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Conserved domains on  [gi|1958804940|ref|XP_038940483|]
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DNA excision repair protein ERCC-5 isoform X1 [Rattus norvegicus]

Protein Classification

rad2 family protein( domain architecture ID 11489416)

rad2 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 11-1007 0e+00

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. 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: 273166 [Multi-domain]  Cd Length: 1034  Bit Score: 1399.64  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940   11 DISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSASIDSRKTTEKL 90
Cdd:TIGR00600   30 DISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDARKTAEKL 109

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940   91 LKTFLKRQALKTAFRSKR--NEVLPSLTQVQREDDIYVLPPLQEEEKHSSEEEDEKQWQARMDQKQALQEEFFHNPHAID 168
Cdd:TIGR00600  110 LATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSEEESEKEWEERMNQKQALQEEFFHNPSAID 189

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  169 IESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLLKKNYLNQHIENVQKEMNQEHSGQIQRQYE 248
Cdd:TIGR00600  190 IESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLLKKNDLNQHIENVTKEMNQQHSGNIQRQYR 269

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  249 DEGGFLKEVESRRVVAEDTSHYILIKGIQGK---KVVDVDLESLPSSSKE-HSVSFNLKSSPYEKVKPESEP--EATPPS 322
Cdd:TIGR00600  270 DEGGFLKEVELRRVVSEDTSHYILIKGIQGKtavKAVDSDDESLPSLSSQlDSNSEDLKSSPWEKLKPESESivEAEPPS 349

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  323 PRTLHAIQVAMLGGSSEEEPESGEGGQSKERSAWATADAGSISPQTCAAIQRALDDDEEERMCASSDN-----LAVEMLL 397
Cdd:TIGR00600  350 PRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIGQALDDDEDKKVSASSDDqaspsKKTKMLL 429

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  398 GNGLKQE-HADEVVVKGGGVPLDTASLLPSVTEVEECVASASNDKEQTASTHASstachpgeVPKETVSPAHVVSEASQI 476
Cdd:TIGR00600  430 ISRIEVEdDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSGHEA--------VPKAVQSLLLGATNDSPI 501

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  477 SSECEVAGRPVPLPSAFIETPCSYASGVLSERELTLAPPI-RTHSHQRTSIDPEEPELQNGLCPPKNTCNSSHLSSDDET 555
Cdd:TIGR00600  502 PSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTeGTQNLQGISDHPEQFEFQNELSPLETKNNESNLSSDAET 581

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  556 EGGQNPASKAGSTVHVPSEAVGNVENVSSSNAEEHGDFQKT-IQLWEMPEAAARELISAPESLGPVEMESEESESDGSFI 634
Cdd:TIGR00600  582 EGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGESADLLLISNPMEVEPMESEKEESESDGSFI 661

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  635 EVQSVISNDELQIESSEISKHLSEKDAEEPKETLEEGSPRNTECLLQDSSDIKAMKEHRKEDRGAEDSPDEWQDVNLEEL 714
Cdd:TIGR00600  662 EVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEEEKDADDFKNEWQDISLEEL 741

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  715 DALESNLLAEQNSLEAQKQQQDRIAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLF 794
Cdd:TIGR00600  742 EALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLF 821

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  795 GARHVYKNFFNKNKFVEYYQYVDFYNQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPGRGLDPLLKFSEWW 874
Cdd:TIGR00600  822 GARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWW 901

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  875 HKAQNNKKAAENPYDTKVKKKLRKLQLTPGFPNPAVADAYLRPVVDDSRGSFLWGKPDVDKIREFCQRYFGWNRMKTDES 954
Cdd:TIGR00600  902 HEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGKPDLDKIREFCQRYFGWNREKTDEV 981

                          970       980       990      1000      1010
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958804940  955 LYPVLKQLNAHQTQLRIDSFFRLAQQEKQDAKHIKSHRLSRAVTCMLRKEREE 1007
Cdd:TIGR00600  982 LLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRKEKEK 1034
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 11-1007 0e+00

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. 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: 273166 [Multi-domain]  Cd Length: 1034  Bit Score: 1399.64  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940   11 DISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSASIDSRKTTEKL 90
Cdd:TIGR00600   30 DISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDARKTAEKL 109

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940   91 LKTFLKRQALKTAFRSKR--NEVLPSLTQVQREDDIYVLPPLQEEEKHSSEEEDEKQWQARMDQKQALQEEFFHNPHAID 168
Cdd:TIGR00600  110 LATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSEEESEKEWEERMNQKQALQEEFFHNPSAID 189

