIKETQRRRTIQMAYNEQHHKTPMTVQKPIT-LNQPIKLKTKSSEQQKAALIKQLTKEMKQAAANQNYELAIEIRD 642
Cdd:PRK05298  560 SMQKAIDETERRREIQIAYNEEHGITPKTIKKKIRdILDSVYKKDKLSKKELEKLIKELEKQMKEAAKNLEFEEAARLRD 639

                         650
                  ....*....|..
gi 1802993127 643 SIFELEKQFRGK 654
Cdd:PRK05298  640 EIKELKEELLGL 651
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
11-650 0e+00

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


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 972.18  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  11 FHLKSNFAPTGDQPAAIAKLAE-FQTNE--QVLLGATGTGKTFTIANVIQKVQLPTVVIAHNKTLAGQLYQELKELFPNN 87
Cdd:COG0556     2 FKLVSPYKPAGDQPQAIEKLVEgIEAGEkhQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPNN 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  88 AVEYFISYFDFYQPEAYLPAKGVYIEKSATVNEEIKRLRVSTLHSLSTRKDVIVVGSVASIYPTSSPADFAQYSLWLVVG 167
Cdd:COG0556    82 AVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRVG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 168 KEYGLSELKTQLIHLNYVVNKQQLTPGKFRFQGDVVEVFPGYAQDYVLRLSFFDQQLEQIARIDPLTNKVLETLNSFKLG 247
Cdd:COG0556   162 EEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTIY 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 248 PADEYIVNQNDLGVALDTIKAELKDRLKYFERLNFPERAQRLQTITEHDLADLKAWGVCSGVENYARHLEHRPPHSKPYN 327
Cdd:COG0556   242 PASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPPT 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 328 IFDYFTKgEWLLVVDESHQTLPQIKGMYNTDISRKQSLIEYGFRLPSALDNRPLSYEEFRQGINKVIYVSATPREEEIQL 407
Cdd:COG0556   322 LLDYFPD-DFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEK 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 408 SHNNVVEQLVRPTYLLDPEVIVKPKDNQVEDLVIEIINQRKHNGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKDIKAL 487
Cdd:COG0556   401 SGGQVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTL 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 488 ERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDADIPGLPRDERSLIQIIGRAARNVHGRVIMYANTISEQMDK 567
Cdd:COG0556   481 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQR 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 568 AIKETQRRRTIQMAYNEQHHKTPMTVQKPI--TLNQPIKLKTKS------------SEQQKAALIKQLTKEMKQAAANQN 633
Cdd:COG0556   561 AIDETNRRREIQEAYNEEHGITPQTIKKSIrdILEGTYEADEETeelvaeadaaklSKEELEKLIKELEKEMKEAAKNLE 640

                         650
                  ....*....|....*..
gi 1802993127 634 YELAIEIRDSIFELEKQ 650
Cdd:COG0556   641 FEEAARLRDEIKELKKE 657
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
 11-418 7.20e-159

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: 458.60  E-value: 7.20e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  11 FHLKSNFAPTGDQPAAIAKLAEFQTN---EQVLLGATGTGKTFTIANVIQKVQLPTVVIAHNKTLAGQLYQELKELFPNN 87
Cdd:cd17916     1 FKLVSPFKPAGDQPQAIAKLVEGLKRgvkFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  88 AVEYFISYFDFYQPEAYLPAKGVYIEKSATVNEEIKRLRVSTLHSLSTRKDVIVVGSVASIYPtsspadfaqyslwlvvg 167
Cdd:cd17916    81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLERRDVIVVASVSCIYE----------------- 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 168 keyglselktqlihlnyvvnkqqltpgkfrfqgdvvevfpgyaqdyvlrlsffdqqleqiaridpltnkvletlnsfklg 247
Cdd:cd17916       --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 248 padeyivnqndlgVALDTIKAELKDRLKYFERLNFPERAQRLQTITEHDLADLKAWGVCSGVENYARHLEHRPPHSKPYN 327
Cdd:cd17916   144 -------------RAIKSIEEELEERLKYFRAQGKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 328 IFDYFTKgEWLLVVDESHQTLPQIKGMYNTDISRKQSLIEYGFRLPSALDNRPLSYEEFRQGINKVIYVSATPREEEIQL 407
Cdd:cd17916   211 LLDYFPD-DFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEH 289

