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Conserved domains on  [gi|1559336361|ref|WP_128152183|]
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excinuclease ABC subunit UvrB [Apibacter raozihei]

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];
2-662 0e+00

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


:

Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1315.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   2 KFEVVSPFQPTGDQPRAIESLSKGILNNERYQTLLGVTGSGKTFTIANVVQNIQRPTIILAHNKTLAAQLYMEFKEFFPN 81
Cdd:COG0556     1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  82 NAVEYFVSYYDYYQPEAFMPTTNTYIEKDLSINENLEKLRLSASSALLSgRRDVLVVSSVSCLYGIGNPQEFQKNLVALE 161
Cdd:COG0556    81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLE-RRDVIVVASVSCIYGLGSPEEYLKMVLSLR 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 162 VGQKITKTKLLQSLVSALYSRSEMNFGRGNFRVKGDVIDVFPAYS-DTGIRIQLFGNEIDRIENVDYVSNNVIDSIENIN 240
Cdd:COG0556   160 VGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSeERAIRIEFFGDEIERISEFDPLTGEVLGELDRVT 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 241 IYPANLFVTSPDTLSQAIKNIQIDLGKQVEYYNEIGKSLEAHRLKERTEFDLEMIKELGYCSGIENYSRYLDGRAPGSRP 320
Cdd:COG0556   240 IYPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPP 319
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 321 FCLLDYFPKDFLMVVDESHVTLPQVHAMYGGDRSRKETLVEYGFRLPAAMDNRPLKFEEFEMMQNQVIYVSATPADYELQ 400
Cdd:COG0556   320 PTLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELE 399
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 401 KSEGVFVEQIIRPTGLLDPEIEVRPSLNQIDDLMAEIQKRIEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDT 480
Cdd:COG0556   400 KSGGQVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDT 479
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 481 LERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADKEGFLRSHRSLTQTAGRAARNIHGKVIMYADKMTDSMK 560
Cdd:COG0556   480 LERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQ 559
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 561 KTIDETSRRREIQNQFNIDHHITPKPLNKKITKISIGDQEAAIETYNVKDDIKTAAEPSvqynnENLEKIISKKQKEMEK 640
Cdd:COG0556   560 RAIDETNRRREIQEAYNEEHGITPQTIKKSIRDILEGTYEADEETEELVAEADAAKLSK-----EELEKLIKELEKEMKE 634
                         650       660
                  ....*....|....*....|..
gi 1559336361 641 AAKNLDFLTAAKFRDEINELKE 662
Cdd:COG0556   635 AAKNLEFEEAARLRDEIKELKK 656
 
Name Accession Description Interval E-value
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
2-662 0e+00

