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Conserved domains on  [gi|93279489|pdb|2FDC|A]
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Chain A, UvrABC system protein B

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

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];
4-657 0e+00

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


:

Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1444.43  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        4 RFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPH 83
Cdd:COG0556   1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       84 NAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRV 163
Cdd:COG0556  81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRV 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      164 GMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGEVLGEREHVAI 243
Cdd:COG0556 161 GEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTI 240
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      244 FPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPY 323
Cdd:COG0556 241 YPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPP 320
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      324 TLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEH 403
Cdd:COG0556 321 TLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEK 400
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      404 SPG-VVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTL 482
Cdd:COG0556 401 SGGqVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTL 480
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      483 ERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEI 562
Cdd:COG0556 481 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQR 560
                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      563 AIQETKRRRAIQEEYNRKHGIVPRTVKKEIRDVIRATYAAEETEMYEAKPA--AAMTKQEREELIRTLEAEMKEAAKALD 640
Cdd:COG0556 561 AIDETNRRREIQEAYNEEHGITPQTIKKSIRDILEGTYEADEETEELVAEAdaAKLSKEELEKLIKELEKEMKEAAKNLE 640
                       650
                ....*....|....*..
2FDC_A      641 FERAAQLRDIIFELKAE 657
Cdd:COG0556 641 FEEAARLRDEIKELKKE 657
 
Name Accession Description Interval E-value
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
4-657 0e+00

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


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1444.43  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        4 RFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPH 83
Cdd:COG0556   1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       84 NAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRV 163
Cdd:COG0556  81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRV 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      164 GMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGEVLGEREHVAI 243
Cdd:COG0556 161 GEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTI 240
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      244 FPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPY 323
Cdd:COG0556 241 YPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPP 320
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      324 TLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEH 403
Cdd:COG0556 321 TLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEK 400
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      404 SPG-VVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTL 482
Cdd:COG0556 401 SGGqVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTL 480
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      483 ERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEI 562
Cdd:COG0556 481 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQR 560
                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      563 AIQETKRRRAIQEEYNRKHGIVPRTVKKEIRDVIRATYAAEETEMYEAKPA--AAMTKQEREELIRTLEAEMKEAAKALD 640
Cdd:COG0556 561 AIDETNRRREIQEAYNEEHGITPQTIKKSIRDILEGTYEADEETEELVAEAdaAKLSKEELEKLIKELEKEMKEAAKNLE 640
                       650
                ....*....|....*..
2FDC_A      641 FERAAQLRDIIFELKAE 657
Cdd:COG0556 641 FEEAARLRDEIKELKKE 657
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
3-657 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1418.66  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A         3 GRFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFP 82
Cdd:PRK05298   3 KPFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEFFP 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        83 HNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLR 162
Cdd:PRK05298  83 ENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLR 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       163 VGMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGEVLGEREHVA 242
Cdd:PRK05298 163 VGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVT 242
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       243 IFPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTP 322
Cdd:PRK05298 243 IYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPP 322
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       323 YTLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELE 402
Cdd:PRK05298 323 YTLLDYFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYELE 402
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       403 HSPG-VVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKT 481
Cdd:PRK05298 403 KSGGvVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDT 482
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       482 LERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSME 561
Cdd:PRK05298 483 LERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQ 562
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       562 IAIQETKRRRAIQEEYNRKHGIVPRTVKKEIRDVIRATYAAEetemyeakpaaAMTKQEREELIRTLEAEMKEAAKALDF 641
Cdd:PRK05298 563 KAIDETERRREIQIAYNEEHGITPKTIKKKIRDILDSVYKKD-----------KLSKKELEKLIKELEKQMKEAAKNLEF 631
                        650
                 ....*....|....*.
2FDC_A       642 ERAAQLRDIIFELKAE 657
Cdd:PRK05298 632 EEAARLRDEIKELKEE 647
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
4-655 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: 1239.48  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A          4 RFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPH 83
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A         84 NAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRV 163
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEV 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        164 GMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGEVLGEREHVAI 243
Cdd:TIGR00631 161 GKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDEFAVRIEFFGDEIERISRVDPLTGEVLRELDSFTI 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        244 FPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPY 323
Cdd:TIGR00631 241 FPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPPY 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        324 TLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEH 403
Cdd:TIGR00631 321 TLLDYFPDDFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELEQ 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        404 SPGVVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLE 483
Cdd:TIGR00631 401 SGNVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLE 480
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        484 RIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIA 563
Cdd:TIGR00631 481 RVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQKA 560
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        564 IQETKRRRAIQEEYNRKHGIVPRTVKKEIRDVIRATYAAEETEMYEAK---PAAAMTKQEREELIRTLEAEMKEAAKALD 640
Cdd:TIGR00631 561 IEETERRRKIQMAYNEEHGITPQTIRKPIRDILDIELKEKEDAAKKKKkgeDLSDLSKKELKKLIKQLEKEMKQAARNLE 640
                         650
                  ....*....|....*
2FDC_A        641 FERAAQLRDIIFELK 655
Cdd:TIGR00631 641 FEEAARLRDEILELK 655
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
5-413 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: 605.74  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        5 FQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPHN 84
Cdd:cd17916   1 FKLVSPFKPAGDQPQAIAKLVEGLKRGVKFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       85 AVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYglgspeeyrelvvslrvg 164
Cdd:cd17916  81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLERRDVIVVASVSCIY------------------ 142
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      165 meiernallrrlvdiqydrndidfrrgtfrvrgdvveifpasrdehcirveffgdeierirevdaltgevlgERehvaif 244
Cdd:cd17916 143 ------------------------------------------------------------------------ER------ 144
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      245 pashfvtreekmrlAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPYT 324
Cdd:cd17916 145 --------------AIKSIEEELEERLKYFRAQGKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      325 LLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEHS 404
Cdd:cd17916 211 LLDYFPDDFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEHS 290