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  169 IESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLLKKNYLNQHIENVQKEMNQEHSGQIQRQYE 248
Cdd:TIGR00600  190 IESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLLKKNDLNQHIENVTKEMNQQHSGNIQRQYR 269

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  249 DEGGFLKEVESRRVVAEDTSHYILIKGIQGK---KVVDVDLESLPSSSKE-HSVSFNLKSSPYEKVKPESEP--EATPPS 322
Cdd:TIGR00600  270 DEGGFLKEVELRRVVSEDTSHYILIKGIQGKtavKAVDSDDESLPSLSSQlDSNSEDLKSSPWEKLKPESESivEAEPPS 349

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  323 PRTLHAIQVAMLGGSSEEEPESGEGGQSKERSAWATADAGSISPQTCAAIQRALDDDEEERMCASSDN-----LAVEMLL 397
Cdd:TIGR00600  350 PRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIGQALDDDEDKKVSASSDDqaspsKKTKMLL 429

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  398 GNGLKQE-HADEVVVKGGGVPLDTASLLPSVTEVEECVASASNDKEQTASTHASstachpgeVPKETVSPAHVVSEASQI 476
Cdd:TIGR00600  430 ISRIEVEdDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSGHEA--------VPKAVQSLLLGATNDSPI 501

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  477 SSECEVAGRPVPLPSAFIETPCSYASGVLSERELTLAPPI-RTHSHQRTSIDPEEPELQNGLCPPKNTCNSSHLSSDDET 555
Cdd:TIGR00600  502 PSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTeGTQNLQGISDHPEQFEFQNELSPLETKNNESNLSSDAET 581

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  556 EGGQNPASKAGSTVHVPSEAVGNVENVSSSNAEEHGDFQKT-IQLWEMPEAAARELISAPESLGPVEMESEESESDGSFI 634
Cdd:TIGR00600  582 EGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGESADLLLISNPMEVEPMESEKEESESDGSFI 661

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  635 EVQSVISNDELQIESSEISKHLSEKDAEEPKETLEEGSPRNTECLLQDSSDIKAMKEHRKEDRGAEDSPDEWQDVNLEEL 714
Cdd:TIGR00600  662 EVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEEEKDADDFKNEWQDISLEEL 741

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  715 DALESNLLAEQNSLEAQKQQQDRIAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLF 794
Cdd:TIGR00600  742 EALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLF 821

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  795 GARHVYKNFFNKNKFVEYYQYVDFYNQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPGRGLDPLLKFSEWW 874
Cdd:TIGR00600  822 GARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWW 901

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  875 HKAQNNKKAAENPYDTKVKKKLRKLQLTPGFPNPAVADAYLRPVVDDSRGSFLWGKPDVDKIREFCQRYFGWNRMKTDES 954
Cdd:TIGR00600  902 HEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGKPDLDKIREFCQRYFGWNREKTDEV 981

                          970       980       990      1000      1010
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958804940  955 LYPVLKQLNAHQTQLRIDSFFRLAQQEKQDAKHIKSHRLSRAVTCMLRKEREE 1007
Cdd:TIGR00600  982 LLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRKEKEK 1034
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 741-960 2.84e-54

FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350216 [Multi-domain]  Cd Length: 209  Bit Score: 188.11  E-value: 2.84e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  741 SVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYN 820
Cdd:cd09868     92 SVTDEMYEEIQELLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSDVFLFGAKRVYKNFFNQNKYVEYYDMEDIER 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  821 QLgldrnklinlayllgsdytegiptvgcvtameilnefpgrgldpllkfsewwhkaqnnkkaaenpydtkvkkklrklq 900
Cdd:cd09868    172 EL------------------------------------------------------------------------------ 173

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  901 ltpgfpnpavadaylrpvvddsrgSFLWGKPDVDKIREFCQRYFGWNRMKTDESLYPVLK 960
Cdd:cd09868    174 ------------------------KFSWGKPDLELLREFCLDKFGWPKEKTDELLLPVLK 209
XPG_I pfam00867
XPG I-region;
758-839 2.38e-29

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 112.22  E-value: 2.38e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  758 GIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNK-----FVEYYQYVDFYNQLGLDRNKLINL 832
Cdd:pfam00867    1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKkkskvPVEEIDLEKILKELGLTREQLIDL 80


                   ....*..
gi 1958804940  833 AYLLGSD 839
Cdd:pfam00867   81 AILLGCD 87
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 724-1028 2.73e-27