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


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1315.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   2 KFEVVSPFQPTGDQPRAIESLSKGILNNERYQTLLGVTGSGKTFTIANVVQNIQRPTIILAHNKTLAAQLYMEFKEFFPN 81
Cdd:COG0556     1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  82 NAVEYFVSYYDYYQPEAFMPTTNTYIEKDLSINENLEKLRLSASSALLSgRRDVLVVSSVSCLYGIGNPQEFQKNLVALE 161
Cdd:COG0556    81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLE-RRDVIVVASVSCIYGLGSPEEYLKMVLSLR 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 162 VGQKITKTKLLQSLVSALYSRSEMNFGRGNFRVKGDVIDVFPAYS-DTGIRIQLFGNEIDRIENVDYVSNNVIDSIENIN 240
Cdd:COG0556   160 VGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSeERAIRIEFFGDEIERISEFDPLTGEVLGELDRVT 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 241 IYPANLFVTSPDTLSQAIKNIQIDLGKQVEYYNEIGKSLEAHRLKERTEFDLEMIKELGYCSGIENYSRYLDGRAPGSRP 320
Cdd:COG0556   240 IYPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPP 319
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 321 FCLLDYFPKDFLMVVDESHVTLPQVHAMYGGDRSRKETLVEYGFRLPAAMDNRPLKFEEFEMMQNQVIYVSATPADYELQ 400
Cdd:COG0556   320 PTLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELE 399
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 401 KSEGVFVEQIIRPTGLLDPEIEVRPSLNQIDDLMAEIQKRIEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDT 480
Cdd:COG0556   400 KSGGQVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDT 479
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 481 LERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADKEGFLRSHRSLTQTAGRAARNIHGKVIMYADKMTDSMK 560
Cdd:COG0556   480 LERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQ 559
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 561 KTIDETSRRREIQNQFNIDHHITPKPLNKKITKISIGDQEAAIETYNVKDDIKTAAEPSvqynnENLEKIISKKQKEMEK 640
Cdd:COG0556   560 RAIDETNRRREIQEAYNEEHGITPQTIKKSIRDILEGTYEADEETEELVAEADAAKLSK-----EELEKLIKELEKEMKE 634
                         650       660
                  ....*....|....*....|..
gi 1559336361 641 AAKNLDFLTAAKFRDEINELKE 662
Cdd:COG0556   635 AAKNLEFEEAARLRDEIKELKK 656
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
1-668 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1274.21  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   1 MKFEVVSPFQPTGDQPRAIESLSKGILNNERYQTLLGVTGSGKTFTIANVVQNIQRPTIILAHNKTLAAQLYMEFKEFFP 80
Cdd:PRK05298    3 KPFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEFFP 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  81 NNAVEYFVSYYDYYQPEAFMPTTNTYIEKDLSINENLEKLRLSASSALLSgRRDVLVVSSVSCLYGIGNPQEFQKNLVAL 160
Cdd:PRK05298   83 ENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLE-RRDVIVVASVSCIYGLGSPEEYLKMVLSL 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 161 EVGQKITKTKLLQSLVSALYSRSEMNFGRGNFRVKGDVIDVFPAYS-DTGIRIQLFGNEIDRIENVDYVSNNVIDSIENI 239
Cdd:PRK05298  162 RVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYeERAIRIEFFGDEIERISEFDPLTGEVLGELDRV 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 240 NIYPANLFVTSPDTLSQAIKNIQIDLGKQVEYYNEIGKSLEAHRLKERTEFDLEMIKELGYCSGIENYSRYLDGRAPGSR 319
Cdd:PRK05298  242 TIYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEP 321
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 320 PFCLLDYFPKDFLMVVDESHVTLPQVHAMYGGDRSRKETLVEYGFRLPAAMDNRPLKFEEFEMMQNQVIYVSATPADYEL 399
Cdd:PRK05298  322 PYTLLDYFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYEL 401
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 400 QKSEGVFVEQIIRPTGLLDPEIEVRPSLNQIDDLMAEIQKRIEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDID 479
Cdd:PRK05298  402 EKSGGVVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDID 481
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 480 TLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADKEGFLRSHRSLTQTAGRAARNIHGKVIMYADKMTDSM 559
Cdd:PRK05298  482 TLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSM 561
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 560 KKTIDETSRRREIQNQFNIDHHITPKPLNKKITKIsigdqeaaIETYNVKDDIKTaaepsvqynnENLEKIISKKQKEME 639
Cdd:PRK05298  562 QKAIDETERRREIQIAYNEEHGITPKTIKKKIRDI--------LDSVYKKDKLSK----------KELEKLIKELEKQMK 623
                         650       660
                  ....*....|....*....|....*....
gi 1559336361 640 KAAKNLDFLTAAKFRDEINELKETLNKNN 668
Cdd:PRK05298  624 EAAKNLEFEEAARLRDEIKELKEELLGLS 652
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
2-661 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: 1075.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   2 KFEVVSPFQPTGDQPRAIESLSKGILNNERYQTLLGVTGSGKTFTIANVVQNIQRPTIILAHNKTLAAQLYMEFKEFFPN 81
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  82 NAVEYFVSYYDYYQPEAFMPTTNTYIEKDLSINENLEKLRLSASSALLSgRRDVLVVSSVSCLYGIGNPQEFQKNLVALE 161
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLE-RRDVIVVASVSCIYGLGSPEEYLKMVLHLE 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 162 VGQKITKTKLLQSLVSALYSRSEMNFGRGNFRVKGDVIDVFPAYSD-TGIRIQLFGNEIDRIENVDYVSNNVIDSIENIN 240
Cdd:TIGR00631 160 VGKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDeFAVRIEFFGDEIERISRVDPLTGEVLRELDSFT 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 241 IYPANLFVTSPDTLSQAIKNIQIDLGKQVEYYNEIGKSLEAHRLKERTEFDLEMIKELGYCSGIENYSRYLDGRAPGSRP 320
Cdd:TIGR00631 240 IFPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPP 319
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 321 FCLLDYFPKDFLMVVDESHVTLPQVHAMYGGDRSRKETLVEYGFRLPAAMDNRPLKFEEFEMMQNQVIYVSATPADYELQ 400
Cdd:TIGR00631 320 YTLLDYFPDDFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELE 399
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 401 KSEGVfVEQIIRPTGLLDPEIEVRPSLNQIDDLMAEIQKRIEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDT 480
Cdd:TIGR00631 400 QSGNV-VEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDT 478
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 481 LERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADKEGFLRSHRSLTQTAGRAARNIHGKVIMYADKMTDSMK 560
Cdd:TIGR00631 479 LERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQ 558
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 561 KTIDETSRRREIQNQFNIDHHITPKPLNKKITKISIGDQEAAIETYNVkddiKTAAEPSVQYNNENLEKIISKKQKEMEK 640
Cdd:TIGR00631 559 KAIEETERRRKIQMAYNEEHGITPQTIRKPIRDILDIELKEKEDAAKK----KKKGEDLSDLSKKELKKLIKQLEKEMKQ 634
                         650       660
                  ....*....|....*....|.
gi 1559336361 641 AAKNLDFLTAAKFRDEINELK 661
Cdd:TIGR00631 635 AARNLEFEEAARLRDEILELK 655
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
3-412 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: 536.02  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   3 FEVVSPFQPTGDQPRAIESLSKGILNNERYQTLLGVTGSGKTFTIANVVQNIQRPTIILAHNKTLAAQLYMEFKEFFPNN 82
Cdd:cd17916     1 FKLVSPFKPAGDQPQAIAKLVEGLKRGVKFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  83 AVEYFVSYYDYYQPEAFMPTTNTYIEKDLSINENLEKLRLSASSALLSgRRDVLVVSSVSCLYgignpqefqknlvalev 162
Cdd:cd17916    81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLE-RRDVIVVASVSCIY----------------- 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 163 gqkitktkllqslvsalysrsemnfgrgnfrvkgdvidvfpaysdtgiriqlfgneidrienvdyvsnnvidsieniniy 242
Cdd:cd17916       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 243 panlfvtspdtlSQAIKNIQIDLGKQVEYYNEIGKSLEAHRLKERTEFDLEMIKELGYCSGIENYSRYLDGRAPGSRPFC 322
Cdd:cd17916   143 ------------ERAIKSIEEELEERLKYFRAQGKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 323 LLDYFPKDFLMVVDESHVTLPQVHAMYGGDRSRKETLVEYGFRLPAAMDNRPLKFEEFEMMQNQVIYVSATPADYELQKS 402
Cdd:cd17916   211 LLDYFPDDFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEHS 290
                         410
                  ....*....|
gi 1559336361 403 eGVFVEQIIR 412
Cdd:cd17916   291 -GQVVEQIIR 299
UvrB_inter pfam17757
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ...
158-247 1.05e-33

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: 123.66  E-value: 1.05e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 158 VALEVGQKITKTKLLQSLVSALYSRSEMNFGRGNFRVKGDVIDVFPAYS-DTGIRIQLFGNEIDRIENVDYVSNNVIDSI 236
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSeDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
                          90
                  ....*....|.
gi 1559336361 237 ENINIYPANLF 247
Cdd:pfam17757  81 DEVTIYPASHY 91
HELICc smart00490
helicase superfamily c-terminal domain;
458-542 1.47e-18

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 80.33  E-value: 1.47e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  458 EELTKYLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADkegflRSHRSLTQTA 537
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-----WSPASYIQRI 75

                   ....*
gi 1559336361  538 GRAAR 542
Cdd:smart00490  76 GRAGR 80
 
Name Accession Description Interval E-value
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
2-662 0e+00