                ....*....
2FDC_A      405 PGVVEQIIR 413
Cdd:cd17916 291 GQVVEQIIR 299
UvrB_inter pfam17757
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ...
159-249 1.53e-46

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: 159.10  E-value: 1.53e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        159 VSLRVGMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGEVLGER 238
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
                          90
                  ....*....|.
2FDC_A        239 EHVAIFPASHF 249
Cdd:pfam17757  81 DEVTIYPASHY 91
HELICc smart00490
helicase superfamily c-terminal domain;
459-543 4.74e-20

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 84.57  E-value: 4.74e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A         459 EDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADkegflRSERSLIQTI 538
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-----WSPASYIQRI 75

                   ....*
2FDC_A         539 GRAAR 543
Cdd:smart00490  76 GRAGR 80
 
Name Accession Description Interval E-value
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
4-657 0e+00

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


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1444.43  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        4 RFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPH 83
Cdd:COG0556   1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       84 NAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRV 163
Cdd:COG0556  81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRV 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      164 GMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGEVLGEREHVAI 243
Cdd:COG0556 161 GEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTI 240
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      244 FPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPY 323
Cdd:COG0556 241 YPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPP 320
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      324 TLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEH 403
Cdd:COG0556 321 TLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEK 400
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      404 SPG-VVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTL 482
Cdd:COG0556 401 SGGqVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTL 480
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      483 ERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEI 562
Cdd:COG0556 481 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQR 560
                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      563 AIQETKRRRAIQEEYNRKHGIVPRTVKKEIRDVIRATYAAEETEMYEAKPA--AAMTKQEREELIRTLEAEMKEAAKALD 640
Cdd:COG0556 561 AIDETNRRREIQEAYNEEHGITPQTIKKSIRDILEGTYEADEETEELVAEAdaAKLSKEELEKLIKELEKEMKEAAKNLE 640
                       650
                ....*....|....*..
2FDC_A      641 FERAAQLRDIIFELKAE 657
Cdd:COG0556 641 FEEAARLRDEIKELKKE 657
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
3-657 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1418.66  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A         3 GRFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFP 82
Cdd:PRK05298   3 KPFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEFFP 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        83 HNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLR 162
Cdd:PRK05298  83 ENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLR 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       163 VGMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGEVLGEREHVA 242
Cdd:PRK05298 163 VGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVT 242
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       243 IFPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTP 322
Cdd:PRK05298 243 IYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPP 322
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       323 YTLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELE 402
Cdd:PRK05298 323 YTLLDYFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYELE 402
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       403 HSPG-VVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKT 481
Cdd:PRK05298 403 KSGGvVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDT 482
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       482 LERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSME 561
Cdd:PRK05298 483 LERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQ 562
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       562 IAIQETKRRRAIQEEYNRKHGIVPRTVKKEIRDVIRATYAAEetemyeakpaaAMTKQEREELIRTLEAEMKEAAKALDF 641
Cdd:PRK05298 563 KAIDETERRREIQIAYNEEHGITPKTIKKKIRDILDSVYKKD-----------KLSKKELEKLIKELEKQMKEAAKNLEF 631
                        650
                 ....*....|....*.
2FDC_A       642 ERAAQLRDIIFELKAE 657
Cdd:PRK05298 632 EEAARLRDEIKELKEE 647
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
4-655 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: 1239.48  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A          4 RFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPH 83
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A         84 NAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRV 163
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEV 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        164 GMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGEVLGEREHVAI 243
Cdd:TIGR00631 161 GKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDEFAVRIEFFGDEIERISRVDPLTGEVLRELDSFTI 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        244 FPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPY 323
Cdd:TIGR00631 241 FPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPPY 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        324 TLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEH 403
Cdd:TIGR00631 321 TLLDYFPDDFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELEQ 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        404 SPGVVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLE 483
Cdd:TIGR00631 401 SGNVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLE 480
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        484 RIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIA 563
Cdd:TIGR00631 481 RVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQKA 560
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        564 IQETKRRRAIQEEYNRKHGIVPRTVKKEIRDVIRATYAAEETEMYEAK---PAAAMTKQEREELIRTLEAEMKEAAKALD 640
Cdd:TIGR00631 561 IEETERRRKIQMAYNEEHGITPQTIRKPIRDILDIELKEKEDAAKKKKkgeDLSDLSKKELKKLIKQLEKEMKQAARNLE 640
                         650
                  ....*....|....*
2FDC_A        641 FERAAQLRDIIFELK 655
Cdd:TIGR00631 641 FEEAARLRDEILELK 655
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
5-413 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: 605.74  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        5 FQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPHN 84
Cdd:cd17916   1 FKLVSPFKPAGDQPQAIAKLVEGLKRGVKFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       85 AVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYglgspeeyrelvvslrvg 164
Cdd:cd17916  81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLERRDVIVVASVSCIY------------------ 142
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      165 meiernallrrlvdiqydrndidfrrgtfrvrgdvveifpasrdehcirveffgdeierirevdaltgevlgERehvaif 244
Cdd:cd17916 143 ------------------------------------------------------------------------ER------ 144
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      245 pashfvtreekmrlAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPYT 324
Cdd:cd17916 145 --------------AIKSIEEELEERLKYFRAQGKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      325 LLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEHS 404
Cdd:cd17916 211 LLDYFPDDFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEHS 290