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 115.49  E-value: 2.73e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  724 EQNSLEAQKQQQDRiAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNF 803
Cdd:PTZ00217   118 EEGDDEEIKKQSKR-TVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNL 196

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  804 FN----KNKFVEyYQYVDFYNQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFpgRGLDPLLKfsewwHKAQN 879
Cdd:PTZ00217   197 NFseakKRPIQE-INLSTVLEELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKY--KSIEEILE-----HLDKT 268

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  880 NKKAAEN-PYdtkvkKKLRKLqltpgFPNPAVADAylrpvvddSRGSFLWGKPDVDKIREFCQRYFGWNRMKTDESLYPV 958
Cdd:PTZ00217   269 KYPVPENfDY-----KEAREL-----FLNPEVTPA--------EEIDLKWNEPDEEGLKKFLVKEKNFNEERVEKYIERL 330

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  959 LKQLNaHQTQLRIDSFFRLAQQEKQDAKHIKShrlsravtcmLRKEREETAGELKKVPETLDKANGKTQK 1028
Cdd:PTZ00217   331 KKAKT-KKTQTRLDSFFTATKKPIKKSNSKAK----------LKKKKKKAGASAVPKSETSQEAKSSGKK 389
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 11-79 3.30e-26

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 103.47  E-value: 3.30e-26
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940    11 DISIWLNQALKGVRDRHGNAIEN-AHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSA 79
Cdd:smart00485   30 DASIWLYQFLTACREKLGTPLPNsKHLMGLFYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRERREEA 99
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 11-1007 0e+00

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. 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: 273166 [Multi-domain]  Cd Length: 1034  Bit Score: 1399.64  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940   11 DISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSASIDSRKTTEKL 90
Cdd:TIGR00600   30 DISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDARKTAEKL 109

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940   91 LKTFLKRQALKTAFRSKR--NEVLPSLTQVQREDDIYVLPPLQEEEKHSSEEEDEKQWQARMDQKQALQEEFFHNPHAID 168
Cdd:TIGR00600  110 LATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSEEESEKEWEERMNQKQALQEEFFHNPSAID 189

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  169 IESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLLKKNYLNQHIENVQKEMNQEHSGQIQRQYE 248
Cdd:TIGR00600  190 IESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLLKKNDLNQHIENVTKEMNQQHSGNIQRQYR 269

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  249 DEGGFLKEVESRRVVAEDTSHYILIKGIQGK---KVVDVDLESLPSSSKE-HSVSFNLKSSPYEKVKPESEP--EATPPS 322
Cdd:TIGR00600  270 DEGGFLKEVELRRVVSEDTSHYILIKGIQGKtavKAVDSDDESLPSLSSQlDSNSEDLKSSPWEKLKPESESivEAEPPS 349

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  323 PRTLHAIQVAMLGGSSEEEPESGEGGQSKERSAWATADAGSISPQTCAAIQRALDDDEEERMCASSDN-----LAVEMLL 397
Cdd:TIGR00600  350 PRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIGQALDDDEDKKVSASSDDqaspsKKTKMLL 429

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  398 GNGLKQE-HADEVVVKGGGVPLDTASLLPSVTEVEECVASASNDKEQTASTHASstachpgeVPKETVSPAHVVSEASQI 476
Cdd:TIGR00600  430 ISRIEVEdDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSGHEA--------VPKAVQSLLLGATNDSPI 501

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  477 SSECEVAGRPVPLPSAFIETPCSYASGVLSERELTLAPPI-RTHSHQRTSIDPEEPELQNGLCPPKNTCNSSHLSSDDET 555
Cdd:TIGR00600  502 PSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTeGTQNLQGISDHPEQFEFQNELSPLETKNNESNLSSDAET 581

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  556 EGGQNPASKAGSTVHVPSEAVGNVENVSSSNAEEHGDFQKT-IQLWEMPEAAARELISAPESLGPVEMESEESESDGSFI 634
Cdd:TIGR00600  582 EGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGESADLLLISNPMEVEPMESEKEESESDGSFI 661

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  635 EVQSVISNDELQIESSEISKHLSEKDAEEPKETLEEGSPRNTECLLQDSSDIKAMKEHRKEDRGAEDSPDEWQDVNLEEL 714
Cdd:TIGR00600  662 EVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEEEKDADDFKNEWQDISLEEL 741

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  715 DALESNLLAEQNSLEAQKQQQDRIAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLF 794
Cdd:TIGR00600  742 EALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLF 821