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


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1315.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   2 KFEVVSPFQPTGDQPRAIESLSKGILNNERYQTLLGVTGSGKTFTIANVVQNIQRPTIILAHNKTLAAQLYMEFKEFFPN 81
Cdd:COG0556     1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  82 NAVEYFVSYYDYYQPEAFMPTTNTYIEKDLSINENLEKLRLSASSALLSgRRDVLVVSSVSCLYGIGNPQEFQKNLVALE 161
Cdd:COG0556    81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLE-RRDVIVVASVSCIYGLGSPEEYLKMVLSLR 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 162 VGQKITKTKLLQSLVSALYSRSEMNFGRGNFRVKGDVIDVFPAYS-DTGIRIQLFGNEIDRIENVDYVSNNVIDSIENIN 240
Cdd:COG0556   160 VGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSeERAIRIEFFGDEIERISEFDPLTGEVLGELDRVT 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 241 IYPANLFVTSPDTLSQAIKNIQIDLGKQVEYYNEIGKSLEAHRLKERTEFDLEMIKELGYCSGIENYSRYLDGRAPGSRP 320
Cdd:COG0556   240 IYPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPP 319
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 321 FCLLDYFPKDFLMVVDESHVTLPQVHAMYGGDRSRKETLVEYGFRLPAAMDNRPLKFEEFEMMQNQVIYVSATPADYELQ 400
Cdd:COG0556   320 PTLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELE 399
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 401 KSEGVFVEQIIRPTGLLDPEIEVRPSLNQIDDLMAEIQKRIEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDT 480
Cdd:COG0556   400 KSGGQVVEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDT 479
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 481 LERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADKEGFLRSHRSLTQTAGRAARNIHGKVIMYADKMTDSMK 560
Cdd:COG0556   480 LERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQ 559
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 561 KTIDETSRRREIQNQFNIDHHITPKPLNKKITKISIGDQEAAIETYNVKDDIKTAAEPSvqynnENLEKIISKKQKEMEK 640
Cdd:COG0556   560 RAIDETNRRREIQEAYNEEHGITPQTIKKSIRDILEGTYEADEETEELVAEADAAKLSK-----EELEKLIKELEKEMKE 634
                         650       660
                  ....*....|....*....|..
gi 1559336361 641 AAKNLDFLTAAKFRDEINELKE 662
Cdd:COG0556   635 AAKNLEFEEAARLRDEIKELKK 656
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
1-668 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1274.21  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   1 MKFEVVSPFQPTGDQPRAIESLSKGILNNERYQTLLGVTGSGKTFTIANVVQNIQRPTIILAHNKTLAAQLYMEFKEFFP 80
Cdd:PRK05298    3 KPFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEFFP 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  81 NNAVEYFVSYYDYYQPEAFMPTTNTYIEKDLSINENLEKLRLSASSALLSgRRDVLVVSSVSCLYGIGNPQEFQKNLVAL 160
Cdd:PRK05298   83 ENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLE-RRDVIVVASVSCIYGLGSPEEYLKMVLSL 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 161 EVGQKITKTKLLQSLVSALYSRSEMNFGRGNFRVKGDVIDVFPAYS-DTGIRIQLFGNEIDRIENVDYVSNNVIDSIENI 239
Cdd:PRK05298  162 RVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYeERAIRIEFFGDEIERISEFDPLTGEVLGELDRV 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 240 NIYPANLFVTSPDTLSQAIKNIQIDLGKQVEYYNEIGKSLEAHRLKERTEFDLEMIKELGYCSGIENYSRYLDGRAPGSR 319
Cdd:PRK05298  242 TIYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEP 321
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 320 PFCLLDYFPKDFLMVVDESHVTLPQVHAMYGGDRSRKETLVEYGFRLPAAMDNRPLKFEEFEMMQNQVIYVSATPADYEL 399
Cdd:PRK05298  322 PYTLLDYFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYEL 401
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 400 QKSEGVFVEQIIRPTGLLDPEIEVRPSLNQIDDLMAEIQKRIEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDID 479
Cdd:PRK05298  402 EKSGGVVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDID 481
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 480 TLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADKEGFLRSHRSLTQTAGRAARNIHGKVIMYADKMTDSM 559
Cdd:PRK05298  482 TLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSM 561
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 560 KKTIDETSRRREIQNQFNIDHHITPKPLNKKITKIsigdqeaaIETYNVKDDIKTaaepsvqynnENLEKIISKKQKEME 639
Cdd:PRK05298  562 QKAIDETERRREIQIAYNEEHGITPKTIKKKIRDI--------LDSVYKKDKLSK----------KELEKLIKELEKQMK 623
                         650       660
                  ....*....|....*....|....*....
gi 1559336361 640 KAAKNLDFLTAAKFRDEINELKETLNKNN 668
Cdd:PRK05298  624 EAAKNLEFEEAARLRDEIKELKEELLGLS 652
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
2-661 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: 1075.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   2 KFEVVSPFQPTGDQPRAIESLSKGILNNERYQTLLGVTGSGKTFTIANVVQNIQRPTIILAHNKTLAAQLYMEFKEFFPN 81
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  82 NAVEYFVSYYDYYQPEAFMPTTNTYIEKDLSINENLEKLRLSASSALLSgRRDVLVVSSVSCLYGIGNPQEFQKNLVALE 161
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLE-RRDVIVVASVSCIYGLGSPEEYLKMVLHLE 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 162 VGQKITKTKLLQSLVSALYSRSEMNFGRGNFRVKGDVIDVFPAYSD-TGIRIQLFGNEIDRIENVDYVSNNVIDSIENIN 240
Cdd:TIGR00631 160 VGKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDeFAVRIEFFGDEIERISRVDPLTGEVLRELDSFT 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 241 IYPANLFVTSPDTLSQAIKNIQIDLGKQVEYYNEIGKSLEAHRLKERTEFDLEMIKELGYCSGIENYSRYLDGRAPGSRP 320
Cdd:TIGR00631 240 IFPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPP 319
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 321 FCLLDYFPKDFLMVVDESHVTLPQVHAMYGGDRSRKETLVEYGFRLPAAMDNRPLKFEEFEMMQNQVIYVSATPADYELQ 400
Cdd:TIGR00631 320 YTLLDYFPDDFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELE 399
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 401 KSEGVfVEQIIRPTGLLDPEIEVRPSLNQIDDLMAEIQKRIEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDT 480
Cdd:TIGR00631 400 QSGNV-VEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDT 478
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 481 LERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADKEGFLRSHRSLTQTAGRAARNIHGKVIMYADKMTDSMK 560
Cdd:TIGR00631 479 LERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQ 558
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 561 KTIDETSRRREIQNQFNIDHHITPKPLNKKITKISIGDQEAAIETYNVkddiKTAAEPSVQYNNENLEKIISKKQKEMEK 640
Cdd:TIGR00631 559 KAIEETERRRKIQMAYNEEHGITPQTIRKPIRDILDIELKEKEDAAKK----KKKGEDLSDLSKKELKKLIKQLEKEMKQ 634
                         650       660
                  ....*....|....*....|.
gi 1559336361 641 AAKNLDFLTAAKFRDEINELK 661
Cdd:TIGR00631 635 AARNLEFEEAARLRDEILELK 655
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
3-412 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: 536.02  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   3 FEVVSPFQPTGDQPRAIESLSKGILNNERYQTLLGVTGSGKTFTIANVVQNIQRPTIILAHNKTLAAQLYMEFKEFFPNN 82
Cdd:cd17916     1 FKLVSPFKPAGDQPQAIAKLVEGLKRGVKFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  83 AVEYFVSYYDYYQPEAFMPTTNTYIEKDLSINENLEKLRLSASSALLSgRRDVLVVSSVSCLYgignpqefqknlvalev 162
Cdd:cd17916    81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLE-RRDVIVVASVSCIY----------------- 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 163 gqkitktkllqslvsalysrsemnfgrgnfrvkgdvidvfpaysdtgiriqlfgneidrienvdyvsnnvidsieniniy 242
Cdd:cd17916       --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 243 panlfvtspdtlSQAIKNIQIDLGKQVEYYNEIGKSLEAHRLKERTEFDLEMIKELGYCSGIENYSRYLDGRAPGSRPFC 322
Cdd:cd17916   143 ------------ERAIKSIEEELEERLKYFRAQGKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 323 LLDYFPKDFLMVVDESHVTLPQVHAMYGGDRSRKETLVEYGFRLPAAMDNRPLKFEEFEMMQNQVIYVSATPADYELQKS 402
Cdd:cd17916   211 LLDYFPDDFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEHS 290
                         410
                  ....*....|
gi 1559336361 403 eGVFVEQIIR 412
Cdd:cd17916   291 -GQVVEQIIR 299
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
418-588 7.35e-113

