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Conserved domains on  [gi|2072548576|ref|WP_218950618|]
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MULTISPECIES: excinuclease ABC subunit UvrB [unclassified Acinetobacter]

Protein Classification

excinuclease ABC subunit UvrB( domain architecture ID 11426127)

excinuclease ABC subunit B is part of the UvrABC repair system, which catalyzes the recognition and processing of DNA lesions

CATH:  3.30.2060.10|3.40.50.300
Gene Ontology:  GO:0003677|GO:0005524|GO:0009381|GO:0006289|GO:0009380|GO:0016887|GO:0004386|GO:0006289
PubMed:  16464004|10946234

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
5-669 0e+00

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


:

Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1360.46  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576   5 PFELVTQYQPAGDQPQAIEKLVKGIEKGMHDQLLLGVTGSGKTYTMANVIARTQRPTIIMAHNKTLAAQLYGEFKAFFPH 84
Cdd:COG0556     1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  85 NAVEYFVSYYDYYQPEAYVPSSDTFIEKDSSINDHIDQMRLSATRALLERRDAIIVASVSAIYGLGDPNAYMSMLLHIVE 164
Cdd:COG0556    81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 165 GDRISRDDIIRRLVEMQYTRNELEFLRGTYRIRGEIIDIFPAESDQNAIRIELFDDEVDSVRWFDPLTGRMVRKVPRITI 244
Cdd:COG0556   161 GEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 245 YPKSHYVTPKDNLQRAIGTIREELAERLGFFRANDKLLEAQRIEQRTRYDLEMMQQLGYTNGIENYSRHLSGRPSGEAPP 324
Cdd:COG0556   241 YPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPP 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 325 TLFDYVPDDALLIIDESHVTVPQIGAMYKGDRSRKENLVNYGFRLPSALDNRPMKFEEWERIIPSTIYVSATPAHYEMEK 404
Cdd:COG0556   321 TLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEK 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 405 SE-QVVEQVVRPTGLVDPEIEIRPVLTQVDDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTV 483
Cdd:COG0556   401 SGgQVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTL 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 484 ERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNLNGKAILYADRMTDSMQK 563
Cdd:COG0556   481 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQR 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 564 AIDETDRRRNLQIAFNLEHGITPRSaVRQNVNDIDTGEVLTDDEidakisdqAKALTADERHLMSDPKLLAKHMNKLEKE 643
Cdd:COG0556   561 AIDETNRRREIQEAYNEEHGITPQT-IKKSIRDILEGTYEADEE--------TEELVAEADAAKLSKEELEKLIKELEKE 631

                         650       660
                  ....*....|....*....|....*.
gi 2072548576 644 MLKASKDLQFEQAARLRDEILRLKAQ 669
Cdd:COG0556   632 MKEAAKNLEFEEAARLRDEIKELKKE 657
 
Name Accession Description Interval E-value
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
5-669 0e+00

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


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1360.46  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576   5 PFELVTQYQPAGDQPQAIEKLVKGIEKGMHDQLLLGVTGSGKTYTMANVIARTQRPTIIMAHNKTLAAQLYGEFKAFFPH 84
Cdd:COG0556     1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  85 NAVEYFVSYYDYYQPEAYVPSSDTFIEKDSSINDHIDQMRLSATRALLERRDAIIVASVSAIYGLGDPNAYMSMLLHIVE 164
Cdd:COG0556    81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 165 GDRISRDDIIRRLVEMQYTRNELEFLRGTYRIRGEIIDIFPAESDQNAIRIELFDDEVDSVRWFDPLTGRMVRKVPRITI 244
Cdd:COG0556   161 GEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 245 YPKSHYVTPKDNLQRAIGTIREELAERLGFFRANDKLLEAQRIEQRTRYDLEMMQQLGYTNGIENYSRHLSGRPSGEAPP 324
Cdd:COG0556   241 YPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPP 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 325 TLFDYVPDDALLIIDESHVTVPQIGAMYKGDRSRKENLVNYGFRLPSALDNRPMKFEEWERIIPSTIYVSATPAHYEMEK 404
Cdd:COG0556   321 TLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEK 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 405 SE-QVVEQVVRPTGLVDPEIEIRPVLTQVDDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTV 483
Cdd:COG0556   401 SGgQVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTL 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 484 ERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNLNGKAILYADRMTDSMQK 563
Cdd:COG0556   481 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQR 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 564 AIDETDRRRNLQIAFNLEHGITPRSaVRQNVNDIDTGEVLTDDEidakisdqAKALTADERHLMSDPKLLAKHMNKLEKE 643
Cdd:COG0556   561 AIDETNRRREIQEAYNEEHGITPQT-IKKSIRDILEGTYEADEE--------TEELVAEADAAKLSKEELEKLIKELEKE 631

                         650       660
                  ....*....|....*....|....*.
gi 2072548576 644 MLKASKDLQFEQAARLRDEILRLKAQ 669
Cdd:COG0556   632 MKEAAKNLEFEEAARLRDEIKELKKE 657
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
4-671 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1342.78  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576   4 QPFELVTQYQPAGDQPQAIEKLVKGIEKGMHDQLLLGVTGSGKTYTMANVIARTQRPTIIMAHNKTLAAQLYGEFKAFFP 83
Cdd:PRK05298    3 KPFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEFFP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  84 HNAVEYFVSYYDYYQPEAYVPSSDTFIEKDSSINDHIDQMRLSATRALLERRDAIIVASVSAIYGLGDPNAYMSMLLHIV 163
Cdd:PRK05298   83 ENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLR 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 164 EGDRISRDDIIRRLVEMQYTRNELEFLRGTYRIRGEIIDIFPAESDQNAIRIELFDDEVDSVRWFDPLTGRMVRKVPRIT 243
Cdd:PRK05298  163 VGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVT 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 244 IYPKSHYVTPKDNLQRAIGTIREELAERLGFFRANDKLLEAQRIEQRTRYDLEMMQQLGYTNGIENYSRHLSGRPSGEAP 323
Cdd:PRK05298  243 IYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPP 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 324 PTLFDYVPDDALLIIDESHVTVPQIGAMYKGDRSRKENLVNYGFRLPSALDNRPMKFEEWERIIPSTIYVSATPAHYEME 403
Cdd:PRK05298  323 YTLLDYFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYELE 402

