NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|502824756|ref|WP_013059732|]
View 

MULTISPECIES: excinuclease ABC subunit UvrB [Priestia]

Protein Classification

excinuclease ABC subunit UvrB( domain architecture ID 11426127)

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

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
4-658 0e+00

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


:

Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1386.65  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   4 QFELVSPYQPQGDQPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTMSNVIKEINKPTLIMAHNKTLAGQLYSEFKEFFPN 83
Cdd:COG0556    1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  84 NAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSSLFERKDVIIIASVSCIYGLGSPEEYKEMVVSLRV 163
Cdd:COG0556   81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 164 GMEKERNQLLRTLVDVQYERNDIDFKRGTFRVRGDVVEIFPVSRDEHCIRVEFFGDEIDRIREVDALTGEIIGDREHVAI 243
Cdd:COG0556  161 GEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTI 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 244 FPASHFVTREEKMRVAIQNIEKELEEQLEKLKEAGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPAGSTPY 323
Cdd:COG0556  241 YPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPP 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 324 TLLDFFPEDFLLVVDESHVTIPQVRGMYNGDQARKQVLVDHGFRLPSALDNRPLKFDEFEQHINQIVHVSATPGPYELEK 403
Cdd:COG0556  321 TLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEK 400

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 404 APDVI-EQIIRPTGLLDPNIEVRPIEGQIDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTL 482
Cdd:COG0556  401 SGGQVvEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTL 480

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 483 ERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADRITNSMDI 562
Cdd:COG0556  481 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQR 560

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 563 AINETKRRRSIQEAYNEEHGITPTTIQKEVRGSIRATVVAEDTETYEEA-PAFDKLNKKEKAKLVEEMEQEMKEAAKALN 641
Cdd:COG0556  561 AIDETNRRREIQEAYNEEHGITPQTIKKSIRDILEGTYEADEETEELVAeADAAKLSKEELEKLIKELEKEMKEAAKNLE 640

                        650
                 ....*....|....*..
gi 502824756 642 FERAAELRDLILELKAE 658
Cdd:COG0556  641 FEEAARLRDEIKELKKE 657
 
Name Accession Description Interval E-value
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
4-658 0e+00

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


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1386.65  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   4 QFELVSPYQPQGDQPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTMSNVIKEINKPTLIMAHNKTLAGQLYSEFKEFFPN 83
Cdd:COG0556    1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  84 NAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSSLFERKDVIIIASVSCIYGLGSPEEYKEMVVSLRV 163
Cdd:COG0556   81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 164 GMEKERNQLLRTLVDVQYERNDIDFKRGTFRVRGDVVEIFPVSRDEHCIRVEFFGDEIDRIREVDALTGEIIGDREHVAI 243
Cdd:COG0556  161 GEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTI 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 244 FPASHFVTREEKMRVAIQNIEKELEEQLEKLKEAGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPAGSTPY 323
Cdd:COG0556  241 YPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPP 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 324 TLLDFFPEDFLLVVDESHVTIPQVRGMYNGDQARKQVLVDHGFRLPSALDNRPLKFDEFEQHINQIVHVSATPGPYELEK 403
Cdd:COG0556  321 TLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEK 400

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 404 APDVI-EQIIRPTGLLDPNIEVRPIEGQIDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTL 482
Cdd:COG0556  401 SGGQVvEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTL 480

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 483 ERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADRITNSMDI 562
Cdd:COG0556  481 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQR 560

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 563 AINETKRRRSIQEAYNEEHGITPTTIQKEVRGSIRATVVAEDTETYEEA-PAFDKLNKKEKAKLVEEMEQEMKEAAKALN 641
Cdd:COG0556  561 AIDETNRRREIQEAYNEEHGITPQTIKKSIRDILEGTYEADEETEELVAeADAAKLSKEELEKLIKELEKEMKEAAKNLE 640

                        650
                 ....*....|....*..
gi 502824756 642 FERAAELRDLILELKAE 658
Cdd:COG0556  641 FEEAARLRDEIKELKKE 657
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
1-658 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1362.04  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   1 MKDQFELVSPYQPQGDQPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTMSNVIKEINKPTLIMAHNKTLAGQLYSEFKEF 80
Cdd:PRK05298   1 MMKPFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  81 FPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSSLFERKDVIIIASVSCIYGLGSPEEYKEMVVS 160
Cdd:PRK05298  81 FPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 161 LRVGMEKERNQLLRTLVDVQYERNDIDFKRGTFRVRGDVVEIFPVSRDEHCIRVEFFGDEIDRIREVDALTGEIIGDREH 240
Cdd:PRK05298 161 LRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDR 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 241 VAIFPASHFVTREEKMRVAIQNIEKELEEQLEKLKEAGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPAGS 320
Cdd:PRK05298 241 VTIYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGE 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 321 TPYTLLDFFPEDFLLVVDESHVTIPQVRGMYNGDQARKQVLVDHGFRLPSALDNRPLKFDEFEQHINQIVHVSATPGPYE 400
Cdd:PRK05298 321 PPYTLLDYFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYE 400

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 401 LEKAPD-VIEQIIRPTGLLDPNIEVRPIEGQIDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEV 479
Cdd:PRK05298 401 LEKSGGvVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDI 480

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 480 KTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADRITNS 559
Cdd:PRK05298 481 DTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDS 560

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 560 MDIAINETKRRRSIQEAYNEEHGITPTTIQKEVRGSIRATVVAedtetyeeapafDKLNKKEKAKLVEEMEQEMKEAAKA 639
Cdd:PRK05298 561 MQKAIDETERRREIQIAYNEEHGITPKTIKKKIRDILDSVYKK------------DKLSKKELEKLIKELEKQMKEAAKN 628