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: 336.14  E-value: 7.35e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 418 DPEIEVRPSLNQIDDLMAEIQKRIEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDV 497
Cdd:cd18790     1 DPEIEVRPTEGQVDDLLGEIRKRVARGERVLVTTLTKRMAEDLTEYLQELGVKVRYLHSEIDTLERVEIIRDLRLGEFDV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 498 LVGVNLLREGLDLPEVSLVAILDADKEGFLRSHRSLTQTAGRAARNIHGKVIMYADKMTDSMKKTIDETSRRREIQNQFN 577
Cdd:cd18790    81 LVGINLLREGLDLPEVSLVAILDADKEGFLRSETSLIQTIGRAARNVNGKVILYADKITDSMQKAIEETERRREIQMEYN 160
                         170
                  ....*....|.
gi 1559336361 578 IDHHITPKPLN 588
Cdd:cd18790   161 EEHGITPKTII 171
UvrB_inter pfam17757
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ...
158-247 1.05e-33

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: 123.66  E-value: 1.05e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 158 VALEVGQKITKTKLLQSLVSALYSRSEMNFGRGNFRVKGDVIDVFPAYS-DTGIRIQLFGNEIDRIENVDYVSNNVIDSI 236
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSeDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
                          90
                  ....*....|.
gi 1559336361 237 ENINIYPANLF 247
Cdd:pfam17757  81 DEVTIYPASHY 91
UvrB pfam12344
Ultra-violet resistance protein B; This domain family is found in bacteria, archaea and ...
550-592 2.26e-21

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: 87.06  E-value: 2.26e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1559336361 550 MYADKMTDSMKKTIDETSRRREIQNQFNIDHHITPKPLNKKIT 592
Cdd:pfam12344   1 LYADKITDSMQRAIDETERRREIQEAYNEEHGITPKTIKKKIR 43
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
430-542 2.68e-20

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


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 86.50  E-value: 2.68e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 430 IDDLMAEIQKriEEDERVLVTTLTKRMAEElTKYLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLD 509
Cdd:pfam00271   3 LEALLELLKK--ERGGKVLIFSQTKKTLEA-ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLD 79
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1559336361 510 LPEVSLVAILDADKegflrSHRSLTQTAGRAAR 542
Cdd:pfam00271  80 LPDVDLVINYDLPW-----NPASYIQRIGRAGR 107
HELICc smart00490
helicase superfamily c-terminal domain;
458-542 1.47e-18

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 80.33  E-value: 1.47e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  458 EELTKYLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADkegflRSHRSLTQTA 537
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-----WSPASYIQRI 75

                   ....*
gi 1559336361  538 GRAAR 542
Cdd:smart00490  76 GRAGR 80
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
324-662 6.30e-18

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 87.77  E-value: 6.30e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 324 LDYFPKDF-LMVVDESHvtlpqvHAmygGDRSRKETLVEYG--FRL-----PAAMDNRPLKFEEFEmmqnQVIYVsatpA 395
Cdd:COG1061   181 LDELGDRFgLVIIDEAH------HA---GAPSYRRILEAFPaaYRLgltatPFRSDGREILLFLFD----GIVYE----Y 243
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 396 DYELQKSEGVFVEQII--RPTGLLDPEIEVRPSLNQIDDLMA-----------EIQKRIEEDERVLVTTLTKRMAEELTK 462
Cdd:COG1061   244 SLKEAIEDGYLAPPEYygIRVDLTDERAEYDALSERLREALAadaerkdkilrELLREHPDDRKTLVFCSSVDHAEALAE 323
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 463 YLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAIldadkegfLRSHRSLT---QTAGR 539
Cdd:COG1061   324 LLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAIL--------LRPTGSPRefiQRLGR 395
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 540 AARNIHGK----VIMYADKMTDSMKKTIDEtsRRREIQNQFNIDHHITPKPLNKKITKISIGDQEAAIETYNVKDDIKTA 615
Cdd:COG1061   396 GLRPAPGKedalVYDFVGNDVPVLEELAKD--LRDLAGYRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLE 473
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 1559336361 616 AEPSVQYNNENLEKIISKKQKEMEKAAKNLDFLTAAKFRDEINELKE 662
Cdd:COG1061   474 DALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLAL 520
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
388-573 2.13e-16

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: 82.23  E-value: 2.13e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 388 IYVSATPADyELQ---KSEGVFVEQI-IRPTG--LLDPEIEVRPSLNQ-------IDDLMAEIQKRIEEDERVLVTTLTK 454
Cdd:COG4098   251 IYLTATPSK-ALQrqvKRGKLKVVKLpARYHGhpLPVPKFKWLGNWKKrlrrgklPRKLLKWLKKRLKEGRQLLIFVPTI 329
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 455 RMAEELTKYLTKF--GIRTRYIHSDiDTlERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSlVAILDADKEGFLRShrS 532
Cdd:COG4098   330 ELLEQLVALLQKLfpEERIAGVHAE-DP-ERKEKVQAFRDGEIPILVTTTILERGVTFPNVD-VAVLGADHPVFTEA--A 404
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1559336361 533 LTQTAGRAARNI---HGKVIMYADKMTDSMKKTIdetsrrREIQ 573
Cdd:COG4098   405 LVQIAGRVGRSAdypTGEVIFFHHGKTRAMKRAI------REIK 442
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
420-542 2.63e-14