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 404 KSE-QVVEQVVRPTGLVDPEIEIRPVLTQVDDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDT 482
Cdd:PRK05298  403 KSGgVVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDT 482

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 483 VERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNLNGKAILYADRMTDSMQ 562
Cdd:PRK05298  483 LERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQ 562

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 563 KAIDETDRRRNLQIAFNLEHGITPRSaVRQNVNDIdtgevltddeIDAKisDQAKALTADErhlmsdpklLAKHMNKLEK 642
Cdd:PRK05298  563 KAIDETERRREIQIAYNEEHGITPKT-IKKKIRDI----------LDSV--YKKDKLSKKE---------LEKLIKELEK 620

                         650       660
                  ....*....|....*....|....*....
gi 2072548576 643 EMLKASKDLQFEQAARLRDEILRLKAQMI 671
Cdd:PRK05298  621 QMKEAAKNLEFEEAARLRDEIKELKEELL 649
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
 5-667 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: 1148.19  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576   5 PFELVTQYQPAGDQPQAIEKLVKGIEKGMHDQLLLGVTGSGKTYTMANVIARTQRPTIIMAHNKTLAAQLYGEFKAFFPH 84
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  85 NAVEYFVSYYDYYQPEAYVPSSDTFIEKDSSINDHIDQMRLSATRALLERRDAIIVASVSAIYGLGDPNAYMSMLLHIVE 164
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 165 GDRISRDDIIRRLVEMQYTRNELEFLRGTYRIRGEIIDIFPAESDQNAIRIELFDDEVDSVRWFDPLTGRMVRKVPRITI 244
Cdd:TIGR00631 161 GKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDEFAVRIEFFGDEIERISRVDPLTGEVLRELDSFTI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 245 YPKSHYVTPKDNLQRAIGTIREELAERLGFFRANDKLLEAQRIEQRTRYDLEMMQQLGYTNGIENYSRHLSGRPSGEAPP 324
Cdd:TIGR00631 241 FPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPPY 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 325 TLFDYVPDDALLIIDESHVTVPQIGAMYKGDRSRKENLVNYGFRLPSALDNRPMKFEEWERIIPSTIYVSATPAHYEMEK 404
Cdd:TIGR00631 321 TLLDYFPDDFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELEQ 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 405 SEQVVEQVVRPTGLVDPEIEIRPVLTQVDDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTVE 484
Cdd:TIGR00631 401 SGNVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLE 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 485 RTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNLNGKAILYADRMTDSMQKA 564
Cdd:TIGR00631 481 RVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQKA 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 565 IDETDRRRNLQIAFNLEHGITPRSaVRQNVNDIDTGEVLTddeidakISDQAKALTADERHLMSDPKLLAKHMNKLEKEM 644
Cdd:TIGR00631 561 IEETERRRKIQMAYNEEHGITPQT-IRKPIRDILDIELKE-------KEDAAKKKKKGEDLSDLSKKELKKLIKQLEKEM 632

                         650       660
                  ....*....|....*....|...
gi 2072548576 645 LKASKDLQFEQAARLRDEILRLK 667
Cdd:TIGR00631 633 KQAARNLEFEEAARLRDEILELK 655
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
 6-414 0e+00

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: 554.90  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576   6 FELVTQYQPAGDQPQAIEKLVKGIEKGMHDQLLLGVTGSGKTYTMANVIARTQRPTIIMAHNKTLAAQLYGEFKAFFPHN 85
Cdd:cd17916     1 FKLVSPFKPAGDQPQAIAKLVEGLKRGVKFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  86 AVEYFVSYYDYYQPEAYVPSSDTFIEKDSSINDHIDQMRLSATRALLERRDAIIVASVSAIYglgdpnaymsmllhiveg 165
Cdd:cd17916    81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLERRDVIVVASVSCIY------------------ 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 166 drisrddiirrlvemqytrneleflrgtyrirgeiidifpaesdqnairielfddevdsvrwfdpltgrmvrkvpritiy 245
Cdd:cd17916       --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 246 pkshyvtpkdnlQRAIGTIREELAERLGFFRANDKLLEAQRIEQRTRYDLEMMQQLGYTNGIENYSRHLSGRPSGEAPPT 325
Cdd:cd17916   143 ------------ERAIKSIEEELEERLKYFRAQGKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 326 LFDYVPDDALLIIDESHVTVPQIGAMYKGDRSRKENLVNYGFRLPSALDNRPMKFEEWERIIPSTIYVSATPAHYEMEKS 405
Cdd:cd17916   211 LLDYFPDDFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEHS 290


                  ....*....
gi 2072548576 406 EQVVEQVVR 414
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 1.57e-43

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: 151.01  E-value: 1.57e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 160 LHIVEGDRISRDDIIRRLVEMQYTRNELEFLRGTYRIRGEIIDIFPAESDQNAIRIELFDDEVDSVRWFDPLTGRMVRKV 239
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80

                          90
                  ....*....|.
gi 2072548576 240 PRITIYPKSHY 250
Cdd:pfam17757  81 DEVTIYPASHY 91
HELICc smart00490
helicase superfamily c-terminal domain;
460-544 1.96e-18

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 80.33  E-value: 1.96e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  460 EDLTSYLKEYGIKVAYLHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADkegflRSERSLIQTI 539
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-----WSPASYIQRI 75


                   ....*
gi 2072548576  540 GRAAR 544
Cdd:smart00490  76 GRAGR 80
 
Name Accession Description Interval E-value
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
5-669 0e+00