                         410
                  ....*....|.
gi 1802993127 408 ShNNVVEQLVR 418
Cdd:cd17916   290 S-GQVVEQIIR 299
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 424-593 8.19e-98

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: 297.23  E-value: 8.19e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 424 DPEVIVKPKDNQVEDLVIEIINQRKHNGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKDIKALERLILLTDLRKGEYEC 503
Cdd:cd18790     1 DPEIEVRPTEGQVDDLLGEIRKRVARGERVLVTTLTKRMAEDLTEYLQELGVKVRYLHSEIDTLERVEIIRDLRLGEFDV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 504 LVGINLLREGLDVPEVSLVAIFDADIPGLPRDERSLIQIIGRAARNVHGRVIMYANTISEQMDKAIKETQRRRTIQMAYN 583
Cdd:cd18790    81 LVGINLLREGLDLPEVSLVAILDADKEGFLRSETSLIQTIGRAARNVNGKVILYADKITDSMQKAIEETERRREIQMEYN 160

                         170
                  ....*....|
gi 1802993127 584 EQHHKTPMTV 593
Cdd:cd18790   161 EEHGITPKTI 170
UvrB_inter pfam17757
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ...
 162-252 1.46e-28

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: 109.41  E-value: 1.46e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 162 LWLVVGKEYGLSELKTQLIHLNYVVNKQQLTPGKFRFQGDVVEVFPGYAQDYVLRLSFFDQQLEQIARIDPLTNKVLETL 241
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80

                          90
                  ....*....|.
gi 1802993127 242 NSFKLGPADEY 252
Cdd:pfam17757  81 DEVTIYPASHY 91
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 438-548 1.22e-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: 87.27  E-value: 1.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 438 DLVIEIInQRKHNGRTFVTVLTIKMAEnLTDFLKERNIKVAYIHKDIKALERLILLTDLRKGEYECLVGINLLREGLDVP 517
Cdd:pfam00271   4 EALLELL-KKERGGKVLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLP 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1802993127 518 EVSLVAIFDadipgLPRDERSLIQIIGRAAR 548
Cdd:pfam00271  82 DVDLVINYD-----LPWNPASYIQRIGRAGR 107
HELICc smart00490
helicase superfamily c-terminal domain;
464-548 5.64e-20

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 84.57  E-value: 5.64e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  464 ENLTDFLKERNIKVAYIHKDIKALERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDadipgLPRDERSLIQII 543
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYD-----LPWSPASYIQRI 75


                   ....*
gi 1802993127  544 GRAAR 548
Cdd:smart00490  76 GRAGR 80
UvrB pfam12344
Ultra-violet resistance protein B; This domain family is found in bacteria, archaea and ...
 556-598 1.64e-18

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: 78.97  E-value: 1.64e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1802993127 556 MYANTISEQMDKAIKETQRRRTIQMAYNEQHHKTPMTVQKPIT 598
Cdd:pfam12344   1 LYADKITDSMQRAIDETERRREIQEAYNEEHGITPKTIKKKIR 43
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 392-574 1.78e-18

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: 88.39  E-value: 1.78e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 392 KVIYVSATPREE---EIQLSHNNVVEQLVR--------PTYLLDPEVIVKPKDNQVEDLVIEIINQR-KHNGRTFVTVLT 459
Cdd:COG4098   249 KLIYLTATPSKAlqrQVKRGKLKVVKLPARyhghplpvPKFKWLGNWKKRLRRGKLPRKLLKWLKKRlKEGRQLLIFVPT 328