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: 69.84  E-value: 2.63e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 420 EIEVRPSLNQIDDLMAEIQKRiEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLV 499
Cdd:cd18787     4 LYVVVEEEEKKLLLLLLLLEK-LKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRVLV 82
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1559336361 500 GVNLLREGLDLPEVSLVAILDA--DKEGFLrsHRsltqtAGRAAR 542
Cdd:cd18787    83 ATDVAARGLDIPGVDHVINYDLprDAEDYV--HR-----IGRTGR 120
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
453-549 3.92e-13

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: 69.58  E-value: 3.92e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 453 TKRMAEELTKYLTKFGIrtryIHSDIDTLERV----EIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADKEGFLR 528
Cdd:cd18804   103 TERVEEELKTLFPEARI----ARIDRDTTRKKgaleKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNADSGLNSP 178
                          90       100
                  ....*....|....*....|....*....
gi 1559336361 529 SHRS-------LTQTAGRAAR-NIHGKVI 549
Cdd:cd18804   179 DFRAserafqlLTQVSGRAGRgDKPGKVI 207
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
440-542 1.38e-12

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 70.18  E-value: 1.38e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 440 RIEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVaI- 518
Cdd:COG0513   237 RDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHV-In 315
                          90       100
                  ....*....|....*....|....*.
gi 1559336361 519 --LDADKEGFLrsHRSltqtaGRAAR 542
Cdd:COG0513   316 ydLPEDPEDYV--HRI-----GRTGR 334
DEXDc smart00487
DEAD-like helicases superfamily;
3-90 2.73e-10

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 60.20  E-value: 2.73e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361    3 FEVVSPFQPTGDQPRAIESlskgILNNERYQTLLGVTGSGKTFTIANVV-----QNIQRPTIILAHNKTLAAQLYMEFKE 77
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEA----LLSGLRDVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKK 76
                           90
                   ....*....|...
gi 1559336361   78 FFPNNAVEYFVSY 90
Cdd:smart00487  77 LGPSLGLKVVGLY 89
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
433-666 5.80e-10

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 62.44  E-value: 5.80e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 433 LMAEIQKRIEE--DERVLVTTLTKRMAEELTKYLTKFGIRT-RYI-HSDIDTL------ERVEIMQDLRLGKFDVLVGVN 502
Cdd:COG1111   340 LREILKEQLGTnpDSRIIVFTQYRDTAEMIVEFLSEPGIKAgRFVgQASKEGDkgltqkEQIEILERFRAGEFNVLVATS 419
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 503 LLREGLDLPEVSLV--------AIldadkegflrshRSLtQTAGRAARNIHGKVIMYadkMTdsmKKTIDET----SRRR 570
Cdd:COG1111   420 VAEEGLDIPEVDLVifyepvpsEI------------RSI-QRKGRTGRKREGRVVVL---IA---KGTRDEAyywsSRRK 480
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 571 EIQNQFNID--HHITPKPLNKKITKISigdqEAAIETYnvkDDIKTAAEpsVQYNNENLEKIISKKQKEMEKAAKNLDFL 648
Cdd:COG1111   481 EKKMKSILKklKKLLDKQEKEKLKESA----QATLDEF---ESIKELAE--DEINEKDLDEIESSENGAHVDWREPVLLQ 551
                         250
                  ....*....|....*...
gi 1559336361 649 TAAKFRDEINELKETLNK 666
Cdd:COG1111   552 VIVSTLAESLELRELGEK 569
PRK13766 PRK13766
Hef nuclease; Provisional
425-634 4.17e-09

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 59.89  E-value: 4.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 425 PSLNQIDDLMAEIQKrIEEDERVLVTTLTKRMAEELTKYLTKFGIRT-RYI-HSDIDTL------ERVEIMQDLRLGKFD 496
Cdd:PRK13766  347 PKLEKLREIVKEQLG-KNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAvRFVgQASKDGDkgmsqkEQIEILDKFRAGEFN 425
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 497 VLVGVNLLREGLDLPEVSLV--------AIldadkegflrshRSLtQTAGRAARNIHGKVIMYadkMTdsmKKTIDET-- 566
Cdd:PRK13766  426 VLVSTSVAEEGLDIPSVDLVifyepvpsEI------------RSI-QRKGRTGRQEEGRVVVL---IA---KGTRDEAyy 486
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1559336361 567 --SRRRE--IQNQF-NIDHHITPKPLNKKITKISIGDQEAAIETYN--VKDDIKTAAEPSVQYNNENLEKIISKK 634
Cdd:PRK13766  487 wsSRRKEkkMKEELkNLKGILNKKLQELDEEQKGEEEEKDEQLSLDdfVKSKGKEEEEEEEKEEKDKETEEDEPE 561
PRK05580 PRK05580
primosome assembly protein PriA; Validated
453-549 4.83e-09

primosome assembly protein PriA; Validated


Pssm-ID: 235514 [Multi-domain]  Cd Length: 679  Bit Score: 59.40  E-value: 4.83e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 453 TKRMAEELTKYLTKFGIrTRYihsDIDTLERV----EIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADkeGFLR 528
Cdd:PRK05580  439 TERLEEELAELFPEARI-LRI---DRDTTRRKgaleQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDAD--LGLF 512
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1559336361 529 SH--RS-------LTQTAGRAAR-NIHGKVI 549
Cdd:PRK05580  513 SPdfRAsertfqlLTQVAGRAGRaEKPGEVL 543
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
423-550 5.05e-09

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


Pssm-ID: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 55.44  E-value: 5.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 423 VRPSLNQIDDLMAEIQKRIEE--DERVLVTTLTKRMAEELTKYLTKF--GIR-TRYI-HSDIDTL------ERVEIMQDL 490
Cdd:cd18801     7 IHPKLEKLEEIVKEHFKKKQEgsDTRVIIFSEFRDSAEEIVNFLSKIrpGIRaTRFIgQASGKSSkgmsqkEQKEVIEQF 86
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 491 RLGKFDVLVGVNLLREGLDLPEVSLVAILDADKegflrSHRSLTQTAGRAARNIHGKVIM 550
Cdd:cd18801    87 RKGGYNVLVATSIGEEGLDIGEVDLIICYDASP-----SPIRMIQRMGRTGRKRQGRVVV 141
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
33-99 2.18e-08