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


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1360.46  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576   5 PFELVTQYQPAGDQPQAIEKLVKGIEKGMHDQLLLGVTGSGKTYTMANVIARTQRPTIIMAHNKTLAAQLYGEFKAFFPH 84
Cdd:COG0556     1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  85 NAVEYFVSYYDYYQPEAYVPSSDTFIEKDSSINDHIDQMRLSATRALLERRDAIIVASVSAIYGLGDPNAYMSMLLHIVE 164
Cdd:COG0556    81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 165 GDRISRDDIIRRLVEMQYTRNELEFLRGTYRIRGEIIDIFPAESDQNAIRIELFDDEVDSVRWFDPLTGRMVRKVPRITI 244
Cdd:COG0556   161 GEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 245 YPKSHYVTPKDNLQRAIGTIREELAERLGFFRANDKLLEAQRIEQRTRYDLEMMQQLGYTNGIENYSRHLSGRPSGEAPP 324
Cdd:COG0556   241 YPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPP 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 325 TLFDYVPDDALLIIDESHVTVPQIGAMYKGDRSRKENLVNYGFRLPSALDNRPMKFEEWERIIPSTIYVSATPAHYEMEK 404
Cdd:COG0556   321 TLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEK 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 405 SE-QVVEQVVRPTGLVDPEIEIRPVLTQVDDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTV 483
Cdd:COG0556   401 SGgQVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTL 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 484 ERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNLNGKAILYADRMTDSMQK 563
Cdd:COG0556   481 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQR 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 564 AIDETDRRRNLQIAFNLEHGITPRSaVRQNVNDIDTGEVLTDDEidakisdqAKALTADERHLMSDPKLLAKHMNKLEKE 643
Cdd:COG0556   561 AIDETNRRREIQEAYNEEHGITPQT-IKKSIRDILEGTYEADEE--------TEELVAEADAAKLSKEELEKLIKELEKE 631

                         650       660
                  ....*....|....*....|....*.
gi 2072548576 644 MLKASKDLQFEQAARLRDEILRLKAQ 669
Cdd:COG0556   632 MKEAAKNLEFEEAARLRDEIKELKKE 657
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
4-671 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1342.78  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576   4 QPFELVTQYQPAGDQPQAIEKLVKGIEKGMHDQLLLGVTGSGKTYTMANVIARTQRPTIIMAHNKTLAAQLYGEFKAFFP 83
Cdd:PRK05298    3 KPFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEFFP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  84 HNAVEYFVSYYDYYQPEAYVPSSDTFIEKDSSINDHIDQMRLSATRALLERRDAIIVASVSAIYGLGDPNAYMSMLLHIV 163
Cdd:PRK05298   83 ENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLR 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 164 EGDRISRDDIIRRLVEMQYTRNELEFLRGTYRIRGEIIDIFPAESDQNAIRIELFDDEVDSVRWFDPLTGRMVRKVPRIT 243
Cdd:PRK05298  163 VGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVT 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 244 IYPKSHYVTPKDNLQRAIGTIREELAERLGFFRANDKLLEAQRIEQRTRYDLEMMQQLGYTNGIENYSRHLSGRPSGEAP 323
Cdd:PRK05298  243 IYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPP 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 324 PTLFDYVPDDALLIIDESHVTVPQIGAMYKGDRSRKENLVNYGFRLPSALDNRPMKFEEWERIIPSTIYVSATPAHYEME 403
Cdd:PRK05298  323 YTLLDYFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYELE 402

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 404 KSE-QVVEQVVRPTGLVDPEIEIRPVLTQVDDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDT 482
Cdd:PRK05298  403 KSGgVVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDT 482

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 483 VERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNLNGKAILYADRMTDSMQ 562
Cdd:PRK05298  483 LERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQ 562

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 563 KAIDETDRRRNLQIAFNLEHGITPRSaVRQNVNDIdtgevltddeIDAKisDQAKALTADErhlmsdpklLAKHMNKLEK 642
Cdd:PRK05298  563 KAIDETERRREIQIAYNEEHGITPKT-IKKKIRDI----------LDSV--YKKDKLSKKE---------LEKLIKELEK 620

                         650       660
                  ....*....|....*....|....*....
gi 2072548576 643 EMLKASKDLQFEQAARLRDEILRLKAQMI 671
Cdd:PRK05298  621 QMKEAAKNLEFEEAARLRDEIKELKEELL 649
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
 5-667 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: 1148.19  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576   5 PFELVTQYQPAGDQPQAIEKLVKGIEKGMHDQLLLGVTGSGKTYTMANVIARTQRPTIIMAHNKTLAAQLYGEFKAFFPH 84
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  85 NAVEYFVSYYDYYQPEAYVPSSDTFIEKDSSINDHIDQMRLSATRALLERRDAIIVASVSAIYGLGDPNAYMSMLLHIVE 164
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 165 GDRISRDDIIRRLVEMQYTRNELEFLRGTYRIRGEIIDIFPAESDQNAIRIELFDDEVDSVRWFDPLTGRMVRKVPRITI 244
Cdd:TIGR00631 161 GKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDEFAVRIEFFGDEIERISRVDPLTGEVLRELDSFTI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 245 YPKSHYVTPKDNLQRAIGTIREELAERLGFFRANDKLLEAQRIEQRTRYDLEMMQQLGYTNGIENYSRHLSGRPSGEAPP 324
Cdd:TIGR00631 241 FPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPPY 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 325 TLFDYVPDDALLIIDESHVTVPQIGAMYKGDRSRKENLVNYGFRLPSALDNRPMKFEEWERIIPSTIYVSATPAHYEMEK 404
Cdd:TIGR00631 321 TLLDYFPDDFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELEQ 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 405 SEQVVEQVVRPTGLVDPEIEIRPVLTQVDDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTVE 484
Cdd:TIGR00631 401 SGNVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLE 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 485 RTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNLNGKAILYADRMTDSMQKA 564
Cdd:TIGR00631 481 RVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQKA 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 565 IDETDRRRNLQIAFNLEHGITPRSaVRQNVNDIDTGEVLTddeidakISDQAKALTADERHLMSDPKLLAKHMNKLEKEM 644
Cdd:TIGR00631 561 IEETERRRKIQMAYNEEHGITPQT-IRKPIRDILDIELKE-------KEDAAKKKKKGEDLSDLSKKELKKLIKQLEKEM 632

                         650       660
                  ....*....|....*....|...
gi 2072548576 645 LKASKDLQFEQAARLRDEILRLK 667
Cdd:TIGR00631 633 KQAARNLEFEEAARLRDEILELK 655
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
 6-414 0e+00