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 460 IKMAENLTDFLKER--NIKVAYIH-KDikaLERLILLTDLRKGEYECLVGINLLREGLDVPEVSlVAIFDADIPGLprDE 536
Cdd:COG4098   329 IELLEQLVALLQKLfpEERIAGVHaED---PERKEKVQAFRDGEIPILVTTTILERGVTFPNVD-VAVLGADHPVF--TE 402

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1802993127 537 RSLIQIIGRAARNV---HGRVIMYANTISEQMDKAIKETQR 574
Cdd:COG4098   403 AALVQIAGRVGRSAdypTGEVIFFHHGKTRAMKRAIREIKR 443
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 426-548 4.96e-16

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: 74.85  E-value: 4.96e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 426 EVIVKPKDNQVEDLVIEIINQRKhNGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKDIKALERLILLTDLRKGEYECLV 505
Cdd:cd18787     4 LYVVVEEEEKKLLLLLLLLEKLK-PGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRVLV 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1802993127 506 GINLLREGLDVPEVSLVAIFDadipgLPRDERSLIQIIGRAAR 548
Cdd:cd18787    83 ATDVAARGLDIPGVDHVINYD-----LPRDAEDYVHRIGRTGR 120
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
397-548 7.12e-12

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 67.86  E-value: 7.12e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 397 SAT-PREeeiqlshnnvVEQLVRpTYLLDPEVI-VKPKDNQVE---------------DLVIEIINQRKhNGRTFVTVLT 459
Cdd:COG0513   183 SATmPPE----------IRKLAK-RYLKNPVRIeVAPENATAEtieqryylvdkrdklELLRRLLRDED-PERAIVFCNT 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 460 IKMAENLTDFLKERNIKVAYIHKDIKALERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDadipgLPRDERSL 539
Cdd:COG0513   251 KRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYD-----LPEDPEDY 325


                  ....*....
gi 1802993127 540 IQIIGRAAR 548
Cdd:COG0513   326 VHRIGRTGR 334
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
366-548 3.24e-11

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 66.20  E-value: 3.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 366 IEYGFRLPSALDN---RPLSYEEfrqginkvIYVSATPREEEIQLSHNNVVEQLVrptylldpevivkPKDNQVEDLVIE 442
Cdd:COG1061   239 IVYEYSLKEAIEDgylAPPEYYG--------IRVDLTDERAEYDALSERLREALA-------------ADAERKDKILRE 297

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 443 IINQRKHNGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKDIKALERLILLTDLRKGEYECLVGINLLREGLDVPEVSLV 522
Cdd:COG1061   298 LLREHPDDRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVA 377

                         170       180
                  ....*....|....*....|....*.
gi 1802993127 523 AIFDAdipglPRDERSLIQIIGRAAR 548
Cdd:COG1061   378 ILLRP-----TGSPREFIQRLGRGLR 398
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
 453-555 3.94e-09

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: 57.64  E-value: 3.94e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 453 TFVTVLTIKMAENLTDFLKERniKVAYIHKDI----KALERLilLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDAD 528
Cdd:cd18804    97 VFKGIGTERVEEELKTLFPEA--RIARIDRDTtrkkGALEKL--LDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNAD 172

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1802993127 529 I----PGLPRDERS---LIQIIGRAAR-NVHGRVI 555
Cdd:cd18804   173 SglnsPDFRASERAfqlLTQVSGRAGRgDKPGKVI 207
DEXDc smart00487
DEAD-like helicases superfamily;
11-95 6.32e-09

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 56.35  E-value: 6.32e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127   11 FHLKSNFAPTGDQPAAIAKLAEFQTNeQVLLGATGTGKTFTIANVI-----QKVQLPTVVIAHNKTLAGQLYQELKELFP 85
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGLRD-VILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKKLGP 79

                           90
                   ....*....|
gi 1802993127   86 NNAVEYFISY 95
Cdd:smart00487  80 SLGLKVVGLY 89
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 429-548 1.25e-08