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


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 53.56  E-value: 2.18e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1559336361  33 QTLLGVTGSGKTFTIANVVqnIQR------PTIILAHNKTLAAQLYMEFKEFF-PNNAVEYFVSYYDYYQPEAF 99
Cdd:cd00046     4 VLITAPTGSGKTLAALLAA--LLLllkkgkKVLVLVPTKALALQTAERLRELFgPGIRVAVLVGGSSAEEREKN 75
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
422-542 2.51e-08

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 52.98  E-value: 2.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 422 EVRPSLNQIDDLMA-EIQKRIEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVG 500
Cdd:cd18794     7 SVRPKDKKDEKLDLlKRIKVEHLGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWLRDKIQVIVA 86
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1559336361 501 VNLLREGLDLPEVSLVAILDADK--EGFLrshrsltQTAGRAAR 542
Cdd:cd18794    87 TVAFGMGIDKPDVRFVIHYSLPKsmESYY-------QESGRAGR 123
ResIII pfam04851
Type III restriction enzyme, res subunit;
15-83 5.45e-08

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 52.67  E-value: 5.45e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1559336361  15 QPRAIESLSKGILNNERYQTLLGVTGSGKTFTIANVVQNIQ-----RPTIILAHNKTLAAQLYMEFKEFFPNNA 83
Cdd:pfam04851   8 QIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFkkgpiKKVLFLVPRKDLLEQALEEFKKFLPNYV 81
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
442-547 6.01e-08

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


Pssm-ID: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 51.41  E-value: 6.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 442 EEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSD-IDTLERVEIMQDL--RLGKFDVLVGVNLLREGLDLPEVSLVAi 518
Cdd:cd18799     4 YVEIKTLIFCVSIEHAEFMAEAFNEAGIDAVALNSDySDRERGDEALILLffGELKPPILVTVDLLTTGVDIPEVDNVV- 82
                          90       100       110
                  ....*....|....*....|....*....|..
gi 1559336361 519 ldadkegFLRSHRSLT---QTAGRAARNIHGK 547
Cdd:cd18799    83 -------FLRPTESRTlflQMLGRGLRLHEGK 107
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
440-570 9.62e-08

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: 51.88  E-value: 9.62e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 440 RIEEDERVLVTTLTKrMAEELTKYLTKFgiRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAIL 519
Cdd:cd18792    35 RIEESEKLDLKSIEA-LAEELKELVPEA--RVALLHGKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIE 111
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1559336361 520 DADKEGFLRSHrsltQTAGRAARnihGKVIMYADKMTDSmKKTIDETSRRR 570
Cdd:cd18792   112 DADRFGLSQLH----QLRGRVGR---GKHQSYCYLLYPD-PKKLTETAKKR 154
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
8-85 1.35e-07

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: 52.03  E-value: 1.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   8 PFQPTGDQPRAIESLSKGILNNERYQTLL-GVTGSGKT----FTIANVVQNiQRPTIILAHNKTLAAQLYMEFKEFFPNN 82
Cdd:cd17918    13 PFSLTKDQAQAIKDIEKDLHSPEPMDRLLsGDVGSGKTlvalGAALLAYKN-GKQVAILVPTEILAHQHYEEARKFLPFI 91

                  ...
gi 1559336361  83 AVE 85
Cdd:cd17918    92 NVE 94
PRK10689 PRK10689
transcription-repair coupling factor; Provisional
33-254 1.49e-07

transcription-repair coupling factor; Provisional


Pssm-ID: 182649 [Multi-domain]  Cd Length: 1147  Bit Score: 54.75  E-value: 1.49e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   33 QTLLG-VTGSGKTFTIANVVQNIQRPTIILAHNKTLAAQLYMEFKEFFPnnaveyfvsyydyyQPEAFMPTTNTYIEKDL 111
Cdd:PRK10689    16 QRQLGeLTGAACATEVAEIAERHAGPVVLIAPDMQNALRLHDEIQQFTD--------------QMVMNLADWETLPYDSF 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  112 SINENLEKLRLSASSALLSGRRDVLVVSsVSCLYGIGNPQEF-QKNLVALEVGQKITKTKLLQSLVSALYSRSEMNFGRG 190
Cdd:PRK10689    82 SPHQDIISSRLSTLYQLPTMQRGVLILP-VNTLMQRVCPHSFlHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHG 160
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1559336361  191 NFRVKGDVIDVFPAYSDTGIRIQLFGNEIDRIENVDYVSNNVIDSIENINIYPANLFVTSPDTL 254
Cdd:PRK10689   161 EYATRGALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAI 224
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
437-561 2.03e-07

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: 51.19  E-value: 2.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 437 IQKRIEEDERvlvttLTKRMAEELTKYLTKFgIRTRY----IHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPE 512
Cdd:cd18811    32 IYPLIEESEK-----LDLKAAVAMYEYLKER-FRPELnvglLHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPN 105
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1559336361 513 VSLVAILDADKEGFLRSHrsltQTAGRAARNIHGK--VIMYADKMTDSMKK 561
Cdd:cd18811   106 ATVMVIEDAERFGLSQLH----QLRGRVGRGDHQSycLLVYKDPLTETAKQ 152
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
453-549 2.33e-07

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


Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 53.97  E-value: 2.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 453 TKRMAEELTKYLTKFGIrTRYihsDIDTLERV----EIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADkEGF-- 526
Cdd:COG1198   490 TERVEEELAELFPDARV-LRM---DRDTTRRKgaleKLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVLDAD-LGLns 564
                          90       100       110
                  ....*....|....*....|....*....|
gi 1559336361 527 --LRSH-RS---LTQTAGRAAR-NIHGKVI 549
Cdd:COG1198   565 pdFRAAeRTfqlLTQVAGRAGRaEKPGEVL 594
UVR pfam02151
UvrB/uvrC motif;
628-662 3.19e-07

UvrB/uvrC motif;


Pssm-ID: 308001 [Multi-domain]  Cd Length: 36  Bit Score: 47.01  E-value: 3.19e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1559336361 628 EKIISKKQKEMEKAAKNLDFLTAAKFRDEINELKE 662
Cdd:pfam02151   1 KKLIKELEEEMEEAAENEDFEKAAKLRDQINALKK 35
DEAD-like_helicase_C cd09300
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ...
497-552 1.02e-06