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: 554.90  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576   6 FELVTQYQPAGDQPQAIEKLVKGIEKGMHDQLLLGVTGSGKTYTMANVIARTQRPTIIMAHNKTLAAQLYGEFKAFFPHN 85
Cdd:cd17916     1 FKLVSPFKPAGDQPQAIAKLVEGLKRGVKFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  86 AVEYFVSYYDYYQPEAYVPSSDTFIEKDSSINDHIDQMRLSATRALLERRDAIIVASVSAIYglgdpnaymsmllhiveg 165
Cdd:cd17916    81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLERRDVIVVASVSCIY------------------ 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 166 drisrddiirrlvemqytrneleflrgtyrirgeiidifpaesdqnairielfddevdsvrwfdpltgrmvrkvpritiy 245
Cdd:cd17916       --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 246 pkshyvtpkdnlQRAIGTIREELAERLGFFRANDKLLEAQRIEQRTRYDLEMMQQLGYTNGIENYSRHLSGRPSGEAPPT 325
Cdd:cd17916   143 ------------ERAIKSIEEELEERLKYFRAQGKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 326 LFDYVPDDALLIIDESHVTVPQIGAMYKGDRSRKENLVNYGFRLPSALDNRPMKFEEWERIIPSTIYVSATPAHYEMEKS 405
Cdd:cd17916   211 LLDYFPDDFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEHS 290


                  ....*....
gi 2072548576 406 EQVVEQVVR 414
Cdd:cd17916   291 GQVVEQIIR 299
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 420-588 2.23e-107

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: 322.27  E-value: 2.23e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 420 DPEIEIRPVLTQVDDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTVERTKIIHELRSGVYDA 499
Cdd:cd18790     1 DPEIEVRPTEGQVDDLLGEIRKRVARGERVLVTTLTKRMAEDLTEYLQELGVKVRYLHSEIDTLERVEIIRDLRLGEFDV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 500 IVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNLNGKAILYADRMTDSMQKAIDETDRRRNLQIAFN 579
Cdd:cd18790    81 LVGINLLREGLDLPEVSLVAILDADKEGFLRSETSLIQTIGRAARNVNGKVILYADKITDSMQKAIEETERRREIQMEYN 160


                  ....*....
gi 2072548576 580 LEHGITPRS 588
Cdd:cd18790   161 EEHGITPKT 169
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
 32-524 9.68e-57

Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];


Pssm-ID: 440810 [Multi-domain]  Cd Length: 1130  Bit Score: 208.38  E-value: 9.68e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576   32 GMHDQLLLGVTGSGKTYTMANVIARTQRPTIIMAHNKTLAAQLYGEFKAFFPHNAVEYFvsyydyyqpeayvPSSDTFIE 111
Cdd:COG1197      1 GGGRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLPDLPVLLF-------------PAWETLPY 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  112 KDSSINDHIDQMRLSATRALLERRDAIIVASVSA-IYGLGDPNAYMSMLLHIVEGDRISRDDIIRRLVEMQYTRNELEFL 190
Cdd:COG1197     68 DRFSPSPDIVSERLATLRRLASGKPGIVVTPVRAlLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEE 147

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  191 RGTYRIRGEIIDIFPAESDqNAIRIELFDDEVDSVRWFDPLTGRMVRKVPRITIYPKSHYVTPKDNLQRAigtiREELAE 270
Cdd:COG1197    148 PGEFAVRGGILDIFPPGSE-HPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERF----RERLRE 222

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  271 RLGFFRANDKLLEAqrIEQRTRYDlemmqqlgytnGIENYSRHLSGRPSgeappTLFDYVPDDALLIIDESHVTVPQIGA 350
Cdd:COG1197    223 LFGLDPKLDELYEA--LSEGIAFA-----------GIEYYLPLFYEELA-----TLFDYLPEDALVVLDEPERIEEAAEE 284

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  351 MYKGDRSRKENLVNYGFRLPSALDNRPMKFEEWERIIPS--TIYVSATPahyEMEKSEQVVEQVVRPtglvdpeieIRPV 428
Cdd:COG1197    285 FWEEIEERYEARRHDRGRPLLPPEELFLDPEELFAALKRrpRVTLSPFA---ALPEGAGVVNLGARP---------LPSF 352

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  429 LTQVDDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSdidtvertkiIHELRSGVYDAIVGInlLRE 508
Cdd:COG1197    353 AGQLEALLEELKRLLKDGGRVLLAAESEGRRERLLELLRDHGIPARLVES----------LAELSPGGVAITVGP--LEH 420

                          490
                   ....*....|....*.
gi 2072548576  509 GLDMPEVSLVAILDAD 524
Cdd:COG1197    421 GFELPDAKLAVITESE 436
UvrB_inter pfam17757
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ...
 160-250 1.57e-43

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: 151.01  E-value: 1.57e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 160 LHIVEGDRISRDDIIRRLVEMQYTRNELEFLRGTYRIRGEIIDIFPAESDQNAIRIELFDDEVDSVRWFDPLTGRMVRKV 239
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80

                          90
                  ....*....|.
gi 2072548576 240 PRITIYPKSHY 250
Cdd:pfam17757  81 DEVTIYPASHY 91
UvrB pfam12344
Ultra-violet resistance protein B; This domain family is found in bacteria, archaea and ...
 552-592 4.13e-20

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: 83.59  E-value: 4.13e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2072548576 552 LYADRMTDSMQKAIDETDRRRNLQIAFNLEHGITPRSAVRQ 592
Cdd:pfam12344   1 LYADKITDSMQRAIDETERRREIQEAYNEEHGITPKTIKKK 41
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 442-544 4.88e-19

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: 82.64  E-value: 4.88e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 442 RKNLNERVLVTTLTKRMAeDLTSYLKEYGIKVAYLHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAIL 521
Cdd:pfam00271  11 KKERGGKVLIFSQTKKTL-EAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINY 89

                          90       100
                  ....*....|....*....|...
gi 2072548576 522 DADKegflrSERSLIQTIGRAAR 544
Cdd:pfam00271  90 DLPW-----NPASYIQRIGRAGR 107
HELICc smart00490
helicase superfamily c-terminal domain;
460-544 1.96e-18

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 80.33  E-value: 1.96e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  460 EDLTSYLKEYGIKVAYLHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADkegflRSERSLIQTI 539
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-----WSPASYIQRI 75


                   ....*
gi 2072548576  540 GRAAR 544
Cdd:smart00490  76 GRAGR 80
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
335-669 1.53e-17