                ....*....
2FDC_A      405 PGVVEQIIR 413
Cdd:cd17916 291 GQVVEQIIR 299
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
419-589 6.51e-115

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: 341.15  E-value: 6.51e-115
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      419 DPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDV 498
Cdd:cd18790   1 DPEIEVRPTEGQVDDLLGEIRKRVARGERVLVTTLTKRMAEDLTEYLQELGVKVRYLHSEIDTLERVEIIRDLRLGEFDV 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      499 LVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYN 578
Cdd:cd18790  81 LVGINLLREGLDLPEVSLVAILDADKEGFLRSETSLIQTIGRAARNVNGKVILYADKITDSMQKAIEETERRREIQMEYN 160
                       170
                ....*....|.
2FDC_A      579 RKHGIVPRTVK 589
Cdd:cd18790 161 EEHGITPKTII 171
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
31-523 6.34e-48

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


Pssm-ID: 440810 [Multi-domain]  Cd Length: 1130  Bit Score: 181.80  E-value: 6.34e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        31 GVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFvsyydyyqpeayvPQTDTYIE 110
Cdd:COG1197    1 GGGRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLPDLPVLLF-------------PAWETLPY 67
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       111 KDAKINDEIDKLRHSATSALFERRDVIIVASV-SCIYGLGSPEEYRELVVSLRVGMEIERNALLRRLVDIQYDRNDIDFR 189
Cdd:COG1197   68 DRFSPSPDIVSERLATLRRLASGKPGIVVTPVrALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEE 147
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       190 RGTFRVRGDVVEIFPASrDEHCIRVEFFGDEIERIREVDALTGEVLGEREHVAIFPASHFVTREEKMRLAIQNIEQELEe 269
Cdd:COG1197  148 PGEFAVRGGILDIFPPG-SEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFG- 225
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       270 rlaelraqgklleaqrLEQRTRYDLEMMREMGFCSGIENYsrhLALRPPGstPYTLLDYFPDDFLIIVDESHVTLPQLRG 349
Cdd:COG1197  226 ----------------LDPKLDELYEALSEGIAFAGIEYY---LPLFYEE--LATLFDYLPEDALVVLDEPERIEEAAEE 284
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       350 MYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKIN--QIIYVSATPgpyELEHSPGVVEQIIRPtglldptidVRPT 427
Cdd:COG1197  285 FWEEIEERYEARRHDRGRPLLPPEELFLDPEELFAALKrrPRVTLSPFA---ALPEGAGVVNLGARP---------LPSF 352
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       428 KGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYlhseiktlerIEIIRDLRLGKYDVLVGInlLRE 507
Cdd:COG1197  353 AGQLEALLEELKRLLKDGGRVLLAAESEGRRERLLELLRDHGIPARL----------VESLAELSPGGVAITVGP--LEH 420
                        490
                 ....*....|....*.
2FDC_A       508 GLDIPEVSLVAILDAD 523
Cdd:COG1197  421 GFELPDAKLAVITESE 436
UvrB_inter pfam17757
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ...
159-249 1.53e-46

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: 159.10  E-value: 1.53e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        159 VSLRVGMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGEVLGER 238
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
                          90
                  ....*....|.
2FDC_A        239 EHVAIFPASHF 249
Cdd:pfam17757  81 DEVTIYPASHY 91
UvrB pfam12344
Ultra-violet resistance protein B; This domain family is found in bacteria, archaea and ...
551-593 8.19e-23

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: 91.30  E-value: 8.19e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
2FDC_A        551 MYADTITKSMEIAIQETKRRRAIQEEYNRKHGIVPRTVKKEIR 593
Cdd:pfam12344   1 LYADKITDSMQRAIDETERRREIQEAYNEEHGITPKTIKKKIR 43
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
429-543 2.28e-21

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: 89.58  E-value: 2.28e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        429 GQIDDLIGEIRErvERNERTLVTTLTKKMAEdlTDYLKEA-GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 507
Cdd:pfam00271   1 EKLEALLELLKK--ERGGKVLIFSQTKKTLE--AELLLEKeGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAER 76
                          90       100       110
                  ....*....|....*....|....*....|....*.
2FDC_A        508 GLDIPEVSLVAILDADKegflrSERSLIQTIGRAAR 543
Cdd:pfam00271  77 GLDLPDVDLVINYDLPW-----NPASYIQRIGRAGR 107
HELICc smart00490
helicase superfamily c-terminal domain;
459-543 4.74e-20

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 84.57  E-value: 4.74e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A         459 EDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADkegflRSERSLIQTI 538
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-----WSPASYIQRI 75

                   ....*
2FDC_A         539 GRAAR 543
Cdd:smart00490  76 GRAGR 80
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
389-575 2.94e-19