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


Pssm-ID: 350171 [Multi-domain]  Cd Length: 59  Bit Score: 46.39  E-value: 1.02e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1559336361 497 VLVGVNLLREGLDLPEVSLVAILDADkegflRSHRSLTQTAGRAARN-IHGKVIMYA 552
Cdd:cd09300     8 VLIAVN*ALTGFDAPELNTIIVDKNL-----RSYRGLNQAFGRANRIyTFGGIVTYR 59
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
435-542 2.54e-06

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: 47.63  E-value: 2.54e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 435 AEIQKRIEEDERVLVTTLTKRMAEELTKyltKFGIRtrYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVS 514
Cdd:cd18789    40 EELLKRHEQGDKIIVFTDNVEALYRYAK---RLLKP--FITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEAN 114
                          90       100
                  ....*....|....*....|....*...
gi 1559336361 515 lVAILDADKEGflrSHRSLTQTAGRAAR 542
Cdd:cd18789   115 -VAIQISGHGG---SRRQEAQRLGRILR 138
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
446-551 6.53e-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: 6.53e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 446 RVLVTTLTKRMAEELTKYLTkfgirtryihsdidtlerveimqdlrlgkfdVLVGVNLLREGLDLPEVSLVAILDADkeg 525
Cdd:cd18785     5 KIIVFTNSIEHAEEIASSLE-------------------------------ILVATNVLGEGIDVPSLDTVIFFDPP--- 50
                          90       100
                  ....*....|....*....|....*...
gi 1559336361 526 flRSHRSLTQTAGRAARN--IHGKVIMY 551
Cdd:cd18785    51 --SSAASYIQRVGRAGRGgkDEGEVILF 76
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
440-570 8.19e-06

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


Pssm-ID: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 46.18  E-value: 8.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 440 RIEEDERVlvttltKRMAEELTKYLtkfgiRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAIL 519
Cdd:cd18810    34 RIESIEKL------ATQLRQLVPEA-----RIAIAHGQMTENELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIIE 102
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1559336361 520 DADKEGFLRSHrsltQTAGRAARnihGKVIMYADKMTDSMKKtIDETSRRR 570
Cdd:cd18810   103 RADKFGLAQLY----QLRGRVGR---SKERAYAYFLYPDQKK-LTEDALKR 145
DEAD-like_helicase_N cd17912
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
33-94 1.46e-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: 43.66  E-value: 1.46e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1559336361  33 QTLLGVTGSGKTFTIANVV---QNIQRPTIILAHNKTLAAQLYMEFKEFFPNNAVEYFVSYYDYY 94
Cdd:cd17912     2 ILHLGPTGSGKTLVAIQKIasaMSSGKSVLVVTPTKLLAHEILIVIDEIQ*ILDPAAGWAWATRA 66
PTZ00424 PTZ00424
helicase 45; Provisional
453-577 2.31e-04

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 44.05  E-value: 2.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 453 TKRMAEELTKYLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILD--ADKEGFLrsH 530
Cdd:PTZ00424  276 TRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDlpASPENYI--H 353
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1559336361 531 RslTQTAGRAARNihGKVIMYAdkmtdsmkkTIDETSRRREIQNQFN 577
Cdd:PTZ00424  354 R--IGRSGRFGRK--GVAINFV---------TPDDIEQLKEIERHYN 387
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
415-542 5.38e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 42.82  E-value: 5.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 415 GLLDPEIEV----RPSLN------QIDDLMAEIQKRIEE--DERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDTLE 482
Cdd:COG0514   189 GLEDPRVFVgsfdRPNLRlevvpkPPDDKLAQLLDFLKEhpGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEE 268
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1559336361 483 RVEIMQDLRLGKFDVLV-----GVnllreGLDLPEVSLVAILDADK--EGFLrshrsltQTAGRAAR 542
Cdd:COG0514   269 REANQDRFLRDEVDVIVatiafGM-----GIDKPDVRFVIHYDLPKsiEAYY-------QEIGRAGR 323
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
402-542 5.65e-04

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 43.01  E-value: 5.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 402 SEGV--FVEQIirptgLLDP-EIEVRPS------LNQ----IDD------LMAEIQKRiEEDERVLVTTLTKRMAEELTK 462
Cdd:PRK11192  190 GDAVqdFAERL-----LNDPvEVEAEPSrrerkkIHQwyyrADDlehktaLLCHLLKQ-PEVTRSIVFVRTRERVHELAG 263
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 463 YLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDADKEGFLRSHRsltqtAGRAAR 542
Cdd:PRK11192  264 WLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHR-----IGRTGR 338
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
15-83 6.72e-04

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 41.01  E-value: 6.72e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1559336361  15 QPRAIESLSKGILNNERYQTLLGVTGSGKTFTIANVVQNIQRPT-----IILAHNKTLAAQLYMEFKEFFPNNA 83
Cdd:cd18032     5 QQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANrkkriLFLAHREELLEQAERSFKEVLPDGS 78
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
626-666 7.19e-04

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


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 42.80  E-value: 7.19e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1559336361 626 NLEKIISKKQKEMEKAAKNLDFLTAAKFRDEINELKETLNK 666
Cdd:COG0322   200 KTKELIKELEEKMEEAAEELEFERAARLRDQIRALEKVQEK 240
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
430-548 7.70e-04

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


Pssm-ID: 350183 [Multi-domain]  Cd Length: 150  Bit Score: 40.33  E-value: 7.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 430 IDDLMAEIQKRIEEDERVLVTTLTKRMAEELTKYL------TKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNL 503
Cdd:cd18796    24 GADAYAEVIFLLERHKSTLVFTNTRSQAERLAQRLrelcpdRVPPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSS 103
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1559336361 504 LREGLDLPEVSLVAILDADKegflrSHRSLTQTAGRAARNIHGKV 548
Cdd:cd18796   104 LELGIDIGDVDLVIQIGSPK-----SVARLLQRLGRSGHRPGAAS 143
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
19-87 7.73e-04

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


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 40.37  E-value: 7.73e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1559336361  19 IESLSKgILNNERYQTLLGV--TGSGKTFTIANVVQNI-QRPTIILAHNKTLAAQLYMEFKEFFPNNAVEYF 87
Cdd:cd17926     6 EEALEA-WLAHKNNRRGILVlpTGSGKTLTALALIAYLkELRTLIVVPTDALLDQWKERFEDFLGDSSIGLI 76
PRK10590 PRK10590
ATP-dependent RNA helicase RhlE; Provisional
445-516 8.42e-04