                        650
                 ....*....|....*....
gi 502824756 640 LNFERAAELRDLILELKAE 658
Cdd:PRK05298 629 LEFEEAARLRDEIKELKEE 647
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
 4-656 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: 1190.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756    4 QFELVSPYQPQGDQPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTMSNVIKEINKPTLIMAHNKTLAGQLYSEFKEFFPN 83
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   84 NAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSSLFERKDVIIIASVSCIYGLGSPEEYKEMVVSLRV 163
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  164 GMEKERNQLLRTLVDVQYERNDIDFKRGTFRVRGDVVEIFPVSRDEHCIRVEFFGDEIDRIREVDALTGEIIGDREHVAI 243
Cdd:TIGR00631 161 GKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDEFAVRIEFFGDEIERISRVDPLTGEVLRELDSFTI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  244 FPASHFVTREEKMRVAIQNIEKELEEQLEKLKEAGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPAGSTPY 323
Cdd:TIGR00631 241 FPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPPY 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  324 TLLDFFPEDFLLVVDESHVTIPQVRGMYNGDQARKQVLVDHGFRLPSALDNRPLKFDEFEQHINQIVHVSATPGPYELEK 403
Cdd:TIGR00631 321 TLLDYFPDDFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELEQ 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  404 APDVIEQIIRPTGLLDPNIEVRPIEGQIDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTLE 483
Cdd:TIGR00631 401 SGNVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLE 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  484 RIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADRITNSMDIA 563
Cdd:TIGR00631 481 RVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQKA 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  564 INETKRRRSIQEAYNEEHGITPTTIQKEVRGSIRATVVAEDTETYEE--APAFDKLNKKEKAKLVEEMEQEMKEAAKALN 641
Cdd:TIGR00631 561 IEETERRRKIQMAYNEEHGITPQTIRKPIRDILDIELKEKEDAAKKKkkGEDLSDLSKKELKKLIKQLEKEMKQAARNLE 640

                         650
                  ....*....|....*
gi 502824756  642 FERAAELRDLILELK 656
Cdd:TIGR00631 641 FEEAARLRDEILELK 655
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
 5-413 0e+00

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


Pssm-ID: 350674 [Multi-domain]  Cd Length: 299  Bit Score: 561.45  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   5 FELVSPYQPQGDQPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTMSNVIKEINKPTLIMAHNKTLAGQLYSEFKEFFPNN 84
Cdd:cd17916    1 FKLVSPFKPAGDQPQAIAKLVEGLKRGVKFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  85 AVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSSLFERKDVIIIASVSCIYglgspeeykemvvslrvg 164
Cdd:cd17916   81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLERRDVIVVASVSCIY------------------ 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 165 mekernqlLRTLVDVQYERNDidfkrgtfrvrgdvveifpvsrdehciRVEFFGDEidrirevdaltgeiigdrehvaif 244
Cdd:cd17916  143 --------ERAIKSIEEELEE---------------------------RLKYFRAQ------------------------ 163

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 245 pashfvtreekmrvaiqniekeleeqleklkeaGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPAGSTPYT 324
Cdd:cd17916  164 ---------------------------------GKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 325 LLDFFPEDFLLVVDESHVTIPQVRGMYNGDQARKQVLVDHGFRLPSALDNRPLKFDEFEQHINQIVHVSATPGPYELEKA 404
Cdd:cd17916  211 LLDYFPDDFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEHS 290


                 ....*....
gi 502824756 405 PDVIEQIIR 413
Cdd:cd17916  291 GQVVEQIIR 299
UvrB_inter pfam17757
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ...
 159-249 8.58e-45

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: 154.47  E-value: 8.58e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  159 VSLRVGMEKERNQLLRTLVDVQYERNDIDFKRGTFRVRGDVVEIFPVSRDEHCIRVEFFGDEIDRIREVDALTGEIIGDR 238
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80

                          90
                  ....*....|.
gi 502824756  239 EHVAIFPASHF 249
Cdd:pfam17757  81 DEVTIYPASHY 91
HELICc smart00490
helicase superfamily c-terminal domain;
459-543 1.11e-18

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 80.72  E-value: 1.11e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   459 EDLTNYLKEIGIKVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADkegflRSERSLIQTI 538
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-----WSPASYIQRI 75


                   ....*
gi 502824756   539 GRAAR 543
Cdd:smart00490  76 GRAGR 80
 
Name Accession Description Interval E-value
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
4-658 0e+00

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


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 1386.65  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   4 QFELVSPYQPQGDQPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTMSNVIKEINKPTLIMAHNKTLAGQLYSEFKEFFPN 83
Cdd:COG0556    1 PFKLVSPYKPAGDQPQAIEKLVEGIEAGEKHQTLLGVTGSGKTFTMANVIERVQRPTLVLAHNKTLAAQLYGEFKEFFPN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  84 NAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSSLFERKDVIIIASVSCIYGLGSPEEYKEMVVSLRV 163
Cdd:COG0556   81 NAVEYFVSYYDYYQPEAYVPSTDTYIEKDSSINEEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLSLRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 164 GMEKERNQLLRTLVDVQYERNDIDFKRGTFRVRGDVVEIFPVSRDEHCIRVEFFGDEIDRIREVDALTGEIIGDREHVAI 243
Cdd:COG0556  161 GEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTI 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 244 FPASHFVTREEKMRVAIQNIEKELEEQLEKLKEAGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPAGSTPY 323
Cdd:COG0556  241 YPASHYVTPRERLERAIESIKEELEERLAEFESEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGEPPP 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 324 TLLDFFPEDFLLVVDESHVTIPQVRGMYNGDQARKQVLVDHGFRLPSALDNRPLKFDEFEQHINQIVHVSATPGPYELEK 403
Cdd:COG0556  321 TLLDYFPDDFLLFIDESHVTVPQIRGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEARVPQTIYVSATPGDYELEK 400

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 404 APDVI-EQIIRPTGLLDPNIEVRPIEGQIDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTL 482
Cdd:COG0556  401 SGGQVvEQIIRPTGLLDPEIEVRPTKGQVDDLLGEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTL 480

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 483 ERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADRITNSMDI 562
Cdd:COG0556  481 ERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQR 560

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 563 AINETKRRRSIQEAYNEEHGITPTTIQKEVRGSIRATVVAEDTETYEEA-PAFDKLNKKEKAKLVEEMEQEMKEAAKALN 641
Cdd:COG0556  561 AIDETNRRREIQEAYNEEHGITPQTIKKSIRDILEGTYEADEETEELVAeADAAKLSKEELEKLIKELEKEMKEAAKNLE 640