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: 91.09  E-value: 2.94e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      389 IIYVSATPGPY--------ELEHS---------PGVVeqiirPTGLLDPTIDVRPTKGQI-DDLIGEIRERVERNERTLV 450
Cdd:COG4098 250 LIYLTATPSKAlqrqvkrgKLKVVklparyhghPLPV-----PKFKWLGNWKKRLRRGKLpRKLLKWLKKRLKEGRQLLI 324
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      451 TTLTKKMAEDLTDYLKE--AGIKVAYLHSEIKtlERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSlVAILDADKEGFl 528
Cdd:COG4098 325 FVPTIELLEQLVALLQKlfPEERIAGVHAEDP--ERKEKVQAFRDGEIPILVTTTILERGVTFPNVD-VAVLGADHPVF- 400
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
2FDC_A      529 rSERSLIQTIGRAARNA---NGHVIMYADTITKSMEIAIQETKR--RRAIQE 575
Cdd:COG4098 401 -TEAALVQIAGRVGRSAdypTGEVIFFHHGKTRAMKRAIREIKRmnREAKKR 451
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
326-657 2.34e-18

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 88.93  E-value: 2.34e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      326 LDYFPDDF-LIIVDESH-VTLPQLRGMYNGDRARkqvlvdhgFRL-----PSALDNRPLTFEEFEQKINQIIYVSATPG- 397
Cdd:COG1061 181 LDELGDRFgLVIIDEAHhAGAPSYRRILEAFPAA--------YRLgltatPFRSDGREILLFLFDGIVYEYSLKEAIEDg 252
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      398 ---PYELEHSPGVVEQIIRPTGLLDPTID--VRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKV 472
Cdd:COG1061 253 ylaPPEYYGIRVDLTDERAEYDALSERLReaLAADAERKDKILRELLREHPDDRKTLVFCSSVDHAEALAELLNEAGIRA 332
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      473 AYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAdkegfLRSERSLIQTIGRAARNANG----H 548
Cdd:COG1061 333 AVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRP-----TGSPREFIQRLGRGLRPAPGkedaL 407
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      549 VIMYADTITKSMEIAIQETKRRRAIQ----EEYNRKHGIVPRTVKKEIRDVIRATYAAEETEMYEAKPAAAMTKQEREEL 624
Cdd:COG1061 408 VYDFVGNDVPVLEELAKDLRDLAGYRveflDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLE 487
                       330       340       350
                ....*....|....*....|....*....|...
2FDC_A      625 IRTLEAEMKEAAKALDFERAAQLRDIIFELKAE 657
Cdd:COG1061 488 LLALALELLELAKAEGKAEEEEEEKELLLLLAL 520
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
443-550 6.60e-15

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: 71.77  E-value: 6.60e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      443 ERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDa 522
Cdd:cd18787  25 LKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVINYD- 103
                        90       100
                ....*....|....*....|....*....
2FDC_A      523 dkegFLRSERSLIQTIGRAAR-NANGHVI 550
Cdd:cd18787 104 ----LPRDAEDYVHRIGRTGRaGRKGTAI 128
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
33-139 6.08e-14

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: 69.35  E-value: 6.08e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       33 KHQTLLGATGTGKTFTISNVIAQVN----KPTLVIAHNKTLAGQLYSELKEFFPHNA-VEYFVSYYDYYQPEAyvpqtdt 107
Cdd:cd00046   2 ENVLITAPTGSGKTLAALLAALLLLlkkgKKVLVLVPTKALALQTAERLRELFGPGIrVAVLVGGSSAEEREK------- 74
                        90       100       110
                ....*....|....*....|....*....|....*.
2FDC_A      108 YIEKDAKI----NDEIDKLRHSATSALFERRDVIIV 139
Cdd:cd00046  75 NKLGDADIiiatPDMLLNLLLREDRLFLKDLKLIIV 110
mfd TIGR00580
transcription-repair coupling factor (mfd); All proteins in this family for which functions ...
176-340 3.23e-13

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: 73.16  E-value: 3.23e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        176 LVDIQYDRNDIDFRRGTFRVRGDVVEIFPASrDEHCIRVEFFGDEIERIREVDALTGEVLGEREHVAIFPASHFVTREEK 255
Cdd:TIGR00580   1 LVELGYERVDLVEEEGEFSVRGEILDIFPPG-SELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFILLEEE 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        256 MRLAIQNIEQELEERlaelraqGKLLEAQRLEQRTRYDlemmremgfcsGIENYSRHLALRPPgstpyTLLDYFPDDFLI 335
Cdd:TIGR00580  80 TIARLKDNAARVEDA-------KHLETIEALSEGTLPA-----------GEEMFLPLFFEDLS-----SLFDYLPDNTPI 136

                  ....*
2FDC_A        336 IVDES 340
Cdd:TIGR00580 137 LLDDP 141
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
441-621 2.01e-12

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 69.41  E-value: 2.01e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      441 RVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVaI- 519
Cdd:COG0513 237 RDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHV-In 315
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      520 --LDADKEGFL-RsersliqtIGRAAR-NANGHVIMYAD--------TITKSMEIAIQETKRRRAiqEEYNRKHgivPRT 587
Cdd:COG0513 316 ydLPEDPEDYVhR--------IGRTGRaGAEGTAISLVTpderrllrAIEKLIGQKIEEEELPGF--EPVEEKR---LER 382
                       170       180       190
                ....*....|....*....|....*....|....
2FDC_A      588 VKKEIRDVIRATYAAEETEMYEAKPAAAMTKQER 621
Cdd:COG0513 383 LKPKIKEKLKGKKAGRGGRPGPKGERKARRGKRR 416
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
434-552 4.22e-11