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  795 GARHVYKNFFNKNKFVEYYQYVDFYNQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPGRGLDPLLKFSEWW 874
Cdd:TIGR00600  822 GARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWW 901

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  875 HKAQNNKKAAENPYDTKVKKKLRKLQLTPGFPNPAVADAYLRPVVDDSRGSFLWGKPDVDKIREFCQRYFGWNRMKTDES 954
Cdd:TIGR00600  902 HEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGKPDLDKIREFCQRYFGWNREKTDEV 981

                          970       980       990      1000      1010
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958804940  955 LYPVLKQLNAHQTQLRIDSFFRLAQQEKQDAKHIKSHRLSRAVTCMLRKEREE 1007
Cdd:TIGR00600  982 LLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRKEKEK 1034
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 741-960 2.84e-54

FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350216 [Multi-domain]  Cd Length: 209  Bit Score: 188.11  E-value: 2.84e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  741 SVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYN 820
Cdd:cd09868     92 SVTDEMYEEIQELLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSDVFLFGAKRVYKNFFNQNKYVEYYDMEDIER 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  821 QLgldrnklinlayllgsdytegiptvgcvtameilnefpgrgldpllkfsewwhkaqnnkkaaenpydtkvkkklrklq 900
Cdd:cd09868    172 EL------------------------------------------------------------------------------ 173

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  901 ltpgfpnpavadaylrpvvddsrgSFLWGKPDVDKIREFCQRYFGWNRMKTDESLYPVLK 960
Cdd:cd09868    174 ------------------------KFSWGKPDLELLREFCLDKFGWPKEKTDELLLPVLK 209
H3TH_XPG cd09904
H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 827-921 2.65e-41

H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease; The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of XPG and other similar eukaryotic 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.


Pssm-ID: 188624 [Multi-domain]  Cd Length: 97  Bit Score: 146.63  E-value: 2.65e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  827 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPgrGLDPLLKFSEWWHKAQNNKK----AAENPYDTKVKKKLRKLQLT 902
Cdd:cd09904      1 DKLIRLALLLGSDYTEGVSGIGPVNAMEILSEFP--GEEDLEKFKDWWENAQPEKSedsdNDKQEFKRKHKNYLKNLILP 78

                           90
                   ....*....|....*....
gi 1958804940  903 PGFPNPAVADAYLRPVVDD 921
Cdd:cd09904     79 PGFPSPAVINAYLNPNVDD 97
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 11-94 9.09e-38

FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350216 [Multi-domain]  Cd Length: 209  Bit Score: 140.73  E-value: 9.09e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940   11 DISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSASIDSRktteKL 90
Cdd:cd09868     29 DASIWLHQFVKGMRDNEGNSVPNAHLLGFFRRICKLLFYGIKPVFVFDGPAPALKRRTLARRRSVTDEMYEEIQ----EL 104


                   ....
gi 1958804940   91 LKTF 94
Cdd:cd09868    105 LRLF 108
XPG_I pfam00867
XPG I-region;
758-839 2.38e-29

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 112.22  E-value: 2.38e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  758 GIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNK-----FVEYYQYVDFYNQLGLDRNKLINL 832
Cdd:pfam00867    1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKkkskvPVEEIDLEKILKELGLTREQLIDL 80


                   ....*..
gi 1958804940  833 AYLLGSD 839
Cdd:pfam00867   81 AILLGCD 87
XPG_N pfam00752
XPG N-terminal domain;
11-79 2.51e-28

XPG N-terminal domain;


Pssm-ID: 395609 [Multi-domain]  Cd Length: 100  Bit Score: 109.76  E-value: 2.51e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940   11 DISIWLNQALKGVRDRHGNAIEN-AHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSA 79
Cdd:pfam00752   31 DASIWLYQFLKAVRDQLGNALQNtSHLMGFFSRLCRLKDFGIKPIFVFDGGPPPLKAETLQKRSARRQEA 100
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 724-1028 2.73e-27

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 115.49  E-value: 2.73e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  724 EQNSLEAQKQQQDRiAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNF 803
Cdd:PTZ00217   118 EEGDDEEIKKQSKR-TVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNL 196

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  804 FN----KNKFVEyYQYVDFYNQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFpgRGLDPLLKfsewwHKAQN 879
Cdd:PTZ00217   197 NFseakKRPIQE-INLSTVLEELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKY--KSIEEILE-----HLDKT 268