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. 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: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 53.75  E-value: 1.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 429 VKPK-DNQVEDLVIEIINQRKHNGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKDIKALERLILLTDLRKGEYECLVGI 507
Cdd:cd18794     8 VRPKdKKDEKLDLLKRIKVEHLGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWLRDKIQVIVAT 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1802993127 508 NLLREGLDVPEVSLVAIFdadipGLPRDERSLIQIIGRAAR 548
Cdd:cd18794    88 VAFGMGIDKPDVRFVIHY-----SLPKSMESYYQESGRAGR 123
UVR pfam02151
UvrB/uvrC motif;
617-650 1.26e-08

UvrB/uvrC motif;


Pssm-ID: 308001 [Multi-domain]  Cd Length: 36  Bit Score: 50.86  E-value: 1.26e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1802993127 617 LIKQLTKEMKQAAANQNYELAIEIRDSIFELEKQ 650
Cdd:pfam02151   3 LIKELEEEMEEAAENEDFEKAAKLRDQINALKKQ 36
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 36-142 1.82e-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: 1.82e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  36 NEQVLLGATGTGKTFTIANVI----QKVQLPTVVIAHNKTLAGQLYQELKELF-PNNAVEYFISYFDFYQPEAY--LPAK 108
Cdd:cd00046     2 ENVLITAPTGSGKTLAALLAAllllLKKGKKVLVLVPTKALALQTAERLRELFgPGIRVAVLVGGSSAEEREKNklGDAD 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1802993127 109 GVYieksATVnEEIKRLRVSTLHSLSTRKDVIVV 142
Cdd:cd00046    82 III----ATP-DMLLNLLLREDRLFLKDLKLIIV 110
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 491-557 5.29e-08

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: 50.40  E-value: 5.29e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1802993127 491 ILLTDLRKGEYEC------LVGINLLREGLDVPEVSLVAIFDAdipglPRDERSLIQIIGRAARN--VHGRVIMY 557
Cdd:cd18785     7 IVFTNSIEHAEEIassleiLVATNVLGEGIDVPSLDTVIFFDP-----PSSAASYIQRVGRAGRGgkDEGEVILF 76
DEAD-like_helicase_C cd09300
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ...
 503-558 7.84e-08

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: 49.47  E-value: 7.84e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1802993127 503 CLVGINLLREGLDVPEVSLVAIFDADipglpRDERSLIQIIGRAARN-VHGRVIMYA 558
Cdd:cd09300     8 VLIAVN*ALTGFDAPELNTIIVDKNL-----RSYRGLNQAFGRANRIyTFGGIVTYR 59
ResIII pfam04851
Type III restriction enzyme, res subunit;
23-142 1.30e-07

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 51.52  E-value: 1.30e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  23 QPAAIAKLAEFQTNEQ---VLLGATGTGKTFTIANVIQKVQL-----PTVVIAHNKTLAGQLYQELKELFPNNAVEYFIS 94
Cdd:pfam04851   8 QIEAIENLLESIKNGQkrgLIVMATGSGKTLTAAKLIARLFKkgpikKVLFLVPRKDLLEQALEEFKKFLPNYVEIGEII 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1802993127  95 YFDFYQPEayLPAKGVYIeksATVNEEIKRLRVSTLHSLSTRKDVIVV 142
Cdd:pfam04851  88 SGDKKDES--VDDNKIVV---TTIQSLYKALELASLELLPDFFDVIII 130
PRK13766 PRK13766
Hef nuclease; Provisional
 431-555 1.44e-07

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 54.88  E-value: 1.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 431 PKDNQVEDLVIEIInQRKHNGRTFV------TvltikmAENLTDFLKERNIKVAYI--------------HKDIKALERL 490
Cdd:PRK13766  347 PKLEKLREIVKEQL-GKNPDSRIIVftqyrdT------AEKIVDLLEKEGIKAVRFvgqaskdgdkgmsqKEQIEILDKF 419