                        650
                 ....*....|....*..
gi 502824756 642 FERAAELRDLILELKAE 658
Cdd:COG0556  641 FEEAARLRDEIKELKKE 657
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
1-658 0e+00

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 1362.04  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   1 MKDQFELVSPYQPQGDQPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTMSNVIKEINKPTLIMAHNKTLAGQLYSEFKEF 80
Cdd:PRK05298   1 MMKPFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNKTLAAQLYSEFKEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  81 FPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSSLFERKDVIIIASVSCIYGLGSPEEYKEMVVS 160
Cdd:PRK05298  81 FPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRHSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 161 LRVGMEKERNQLLRTLVDVQYERNDIDFKRGTFRVRGDVVEIFPVSRDEHCIRVEFFGDEIDRIREVDALTGEIIGDREH 240
Cdd:PRK05298 161 LRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDR 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 241 VAIFPASHFVTREEKMRVAIQNIEKELEEQLEKLKEAGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPAGS 320
Cdd:PRK05298 241 VTIYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLDGRKPGE 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 321 TPYTLLDFFPEDFLLVVDESHVTIPQVRGMYNGDQARKQVLVDHGFRLPSALDNRPLKFDEFEQHINQIVHVSATPGPYE 400
Cdd:PRK05298 321 PPYTLLDYFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYE 400

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 401 LEKAPD-VIEQIIRPTGLLDPNIEVRPIEGQIDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEV 479
Cdd:PRK05298 401 LEKSGGvVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDI 480

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 480 KTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADRITNS 559
Cdd:PRK05298 481 DTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDS 560

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 560 MDIAINETKRRRSIQEAYNEEHGITPTTIQKEVRGSIRATVVAedtetyeeapafDKLNKKEKAKLVEEMEQEMKEAAKA 639
Cdd:PRK05298 561 MQKAIDETERRREIQIAYNEEHGITPKTIKKKIRDILDSVYKK------------DKLSKKELEKLIKELEKQMKEAAKN 628

                        650
                 ....*....|....*....
gi 502824756 640 LNFERAAELRDLILELKAE 658
Cdd:PRK05298 629 LEFEEAARLRDEIKELKEE 647
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
 4-656 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: 1190.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756    4 QFELVSPYQPQGDQPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTMSNVIKEINKPTLIMAHNKTLAGQLYSEFKEFFPN 83
Cdd:TIGR00631   1 LFKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKTLAAQLYNEFKEFFPE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   84 NAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSSLFERKDVIIIASVSCIYGLGSPEEYKEMVVSLRV 163
Cdd:TIGR00631  81 NAVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  164 GMEKERNQLLRTLVDVQYERNDIDFKRGTFRVRGDVVEIFPVSRDEHCIRVEFFGDEIDRIREVDALTGEIIGDREHVAI 243
Cdd:TIGR00631 161 GKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDEFAVRIEFFGDEIERISRVDPLTGEVLRELDSFTI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  244 FPASHFVTREEKMRVAIQNIEKELEEQLEKLKEAGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPAGSTPY 323
Cdd:TIGR00631 241 FPASHYVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRAPGEPPY 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  324 TLLDFFPEDFLLVVDESHVTIPQVRGMYNGDQARKQVLVDHGFRLPSALDNRPLKFDEFEQHINQIVHVSATPGPYELEK 403
Cdd:TIGR00631 321 TLLDYFPDDFLLVIDESHVTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATPGPYELEQ 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  404 APDVIEQIIRPTGLLDPNIEVRPIEGQIDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTLE 483
Cdd:TIGR00631 401 SGNVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLE 480

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  484 RIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADRITNSMDIA 563
Cdd:TIGR00631 481 RVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQKA 560

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  564 INETKRRRSIQEAYNEEHGITPTTIQKEVRGSIRATVVAEDTETYEE--APAFDKLNKKEKAKLVEEMEQEMKEAAKALN 641
Cdd:TIGR00631 561 IEETERRRKIQMAYNEEHGITPQTIRKPIRDILDIELKEKEDAAKKKkkGEDLSDLSKKELKKLIKQLEKEMKQAARNLE 640

                         650
                  ....*....|....*
gi 502824756  642 FERAAELRDLILELK 656
Cdd:TIGR00631 641 FEEAARLRDEILELK 655
DEXHc_UvrB cd17916
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ...
 5-413 0e+00

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


Pssm-ID: 350674 [Multi-domain]  Cd Length: 299  Bit Score: 561.45  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   5 FELVSPYQPQGDQPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTMSNVIKEINKPTLIMAHNKTLAGQLYSEFKEFFPNN 84
Cdd:cd17916    1 FKLVSPFKPAGDQPQAIAKLVEGLKRGVKFQTLLGVTGSGKTFTIANVIAQVNKPTLVIAHNKTLAAQLYSEFKEFFPEN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  85 AVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSSLFERKDVIIIASVSCIYglgspeeykemvvslrvg 164
Cdd:cd17916   81 AVEYFVSYYDYYQPEAYVPQTDTYIEKDASINDEIDRLRHSATRSLLERRDVIVVASVSCIY------------------ 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 165 mekernqlLRTLVDVQYERNDidfkrgtfrvrgdvveifpvsrdehciRVEFFGDEidrirevdaltgeiigdrehvaif 244
Cdd:cd17916  143 --------ERAIKSIEEELEE---------------------------RLKYFRAQ------------------------ 163

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 245 pashfvtreekmrvaiqniekeleeqleklkeaGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPAGSTPYT 324
Cdd:cd17916  164 ---------------------------------GKLLEAQRLEQRTRYDLEMLREMGFCSGIENYSRHLSGRKPGEPPYT 210

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 325 LLDFFPEDFLLVVDESHVTIPQVRGMYNGDQARKQVLVDHGFRLPSALDNRPLKFDEFEQHINQIVHVSATPGPYELEKA 404
Cdd:cd17916  211 LLDYFPDDFLLVIDESHVTVPQLRGMYNGDRSRKQSLVDYGFRLPSALDNRPLKFEEFEEKVNQVIYVSATPGDYELEHS 290