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 86.23  E-value: 1.53e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 335 LLIIDESHvtvpQIGA-MYKgdrsRKENLVNYGFRL-----PSALDNRPMKFEEWERIIPSTIYVSA------TPAHYEM 402
Cdd:COG1061   190 LVIIDEAH----HAGApSYR----RILEAFPAAYRLgltatPFRSDGREILLFLFDGIVYEYSLKEAiedgylAPPEYYG 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 403 EKSEQVVEQVVRPTGLVDPEIEIRPVLTQVDDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDT 482
Cdd:COG1061   262 IRVDLTDERAEYDALSERLREALAADAERKDKILRELLREHPDDRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPK 341

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 483 VERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDAdkegfLRSERSLIQTIGRAARNLNGK--AILY------- 553
Cdd:COG1061   342 KEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRP-----TGSPREFIQRLGRGLRPAPGKedALVYdfvgndv 416

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 554 ------ADRMTDSMQKAIDETDRRRNLQIAFNLEHGITPRSAVRQNVNDIDTGEVLTDDEIDAKISDQAKALTADERHLM 627
Cdd:COG1061   417 pvleelAKDLRDLAGYRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELL 496

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 2072548576 628 SDPKLLAKHMNKLEKEMLKASKDLQFEQAARLRDEILRLKAQ 669
Cdd:COG1061   497 ELAKAEGKAEEEEEEKELLLLLALAKLLKLLLLLLLLLLLEL 538
mfd TIGR00580
transcription-repair coupling factor (mfd); All proteins in this family for which functions ...
 177-509 3.84e-17

transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273152 [Multi-domain]  Cd Length: 926  Bit Score: 85.87  E-value: 3.84e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 177 LVEMQYTRNELEFLRGTYRIRGEIIDIFPAESdQNAIRIELFDDEVDSVRWFDPLTGRMVRKVPRITIYPKSHYVTPKDN 256
Cdd:TIGR00580   1 LVELGYERVDLVEEEGEFSVRGEILDIFPPGS-ELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFILLEEE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 257 LqRAigtiREELAERLGFFRANDKLLEAqRIEQRTRYDLEMMQQLGYtngienysrhlsgrpsgEAPPTLFDYVPDDALL 336
Cdd:TIGR00580  80 T-IA----RLKDNAARVEDAKHLETIEA-LSEGTLPAGEEMFLPLFF-----------------EDLSSLFDYLPDNTPI 136

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 337 IIDEshvtvpqigamYKGDRSRKENLVNYGFRL------PSALDNRPMKFEEWERIIPSTIYVSATPAHYEMEKSEQVVE 410
Cdd:TIGR00580 137 LLDD-----------PERFHSAARFLQRELEEFynaleeAKKLINPPRLDLDPSELAFEASAISLSRVQLENEHLSLKAS 205

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 411 QVVRPTGLVdPEIEIRPVLTQVDDVLSEINNrknlNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSD--IDTVERTKI 488
Cdd:TIGR00580 206 EAIEGAQKH-SRLEFGEILAFKEELFRWLKA----GFKITVAAESESQAERLKSLLAEHDIAAQVIDESciIIPAVRYVM 280

                         330       340
                  ....*....|....*....|.
gi 2072548576 489 IHELRSGVYDAIVGINLLREG 509
Cdd:TIGR00580 281 IGALSSGFILPTAGLAVITES 301
PRK10689 PRK10689
transcription-repair coupling factor; Provisional
 35-337 9.32e-14

transcription-repair coupling factor; Provisional


Pssm-ID: 182649 [Multi-domain]  Cd Length: 1147  Bit Score: 75.17  E-value: 9.32e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576   35 DQLLLG-VTGSGKTYTMANVIARTQRPTIIMAHNKTLAAQLYGEFKAFFPH---NAVEYFVSYYDYYQPEAYVPSSdtfi 110
Cdd:PRK10689    15 DQRQLGeLTGAACATEVAEIAERHAGPVVLIAPDMQNALRLHDEIQQFTDQmvmNLADWETLPYDSFSPHQDIISS---- 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  111 ekdssindhidqmRLSATRALLERRDAIIVASVSAIYGLGDPNAYM-SMLLHIVEGDRISRDDIIRRLVEMQYTRNELEF 189
Cdd:PRK10689    91 -------------RLSTLYQLPTMQRGVLILPVNTLMQRVCPHSFLhGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVM 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  190 LRGTYRIRGEIIDIFPAESDQnAIRIELFDDEVDSVRWFDPLTGRMVRKVPRITIYPKSHYVTPKDnlqrAIGTIREELA 269
Cdd:PRK10689   158 EHGEYATRGALLDLFPMGSEE-PYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKA----AIELFRSQWR 232

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2072548576  270 ERLGFFRANDKLLeaQRIEQRTrydlemmqqlgYTNGIENYSRHLSGRPSgeapPTLFDYVPDDALLI 337
Cdd:PRK10689   233 DTFEVKRDAEHIY--QQVSKGT-----------LPAGIEYWQPLFFSEPL----PPLFSYFPANTLLV 283
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 389-567 4.82e-13

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: 71.83  E-value: 4.82e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 389 STIYVSATPahyemekSEQVVEQV-----------VRPTG--LVDPEIEIRPVLTQV-------DDVLSEINNRKNLNER 448
Cdd:COG4098   249 KLIYLTATP-------SKALQRQVkrgklkvvklpARYHGhpLPVPKFKWLGNWKKRlrrgklpRKLLKWLKKRLKEGRQ 321

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 449 VLVTTLTKRMAEDLTSYLKEY--GIKVAYLHSDiDTvERTKIIHELRSGVYDAIVGINLLREGLDMPEVSlVAILDADKE 526
Cdd:COG4098   322 LLIFVPTIELLEQLVALLQKLfpEERIAGVHAE-DP-ERKEKVQAFRDGEIPILVTTTILERGVTFPNVD-VAVLGADHP 398

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2072548576 527 GFlrSERSLIQTIGRAARNL---NGKAILYADRMTDSMQKAIDE 567
Cdd:COG4098   399 VF--TEAALVQIAGRVGRSAdypTGEVIFFHHGKTRAMKRAIRE 440
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 433-552 6.60e-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: 65.99  E-value: 6.60e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 433 DDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDM 512
Cdd:cd18787    14 KLLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDI 93

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2072548576 513 PEVSLVAILDadkegFLRSERSLIQTIGRAAR-NLNGKAIL 552
Cdd:cd18787    94 PGVDHVINYD-----LPRDAEDYVHRIGRTGRaGRKGTAIT 129
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
 455-552 6.72e-11