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  880 NKKAAEN-PYdtkvkKKLRKLqltpgFPNPAVADAylrpvvddSRGSFLWGKPDVDKIREFCQRYFGWNRMKTDESLYPV 958
Cdd:PTZ00217   269 KYPVPENfDY-----KEAREL-----FLNPEVTPA--------EEIDLKWNEPDEEGLKKFLVKEKNFNEERVEKYIERL 330

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  959 LKQLNaHQTQLRIDSFFRLAQQEKQDAKHIKShrlsravtcmLRKEREETAGELKKVPETLDKANGKTQK 1028
Cdd:PTZ00217   331 KKAKT-KKTQTRLDSFFTATKKPIKKSNSKAK----------LKKKKKKAGASAVPKSETSQEAKSSGKK 389
fen_arch TIGR03674
flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap ...
 691-975 4.13e-27

flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA


Pssm-ID: 274717 [Multi-domain]  Cd Length: 338  Bit Score: 113.88  E-value: 4.13e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  691 EHRKEDRgaEDSPDEWQDvnleeldALESNLLAEQNSLEAQkqqqdriAASVTGQMFLESQELLRLFGIPYIQAPMEAEA 770
Cdd:TIGR03674   92 EERREIR--EEAEEKWEE-------ALEKGDLEEARKYAQR-------SSRLTSEIVESSKKLLDLMGIPYVQAPSEGEA 155

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  771 QCAILDLTDQTSGTITDDSDIWLFGARHVYKNF--FNKNKFVEYYQYVDFY----------NQLGLDRNKLINLAYLLGS 838
Cdd:TIGR03674  156 QAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLtiSGKRKLPGKNIYVEVKpelieleevlSELGITREQLIDIAILVGT 235

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  839 DYTEGIPTVGCVTAMEILNEFpgRGLDPLLKFSEWwhkaqnnkkAAENPydtkvkKKLRKLqltpgFPNPAVADAYlrpv 918
Cdd:TIGR03674  236 DYNEGVKGIGPKTALKLIKEH--GDLEKVLKARGE---------DIENY------DEIREF-----FLNPPVTDDY---- 289

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958804940  919 vddsrgSFLWGKPDVDKIREF-CQRY-FGWNRMKtdeslyPVLKQLNA--HQTQLRIDSFF 975
Cdd:TIGR03674  290 ------ELEWRKPDKEGIIEFlCDEHdFSEDRVE------RALERLEAayKSKQKTLDRWF 338
PRK03980 PRK03980
flap endonuclease-1; Provisional
 722-939 1.78e-26

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 110.68  E-value: 1.78e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  722 LAEQNSLEAQKQQQDriAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYK 801
Cdd:PRK03980    62 KEEGDLEEARKYAQR--SSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVR 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  802 NF--------FNKNKFVEYY-QYVDF---YNQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPgrgldpllk 869
Cdd:PRK03980   140 NLtisgkrklPGKNVYVEVKpELIELeevLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHG--------- 210

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  870 fSEWwhKAQNNKKAAENPYDtkvkkKLRKLqltpgFPNPAVADAYlrpvvddsrgSFLWGKPDVDKIREF 939
Cdd:PRK03980   211 -DLE--KVLEERGFEIENYD-----EIREF-----FLNPPVTDDY----------ELKWKEPDKEGIIEF 257
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 11-79 3.30e-26

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 103.47  E-value: 3.30e-26
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940    11 DISIWLNQALKGVRDRHGNAIEN-AHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSA 79
Cdd:smart00485   30 DASIWLYQFLTACREKLGTPLPNsKHLMGLFYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRERREEA 99
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
 755-824 9.44e-25

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 98.42  E-value: 9.44e-25
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958804940   755 RLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNK-FVEYYQYV--DFYNQLGL 824
Cdd:smart00484    1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKkKLEFRIIDleSVLKELGL 73
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 11-89 4.06e-18

FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, divalent-metal-ion dependent, 5' nucleases; PIN (PilT N terminus) domain of Flap endonuclease-1 (FEN1)-like nucleases: FEN1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Nucleases in this subfamily are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350206 [Multi-domain]  Cd Length: 235  Bit Score: 84.90  E-value: 4.06e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958804940   11 DISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSASIDSRKTTEK 89
Cdd:cd09856     26 DASIWIYQFLTAVRGQGGNGVSNSHIRGLFYRIIRLLENGIKPVFVFDGEPPKLKKRTRRKRKERRQGAEESAKSAVED 104
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 749-828 5.54e-18

FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Gap Endonuclease 1 (GEN1) is a Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350217 [Multi-domain]  Cd Length: 227  Bit Score: 84.19  E-value: 5.54e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  749 ESQELLRLFGIPYIQAPMEAEAQCAILD---LTDqtsGTITDDSDIWLFGARHVYKNF--FNKNKFVEYYQYVDFYNQLG 823
Cdd:cd09869    116 ECEELLELLGVPVVQAPGEAEALCALLNaegLVD---GCITNDGDAFLYGARTVYRNFslNTKDGSVECYDMSDIEKRLS 192


                   ....*
gi 1958804940  824 LDRNK 828
Cdd:cd09869    193 LRWRR 197
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 716-819 1.27e-17

FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, divalent-metal-ion dependent, 5' nucleases; PIN (PilT N terminus) domain of Flap endonuclease-1 (FEN1)-like nucleases: FEN1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Nucleases in this subfamily are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350206 [Multi-domain]  Cd Length: 235  Bit Score: 83.36  E-value: 1.27e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  716 ALESNLLAEQNSLEAQKQQQDRIAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFG 795
Cdd:cd09856     94 AEESAKSAVEDELFEEQSKDKKRSGTVTKVMTAECKHLLSLFGIPYVDAPGEAEAQCAYLEQQGIVDAVLTEDVDTFLFG 173

                           90       100
                   ....*....|....*....|....
gi 1958804940  796 ARHVYKNFFNKNKfveyYQYVDFY 819
Cdd:cd09856    174 SPVVYRNLTSEGK----KTHVELY 193
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 741-813 1.09e-16

FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like nucleases, structure-specific, divalent-metal-ion dependent, 5' nucleases; PIN (PilT N terminus) domain of Flap endonuclease-1 (FEN1) and exonuclease-1 (EXO1)-like nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350200 [Multi-domain]  Cd Length: 162  Bit Score: 78.57  E-value: 1.09e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958804940  741 SVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYY 813
Cdd:cd00128     83 TITKKMYQECKHLLSLFGIPYVVAPYEAEAQCAYLLKAGIVDAAITEDSDCLLFGAPRVIRNMTFEGPHVEEF 155
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 737-803 3.82e-15

FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium thermophilum junction-resolving enzyme GEN1, and fungal homologs; Fungal Endonuclease 1 (YEN1 and GEN1, GEN1 is known as YEN1 in Saccharomyces cerevisiae) is a four-way (Holliday) junction resolvase. Members of this subgroup belong to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350218 [Multi-domain]  Cd Length: 229  Bit Score: 76.16  E-value: 3.82e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958804940  737 RIAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILdltdQTSGTI----TDDSDIWLFGARHVYKNF 803
Cdd:cd09870     99 KVGKSTPHWLTKLFKELLDAFGFPWHEAPGEAEAELARL----QRLGVVdavlTDDSDALVFGATTVLRNF 165
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 722-817 1.21e-14

FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. FEN1 belongs to the FEN1-EXO1-like subfamily of structure-specific, 5' nucleases (FEN-like family). Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA.


Pssm-ID: 350215 [Multi-domain]  Cd Length: 251  Bit Score: 75.13  E-value: 1.21e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  722 LAEQNSLEAQKQQQdrIAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYK 801
Cdd:cd09867    107 LEEGDLEEARKYAK--RTVRVTKEMVEEAKKLLDLMGIPYVQAPSEGEAQAAYLVKKGDVYAVASQDYDSLLFGAPRLVR 184

                           90
                   ....*....|....*.
gi 1958804940  802 NFFNKNKFVEYYQYVD 817
Cdd:cd09867    185 NLTISGKRKLKGVYRK 200
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 11-74 2.16e-12

FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Gap Endonuclease 1 (GEN1) is a Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350217 [Multi-domain]  Cd Length: 227  Bit Score: 68.01  E-value: 2.16e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958804940   11 DISIWLNQALKgVRDRHGNaIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQ 74
Cdd:cd09869     29 DLSIWICEAQT-VLALFET-VPKPHLRNLFFRTVNLLRLGIKPVFVLDGDAPELKLQTIKKRNA 90
H3TH_XPG-like cd09900
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 ...
 827-860 2.62e-12

H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (archaeal), GEN1, YEN1, and XPG; The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of archaeal Flap Endonuclease-1 (FEN1), Gap Endonuclease 1 (GEN1), Yeast Endonuclease 1 (YEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.