                 ....*....
gi 502824756 405 PDVIEQIIR 413
Cdd:cd17916  291 GQVVEQIIR 299
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 419-588 2.88e-112

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: 334.60  E-value: 2.88e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 419 DPNIEVRPIEGQIDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTLERIEIIRELRLGKYDV 498
Cdd:cd18790    1 DPEIEVRPTEGQVDDLLGEIRKRVARGERVLVTTLTKRMAEDLTEYLQELGVKVRYLHSEIDTLERVEIIRDLRLGEFDV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 499 LVGINLLREGLDIPEVSLVTILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADRITNSMDIAINETKRRRSIQEAYN 578
Cdd:cd18790   81 LVGINLLREGLDLPEVSLVAILDADKEGFLRSETSLIQTIGRAARNVNGKVILYADKITDSMQKAIEETERRREIQMEYN 160

                        170
                 ....*....|
gi 502824756 579 EEHGITPTTI 588
Cdd:cd18790  161 EEHGITPKTI 170
UvrB_inter pfam17757
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ...
 159-249 8.58e-45

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: 154.47  E-value: 8.58e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  159 VSLRVGMEKERNQLLRTLVDVQYERNDIDFKRGTFRVRGDVVEIFPVSRDEHCIRVEFFGDEIDRIREVDALTGEIIGDR 238
Cdd:pfam17757   1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80

                          90
                  ....*....|.
gi 502824756  239 EHVAIFPASHF 249
Cdd:pfam17757  81 DEVTIYPASHY 91
Mfd COG1197
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ...
 31-523 1.78e-43

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


Pssm-ID: 440810 [Multi-domain]  Cd Length: 1130  Bit Score: 168.32  E-value: 1.78e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   31 GKQHQVLLGATGTGKTFTMSNVIKEINKPTLIMAHNKTLAGQLYSEFKEFFPNNAVEYFvsyydyyqpeayvPQTDTFIE 110
Cdd:COG1197     1 GGGRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLPDLPVLLF-------------PAWETLPY 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  111 KDASINDEIDKLRHSATSSLFERKDVIIIASV-SCIYGLGSPEEYKEMVVSLRVGMEKERNQLLRTLVDVQYERNDIDFK 189
Cdd:COG1197    68 DRFSPSPDIVSERLATLRRLASGKPGIVVTPVrALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEE 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  190 RGTFRVRGDVVEIFPVSrDEHCIRVEFFGDEIDRIREVDALTGEIIGDREHVAIFPASHFVTREEKMRVAIQNIEkelee 269
Cdd:COG1197   148 PGEFAVRGGILDIFPPG-SEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLR----- 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  270 qleklkeagkllEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPAgstpyTLLDFFPEDFLLVVDESHVTIPQVRG 349
Cdd:COG1197   222 ------------ELFGLDPKLDELYEALSEGIAFAGIEYYLPLFYEELA-----TLFDYLPEDALVVLDEPERIEEAAEE 284

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  350 MYNGDQARKQVLVDHGFRLPSALDNRPLKFDEFEQHINQIVHVSATPGPyELEKAPDVIEQIIRPtglldpnieVRPIEG 429
Cdd:COG1197   285 FWEEIEERYEARRHDRGRPLLPPEELFLDPEELFAALKRRPRVTLSPFA-ALPEGAGVVNLGARP---------LPSFAG 354

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  430 QIDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYlhsevktlerIEIIRELRLGKYDVLVGInlLREGL 509
Cdd:COG1197   355 QLEALLEELKRLLKDGGRVLLAAESEGRRERLLELLRDHGIPARL----------VESLAELSPGGVAITVGP--LEHGF 422

                         490
                  ....*....|....
gi 502824756  510 DIPEVSLVTILDAD 523
Cdd:COG1197   423 ELPDAKLAVITESE 436
UvrB pfam12344
Ultra-violet resistance protein B; This domain family is found in bacteria, archaea and ...
 551-593 5.66e-23

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


Pssm-ID: 463540 [Multi-domain]  Cd Length: 43  Bit Score: 91.68  E-value: 5.66e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 502824756  551 MYADRITNSMDIAINETKRRRSIQEAYNEEHGITPTTIQKEVR 593
Cdd:pfam12344   1 LYADKITDSMQRAIDETERRREIQEAYNEEHGITPKTIKKKIR 43
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 429-543 3.82e-19

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


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 83.03  E-value: 3.82e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  429 GQIDDLIGEIHDriKRNERVLVTTLTKKMSeDLTNYLKEIGIKVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREG 508
Cdd:pfam00271   1 EKLEALLELLKK--ERGGKVLIFSQTKKTL-EAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERG 77

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 502824756  509 LDIPEVSLVTILDADKegflrSERSLIQTIGRAAR 543
Cdd:pfam00271  78 LDLPDVDLVINYDLPW-----NPASYIQRIGRAGR 107
HELICc smart00490
helicase superfamily c-terminal domain;
459-543 1.11e-18

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 80.72  E-value: 1.11e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   459 EDLTNYLKEIGIKVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADkegflRSERSLIQTI 538
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-----WSPASYIQRI 75


                   ....*
gi 502824756   539 GRAAR 543
Cdd:smart00490  76 GRAGR 80
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 414-569 1.86e-17

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: 85.31  E-value: 1.86e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 414 PTGLLDPNIEVRPIEGQI-DDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEI--GIKVQYLHSEVKtlERIEIIRE 490
Cdd:COG4098  287 PKFKWLGNWKKRLRRGKLpRKLLKWLKKRLKEGRQLLIFVPTIELLEQLVALLQKLfpEERIAGVHAEDP--ERKEKVQA 364

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 491 LRLGKYDVLVGINLLREGLDIPEVSlVTILDADKEGFlrSERSLIQTIGRAARNA---NGHVIMYADRITNSMDIAINET 567
Cdd:COG4098  365 FRDGEIPILVTTTILERGVTFPNVD-VAVLGADHPVF--TEAALVQIAGRVGRSAdypTGEVIFFHHGKTRAMKRAIREI 441