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: 63.03  E-value: 6.72e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 455 TKRMAEDLTSYLKEYgiKVAYLhsDIDTVER----TKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKEGFL- 529
Cdd:cd18804   103 TERVEEELKTLFPEA--RIARI--DRDTTRKkgalEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNADSGLNSp 178

                          90       100       110
                  ....*....|....*....|....*....|
gi 2072548576 530 --RS-ERS---LIQTIGRAAR-NLNGKAIL 552
Cdd:cd18804   179 dfRAsERAfqlLTQVSGRAGRgDKPGKVII 208
DEXDc smart00487
DEAD-like helicases superfamily;
6-93 1.76e-10

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 60.97  E-value: 1.76e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576    6 FELVTQYQPAGDQPQAIEKlvkgIEKGMHDQLLLGVTGSGKTYTMANVIART-----QRPTIIMAHNKTLAAQLYGEFKA 80
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEA----LLSGLRDVILAAPTGSGKTLAALLPALEAlkrgkGGRVLVLVPTRELAEQWAEELKK 76

                           90
                   ....*....|...
gi 2072548576   81 FFPHNAVEYFVSY 93
Cdd:smart00487  77 LGPSLGLKVVGLY 89
ResIII pfam04851
Type III restriction enzyme, res subunit;
18-83 2.78e-10

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 59.22  E-value: 2.78e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2072548576  18 QPQAIEKLVKGIEKGMHDQLLLGVTGSGKTYTMANVIAR-----TQRPTIIMAHNKTLAAQLYGEFKAFFP 83
Cdd:pfam04851   8 QIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARlfkkgPIKKVLFLVPRKDLLEQALEEFKKFLP 78
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
397-565 3.31e-10

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 62.47  E-value: 3.31e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 397 PAHYEMEKSEQV---VEQVVRPtglVDPEiEIRPVLTqvdDVLSEINNrknlnERVLVTTLTKRMAEDLTSYLKEYGIKV 473
Cdd:COG0513   201 PVRIEVAPENATaetIEQRYYL---VDKR-DKLELLR---RLLRDEDP-----ERAIVFCNTKRGADRLAEKLQKRGISA 268

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 474 AYLHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVaI---LDADKEGFL-RsersliqtIGRAAR-NLNG 548
Cdd:COG0513   269 AALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHV-InydLPEDPEDYVhR--------IGRTGRaGAEG 339

                         170
                  ....*....|....*..
gi 2072548576 549 KAILYADRMTDSMQKAI 565
Cdd:COG0513   340 TAISLVTPDERRLLRAI 356
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 34-140 9.60e-09

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: 54.72  E-value: 9.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  34 HDQLLLGVTGSGKTYTMANVI---ARTQRP-TIIMAHNKTLAAQLYGEFKAFFPHNA-VEYFVSYYDYYQPEAYvpssdt 108
Cdd:cd00046     2 ENVLITAPTGSGKTLAALLAAlllLLKKGKkVLVLVPTKALALQTAERLRELFGPGIrVAVLVGGSSAEEREKN------ 75

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2072548576 109 fIEKDSSI----NDHIDQMRLSATRALLERRDAIIV 140
Cdd:cd00046    76 -KLGDADIiiatPDMLLNLLLREDRLFLKDLKLIIV 110
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 447-549 6.34e-08

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: 51.41  E-value: 6.34e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 447 ERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSD-IDTVERTKIIHELRSG--VYDAIVGINLLREGLDMPEVSLVAilda 523
Cdd:cd18799     7 IKTLIFCVSIEHAEFMAEAFNEAGIDAVALNSDySDRERGDEALILLFFGelKPPILVTVDLLTTGVDIPEVDNVV---- 82

                          90       100
                  ....*....|....*....|....*....
gi 2072548576 524 dkegFLRSERSLI---QTIGRAARNLNGK 549
Cdd:cd18799    83 ----FLRPTESRTlflQMLGRGLRLHEGK 107
UVR pfam02151
UvrB/uvrC motif;
638-669 2.74e-07

UvrB/uvrC motif;


Pssm-ID: 308001 [Multi-domain]  Cd Length: 36  Bit Score: 47.01  E-value: 2.74e-07
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2072548576 638 NKLEKEMLKASKDLQFEQAARLRDEILRLKAQ 669
Cdd:pfam02151   5 KELEEEMEEAAENEDFEKAAKLRDQINALKKQ 36
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 425-552 4.62e-07

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: 49.66  E-value: 4.62e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 425 IRPVLTQVDDVLSEINNRKNL--NERVLVTTLTKRMAEDLTSYLKEY--GIKVAYL--HSDIDTV------ERTKIIHEL 492
Cdd:cd18801     7 IHPKLEKLEEIVKEHFKKKQEgsDTRVIIFSEFRDSAEEIVNFLSKIrpGIRATRFigQASGKSSkgmsqkEQKEVIEQF 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 493 RSGVYDAIVGINLLREGLDMPEVSLVAILDADKegflrSERSLIQTIGRAARNLNGKAIL 552
Cdd:cd18801    87 RKGGYNVLVATSIGEEGLDIGEVDLIICYDASP-----SPIRMIQRMGRTGRKRQGRVVV 141
DEAD-like_helicase_C cd09300
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ...
 501-545 1.09e-06

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: 46.00  E-value: 1.09e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2072548576 501 VGINLLREGLDMPEVSLVAILDADkegflRSERSLIQTIGRAARN 545
Cdd:cd09300    10 IAVN*ALTGFDAPELNTIIVDKNL-----RSYRGLNQAFGRANRI 49
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 18-90 1.54e-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: 48.07  E-value: 1.54e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2072548576  18 QPQAIEKLVKGIEKgmhDQLLLG-VTGSGKTYTMANVIA-RTQRPTIIMAHNKTLAAQLYGEFKAFFPHNAVEYF 90
Cdd:cd17926     5 QEEALEAWLAHKNN---RRGILVlPTGSGKTLTALALIAyLKELRTLIVVPTDALLDQWKERFEDFLGDSSIGLI 76
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 433-544 1.61e-06

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: 47.97  E-value: 1.61e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 433 DDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDM 512
Cdd:cd18794    17 KLDLLKRIKVEHLGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDK 96