Pssm-ID: 188620 [Multi-domain]  Cd Length: 52  Bit Score: 62.50  E-value: 2.62e-12
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1958804940  827 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFP 860
Cdd:cd09900      1 EQLILLALLLGTDYNPGVPGIGPKTALELLKEFG 34
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 11-96 5.58e-12

FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium thermophilum junction-resolving enzyme GEN1, and fungal homologs; Fungal Endonuclease 1 (YEN1 and GEN1, GEN1 is known as YEN1 in Saccharomyces cerevisiae) is a four-way (Holliday) junction resolvase. Members of this subgroup belong to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350218 [Multi-domain]  Cd Length: 229  Bit Score: 66.91  E-value: 5.58e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940   11 DISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDA-PLLKkqtlakrRQKKDSASIDSRKTteK 89
Cdd:cd09870     40 DASIWLFHAQSSFGGGHIQAGENPELRTLFYRLARLLSLPIQPVFVFDGPNrPPFK-------RGKKVGKSTPHWLT--K 110


                   ....*..
gi 1958804940   90 LLKTFLK 96
Cdd:cd09870    111 LFKELLD 117
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 11-108 8.51e-12

FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. FEN1 belongs to the FEN1-EXO1-like subfamily of structure-specific, 5' nucleases (FEN-like family). Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA.


Pssm-ID: 350215 [Multi-domain]  Cd Length: 251  Bit Score: 66.65  E-value: 8.51e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940   11 DISIWLNQALKGVRDRHGNAIENA------HLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSAsidsr 84
Cdd:cd09867     25 DASNALYQFLSAIRQPDGTPLTDSkgrvtsHLSGLFYRTINLLENGIKPVYVFDGKPPELKSGELEKRRERREEA----- 99

                           90       100
                   ....*....|....*....|....*
gi 1958804940   85 kttEKLLKTFLKRQALKTAFR-SKR 108
Cdd:cd09867    100 ---EEKLEEALEEGDLEEARKyAKR 121
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 11-77 1.47e-11

FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like nucleases, structure-specific, divalent-metal-ion dependent, 5' nucleases; PIN (PilT N terminus) domain of Flap endonuclease-1 (FEN1) and exonuclease-1 (EXO1)-like nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350200 [Multi-domain]  Cd Length: 162  Bit Score: 63.93  E-value: 1.47e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958804940   11 DISIWLNQALKGVRDRHG-NAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKD 77
Cdd:cd00128     25 DASIWVYQFLTAKREQGGdIGVTNSHLRGLFYRIIKLLSNGIKPIFVFDGGPPPLKKETITKKMYQEC 92
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 689-820 1.14e-10

FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR)), recombination, and telomere integrity. EXO1 functions in the MMS2 error-free branch of the PRR pathway in the maintenance and repair of stalled replication forks. Studies also suggest that EXO1 plays both structural and catalytic roles during MMR-mediated mutation avoidance. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively.


Pssm-ID: 350207 [Multi-domain]  Cd Length: 202  Bit Score: 62.42  E-value: 1.14e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  689 MKEH----RKEDRgaedspdewqDVNLEEldALEsnLLAEQNSLEAQKQ-QQdriAASVTGQMFLESQELLRLFGIPYIQ 763
Cdd:cd09857     84 SKAGteeeRRERR----------EEALEK--ALE--LLREGKKSEARECfQR---AVDITPEMAHELIKALRKENVEYIV 146

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958804940  764 APMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHV-YKnfFNKNKFVEYYQYVDFYN 820
Cdd:cd09857    147 APYEADAQLAYLAKTGYVDAVITEDSDLLAFGCPKVlFK--LDKDGNGQEIDRDDLGK 202
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 11-127 1.81e-10

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 64.26  E-value: 1.81e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940   11 DISIWLNQALKGVRD--RHGNAIENA-----HLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSASIDS 83
Cdd:PTZ00217    34 DASMALYQFLIAIRDdsQGGNLTNEAgevtsHISGLFNRTIRLLEAGIKPVYVFDGKPPELKSGELEKRRERREEAEEEL 113

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1958804940   84 RKTTEKllktFLKRQALKTAFRSKRnevlpsLTQVQREDDIYVL 127
Cdd:PTZ00217   114 EKAIEE----GDDEEIKKQSKRTVR------VTKEQNEDAKKLL 147
H3TH_FEN1-XPG-like cd09897
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases; The 5' ...
 827-915 3.47e-10

H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases; The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.