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 66.29  E-value: 4.22e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      434 LIGEIRErVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYL-----HSEIKTL---ERIEIIRDLRLGKYDVLVGINLL 505
Cdd:COG1111 343 ILKEQLG-TNPDSRIIVFTQYRDTAEMIVEFLSEPGIKAGRFvgqasKEGDKGLtqkEQIEILERFRAGEFNVLVATSVA 421
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
2FDC_A      506 REGLDIPEVSLVAILDAdkegfLRSE-RSlIQTIGRAARNANGHVIMY 552
Cdd:COG1111 422 EEGLDIPEVDLVIFYEP-----VPSEiRS-IQRKGRTGRKREGRVVVL 463
DEXDc smart00487
DEAD-like helicases superfamily;
10-92 4.69e-11

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 62.51  E-value: 4.69e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A          10 PYEPQGDQPQAIAKLVDGLRRGVkhqtLLGATGTGKTFTISNVIAQ-----VNKPTLVIAHNKTLAGQLYSELKEFFPHN 84
Cdd:smart00487   6 FEPLRPYQKEAIEALLSGLRDVI----LAAPTGSGKTLAALLPALEalkrgKGGRVLVLVPTRELAEQWAEELKKLGPSL 81

                   ....*...
2FDC_A          85 AVEYFVSY 92
Cdd:smart00487  82 GLKVVGLY 89
DEAD-like_helicase_N cd17912
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
34-104 1.50e-10

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: 57.91  E-value: 1.50e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
2FDC_A       34 HQTLLGATGTGKTFTISNVIAQVN---KPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYVPQ 104
Cdd:cd17912   1 NILHLGPTGSGKTLVAIQKIASAMssgKSVLVVTPTKLLAHEILIVIDEIQ*ILDPAAGWAWATRALLGLKAEK 74
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
442-543 2.81e-10

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: 57.95  E-value: 2.81e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      442 VERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLER-IEIIRDL--RLGKYDVLVGINLLREGLDIPEVSLVA 518
Cdd:cd18799   3 KYVEIKTLIFCVSIEHAEFMAEAFNEAGIDAVALNSDYSDRERgDEALILLffGELKPPILVTVDLLTTGVDIPEVDNVV 82
                        90       100
                ....*....|....*....|....*...
2FDC_A      519 ildadkegFLRSERSLI---QTIGRAAR 543
Cdd:cd18799  83 --------FLRPTESRTlflQMLGRGLR 102
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
454-550 2.83e-10

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: 61.11  E-value: 2.83e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      454 TKKMAEDLTDYLKEAgiKVAYLHSEIKTLERI--EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFL--- 528
Cdd:cd18804 103 TERVEEELKTLFPEA--RIARIDRDTTRKKGAleKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNADSGLNSpdf 180
                        90       100
                ....*....|....*....|....*..
2FDC_A      529 RS-ERS---LIQTIGRAAR-NANGHVI 550
Cdd:cd18804 181 RAsERAfqlLTQVSGRAGRgDKPGKVI 207
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
421-543 5.31e-09

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: 54.91  E-value: 5.31e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      421 TIDVRP--TKGQIDDLIGEIRERvERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDV 498
Cdd:cd18794   5 FYSVRPkdKKDEKLDLLKRIKVE-HLGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWLRDKIQV 83
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
2FDC_A      499 LVGINLLREGLDIPEVSLVAILDADK--EGFLrsersliQTIGRAAR 543
Cdd:cd18794  84 IVATVAFGMGIDKPDVRFVIHYSLPKsmESYY-------QESGRAGR 123
UVR pfam02151
UvrB/uvrC motif;
622-657 3.97e-08

UvrB/uvrC motif;


Pssm-ID: 308001 [Multi-domain]  Cd Length: 36  Bit Score: 49.32  E-value: 3.97e-08
                          10        20        30
                  ....*....|....*....|....*....|....*.
2FDC_A        622 EELIRTLEAEMKEAAKALDFERAAQLRDIIFELKAE 657
Cdd:pfam02151   1 KKLIKELEEEMEEAAENEDFEKAAKLRDQINALKKQ 36
DEAD-like_helicase_C cd09300
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ...
498-553 4.00e-08

C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases is composed of two superfamilies, SF1 and SF2, that share almost identical folds and extensive structural similarity in their catalytic core. Helicases are involved in ATP-dependent RNA or DNA unwinding. Two distinct types of helicases exist, those forming toroidal, predominantly hexameric structures, and those that do not. SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Their conserved helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350171 [Multi-domain]  Cd Length: 59  Bit Score: 50.24  E-value: 4.00e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
2FDC_A      498 VLVGINLLREGLDIPEVSLVAILDADkegflRSERSLIQTIGRAARNAN-GHVIMYA 553
Cdd:cd09300   8 VLIAVN*ALTGFDAPELNTIIVDKNL-----RSYRGLNQAFGRANRIYTfGGIVTYR 59
ResIII pfam04851
Type III restriction enzyme, res subunit;
17-82 6.53e-08

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 52.67  E-value: 6.53e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
2FDC_A         17 QPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNK-----PTLVIAHNKTLAGQLYSELKEFFP 82
Cdd:pfam04851   8 QIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKkgpikKVLFLVPRKDLLEQALEEFKKFLP 78
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
483-551 8.89e-08

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: 51.59  E-value: 8.89e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
2FDC_A      483 ERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKegflrSERSLIQTIGRAARNANGHVIM 551
Cdd:cd18801  78 EQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASP-----SPIRMIQRMGRTGRKRQGRVVV 141
PRK13766 PRK13766
Hef nuclease; Provisional
433-643 2.68e-07