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1802993127 491 illtdlRKGEYECLVGINLLREGLDVPEVSLVAIFDAdipgLPRDERSlIQIIGRAARNVHGRVI 555
Cdd:PRK13766  420 ------RAGEFNVLVSTSVAEEGLDIPSVDLVIFYEP----VPSEIRS-IQRKGRTGRQEEGRVV 473
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
431-563 1.61e-07

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 54.74  E-value: 1.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 431 PKDNQVEDLVIEIINQRKhNGRTFVTVLTIKMAENLTDFLKERNIKV--------AYIHKDIKALERLILLTDLRKGEYE 502
Cdd:COG1111   335 PKLSKLREILKEQLGTNP-DSRIIVFTQYRDTAEMIVEFLSEPGIKAgrfvgqasKEGDKGLTQKEQIEILERFRAGEFN 413

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1802993127 503 CLVGINLLREGLDVPEVSLVAIFDAdipgLPRDERSlIQIIGRAARNVHGRVI--MYANTISE 563
Cdd:COG1111   414 VLVATSVAEEGLDIPEVDLVIFYEP----VPSEIRS-IQRKGRTGRKREGRVVvlIAKGTRDE 471
PTZ00424 PTZ00424
helicase 45; Provisional
 450-593 2.07e-07

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 53.68  E-value: 2.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 450 NGRTFVTVLTIKMaenltdflKERNIKVAYIHKDIKALERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDadi 529
Cdd:PTZ00424  275 NTRRKVDYLTKKM--------HERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYD--- 343

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1802993127 530 pgLPRDERSLIQIIGRAARnvHGRVIMYANTISEQmdkaikETQRRRTIQMAYNEQHHKTPMTV 593
Cdd:PTZ00424  344 --LPASPENYIHRIGRSGR--FGRKGVAINFVTPD------DIEQLKEIERHYNTQIEEMPMEV 397
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 452-548 2.12e-07

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: 49.87  E-value: 2.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 452 RTFVTVLTIKMAENLTDFLKERNIKVAYIHKDIKALER----LILLTDlRKGEYECLVGINLLREGLDVPEVSLVAIFda 527
Cdd:cd18799     8 KTLIFCVSIEHAEFMAEAFNEAGIDAVALNSDYSDRERgdeaLILLFF-GELKPPILVTVDLLTTGVDIPEVDNVVFL-- 84

                          90       100
                  ....*....|....*....|....
gi 1802993127 528 dipglpRDERSLI---QIIGRAAR 548
Cdd:cd18799    85 ------RPTESRTlflQMLGRGLR 102
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 493-546 5.88e-07

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: 49.13  E-value: 5.88e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1802993127 493 LTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDadipgLPRDERSLIQIIGRA 546
Cdd:cd18802    83 LDKFRDGELNLLIATSVLEEGIDVPACNLVIRFD-----LPKTLRSYIQSRGRA 131
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
23-86 1.13e-06

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 51.56  E-value: 1.13e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1802993127  23 QPAAIAKLAEFQTNEQ---VLLGATGTGKTFTIANVIQKVQL--PTVVIAHNKTLAGQLYQELKELFPN 86
Cdd:COG1061    85 QQEALEALLAALERGGgrgLVVAPTGTGKTVLALALAAELLRgkRVLVLVPRRELLEQWAEELRRFLGD 153
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 457-551 1.84e-06

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: 48.11  E-value: 1.84e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 457 VLTIKMAENLTDFLKER---NIKVAYIHKDIKALERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDADIPGLP 533
Cdd:cd18811    41 KLDLKAAVAMYEYLKERfrpELNVGLLHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLS 120

                          90
                  ....*....|....*...
gi 1802993127 534 RdersLIQIIGRAARNVH 551
Cdd:cd18811   121 Q----LHQLRGRVGRGDH 134
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 429-556 3.02e-06