                 ..
gi 502824756 568 KR 569
Cdd:COG4098  442 KR 443
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
326-658 2.90e-16

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 82.38  E-value: 2.90e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 326 LDFFPEDF-LLVVDESH-VTIPQVRGMYNGDQARkqvlvdhgFRL-----PSALDNRPLKFDEFEqhinqivHVSATPGP 398
Cdd:COG1061  181 LDELGDRFgLVIIDEAHhAGAPSYRRILEAFPAA--------YRLgltatPFRSDGREILLFLFD-------GIVYEYSL 245

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 399 YELEKA-----PDVIEqiiRPTGLLDPNIEVRPIEGQIDDLIG-----------EIHDRIKRNERVLVTTLTKKMSEDLT 462
Cdd:COG1061  246 KEAIEDgylapPEYYG---IRVDLTDERAEYDALSERLREALAadaerkdkilrELLREHPDDRKTLVFCSSVDHAEALA 322

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 463 NYLKEIGIKVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDAdkegfLRSERSLIQTIGRAA 542
Cdd:COG1061  323 ELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRP-----TGSPREFIQRLGRGL 397

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 543 RNANG----HVIMYADRITNSMDIAINETKRRRSIQEAYNEEHGITPTTIQKEVRGSIRATVVAEDTETYEEAPAFDKLN 618
Cdd:COG1061  398 RPAPGkedaLVYDFVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALL 477

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 502824756 619 KKEKAKLVEEMEQEMKEAAKALNFERAAELRDLILELKAE 658
Cdd:COG1061  478 LVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLL 517
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 432-550 4.51e-13

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 66.38  E-value: 4.51e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 432 DDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDI 511
Cdd:cd18787   14 KLLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDI 93

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 502824756 512 PEVSLVTILDadkegFLRSERSLIQTIGRAAR-NANGHVI 550
Cdd:cd18787   94 PGVDHVINYD-----LPRDAEDYVHRIGRTGRaGRKGTAI 128
ResIII pfam04851
Type III restriction enzyme, res subunit;
17-139 8.26e-12

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 63.85  E-value: 8.26e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756   17 QPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTMSNVIKEINK-----PTLIMAHNKTLAGQLYSEFKEFFPNnaveyfvs 91
Cdd:pfam04851   8 QIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKkgpikKVLFLVPRKDLLEQALEEFKKFLPN-------- 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 502824756   92 yyDYYQPEAYVPQTDTFIEKDASIN----DEIDKLRHSATSSLF-ERKDVIII 139
Cdd:pfam04851  80 --YVEIGEIISGDKKDESVDDNKIVvttiQSLYKALELASLELLpDFFDVIII 130
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
442-571 2.04e-11

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 67.06  E-value: 2.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 442 IKRNERVLVTTLTKKMSEDLTNYLKEIGIKV-----QYLHSEVKTL---ERIEIIRELRLGKYDVLVGINLLREGLDIPE 513
Cdd:COG1111  350 TNPDSRIIVFTQYRDTAEMIVEFLSEPGIKAgrfvgQASKEGDKGLtqkEQIEILERFRAGEFNVLVATSVAEEGLDIPE 429

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 514 VSLVTILDAdkegfLRSE-RSlIQTIGRAARNANGHVIMYadrITN-SMDIAINETKRRR 571
Cdd:COG1111  430 VDLVIFYEP-----VPSEiRS-IQRKGRTGRKREGRVVVL---IAKgTRDEAYYWSSRRK 480
DEXDc smart00487
DEAD-like helicases superfamily;
5-92 2.47e-11

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 63.28  E-value: 2.47e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756     5 FELVSPYQPQGDQPKAIEKIVKGIKegkqHQVLLGATGTGKTFTMSNVI-----KEINKPTLIMAHNKTLAGQLYSEFKE 79
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGLR----DVILAAPTGSGKTLAALLPAlealkRGKGGRVLVLVPTRELAEQWAEELKK 76

                           90
                   ....*....|...
gi 502824756    80 FFPNNAVEYFVSY 92
Cdd:smart00487  77 LGPSLGLKVVGLY 89
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 34-139 2.88e-11

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: 61.65  E-value: 2.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  34 HQVLLGATGTGKTFTMSNVIKEIN----KPTLIMAHNKTLAGQLYSEFKEFF-PNNAVEYFVSYYDYYQPEAYvpqtdtf 108
Cdd:cd00046    3 NVLITAPTGSGKTLAALLAALLLLlkkgKKVLVLVPTKALALQTAERLRELFgPGIRVAVLVGGSSAEEREKN------- 75

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 502824756 109 IEKDASI----NDEIDKLRHSATSSLFERKDVIII 139
Cdd:cd00046   76 KLGDADIiiatPDMLLNLLLREDRLFLKDLKLIIV 110
mfd TIGR00580
transcription-repair coupling factor (mfd); All proteins in this family for which functions ...
 176-257 4.52e-11

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


Pssm-ID: 273152 [Multi-domain]  Cd Length: 926  Bit Score: 66.23  E-value: 4.52e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  176 LVDVQYERNDIDFKRGTFRVRGDVVEIFPVSrDEHCIRVEFFGDEIDRIREVDALTGEIIGDREHVAIFPASHFVTREEK 255
Cdd:TIGR00580   1 LVELGYERVDLVEEEGEFSVRGEILDIFPPG-SELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFILLEEE 79


                  ..
gi 502824756  256 MR 257
Cdd:TIGR00580  80 TI 81
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 445-551 2.46e-09

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


Pssm-ID: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 56.21  E-value: 2.46e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 445 NERVLVTTLTKKMSEDLTNYLKEI--GIKVQYL--HSEVKTL------ERIEIIRELRLGKYDVLVGINLLREGLDIPEV 514
Cdd:cd18801   30 DTRVIIFSEFRDSAEEIVNFLSKIrpGIRATRFigQASGKSSkgmsqkEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEV 109