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 53.72  E-value: 2.68e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       433 DLIGEIRERvERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYL-----HSEIKTL---ERIEIIRDLRLGKYDVLVGINL 504
Cdd:PRK13766 354 EIVKEQLGK-NPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFvgqasKDGDKGMsqkEQIEILDKFRAGEFNVLVSTSV 432
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       505 LREGLDIPEVSLVAILDAdkegfLRSE-RSlIQTIGRAARNANGHVIMYadtITKSMEiaiQETKRRRAIQEEYNRKHGI 583
Cdd:PRK13766 433 AEEGLDIPSVDLVIFYEP-----VPSEiRS-IQRKGRTGRQEEGRVVVL---IAKGTR---DEAYYWSSRRKEKKMKEEL 500
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       584 vpRTVKKEIRDVIRATYAAEETEMYEAKPAAAMTKQEREELIRTLEAEMKEAAKALDFER 643
Cdd:PRK13766 501 --KNLKGILNKKLQELDEEQKGEEEEKDEQLSLDDFVKSKGKEEEEEEEKEEKDKETEED 558
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
622-656 3.00e-07

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


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 53.59  E-value: 3.00e-07
                        10        20        30
                ....*....|....*....|....*....|....*
2FDC_A      622 EELIRTLEAEMKEAAKALDFERAAQLRDIIFELKA 656
Cdd:COG0322 202 KELIKELEEKMEEAAEELEFERAARLRDQIRALEK 236
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
17-85 4.98e-07

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: 49.87  E-value: 4.98e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
2FDC_A       17 QPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQV-----NKPTLVIAHNKTLAGQLYSELKEFFPHNA 85
Cdd:cd18032   5 QQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKRLleanrKKRILFLAHREELLEQAERSFKEVLPDGS 78
uvrC PRK00558
excinuclease ABC subunit UvrC;
622-651 1.91e-06

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 50.89  E-value: 1.91e-06
                         10        20        30
                 ....*....|....*....|....*....|
2FDC_A       622 EELIRTLEAEMKEAAKALDFERAAQLRDII 651
Cdd:PRK00558 201 DEVLKELEEKMEEASENLEFERAARYRDQI 230
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
456-575 2.20e-06

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


Pssm-ID: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 48.03  E-value: 2.20e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      456 KMAEDLTDYLKEAgiKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFlrseRSLI 535
Cdd:cd18792  49 ALAEELKELVPEA--RVALLHGKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGL----SQLH 122
                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
2FDC_A      536 QTIGRAARnanGHVIMYADTITKSMEIAIQETKRR-RAIQE 575
Cdd:cd18792 123 QLRGRVGR---GKHQSYCYLLYPDPKKLTETAKKRlRAIAE 160
PRK05580 PRK05580
primosome assembly protein PriA; Validated
486-550 2.68e-06

primosome assembly protein PriA; Validated


Pssm-ID: 235514 [Multi-domain]  Cd Length: 679  Bit Score: 50.54  E-value: 2.68e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
2FDC_A       486 EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAD---KEGFLR-SERS---LIQTIGRAAR-NANGHVI 550
Cdd:PRK05580 471 QLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADlglFSPDFRaSERTfqlLTQVAGRAGRaEKPGEVL 543
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
445-551 2.71e-06

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


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 47.20  E-value: 2.71e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      445 NERTLVTTLTKKMAEDLtdyLKEAGIKVAYL--HSEIKTLER--------IEIIRDLRLGKYDVLVGINLLREGLDIPEV 514
Cdd:cd18802  33 ERRATAVVLSRLLKEHP---STLAFIRCGFLigRGNSSQRKRslmtqrkqKETLDKFRDGELNLLIATSVLEEGIDVPAC 109
                        90       100       110
                ....*....|....*....|....*....|....*...
2FDC_A      515 SLVAILDadkegFLRSERSLIQTIGRA-ARNANgHVIM 551
Cdd:cd18802 110 NLVIRFD-----LPKTLRSYIQSRGRArAPNSK-YILM 141
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
446-543 3.10e-06

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 49.94  E-value: 3.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       446 ERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADke 525
Cdd:PRK11192 246 TRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMP-- 323
                         90
                 ....*....|....*...
2FDC_A       526 gflRSERSLIQTIGRAAR 543
Cdd:PRK11192 324 ---RSADTYLHRIGRTGR 338
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
447-546 4.83e-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: 44.62  E-value: 4.83e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      447 RTLVTTLTKKMAEDLTDYLKeagikvaylhseiktlerieiirdlrlgkydVLVGINLLREGLDIPEVSLVAILDADkeg 526
Cdd:cd18785   5 KIIVFTNSIEHAEEIASSLE-------------------------------ILVATNVLGEGIDVPSLDTVIFFDPP--- 50
                        90       100
                ....*....|....*....|
2FDC_A      527 flRSERSLIQTIGRAARNAN 546
Cdd:cd18785  51 --SSAASYIQRVGRAGRGGK 68
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
442-552 4.97e-06

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ 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: 350184 [Multi-domain]  Cd Length: 146  Bit Score: 46.48  E-value: 4.97e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      442 VERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTL-------ERIEIIRDLRLGKYDVLVGINLLREGLDIPev 514
Cdd:cd18797  32 VRAGVKTIVFCRSRKLAELLLRYLKARLVEEGPLASKVASYragylaeDRREIEAELFNGELLGVVATNALELGIDIG-- 109
                        90       100       110
                ....*....|....*....|....*....|....*...
2FDC_A      515 SLVAILDAdkeGFLRSERSLIQTIGRAARNANGHVIMY 552
Cdd:cd18797 110 GLDAVVLA---GYPGSLASLWQQAGRAGRRGKDSLVIL 144
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
486-550 1.05e-05