Pssm-ID: 188617 [Multi-domain]  Cd Length: 68  Bit Score: 56.84  E-value: 3.47e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  827 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPgrgldPLLKFSEWWHkaQNNKKAAENPYDtkvkkklrklqltpgFP 906
Cdd:cd09897      1 EQFIDLCILSGCDYLPGLPGIGPKTALKLIKEYG-----SLEKVLKALR--DDKKDKVPVPYD---------------FP 58


                   ....*....
gi 1958804940  907 NPAVADAYL 915
Cdd:cd09897     59 YKKARELFL 67
PRK03980 PRK03980
flap endonuclease-1; Provisional
 24-79 3.18e-08

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 56.37  E-value: 3.18e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958804940   24 RDRHGNaiENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSA 79
Cdd:PRK03980     1 MDSKGR--ITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEA 54
H3TH_GEN1 cd09905
H3TH domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' ...
 826-917 3.14e-07

H3TH domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease; Gap Endonuclease 1 (GEN1): Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of GEN1 and other similar eukaryotic 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.


Pssm-ID: 188625  Cd Length: 108  Bit Score: 50.04  E-value: 3.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804940  826 RNKLINLAYLLGSDYTE-GIPTVGCVTAMEILNEFPGRGLdpLLKFSEWWHKAQNNKKAAE------------NPYDTKV 892
Cdd:cd09905      1 REKLIALALLCGCDYNPkGVPGVGKERALRLVNIVSSDEV--LDRLRNWRATSDPSSPQELkkkdknhcsncgHLGKKQE 78

                           90       100       110
                   ....*....|....*....|....*....|
gi 1958804940  893 KKKL-----RKLQLTPGFPNPAVADAYLRP 917
Cdd:cd09905     79 HIKSgcedcDKALLDPGFPNEEIIEEFLSR 108
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 41-101 2.89e-06

FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR)), recombination, and telomere integrity. EXO1 functions in the MMS2 error-free branch of the PRR pathway in the maintenance and repair of stalled replication forks. Studies also suggest that EXO1 plays both structural and catalytic roles during MMR-mediated mutation avoidance. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively.


Pssm-ID: 350207 [Multi-domain]  Cd Length: 202  Bit Score: 49.33  E-value: 2.89e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958804940   41 HRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSAsidsRKTTEKLLKTFLKRQALK 101
Cdd:cd09857     61 KRVNMLLHHGITPILVFDGAPLPSKAGTEEERRERREEA----LEKALELLREGKKSEARE 117
HhH2 smart00279
Helix-hairpin-helix class 2 (Pol1 family) motifs;
826-859 8.04e-06

Helix-hairpin-helix class 2 (Pol1 family) motifs;


Pssm-ID: 197623 [Multi-domain]  Cd Length: 36  Bit Score: 43.59  E-value: 8.04e-06
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 1958804940   826 RNKLINLAYLLG--SDYTEGIPTVGCVTAMEILNEF 859
Cdd:smart00279    1 PEQFIDYAILVGdySDNIPGVKGIGPKTALKLLREF 36
H3TH_StructSpec-5'-nucleases cd00080
H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA ...
 827-889 7.71e-04

H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.


Pssm-ID: 188616 [Multi-domain]  Cd Length: 71  Bit Score: 39.28  E-value: 7.71e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958804940  827 NKLINLAYLLGSDYTE--GIPTVGCVTAMEILNEFpGRgLDPLLKFSEWWHKAQNNKKAAENPYD 889
Cdd:cd00080      1 EQFIDLCALVGCDYSDnpGVPGIGPKTAAKLALKY-GS-LEGILENLDELKGKKREKLEEPKEYA 63
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 42-97 4.51e-03

FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Structure-specific 5' nucleases are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner. The family includes the PIN (PilT N terminus) domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the PIN domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4- and T5-5' nucleases, and other homologs. Canonical members of this FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350204 [Multi-domain]  Cd Length: 174  Bit Score: 39.39  E-value: 4.51e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958804940   42 RLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSAsIDSRKTTEKLLKTFLKR 97
Cdd:cd09853     35 DLVKKLKPGIKPILLFDGGKPKAKKGNRDKRRERRARE-EDRKKGQLKEHKEFDKR 89
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 751-800 6.67e-03

FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Structure-specific 5' nucleases are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner. The family includes the PIN (PilT N terminus) domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the PIN domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4- and T5-5' nucleases, and other homologs. Canonical members of this FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350204 [Multi-domain]  Cd Length: 174  Bit Score: 39.00  E-value: 6.67e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958804940  751 QELLRLF-GIPYIQAPMEAEAQCAILDLTDQTSGT----ITDDSDIWLFGARHVY 800
Cdd:cd09853    102 FELLKHFmGIPVMDAPGEAEDEIAYLVKKHKHLGTvhliISTDGDFLLLGTDHPY 156
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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