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2072548576 513 PEVSLVAILDADK--EGFLrsersliQTIGRAAR 544
Cdd:cd18794    97 PDVRFVIHYSLPKsmESYY-------QESGRAGR 123
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 448-553 1.93e-06

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: 45.77  E-value: 1.93e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 448 RVLVTTLTKRMAEDLTSYLKeygikvaylhsdidtvertkiihelrsgvydAIVGINLLREGLDMPEVSLVAILDADkeg 527
Cdd:cd18785     5 KIIVFTNSIEHAEEIASSLE-------------------------------ILVATNVLGEGIDVPSLDTVIFFDPP--- 50

                          90       100
                  ....*....|....*....|....*...
gi 2072548576 528 flRSERSLIQTIGRAARN--LNGKAILY 553
Cdd:cd18785    51 --SSAASYIQRVGRAGRGgkDEGEVILF 76
PRK05580 PRK05580
primosome assembly protein PriA; Validated
 455-552 7.36e-06

primosome assembly protein PriA; Validated


Pssm-ID: 235514 [Multi-domain]  Cd Length: 679  Bit Score: 49.38  E-value: 7.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 455 TKRMAEDLTSYLKEYGIKVAylhsDIDTVeRTK-----IIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDAD---KE 526
Cdd:PRK05580  439 TERLEEELAELFPEARILRI----DRDTT-RRKgaleqLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADlglFS 513

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2072548576 527 GFLR-SERS---LIQTIGRAAR-NLNGKAIL 552
Cdd:PRK05580  514 PDFRaSERTfqlLTQVAGRAGRaEKPGEVLI 544
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 18-86 1.08e-05

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: 46.02  E-value: 1.08e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2072548576  18 QPQAIEKLVKGIEKGMHDQLLLGVTGSGKTYTMANVIAR----TQRPTI-IMAHNKTLAAQLYGEFKAFFPHNA 86
Cdd:cd18032     5 QQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKRlleaNRKKRIlFLAHREELLEQAERSFKEVLPDGS 78
PTZ00424 PTZ00424
helicase 45; Provisional
 455-576 1.10e-05

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 48.28  E-value: 1.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 455 TKRMAEDLTSYLKEYGIKVAYLHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKegflrSERS 534
Cdd:PTZ00424  276 TRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPA-----SPEN 350

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2072548576 535 LIQTIGRAAR-NLNGKAILYadrMTDSMQKAIDETDRRRNLQI 576
Cdd:PTZ00424  351 YIHRIGRSGRfGRKGVAINF---VTPDDIEQLKEIERHYNTQI 390
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
637-668 1.24e-05

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


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 48.58  E-value: 1.24e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2072548576 637 MNKLEKEMLKASKDLQFEQAARLRDEILRLKA 668
Cdd:COG0322   205 IKELEEKMEEAAEELEFERAARLRDQIRALEK 236
uvrC PRK00558
excinuclease ABC subunit UvrC;
637-667 1.54e-05

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 48.19  E-value: 1.54e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2072548576 637 MNKLEKEMLKASKDLQFEQAARLRDEILRLK 667
Cdd:PRK00558  204 LKELEEKMEEASENLEFERAARYRDQIQALR 234
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
435-614 1.73e-05

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 48.19  E-value: 1.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 435 VLSEINNR--KNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYL--HSDIDTV------ERTKIIHELRSGVYDAIVGIN 504
Cdd:COG1111   340 LREILKEQlgTNPDSRIIVFTQYRDTAEMIVEFLSEPGIKAGRFvgQASKEGDkgltqkEQIEILERFRAGEFNVLVATS 419

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 505 LLREGLDMPEVSLVAILDAdkegfLRSE-RSlIQTIGRAARNLNGKAILY-----------------ADRMTDSMQKAID 566
Cdd:COG1111   420 VAEEGLDIPEVDLVIFYEP-----VPSEiRS-IQRKGRTGRKREGRVVVLiakgtrdeayywssrrkEKKMKSILKKLKK 493

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2072548576 567 ETDRRRNLQIAFNLEHGITprsavrqnvnDIDTGEVLTDDEIDAKISD 614
Cdd:COG1111   494 LLDKQEKEKLKESAQATLD----------EFESIKELAEDEINEKDLD 531
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
 12-88 3.01e-05

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: 45.10  E-value: 3.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  12 YQPAGDQPQAIeklvKGIEKGMH-----DQLLLGVTGSGKT--YTMANVIA-RTQRPTIIMAHNKTLAAQLYGEFKAFFP 83
Cdd:cd17918    14 FSLTKDQAQAI----KDIEKDLHspepmDRLLSGDVGSGKTlvALGAALLAyKNGKQVAILVPTEILAHQHYEEARKFLP 89


                  ....*
gi 2072548576  84 HNAVE 88
Cdd:cd17918    90 FINVE 94
DEAD-like_helicase_N cd17912
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 36-75 3.98e-05

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: 42.51  E-value: 3.98e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2072548576  36 QLLLGVTGSGKTYTMANVIA---RTQRPTIIMAHNKTLAAQLY 75
Cdd:cd17912     2 ILHLGPTGSGKTLVAIQKIAsamSSGKSVLVVTPTKLLAHEIL 44
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 446-553 1.85e-04

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: 42.24  E-value: 1.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 446 NERVLVTTLTKRMAEDLTSYLKEYGIkvaylHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDMPEVSlVAILDADK 525
Cdd:cd18789    49 GDKIIVFTDNVEALYRYAKRLLKPFI-----TGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEAN-VAIQISGH 122

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2072548576 526 EGflrSERSLIQTIG---RAARNLNGKAILY 553
Cdd:cd18789   123 GG---SRRQEAQRLGrilRPKKGGGKNAFFY 150
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 415-549 3.39e-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: 41.48  E-value: 3.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 415 PTGLVDPEIEIRPVLTQVDDVLSEinNRKNLnervlVTTLTKRMAEDLTSYLKEY------GIKVAYLHSDIDTVERTKI 488
Cdd:cd18796    14 PEIFPWAGESGADAYAEVIFLLER--HKSTL-----VFTNTRSQAERLAQRLRELcpdrvpPDFIALHHGSLSRELREEV 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2072548576 489 IHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKegflrSERSLIQTIGRAARNLNGK 549
Cdd:cd18796    87 EAALKRGDLKVVVATSSLELGIDIGDVDLVIQIGSPK-----SVARLLQRLGRSGHRPGAA 142
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 419-544 3.82e-04