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


Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 48.58  E-value: 1.05e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
2FDC_A      486 EIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADkEGF----LR-SERS---LIQTIGRAAR-NANGHVI 550
Cdd:COG1198 522 KLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVLDAD-LGLnspdFRaAERTfqlLTQVAGRAGRaEKPGEVL 594
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
10-87 1.49e-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: 45.87  E-value: 1.49e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       10 PYEPQGDQPQAIAKLVDGLRRGVKHQTLL-GATGTGKT--FTISNVIAQVN-KPTLVIAHNKTLAGQLYSELKEFFPHNA 85
Cdd:cd17918  13 PFSLTKDQAQAIKDIEKDLHSPEPMDRLLsGDVGSGKTlvALGAALLAYKNgKQVAILVPTEILAHQHYEEARKFLPFIN 92

                ..
2FDC_A       86 VE 87
Cdd:cd17918  93 VE 94
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
431-543 1.61e-05

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: 45.33  E-value: 1.61e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      431 IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEA------GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINL 504
Cdd:cd18796  24 GADAYAEVIFLLERHKSTLVFTNTRSQAERLAQRLRELcpdrvpPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSS 103
                        90       100       110
                ....*....|....*....|....*....|....*....
2FDC_A      505 LREGLDIPEVSLVAILDADKegflrSERSLIQTIGRAAR 543
Cdd:cd18796 104 LELGIDIGDVDLVIQIGSPK-----SVARLLQRLGRSGH 137
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
456-543 1.73e-05

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: 45.41  E-value: 1.73e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      456 KMAEDLTDYLKE---AGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFlrseR 532
Cdd:cd18811  45 KAAVAMYEYLKErfrPELNVGLLHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGL----S 120
                        90
                ....*....|.
2FDC_A      533 SLIQTIGRAAR 543
Cdd:cd18811 121 QLHQLRGRVGR 131
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
442-543 2.00e-05

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: 47.91  E-value: 2.00e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      442 VERNERTLVTTLTKKMAEDLTDYLKEA------GIKVA-----YLHSEiktleRIEIIRDLRLGKYDVLVGINLLREGLD 510
Cdd:COG1205 285 VREGLRTLVFTRSRRGAELLARYARRAlrepdlADRVAayragYLPEE-----RREIERGLRSGELLGVVSTNALELGID 359
                        90       100       110
                ....*....|....*....|....*....|...
2FDC_A      511 IPEVSLVaILDadkeGFLRSERSLIQTIGRAAR 543
Cdd:COG1205 360 IGGLDAV-VLA----GYPGTRASFWQQAGRAGR 387
DEAD-like_helicase_N cd17912
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
313-395 2.25e-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: 42.89  E-value: 2.25e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      313 LALRPPGSTPY-TLLDYFPDDFLIIVDESHVTLPQLRGMYNgdrarkqvlvdhgfrlpsaldnrpLTFEEFEQKINQIIY 391
Cdd:cd17912  22 SAMSSGKSVLVvTPTKLLAHEILIVIDEIQ*ILDPAAGWAW------------------------ATRALLGLKAEKVIG 77

                ....
2FDC_A      392 VSAT 395
Cdd:cd17912  78 VGAT 81
PRK10689 PRK10689
transcription-repair coupling factor; Provisional
164-258 2.66e-05

transcription-repair coupling factor; Provisional


Pssm-ID: 182649 [Multi-domain]  Cd Length: 1147  Bit Score: 47.43  E-value: 2.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A        164 GMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASrDEHCIRVEFFGDEIERIREVDALTGEVLGEREHVAI 243
Cdd:PRK10689  133 GQRLSRDALRAQLEQAGYRHVDQVMEHGEYATRGALLDLFPMG-SEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINL 211
                          90
                  ....*....|....*
2FDC_A        244 FPASHFVTREEKMRL 258
Cdd:PRK10689  212 LPAHEFPTDKAAIEL 226
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
40-149 6.24e-05

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: 43.45  E-value: 6.24e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       40 ATGTGKTFTISNVIAQV-NKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYV----PQTDTYIEKDAK 114
Cdd:cd17926  26 PTGSGKTLTALALIAYLkELRTLIVVPTDALLDQWKERFEDFLGDSSIGLIGGGKKKDFDDANVvvatYQSLSNLAEEEK 105
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
2FDC_A      115 ---------INDEIdklrHSATSALFERrdviIVASVSCIYGLG 149
Cdd:cd17926 106 dlfdqfgllIVDEA----HHLPAKTFSE----ILKELNAKYRLG 141
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
456-575 1.03e-04

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


Pssm-ID: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 43.10  E-value: 1.03e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      456 KMAEDLTDYLKEAgiKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRsersLI 535
Cdd:cd18810  40 KLATQLRQLVPEA--RIAIAHGQMTENELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIIERADKFGLAQ----LY 113
                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
2FDC_A      536 QTIGRAARnanGHVIMYAD-TITKSMEIAIQETKRRRAIQE 575
Cdd:cd18810 114 QLRGRVGR---SKERAYAYfLYPDQKKLTEDALKRLEAIQE 151
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
422-544 1.85e-04