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: 47.35  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 429 VKPKDNQVEDLVIEIINQRKHNGRTFVTVLTI--KMAENLTDFLKE--RNIKVA-YI----HKDIKAL---ERLILLTDL 496
Cdd:cd18801     7 IHPKLEKLEEIVKEHFKKKQEGSDTRVIIFSEfrDSAEEIVNFLSKirPGIRATrFIgqasGKSSKGMsqkEQKEVIEQF 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 497 RKGEYECLVGINLLREGLDVPEVSLVAIFDADIPGLprderSLIQIIGRAARNVHGRVIM 556
Cdd:cd18801    87 RKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPI-----RMIQRMGRTGRKRQGRVVV 141
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
605-655 3.45e-06

Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 50.12  E-value: 3.45e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1802993127 605 LKTKSSEqqkaaLIKQLTKEMKQAAANQNYELAIEIRDSIFELEK-QFRGKI 655
Cdd:COG0322   197 LEGKTKE-----LIKELEEKMEEAAEELEFERAARLRDQIRALEKvQEKQKV 243
DEAD-like_helicase_N cd17912
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 38-100 5.07e-06

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: 44.82  E-value: 5.07e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1802993127  38 QVLLGATGTGKTFTIANVIQKVQL---PTVVIAHNKTLAGQLY---QELKELFPNNAVEYFISYFDFYQ 100
Cdd:cd17912     2 ILHLGPTGSGKTLVAIQKIASAMSsgkSVLVVTPTKLLAHEILiviDEIQ*ILDPAAGWAWATRALLGL 70
PRK05580 PRK05580
primosome assembly protein PriA; Validated
 485-555 8.39e-06

primosome assembly protein PriA; Validated


Pssm-ID: 235514 [Multi-domain]  Cd Length: 679  Bit Score: 49.00  E-value: 8.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 485 KALERLilLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDADIpGL----PR-DERS---LIQIIGRAARNVH-GRVI 555
Cdd:PRK05580  467 GALEQL--LAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADL-GLfspdFRaSERTfqlLTQVAGRAGRAEKpGEVL 543
SF2_C_reverse_gyrase cd18798
C-terminal helicase domain of the reverse gyrase; Reverse gyrase modifies the topological ...
 411-548 9.61e-05

C-terminal helicase domain of the reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase 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: 350185 [Multi-domain]  Cd Length: 174  Bit Score: 43.45  E-value: 9.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 411 NVVEqlvrpTYLLDPEVIVKpkdnqvedlVIEIINQRKHNGRTFVTV-LTIKMAENLTDFLKERNIKVA-YIHKDIKALE 488
Cdd:cd18798     1 NIVD-----VYIEDSDSLEK---------LLELVKKLGDGGLIFVSIdYGKEYAEELKEFLERHGIKAElALSSTEKNLE 66

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1802993127 489 rlilltDLRKGEYECLVGI----NLLREGLDVPEVSLVAIFdADIPglprdERSLIQIIGRAAR 548
Cdd:cd18798    67 ------KFEEGEIDVLIGVasyyGVLVRGIDLPERIKYAIF-YGVP-----VTTYIQASGRTSR 118
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 429-576 1.21e-04

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: 42.72  E-value: 1.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 429 VKPKDnqveDLVIEIINQRKH--NGRTFVTVLTIKMAENLTDFLKE--RNIKVAYIHKDIKA--LERLILltDLRKGEYE 502
Cdd:cd18810     6 VMPYD----DELIREAIERELlrGGQVFYVHNRIESIEKLATQLRQlvPEARIAIAHGQMTEneLEEVML--EFAKGEYD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1802993127 503 CLVGINLLREGLDVPEVSLVAIFDADIPGLPRdersLIQIIGRAARnvhGRVIMYANTISEQmDKAIKETQRRR 576
Cdd:cd18810    80 ILVCTTIIESGIDIPNANTIIIERADKFGLAQ----LYQLRGRVGR---SKERAYAYFLYPD-QKKLTEDALKR 145
uvrC PRK00558
excinuclease ABC subunit UvrC;
617-649 1.22e-04