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 502824756 515 SLVTILDADKegflrSERSLIQTIGRAARNANGHVIM 551
Cdd:cd18801  110 DLIICYDASP-----SPIRMIQRMGRTGRKRQGRVVV 141
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
441-554 6.60e-09

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 58.62  E-value: 6.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 441 RIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVtI- 519
Cdd:COG0513  237 RDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHV-In 315

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 502824756 520 --LDADKEGFL-RsersliqtIGRAAR-NANGHVIMYAD 554
Cdd:COG0513  316 ydLPEDPEDYVhR--------IGRTGRaGAEGTAISLVT 346
UVR pfam02151
UvrB/uvrC motif;
624-658 1.17e-08

UvrB/uvrC motif;


Pssm-ID: 308001 [Multi-domain]  Cd Length: 36  Bit Score: 50.86  E-value: 1.17e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 502824756  624 KLVEEMEQEMKEAAKALNFERAAELRDLILELKAE 658
Cdd:pfam02151   2 KLIKELEEEMEEAAENEDFEKAAKLRDQINALKKQ 36
DEAD-like_helicase_C cd09300
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ...
 498-553 1.72e-08

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


Pssm-ID: 350171 [Multi-domain]  Cd Length: 59  Bit Score: 51.01  E-value: 1.72e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 502824756 498 VLVGINLLREGLDIPEVSLVTILDADkegflRSERSLIQTIGRAARNAN-GHVIMYA 553
Cdd:cd09300    8 VLIAVN*ALTGFDAPELNTIIVDKNL-----RSYRGLNQAFGRANRIYTfGGIVTYR 59
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
 462-550 1.84e-08

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


Pssm-ID: 350191 [Multi-domain]  Cd Length: 238  Bit Score: 55.71  E-value: 1.84e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 462 TNYLKEIGIKVQYLHSEVKTL---ERI---------------EIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDAD 523
Cdd:cd18804   93 SEDLVFKGIGTERVEEELKTLfpeARIaridrdttrkkgaleKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNAD 172

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 502824756 524 KEGFL---RS-ERS---LIQTIGRAAR-NANGHVI 550
Cdd:cd18804  173 SGLNSpdfRAsERAfqlLTQVSGRAGRgDKPGKVI 207
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 17-85 2.99e-08

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: 53.33  E-value: 2.99e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 502824756  17 QPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTMSNVIKEI-----NKPTLIMAHNKTLAGQLYSEFKEFFPNNA 85
Cdd:cd18032    5 QQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKRLleanrKKRILFLAHREELLEQAERSFKEVLPDGS 78
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 17-149 3.86e-08

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: 52.69  E-value: 3.86e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  17 QPKAIEKIVKgiKEGKQHQVLLGATGTGKTFTMSNVIKEI-NKPTLIMAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDY 95
Cdd:cd17926    5 QEEALEAWLA--HKNNRRGILVLPTGSGKTLTALALIAYLkELRTLIVVPTDALLDQWKERFEDFLGDSSIGLIGGGKKK 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 502824756  96 YQPEAYV----PQTDTFIEKDAS---------INDEIdklrHSATSSLFERkdviIIASVSCIYGLG 149
Cdd:cd17926   83 DFDDANVvvatYQSLSNLAEEEKdlfdqfgllIVDEA----HHLPAKTFSE----ILKELNAKYRLG 141
DEAD-like_helicase_N cd17912
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 34-104 4.98e-08

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: 50.60  E-value: 4.98e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 502824756  34 HQVLLGATGTGKTFTMSNVIKEIN---KPTLIMAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPQ 104
Cdd:cd17912    1 NILHLGPTGSGKTLVAIQKIASAMssgKSVLVVTPTKLLAHEILIVIDEIQ*ILDPAAGWAWATRALLGLKAEK 74
PRK13766 PRK13766
Hef nuclease; Provisional
 442-550 5.89e-08

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 56.04  E-value: 5.89e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 442 IKRNERVLVTTLTKKMSEDLTNYLKEIGIKV-----QYLHSEVKTL---ERIEIIRELRLGKYDVLVGINLLREGLDIPE 513
Cdd:PRK13766 362 KNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAvrfvgQASKDGDKGMsqkEQIEILDKFRAGEFNVLVSTSVAEEGLDIPS 441

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 502824756 514 VSLVTILDAdkegfLRSE-RSlIQTIGRAARNANGHVI 550
Cdd:PRK13766 442 VDLVIFYEP-----VPSEiRS-IQRKGRTGRQEEGRVV 473
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
624-652 4.95e-07

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


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 52.82  E-value: 4.95e-07
                         10        20
                 ....*....|....*....|....*....
gi 502824756 624 KLVEEMEQEMKEAAKALNFERAAELRDLI 652
Cdd:COG0322  203 ELIKELEEKMEEAAEELEFERAARLRDQI 231
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 444-543 1.13e-06

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


Pssm-ID: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 47.55  E-value: 1.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 444 RNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTLER-IEIIREL--RLGKYDVLVGINLLREGLDIPEVslVTIL 520
Cdd:cd18799    5 VEIKTLIFCVSIEHAEFMAEAFNEAGIDAVALNSDYSDRERgDEALILLffGELKPPILVTVDLLTTGVDIPEV--DNVV 82

                         90       100
                 ....*....|....*....|....*.
gi 502824756 521 dadkegFLRSERSLI---QTIGRAAR 543
Cdd:cd18799   83 ------FLRPTESRTlflQMLGRGLR 102
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 447-546 1.99e-06

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 45.77  E-value: 1.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 447 RVLVTTLTKKMSEDLTNYLKeigikvqylhsevktlerieiirelrlgkydVLVGINLLREGLDIPEVSLVTILDADkeg 526
Cdd:cd18785    5 KIIVFTNSIEHAEEIASSLE-------------------------------ILVATNVLGEGIDVPSLDTVIFFDPP--- 50

                         90       100
                 ....*....|....*....|
gi 502824756 527 flRSERSLIQTIGRAARNAN 546
Cdd:cd18785   51 --SSAASYIQRVGRAGRGGK 68
uvrC PRK00558
excinuclease ABC subunit UvrC;
624-652 2.80e-06