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


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 44.69  E-value: 1.85e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      422 IDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAG--IKVAYLHSEIKTLERIEIIRDLRL----GK 495
Cdd:COG1203 343 VELKEGPLSDEELAELILEALHKGKSVLVIVNTVKDAQELYEALKEKLpdEEVYLLHSRFCPADRSEIEKEIKErlerGK 422
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
2FDC_A      496 YDVLVGINLLREGLDIpevslvailDADkegFLRSE----RSLIQTIGRAARN 544
Cdd:COG1203 423 PCILVSTQVVEAGVDI---------DFD---VVIRDlaplDSLIQRAGRCNRH 463
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
437-543 2.14e-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: 2.14e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      437 EIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIkvaylHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSl 516
Cdd:cd18789  41 ELLKRHEQGDKIIVFTDNVEALYRYAKRLLKPFI-----TGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEAN- 114
                        90       100
                ....*....|....*....|....*..
2FDC_A      517 VAILDADKEGflrSERSLIQTIGRAAR 543
Cdd:cd18789 115 VAIQISGHGG---SRRQEAQRLGRILR 138
PTZ00424 PTZ00424
helicase 45; Provisional
445-543 2.14e-04

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 44.05  E-value: 2.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       445 NERTLVTTLTKKMAE-DLTdylkeagikVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAD 523
Cdd:PTZ00424 275 NTRRKVDYLTKKMHErDFT---------VSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLP 345
                         90       100
                 ....*....|....*....|
2FDC_A       524 KegflrSERSLIQTIGRAAR 543
Cdd:PTZ00424 346 A-----SPENYIHRIGRSGR 360
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
463-499 4.59e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 43.21  E-value: 4.59e-04
                        10        20        30
                ....*....|....*....|....*....|....*..
2FDC_A      463 DYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVL 499
Cdd:COG0514  75 DALRAAGIRAAFLNSSLSAEERREVLRALRAGELKLL 111
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
463-543 6.13e-04

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 42.85  E-value: 6.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       463 DYLKEA-----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDadkegFLRSERSLIQT 537
Cdd:PLN00206 381 DLLANAitvvtGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFD-----MPNTIKEYIHQ 455

                 ....*.
2FDC_A       538 IGRAAR 543
Cdd:PLN00206 456 IGRASR 461
uvrC PRK14666
excinuclease ABC subunit C; Provisional
594-651 7.55e-04

excinuclease ABC subunit C; Provisional


Pssm-ID: 237782 [Multi-domain]  Cd Length: 694  Bit Score: 42.57  E-value: 7.55e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A       594 DVIRATYAA--EETEMYEAKPAAamtkqereELIRTLEAEMKEAAKALDFERAAQLRDII 651
Cdd:PRK14666 178 DVPRETYAAlvRKVEMLLSGRSG--------ELVDALRTEMEAASEALEFERAAVLRDQI 229
SF2_C_reverse_gyrase cd18798
C-terminal helicase domain of the reverse gyrase; Reverse gyrase modifies the topological ...
455-569 7.74e-04

C-terminal helicase domain of the reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350185 [Multi-domain]  Cd Length: 174  Bit Score: 40.75  E-value: 7.74e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      455 KKMAEDLTDYLKEAGIKVA-YLHSEIKTLErieiirDLRLGKYDVLVGI----NLLREGLDIPEVSLVAIldadkegFLR 529
Cdd:cd18798  37 KEYAEELKEFLERHGIKAElALSSTEKNLE------KFEEGEIDVLIGVasyyGVLVRGIDLPERIKYAI-------FYG 103
                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
2FDC_A      530 SE-RSLIQTIGRAARnanghviMYADTITKSMEIAIQETKR 569
Cdd:cd18798 104 VPvTTYIQASGRTSR-------LYAGGLTKGLSVVLVDDPE 137
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
431-504 7.89e-04

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 42.52  E-value: 7.89e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      431 IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKY-DVL--------VG 501
Cdd:COG0553 535 LEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPEaPVFlislkaggEG 614

                ...
2FDC_A      502 INL 504
Cdd:COG0553 615 LNL 617
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
431-504 9.31e-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: 39.77  E-value: 9.31e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      431 IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDL-RLGKYDVL--------VG 501
Cdd:cd18793  13 LEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFnEDPDIRVFllstkaggVG 92

                ...
2FDC_A      502 INL 504
Cdd:cd18793  93 LNL 95
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
325-395 2.26e-03

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: 38.92  E-value: 2.26e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
2FDC_A      325 LLDYFPDDFLIIVDESHVTLPQLRGMYNGDrarkqvlvdhgfrlpsaldnrpLTFEEFEQKINQIIYVSAT 395
Cdd:cd00046  98 DRLFLKDLKLIIVDEAHALLIDSRGALILD----------------------LAVRKAGLKNAQVILLSAT 146
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
430-523 3.26e-03

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


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 40.80  E-value: 3.26e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FDC_A      430 QIDDLIGEIRERVERNER-----TLVT---TLTKKMAEDLTDYLKEA--GIKVAYLHSEIKTLERIEIIRDLRLGKYDVL 499
Cdd:COG1200 454 RRDEVYERIREEIAKGRQayvvcPLIEeseKLDLQAAEETYEELREAfpGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVL 533
                        90       100
                ....*....|....*....|....*...
2FDC_A      500 VG---InllrE-GLDIPEVSLVAILDAD 523
Cdd:COG1200 534 VAttvI----EvGVDVPNATVMVIENAE 557
 
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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