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: 43.67  E-value: 3.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 419 VDPEIEIRPVLTQVDDVLSEINnRKNLneRVLVTTLTKRMAEDLTSYLKE------YGIKVA-----YLHSdidtvERTK 487
Cdd:COG1205   264 LVDDGIRRSALAEAARLLADLV-REGL--RTLVFTRSRRGAELLARYARRalrepdLADRVAayragYLPE-----ERRE 335

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2072548576 488 IIHELRSGVYDAIVGINLLREGLDMPEVSLVaILDadkeGFLRSERSLIQTIGRAAR 544
Cdd:COG1205   336 IERGLRSGELLGVVSTNALELGIDIGGLDAV-VLA----GYPGTRASFWQQAGRAGR 387
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 421-505 5.68e-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: 40.54  E-value: 5.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 421 PEIEIRPVLTQVDDVLSEINNRKNLNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTVERTKIIHELRSGVYDAI 500
Cdd:cd18793     2 PPKIEEVVSGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDIRV 81

                          90
                  ....*....|....
gi 2072548576 501 ---------VGINL 505
Cdd:cd18793    82 fllstkaggVGLNL 95
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 17-93 6.33e-04

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 41.07  E-value: 6.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576  17 DQPQAIEKLVKGiekgmHDQLLLGVTGSGKT----YTMANVIARTQRP--TIIMAHNKTLAAQLYGEFKAFFPHNAVEYF 90
Cdd:pfam00270   3 IQAEAIPAILEG-----RDVLVQAPTGSGKTlaflLPALEALDKLDNGpqALVLAPTRELAEQIYEELKKLGKGLGLKVA 77


                  ...
gi 2072548576  91 VSY 93
Cdd:pfam00270  78 SLL 80
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 418-505 1.56e-03

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 41.75  E-value: 1.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 418 LVDPEIEIRPV----LTQVDDVLSEINNRknlNERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTVERTKIIHELR 493
Cdd:COG0553   520 LLLEEGAELSGrsakLEALLELLEELLAE---GEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQ 596

                          90       100
                  ....*....|....*....|.
gi 2072548576 494 SGVYDAIV---------GINL 505
Cdd:COG0553   597 EGPEAPVFlislkaggeGLNL 617
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
 479-552 2.01e-03

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


Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 41.26  E-value: 2.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 479 DIDTVER----TKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADkEGF----LR-SERS---LIQTIGRAAR-N 545
Cdd:COG1198   510 DRDTTRRkgalEKLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVLDAD-LGLnspdFRaAERTfqlLTQVAGRAGRaE 588


                  ....*..
gi 2072548576 546 LNGKAIL 552
Cdd:COG1198   589 KPGEVLI 595
PRK13766 PRK13766
Hef nuclease; Provisional
 427-551 2.22e-03

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 41.40  E-value: 2.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 427 PVLTQVDDVLSEINNRKNlNERVLVTTLTKRMAEDLTSYLKEYGIKVA--YLHSDIDTV------ERTKIIHELRSGVYD 498
Cdd:PRK13766  347 PKLEKLREIVKEQLGKNP-DSRIIVFTQYRDTAEKIVDLLEKEGIKAVrfVGQASKDGDkgmsqkEQIEILDKFRAGEFN 425

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2072548576 499 AIVGINLLREGLDMPEVSLVAILDAdkegfLRSE-RSlIQTIGRAARNLNGKAI 551
Cdd:PRK13766  426 VLVSTSVAEEGLDIPSVDLVIFYEP-----VPSEiRS-IQRKGRTGRQEEGRVV 473
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
 18-89 2.78e-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: 39.11  E-value: 2.78e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2072548576  18 QPQAIEKLVKGIEkGMHDQLLLGVTGSGKT----YTMANVIARtQRPTIIMAHNKTLAAQLYGEFKAFFPHNAVEY 89
Cdd:cd17929     1 QRKAYEAIVSSLG-GFKTFLLHGVTGSGKTevyiELIEKVLAK-GKQVLVLVPEISLTPQLIKRFKKRFGDKVAVL 74
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 457-572 2.83e-03

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: 38.79  E-value: 2.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 457 RMAEDLTSYLKEYgiKVAYLHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKEGFlrseRSLI 536
Cdd:cd18792    49 ALAEELKELVPEA--RVALLHGKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGL----SQLH 122

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2072548576 537 QTIGRAARnlnGKAILYADRMTDSmQKAIDETDRRR 572
Cdd:cd18792   123 QLRGRVGR---GKHQSYCYLLYPD-PKKLTETAKKR 154
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 472-577 3.03e-03

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: 38.86  E-value: 3.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 472 KVAYLHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKEGFLRsersLIQTIGRAARnlnGKAI 551
Cdd:cd18810    53 RIAIAHGQMTENELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIIERADKFGLAQ----LYQLRGRVGR---SKER 125

                          90       100
                  ....*....|....*....|....*.
gi 2072548576 552 LYADRMTDSmQKAIDETDRRRNLQIA 577
Cdd:cd18810   126 AYAYFLYPD-QKKLTEDALKRLEAIQ 150
PTZ00110 PTZ00110
helicase; Provisional
 446-544 3.60e-03

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 40.53  E-value: 3.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 446 NERVLVTTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDadk 525
Cdd:PTZ00110  377 GDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFD--- 453

                          90
                  ....*....|....*....
gi 2072548576 526 egFLRSERSLIQTIGRAAR 544
Cdd:PTZ00110  454 --FPNQIEDYVHRIGRTGR 470
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 458-544 7.60e-03

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: 37.71  E-value: 7.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2072548576 458 MAEDLTSYLK-EYgiKVAYLHSDIDTVERTKIIHELRSGVYDAIVGINLLREGLDMPEVSLVAILDADKEGFlrseRSLI 536
Cdd:cd18811    50 MYEYLKERFRpEL--NVGLLHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGL----SQLH 123


                  ....*...
gi 2072548576 537 QTIGRAAR 544
Cdd:cd18811   124 QLRGRVGR 131
 
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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