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 50.50  E-value: 2.80e-06
                         10        20
                 ....*....|....*....|....*....
gi 502824756 624 KLVEEMEQEMKEAAKALNFERAAELRDLI 652
Cdd:PRK00558 202 EVLKELEEKMEEASENLEFERAARYRDQI 230
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 445-551 4.27e-06

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


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 46.82  E-value: 4.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 445 NERVLVTTLTKKMSEdltNYLKEIGIKVQYL--HSEVKTLER--------IEIIRELRLGKYDVLVGINLLREGLDIPEV 514
Cdd:cd18802   33 ERRATAVVLSRLLKE---HPSTLAFIRCGFLigRGNSSQRKRslmtqrkqKETLDKFRDGELNLLIATSVLEEGIDVPAC 109

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 502824756 515 SLVTILDadkegFLRSERSLIQTIGRA-ARNANgHVIM 551
Cdd:cd18802  110 NLVIRFD-----LPKTLRSYIQSRGRArAPNSK-YILM 141
PRK05580 PRK05580
primosome assembly protein PriA; Validated
 486-550 8.35e-06

primosome assembly protein PriA; Validated


Pssm-ID: 235514 [Multi-domain]  Cd Length: 679  Bit Score: 49.00  E-value: 8.35e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 502824756 486 EIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDAD---KEGFLR-SERS---LIQTIGRAAR-NANGHVI 550
Cdd:PRK05580 471 QLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADlglFSPDFRaSERTfqlLTQVAGRAGRaEKPGEVL 543
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
 10-87 1.02e-05

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


Pssm-ID: 350676 [Multi-domain]  Cd Length: 180  Bit Score: 46.64  E-value: 1.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  10 PYQPQGDQPKAIEKIVKGIKEGKQHQVLL-GATGTGKTFTMSNVIK---EINKPTLIMAHNKTLAGQLYSEFKEFFPNNA 85
Cdd:cd17918   13 PFSLTKDQAQAIKDIEKDLHSPEPMDRLLsGDVGSGKTLVALGAALlayKNGKQVAILVPTEILAHQHYEEARKFLPFIN 92


                 ..
gi 502824756  86 VE 87
Cdd:cd17918   93 VE 94
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 442-552 2.22e-05

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350184 [Multi-domain]  Cd Length: 146  Bit Score: 44.94  E-value: 2.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 442 IKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTL-------ERIEIIRELRLGKYDVLVGINLLREGLDIPEV 514
Cdd:cd18797   32 VRAGVKTIVFCRSRKLAELLLRYLKARLVEEGPLASKVASYragylaeDRREIEAELFNGELLGVVATNALELGIDIGGL 111

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 502824756 515 SlVTILDadkeGFLRSERSLIQTIGRAARNANGHVIMY 552
Cdd:cd18797  112 D-AVVLA----GYPGSLASLWQQAGRAGRRGKDSLVIL 144
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 420-543 2.31e-05

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: 44.51  E-value: 2.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 420 PNI--EVRPIEG--QIDDLIGEIHDRiKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTLERIEIIRELRLGK 495
Cdd:cd18794    2 PNLfySVRPKDKkdEKLDLLKRIKVE-HLGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWLRDK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 502824756 496 YDVLVGINLLREGLDIPEVSLVTILDADK--EGFLrsersliQTIGRAAR 543
Cdd:cd18794   81 IQVIVATVAFGMGIDKPDVRFVIHYSLPKsmESYY-------QESGRAGR 123
PriA COG1198
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ...
 486-550 2.87e-05

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


Pssm-ID: 440811 [Multi-domain]  Cd Length: 728  Bit Score: 47.42  E-value: 2.87e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 502824756 486 EIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADkEGF----LR-SERS---LIQTIGRAAR-NANGHVI 550
Cdd:COG1198  522 KLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVLDAD-LGLnspdFRaAERTfqlLTQVAGRAGRaEKPGEVL 594
PTZ00424 PTZ00424
helicase 45; Provisional
 445-543 4.68e-05

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 46.36  E-value: 4.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 445 NERVLVTTLTKKMSE-DLTnylkeigikVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDAD 523
Cdd:PTZ00424 275 NTRRKVDYLTKKMHErDFT---------VSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLP 345

                         90       100
                 ....*....|....*....|
gi 502824756 524 KegflrSERSLIQTIGRAAR 543
Cdd:PTZ00424 346 A-----SPENYIHRIGRSGR 360
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 437-543 7.45e-05

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: 43.39  E-value: 7.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 437 EIHDRIKRNERVLVTTLTKkmsEDLTNYLKEIGIkvQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSL 516
Cdd:cd18789   41 ELLKRHEQGDKIIVFTDNV---EALYRYAKRLLK--PFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANV 115

                         90       100
                 ....*....|....*....|....*..
gi 502824756 517 VTILdadkEGFLRSERSLIQTIGRAAR 543
Cdd:cd18789  116 AIQI----SGHGGSRRQEAQRLGRILR 138
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 456-559 7.68e-05

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


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 43.49  E-value: 7.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 456 KMSEDLTNYLKEI---GIKVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADKEGFlrseR 532
Cdd:cd18811   45 KAAVAMYEYLKERfrpELNVGLLHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGL----S 120

                         90       100
                 ....*....|....*....|....*....
gi 502824756 533 SLIQTIGRAARNANGH--VIMYADRITNS 559
Cdd:cd18811  121 QLHQLRGRVGRGDHQSycLLVYKDPLTET 149
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 389-544 1.04e-04

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


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 45.46  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 389 IVHVSATPGPYELEKAPDVIEQIIRPTG--------LLDPNIEVRPIEGQIDDLIGEIHDRIKRNERVLVTTLTKKMSED 460
Cdd:COG1203  302 VILMTATLPPLLREELLEAYELIPDEPEelpeyfraFVRKRVELKEGPLSDEELAELILEALHKGKSVLVIVNTVKDAQE 381