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 45.11  E-value: 1.22e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1802993127 617 LIKQLTKEMKQAAANQNYELAIEIRDSIFELEK 649
Cdd:PRK00558  203 VLKELEEKMEEASENLEFERAARYRDQIQALRR 235
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 460-548 1.53e-04

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: 42.64  E-value: 1.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 460 IKMAENLTDFLKERniKVAYIHKDIKALERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDADIPGLPRdersL 539
Cdd:cd18792    48 EALAEELKELVPEA--RVALLHGKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQ----L 121


                  ....*....
gi 1802993127 540 IQIIGRAAR 548
Cdd:cd18792   122 HQLRGRVGR 130
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
 17-127 2.53e-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: 42.40  E-value: 2.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127  17 FAPTGDQPAAIAKLAEFQTNE----QVLLGATGTGKT--FTIANVIQ-KVQLPTVVIAHNKTLAGQLYQELKELFPNNAV 89
Cdd:cd17918    14 FSLTKDQAQAIKDIEKDLHSPepmdRLLSGDVGSGKTlvALGAALLAyKNGKQVAILVPTEILAHQHYEEARKFLPFINV 93

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1802993127  90 EYFISYFDfyqpEAYLPAKGVYIEKSATVNEEIKRLRV 127
Cdd:cd17918    94 ELVTGGTK----AQILSGISLLVGTHALLHLDVKFKNL 127
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
 486-555 3.10e-04

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


Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 43.95  E-value: 3.10e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1802993127 486 ALERLilLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDADIpGL----PR-DERS---LIQIIGRAAR-NVHGRVI 555
Cdd:COG1198   519 ALEKL--LEAFARGEADILVGTQMLAKGHDFPNVTLVGVLDADL-GLnspdFRaAERTfqlLTQVAGRAGRaEKPGEVL 594
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 23-92 8.17e-04

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: 40.37  E-value: 8.17e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1802993127  23 QPAAIAKLAEFQTNEQ-VLLGATGTGKTFTIANVIQKV-QLPTVVIAHNKTLAGQLYQELKELFPNNAVEYF 92
Cdd:cd17926     5 QEEALEAWLAHKNNRRgILVLPTGSGKTLTALALIAYLkELRTLIVVPTDALLDQWKERFEDFLGDSSIGLI 76
PTZ00110 PTZ00110
helicase; Provisional
 450-548 5.02e-03

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 39.76  E-value: 5.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 450 NGRTFVTVLTIKMAENLTDFLKERNIKVAYIHKDIKALERLILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDadi 529
Cdd:PTZ00110  377 GDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFD--- 453

                          90
                  ....*....|....*....
gi 1802993127 530 pgLPRDERSLIQIIGRAAR 548
Cdd:PTZ00110  454 --FPNQIEDYVHRIGRTGR 470
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 23-88 6.24e-03

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: 37.93  E-value: 6.24e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1802993127  23 QPAAIAKL-AEFQTNEQVLL--GATGTGKTFTIANVIQKVqLP------TVVIAHNKTLAGQLYQELKELFPNNA 88
Cdd:cd18032     5 QQEAIEALeEAREKGQRRALlvMATGTGKTYTAAFLIKRL-LEanrkkrILFLAHREELLEQAERSFKEVLPDGS 78
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 423-554 6.94e-03

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: 37.63  E-value: 6.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802993127 423 LDPEVI--VKPKDNQVE-----DLVIEIINQRKHNGRTFVTVLTIKMAENLTDFLKER------NIKVAYIHKDIKALER 489
Cdd:cd18796     4 LDIKVIlpVAPEIFPWAgesgaDAYAEVIFLLERHKSTLVFTNTRSQAERLAQRLRELcpdrvpPDFIALHHGSLSRELR 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1802993127 490 LILLTDLRKGEYECLVGINLLREGLDVPEVSLVAIFDAdipglPRDERSLIQIIGRAARNVHGRV 554
Cdd:cd18796    84 EEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIQIGS-----PKSVARLLQRLGRSGHRPGAAS 143
 
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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