ATP-dependent RNA helicase RhlE; Provisional


Pssm-ID: 236722 [Multi-domain]  Cd Length: 456  Bit Score: 42.49  E-value: 8.42e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1559336361 445 ERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLV 516
Cdd:PRK10590  246 QQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHV 317
uvrC PRK00558
excinuclease ABC subunit UvrC;
628-666 8.92e-04

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 42.41  E-value: 8.92e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1559336361 628 EKIISKKQKEMEKAAKNLDFLTAAKFRDEINELKETLNK 666
Cdd:PRK00558  201 DEVLKELEEKMEEASENLEFERAARYRDQIQALRRVQEK 239
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
8-81 9.84e-04

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 42.44  E-value: 9.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   8 PFQPTGDQPRAIESLSKGILNNERYQTLL-GVTGSGKT----FTIANVVQNIQR-----PTIIlahnktLAAQLYMEFKE 77
Cdd:PRK10917  259 PFELTGAQKRVVAEILADLASPKPMNRLLqGDVGSGKTvvaaLAALAAIEAGYQaalmaPTEI------LAEQHYENLKK 332

                  ....
gi 1559336361  78 FFPN 81
Cdd:PRK10917  333 LLEP 336
DEXHc_RecG cd17992
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ...
2-81 2.38e-03

DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. It is a member 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: 350750 [Multi-domain]  Cd Length: 225  Bit Score: 39.82  E-value: 2.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361   2 KFEVVSPFQPTGDQPRAIESLSKGILNNERYQTLL-GVTGSGKT----FTIANVVQN-----IQRPTIILAHnktlaaQL 71
Cdd:cd17992    37 KFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLqGDVGSGKTvvaaLAMLAAVENgyqvaLMAPTEILAE------QH 110
                          90
                  ....*....|
gi 1559336361  72 YMEFKEFFPN 81
Cdd:cd17992   111 YDSLKKLLEP 120
SF2_C_reverse_gyrase cd18798
C-terminal helicase domain of the reverse gyrase; Reverse gyrase modifies the topological ...
418-518 2.59e-03

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: 39.21  E-value: 2.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 418 DPEIEVRPSLNQIddlmAEIQKRIEEDERVLVTT-LTKRMAEELTKYLTKFGIRTRYIHSDidtleRVEIMQDLRLGKFD 496
Cdd:cd18798     4 DVYIEDSDSLEKL----LELVKKLGDGGLIFVSIdYGKEYAEELKEFLERHGIKAELALSS-----TEKNLEKFEEGEID 74
                          90       100
                  ....*....|....*....|....*.
gi 1559336361 497 VLVGV----NLLREGLDLPEVSLVAI 518
Cdd:cd18798    75 VLIGVasyyGVLVRGIDLPERIKYAI 100
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
12-79 3.42e-03

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 38.76  E-value: 3.42e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1559336361  12 TGDQPRAIESLSKG--ILnneryqtLLGVTGSGKT--FTIAnVVQNIQRP-----TIILAHNKTLAAQLYMEFKEFF 79
Cdd:pfam00270   1 TPIQAEAIPAILEGrdVL-------VQAPTGSGKTlaFLLP-ALEALDKLdngpqALVLAPTRELAEQIYEELKKLG 69
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
457-542 3.48e-03

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 40.54  E-value: 3.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 457 AEELTKYLTKF-GIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILDadkegFLRSHRSLTQ 535
Cdd:PLN00206  380 ADLLANAITVVtGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFD-----MPNTIKEYIH 454

                  ....*..
gi 1559336361 536 TAGRAAR 542
Cdd:PLN00206  455 QIGRASR 461
DEADc_DDX52 cd17957
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ...
10-78 3.72e-03

DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 is a member of the DEAD-box 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: 350715 [Multi-domain]  Cd Length: 198  Bit Score: 39.11  E-value: 3.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361  10 QPTGDQPRAIESLSKGIlnneryqTLLGV--TGSGKT--FTIAnVVQNIQRP-------TIILAHNKTLAAQLYMEFKEF 78
Cdd:cd17957    12 EPTPIQMQAIPILLHGR-------DLLACapTGSGKTlaFLIP-ILQKLGKPrkkkglrALILAPTRELASQIYRELLKL 83
PTZ00110 PTZ00110
helicase; Provisional
420-516 5.18e-03

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 39.76  E-value: 5.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 420 EIEVRPSLNQIDDLMAEIQKRIEEDERVLVTTLTKRMAEELTKYLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLV 499
Cdd:PTZ00110  353 EVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMI 432
                          90
                  ....*....|....*..
gi 1559336361 500 GVNLLREGLDLPEVSLV 516
Cdd:PTZ00110  433 ATDVASRGLDVKDVKYV 449
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
453-542 7.92e-03

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 39.45  E-value: 7.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 453 TKRMAEELTKYLTKFGIRTRYIHSDIDTLERVEIMQDLRLGKFDVLVGVNLLREGLDLPEVSLVAILD--ADKEGFLrsH 530
Cdd:PRK11634  254 TKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDipMDSESYV--H 331
                          90
                  ....*....|...
gi 1559336361 531 R-SLTQTAGRAAR 542
Cdd:PRK11634  332 RiGRTGRAGRAGR 344
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
440-522 8.32e-03

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


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 39.26  E-value: 8.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 440 RIEEDERVLVTTLTKRmAEELTKYLTkfGIRTRYIHSDIDTLERVEIMQDLRLGKFDVL-------VGVnllreglDLPE 512
Cdd:COG1200   478 LIEESEKLDLQAAEET-YEELREAFP--GLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLvattvieVGV-------DVPN 547
                          90
                  ....*....|
gi 1559336361 513 VSLVAILDAD 522
Cdd:COG1200   548 ATVMVIENAE 557
DDXDc_reverse_gyrase cd17924
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ...
450-532 9.00e-03

DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350682 [Multi-domain]  Cd Length: 189  Bit Score: 37.69  E-value: 9.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559336361 450 TTLTKRMAEELTKYLTKFGIRTR--YIHSDIDTLERVEIMQDLRLGKFDVLVGVN-LLREGLDL---PEVSLVAILDADk 523
Cdd:cd17924    70 KSLVKQAYERLSKYAEKAGVEVKilVYHSRLKKKEKEELLEKIEKGDFDILVTTNqFLSKNFDLlsnKKFDFVFVDDVD- 148

                  ....*....
gi 1559336361 524 eGFLRSHRS 532
Cdd:cd17924   149 -AVLKSSKN 156
 
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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