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 461 LTNYLKEIG--IKVQYLHSEVKTLERIEIIRELRL----GKYDVLVGINLLREGLDIpevslvtilDADkegFLRSE--- 531
Cdd:COG1203  382 LYEALKEKLpdEEVYLLHSRFCPADRSEIEKEIKErlerGKPCILVSTQVVEAGVDI---------DFD---VVIRDlap 449

                        170
                 ....*....|....
gi 502824756 532 -RSLIQTIGRAARN 544
Cdd:COG1203  450 lDSLIQRAGRCNRH 463
PRK10689 PRK10689
transcription-repair coupling factor; Provisional
 164-254 1.10e-04

transcription-repair coupling factor; Provisional


Pssm-ID: 182649 [Multi-domain]  Cd Length: 1147  Bit Score: 45.51  E-value: 1.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756  164 GMEKERNQLLRTLVDVQYERNDIDFKRGTFRVRGDVVEIFPVSrDEHCIRVEFFGDEIDRIREVDALTGEIIGDREHVAI 243
Cdd:PRK10689  133 GQRLSRDALRAQLEQAGYRHVDQVMEHGEYATRGALLDLFPMG-SEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINL 211

                          90
                  ....*....|.
gi 502824756  244 FPASHFVTREE 254
Cdd:PRK10689  212 LPAHEFPTDKA 222
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 438-571 1.58e-04

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


Pssm-ID: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 42.64  E-value: 1.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 438 IHDRIKRNERVLVTTLTKkMSEDLTNYLKEIgiKVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLV 517
Cdd:cd18792   32 VYPRIEESEKLDLKSIEA-LAEELKELVPEA--RVALLHGKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTM 108

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 502824756 518 TILDADKEGFlrseRSLIQTIGRAARnanGHVIMYADRITNSmDIAINETKRRR 571
Cdd:cd18792  109 IIEDADRFGL----SQLHQLRGRVGR---GKHQSYCYLLYPD-PKKLTETAKKR 154
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 446-543 3.21e-04

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 43.78  E-value: 3.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 446 ERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDADke 525
Cdd:PRK11192 246 TRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMP-- 323

                         90
                 ....*....|....*...
gi 502824756 526 gflRSERSLIQTIGRAAR 543
Cdd:PRK11192 324 ---RSADTYLHRIGRTGR 338
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
 17-88 3.23e-04

DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350687 [Multi-domain]  Cd Length: 178  Bit Score: 41.81  E-value: 3.23e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 502824756  17 QPKAIEKIVKGIKEGKQHqVLLGATGTGKTFTMSNVIKEI---NKPTLIMAHNKTLAGQLYSEFKEFFPNNAVEY 88
Cdd:cd17929    1 QRKAYEAIVSSLGGFKTF-LLHGVTGSGKTEVYIELIEKVlakGKQVLVLVPEISLTPQLIKRFKKRFGDKVAVL 74
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 438-575 3.34e-04

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


Pssm-ID: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 41.56  E-value: 3.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 438 IHDRIKRNERVlvttltKKMSEDLTNYLKeigikVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLV 517
Cdd:cd18810   31 VHNRIESIEKL------ATQLRQLVPEAR-----IAIAHGQMTENELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTI 99

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 518 TILDADKEGFLRsersLIQTIGRAARnanGHVIMYADRITNSmDIAINET--KRRRSIQE 575
Cdd:cd18810  100 IIERADKFGLAQ----LYQLRGRVGR---SKERAYAYFLYPD-QKKLTEDalKRLEAIQE 151
HsdR COG4096
Type I site-specific restriction endonuclease, part of a restriction-modification system ...
 17-84 6.14e-04

Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];


Pssm-ID: 443272 [Multi-domain]  Cd Length: 806  Bit Score: 42.91  E-value: 6.14e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 502824756  17 QPKAIEKIVKGIKEGKQHQVLLGATGTGKTFTM---------SNVIKEInkptLIMAHNKTLAGQLYSEFKEFFPNN 84
Cdd:COG4096  163 QIEAIRRVEEAIAKGQRRALLVMATGTGKTRTAialiyrllkAGRAKRI----LFLADRNALVDQAKNAFKPFLPDL 235
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 469-543 1.74e-03

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 41.31  E-value: 1.74e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 502824756 469 GIKVQYLHSEVKTLERIEIIRELRLGKYDVLVGINLLREGLDIPEVSLVTILDadkegFLRSERSLIQTIGRAAR 543
Cdd:PLN00206 392 GLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFD-----MPNTIKEYIHQIGRASR 461
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 431-543 2.43e-03

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


Pssm-ID: 350183 [Multi-domain]  Cd Length: 150  Bit Score: 38.78  E-value: 2.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 431 IDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEI------GIKVQYLHSEVKTLERIEIIRELRLGKYDVLVGINL 504
Cdd:cd18796   24 GADAYAEVIFLLERHKSTLVFTNTRSQAERLAQRLRELcpdrvpPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSS 103

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 502824756 505 LREGLDIPEVSLVTILDADKegflrSERSLIQTIGRAAR 543
Cdd:cd18796  104 LELGIDIGDVDLVIQIGSPK-----SVARLLQRLGRSGH 137
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 417-504 2.96e-03

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 40.59  E-value: 2.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 417 LLDPNIEVRPIE-GQIDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTLERIEIIRELRLGK 495
Cdd:COG0553  520 LLLEEGAELSGRsAKLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGP 599

                         90
                 ....*....|....*...
gi 502824756 496 Y-DVL--------VGINL 504
Cdd:COG0553  600 EaPVFlislkaggEGLNL 617
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 420-504 3.60e-03

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


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 38.23  E-value: 3.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502824756 420 PNIEVRPIEGQIDDLIGEIHDRIKRNERVLVTTLTKKMSEDLTNYLKEIGIKVQYLHSEVKTLERIEIIREL-RLGKYDV 498
Cdd:cd18793    2 PPKIEEVVSGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFnEDPDIRV 81

                         90
                 ....*....|....
gi 502824756 499 L--------VGINL 504
Cdd:cd18793   82 FllstkaggVGLNL 95
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH