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Conserved domains on  [gi|1780199937|ref|NP_000114|]
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DNA excision repair protein ERCC-5 [Homo sapiens]

Protein Classification

Rad2 family DNA repair protein; XPG/RAD2 family endonuclease( domain architecture ID 11489416)

Rad2 family DNA repair protein, similar to DNA repair protein XPG (also known as ERCC5), a homolog of UVH3 and RAD2 proteins, which are involved in nucleotide excision repair (NER) and other DNA repair pathways| XPG/RAD2 family endonuclease similar to Saccharomyces cerevisiae DNA repair protein RAD2, a single-stranded DNA endonuclease involved in excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents, and Homo sapiens Xeroderma pigmentosum group G-complementing protein (XPG), a single-stranded structure-specific DNA endonuclease involved in DNA excision repair

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 ...
 1-1029 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: 1567.58  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    1 MGVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIENPHLLTLFHRLCKLLFFRIRPIFVFDGDA 80
Cdd:TIGR00600    1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937   81 PLLKKQTLVKRRQRKDLASSDSRKTTEKLLKTFLKRQAIKTAFRSKR--DEALPSLTQVRRENDLYVLPPLQEEEKHSSE 158
Cdd:TIGR00600   81 PLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  159 EEDEKEWQERMNQKQALQEEFFHNPQAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESDDFSQYQLKGLL 238
Cdd:TIGR00600  161 EESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  239 KKNYLNQHIEHVQKEMNQQHSGHIRRQYEDEGGFLKEVESRRVVSEDTSHYILIKGIQAKT-VAEVDS--ESLPS-SSKM 314
Cdd:TIGR00600  241 KKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKTaVKAVDSddESLPSlSSQL 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  315 HGMSFDVKSSPCEKLKTEKEP--DATPPSPRTLLAMQAALLGSSSEEELESENRRQARGRNAPAAVDEGSISPRTLSAIK 392
Cdd:TIGR00600  321 DSNSEDLKSSPWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIG 400

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  393 RALDDDEDVKVCAGDDVQTGGPGAEEMRINSSTENSDEGLKVRD-GKGIPFTATLASSSVNSAEEHVASTNEGREPTDS- 470
Cdd:TIGR00600  401 QALDDDEDKKVSASSDDQASPSKKTKMLLISRIEVEDDDLDYLDqGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSg 480

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  471 ---VPKEQMSLVHVGTEAFPISDESMIKDRKDRLPLESAVVRHSDAPGLPNGRELTPASPTC-TNSVSKNETHAEVLEQQ 546
Cdd:TIGR00600  481 heaVPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTEgTQNLQGISDHPEQFEFQ 560

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  547 NELCPYESKFDSSLLSSDDETKCKPNSAsevigpvslQETSSIVSVPSEAVDNVENVVSFNAKEHENFLET-IQEQQTTE 625
Cdd:TIGR00600  561 NELSPLETKNNESNLSSDAETEGSPNPE---------MPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGE 631

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  626 SAGQDLISIPKAVEPMEIDSEESESDGSFIEVQSVISDEELQAEFPETSKPPSEQGEEELVGTREGEAPAESESLLRDNS 705
Cdd:TIGR00600  632 SADLLLISNPMEVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDES 711

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  706 ERDDVDGePQEAEKDAEDSLHEWQDINLEELETLESNLLAQQNSLKAQKQQQERIAATVTGQMFLESQELLRLFGIPYIQ 785
Cdd:TIGR00600  712 EEDNIVG-MIEEEKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIV 790

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  786 APMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFFNKNKFVEYYQYVDFHNQLGLDRNKLINLAYLLGSDYTEG 865
Cdd:TIGR00600  791 APMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEG 870

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  866 IPTVGCVTAMEILNEFPGHGLEPLLKFSEWWHEAQKNPKIRPNPHDTKVKKKLRTLQLTPGFPNPAVAEAYLKPVVDDSK 945
Cdd:TIGR00600  871 IPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSK 950

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  946 GSFLWGKPDLDKIREFCQRYFGWNRTKTDESLFPVLKQLDAQQTQLRIDSFFRLAQQEKEDAKRIKSQRLNRAVTCMLRK 1025
Cdd:TIGR00600  951 GSFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRK 1030


                   ....
gi 1780199937 1026 EKEA 1029
Cdd:TIGR00600 1031 EKEK 1034
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-1029 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: 1567.58  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    1 MGVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIENPHLLTLFHRLCKLLFFRIRPIFVFDGDA 80
Cdd:TIGR00600    1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937   81 PLLKKQTLVKRRQRKDLASSDSRKTTEKLLKTFLKRQAIKTAFRSKR--DEALPSLTQVRRENDLYVLPPLQEEEKHSSE 158
Cdd:TIGR00600   81 PLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  159 EEDEKEWQERMNQKQALQEEFFHNPQAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESDDFSQYQLKGLL 238
Cdd:TIGR00600  161 EESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  239 KKNYLNQHIEHVQKEMNQQHSGHIRRQYEDEGGFLKEVESRRVVSEDTSHYILIKGIQAKT-VAEVDS--ESLPS-SSKM 314
Cdd:TIGR00600  241 KKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKTaVKAVDSddESLPSlSSQL 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  315 HGMSFDVKSSPCEKLKTEKEP--DATPPSPRTLLAMQAALLGSSSEEELESENRRQARGRNAPAAVDEGSISPRTLSAIK 392
Cdd:TIGR00600  321 DSNSEDLKSSPWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIG 400

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  393 RALDDDEDVKVCAGDDVQTGGPGAEEMRINSSTENSDEGLKVRD-GKGIPFTATLASSSVNSAEEHVASTNEGREPTDS- 470
Cdd:TIGR00600  401 QALDDDEDKKVSASSDDQASPSKKTKMLLISRIEVEDDDLDYLDqGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSg 480

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  471 ---VPKEQMSLVHVGTEAFPISDESMIKDRKDRLPLESAVVRHSDAPGLPNGRELTPASPTC-TNSVSKNETHAEVLEQQ 546
Cdd:TIGR00600  481 heaVPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTEgTQNLQGISDHPEQFEFQ 560

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  547 NELCPYESKFDSSLLSSDDETKCKPNSAsevigpvslQETSSIVSVPSEAVDNVENVVSFNAKEHENFLET-IQEQQTTE 625
Cdd:TIGR00600  561 NELSPLETKNNESNLSSDAETEGSPNPE---------MPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGE 631

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  626 SAGQDLISIPKAVEPMEIDSEESESDGSFIEVQSVISDEELQAEFPETSKPPSEQGEEELVGTREGEAPAESESLLRDNS 705
Cdd:TIGR00600  632 SADLLLISNPMEVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDES 711

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  706 ERDDVDGePQEAEKDAEDSLHEWQDINLEELETLESNLLAQQNSLKAQKQQQERIAATVTGQMFLESQELLRLFGIPYIQ 785
Cdd:TIGR00600  712 EEDNIVG-MIEEEKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIV 790

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  786 APMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFFNKNKFVEYYQYVDFHNQLGLDRNKLINLAYLLGSDYTEG 865
Cdd:TIGR00600  791 APMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEG 870

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  866 IPTVGCVTAMEILNEFPGHGLEPLLKFSEWWHEAQKNPKIRPNPHDTKVKKKLRTLQLTPGFPNPAVAEAYLKPVVDDSK 945
Cdd:TIGR00600  871 IPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSK 950

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  946 GSFLWGKPDLDKIREFCQRYFGWNRTKTDESLFPVLKQLDAQQTQLRIDSFFRLAQQEKEDAKRIKSQRLNRAVTCMLRK 1025
Cdd:TIGR00600  951 GSFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRK 1030


                   ....
gi 1780199937 1026 EKEA 1029
Cdd:TIGR00600 1031 EKEK 1034
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 2-113 8.94e-56

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: 192.35  E-value: 8.94e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    2 GVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIENPHLLTLFHRLCKLLFFRIRPIFVFDGDAP 81
Cdd:cd09868      1 GVKGLWKLLEPTGRPVSLESLEGKVLAVDASIWLHQFVKGMRDNEGNSVPNAHLLGFFRRICKLLFYGIKPVFVFDGPAP 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1780199937   82 LLKKQTLVKRRQRkdlaSSDSRKTTEKLLKTF 113
Cdd:cd09868     81 ALKRRTLARRRSV----TDEMYEEIQELLRLF 108
XPG_N pfam00752
XPG N-terminal domain;
2-98 3.56e-42

XPG N-terminal domain;


Pssm-ID: 395609 [Multi-domain]  Cd Length: 100  Bit Score: 149.43  E-value: 3.56e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    2 GVQGLWKLLECSG--RQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIEN-PHLLTLFHRLCKLLFFRIRPIFVFDG 78
Cdd:pfam00752    1 GIKGLLPILKPVAliRPVDIEALEGKTLAIDASIWLYQFLKAVRDQLGNALQNtSHLMGFFSRLCRLKDFGIKPIFVFDG 80

                           90       100
                   ....*....|....*....|
gi 1780199937   79 DAPLLKKQTLVKRRQRKDLA 98
Cdd:pfam00752   81 GPPPLKAETLQKRSARRQEA 100
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 1-98 1.53e-41

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 147.38  E-value: 1.53e-41
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937     1 MGVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIEN-PHLLTLFHRLCKLLFFRIRPIFVFDGD 79
Cdd:smart00485    1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKLGTPLPNsKHLMGLFYRTCRLLEFGIKPIFVFDGK 80

                            90
                    ....*....|....*....
gi 1780199937    80 APLLKKQTLVKRRQRKDLA 98
Cdd:smart00485   81 PPPLKSETLAKRRERREEA 99
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 711-1033 7.69e-26

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 111.25  E-value: 7.69e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  711 DGEPQEAEKDAEDSLHEWQDINLEELETlesnllAQQNSLKAQKQQQERIAATVTGQMFLESQELLRLFGIPYIQAPMEA 790
Cdd:PTZ00217    88 DGKPPELKSGELEKRRERREEAEEELEK------AIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEA 161

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  791 EAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFF---NKNKFVEYYQYVDFHNQLGLDRNKLINLAYLLGSDYTEGIP 867
Cdd:PTZ00217   162 EAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNfseAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTIK 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  868 TVGCVTAMEILNEFpgHGLEPLLKfsewwheaqknpkirpnpHDTKVKKklrtlQLTPGFPNPAVAEAYLKP-VVDDSKG 946
Cdd:PTZ00217   242 GIGPKTAYKLIKKY--KSIEEILE------------------HLDKTKY-----PVPENFDYKEARELFLNPeVTPAEEI 296

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  947 SFLWGKPDLDKIREFCQRYFGWNRTKTDESLfPVLKQLDAQQTQLRIDSFF-----RLAQQEKEDAKRIKSQRLNRAVTC 1021
Cdd:PTZ00217   297 DLKWNEPDEEGLKKFLVKEKNFNEERVEKYI-ERLKKAKTKKTQTRLDSFFtatkkPIKKSNSKAKLKKKKKKAGASAVP 375

                          330
                   ....*....|..
gi 1780199937 1022 MLRKEKEAAASE 1033
Cdd:PTZ00217   376 KSETSQEAKSSG 387
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-1029 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: 1567.58  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    1 MGVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIENPHLLTLFHRLCKLLFFRIRPIFVFDGDA 80
Cdd:TIGR00600    1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937   81 PLLKKQTLVKRRQRKDLASSDSRKTTEKLLKTFLKRQAIKTAFRSKR--DEALPSLTQVRRENDLYVLPPLQEEEKHSSE 158
Cdd:TIGR00600   81 PLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  159 EEDEKEWQERMNQKQALQEEFFHNPQAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESDDFSQYQLKGLL 238
Cdd:TIGR00600  161 EESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  239 KKNYLNQHIEHVQKEMNQQHSGHIRRQYEDEGGFLKEVESRRVVSEDTSHYILIKGIQAKT-VAEVDS--ESLPS-SSKM 314
Cdd:TIGR00600  241 KKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKTaVKAVDSddESLPSlSSQL 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  315 HGMSFDVKSSPCEKLKTEKEP--DATPPSPRTLLAMQAALLGSSSEEELESENRRQARGRNAPAAVDEGSISPRTLSAIK 392
Cdd:TIGR00600  321 DSNSEDLKSSPWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIG 400

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  393 RALDDDEDVKVCAGDDVQTGGPGAEEMRINSSTENSDEGLKVRD-GKGIPFTATLASSSVNSAEEHVASTNEGREPTDS- 470
Cdd:TIGR00600  401 QALDDDEDKKVSASSDDQASPSKKTKMLLISRIEVEDDDLDYLDqGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSg 480

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  471 ---VPKEQMSLVHVGTEAFPISDESMIKDRKDRLPLESAVVRHSDAPGLPNGRELTPASPTC-TNSVSKNETHAEVLEQQ 546
Cdd:TIGR00600  481 heaVPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTEgTQNLQGISDHPEQFEFQ 560

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  547 NELCPYESKFDSSLLSSDDETKCKPNSAsevigpvslQETSSIVSVPSEAVDNVENVVSFNAKEHENFLET-IQEQQTTE 625
Cdd:TIGR00600  561 NELSPLETKNNESNLSSDAETEGSPNPE---------MPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGE 631

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  626 SAGQDLISIPKAVEPMEIDSEESESDGSFIEVQSVISDEELQAEFPETSKPPSEQGEEELVGTREGEAPAESESLLRDNS 705
Cdd:TIGR00600  632 SADLLLISNPMEVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDES 711

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  706 ERDDVDGePQEAEKDAEDSLHEWQDINLEELETLESNLLAQQNSLKAQKQQQERIAATVTGQMFLESQELLRLFGIPYIQ 785
Cdd:TIGR00600  712 EEDNIVG-MIEEEKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIV 790

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  786 APMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFFNKNKFVEYYQYVDFHNQLGLDRNKLINLAYLLGSDYTEG 865
Cdd:TIGR00600  791 APMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEG 870

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  866 IPTVGCVTAMEILNEFPGHGLEPLLKFSEWWHEAQKNPKIRPNPHDTKVKKKLRTLQLTPGFPNPAVAEAYLKPVVDDSK 945
Cdd:TIGR00600  871 IPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSK 950

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  946 GSFLWGKPDLDKIREFCQRYFGWNRTKTDESLFPVLKQLDAQQTQLRIDSFFRLAQQEKEDAKRIKSQRLNRAVTCMLRK 1025
Cdd:TIGR00600  951 GSFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRK 1030


                   ....
gi 1780199937 1026 EKEA 1029
Cdd:TIGR00600 1031 EKEK 1034
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 2-113 8.94e-56

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: 192.35  E-value: 8.94e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    2 GVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIENPHLLTLFHRLCKLLFFRIRPIFVFDGDAP 81
Cdd:cd09868      1 GVKGLWKLLEPTGRPVSLESLEGKVLAVDASIWLHQFVKGMRDNEGNSVPNAHLLGFFRRICKLLFYGIKPVFVFDGPAP 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1780199937   82 LLKKQTLVKRRQRkdlaSSDSRKTTEKLLKTF 113
Cdd:cd09868     81 ALKRRTLARRRSV----TDEMYEEIQELLRLF 108
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 750-982 1.21e-55

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: 191.96  E-value: 1.21e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  750 LKAQKQQQERiaaTVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFFNKN 829
Cdd:cd09868     82 LKRRTLARRR---SVTDEMYEEIQELLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSDVFLFGAKRVYKNFFNQN 158

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  830 KFVEYYQYVDFHNQLgldrnklinlayllgsdytegiptvgcvtameilnefpghglepllkfsewwheaqknpkirpnp 909
Cdd:cd09868    159 KYVEYYDMEDIEREL----------------------------------------------------------------- 173

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1780199937  910 hdtkvkkklrtlqltpgfpnpavaeaylkpvvddskgSFLWGKPDLDKIREFCQRYFGWNRTKTDESLFPVLK 982
Cdd:cd09868    174 -------------------------------------KFSWGKPDLELLREFCLDKFGWPKEKTDELLLPVLK 209
XPG_N pfam00752
XPG N-terminal domain;
2-98 3.56e-42

XPG N-terminal domain;


Pssm-ID: 395609 [Multi-domain]  Cd Length: 100  Bit Score: 149.43  E-value: 3.56e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    2 GVQGLWKLLECSG--RQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIEN-PHLLTLFHRLCKLLFFRIRPIFVFDG 78
Cdd:pfam00752    1 GIKGLLPILKPVAliRPVDIEALEGKTLAIDASIWLYQFLKAVRDQLGNALQNtSHLMGFFSRLCRLKDFGIKPIFVFDG 80

                           90       100
                   ....*....|....*....|
gi 1780199937   79 DAPLLKKQTLVKRRQRKDLA 98
Cdd:pfam00752   81 GPPPLKAETLQKRSARRQEA 100
H3TH_XPG cd09904
H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 849-943 1.13e-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: 147.78  E-value: 1.13e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  849 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPGHglEPLLKFSEWWHEAQKNPKIRPN----PHDTKVKKKLRTLQLT 924
Cdd:cd09904      1 DKLIRLALLLGSDYTEGVSGIGPVNAMEILSEFPGE--EDLEKFKDWWENAQPEKSEDSDndkqEFKRKHKNYLKNLILP 78

                           90
                   ....*....|....*....
gi 1780199937  925 PGFPNPAVAEAYLKPVVDD 943
Cdd:cd09904     79 PGFPSPAVINAYLNPNVDD 97
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 1-98 1.53e-41

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 147.38  E-value: 1.53e-41
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937     1 MGVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIEN-PHLLTLFHRLCKLLFFRIRPIFVFDGD 79
Cdd:smart00485    1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKLGTPLPNsKHLMGLFYRTCRLLEFGIKPIFVFDGK 80

                            90
                    ....*....|....*....
gi 1780199937    80 APLLKKQTLVKRRQRKDLA 98
Cdd:smart00485   81 PPPLKSETLAKRRERREEA 99
XPG_I pfam00867
XPG I-region;
780-861 1.43e-29

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 112.99  E-value: 1.43e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  780 GIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFFNKNK-----FVEYYQYVDFHNQLGLDRNKLINL 854
Cdd:pfam00867    1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKkkskvPVEEIDLEKILKELGLTREQLIDL 80


                   ....*..
gi 1780199937  855 AYLLGSD 861
Cdd:pfam00867   81 AILLGCD 87
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 5-108 6.95e-27

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: 110.32  E-value: 6.95e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    5 GLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIENPHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLK 84
Cdd:cd09856      1 GFWKIIGPSKRRISLESLRGKRVAIDASIWIYQFLTAVRGQGGNGVSNSHIRGLFYRIIRLLENGIKPVFVFDGEPPKLK 80

                           90       100
                   ....*....|....*....|....
gi 1780199937   85 KQTLVKRRQRKDLASSDSRKTTEK 108
Cdd:cd09856     81 KRTRRKRKERRQGAEESAKSAVED 104
fen_arch TIGR03674
flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap ...
 711-997 5.70e-26

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: 110.42  E-value: 5.70e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  711 DGEPQEAeKDAEdsLHEWQDINLEELETLEsNLLAQQNSLKAQKQQQEriAATVTGQMFLESQELLRLFGIPYIQAPMEA 790
Cdd:TIGR03674   80 DGKPPEL-KAET--LEERREIREEAEEKWE-EALEKGDLEEARKYAQR--SSRLTSEIVESSKKLLDLMGIPYVQAPSEG 153

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  791 EAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNF--FNKNKFVEYYQYVDFH----------NQLGLDRNKLINLAYLL 858
Cdd:TIGR03674  154 EAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLtiSGKRKLPGKNIYVEVKpelieleevlSELGITREQLIDIAILV 233

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  859 GSDYTEGIPTVGCVTAMEILNEfpgHG-LEPLLKfsewwhEAQKNPkirPNPhdtkvkKKLRTLqltpgFPNPAVAEAYl 937
Cdd:TIGR03674  234 GTDYNEGVKGIGPKTALKLIKE---HGdLEKVLK------ARGEDI---ENY------DEIREF-----FLNPPVTDDY- 289

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1780199937  938 kpvvddskgSFLWGKPDLDKIREF-CQRY-FGWNRTKtdeslfPVLKQLDA--QQTQLRIDSFF 997
Cdd:TIGR03674  290 ---------ELEWRKPDKEGIIEFlCDEHdFSEDRVE------RALERLEAayKSKQKTLDRWF 338
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 711-1033 7.69e-26

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 111.25  E-value: 7.69e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  711 DGEPQEAEKDAEDSLHEWQDINLEELETlesnllAQQNSLKAQKQQQERIAATVTGQMFLESQELLRLFGIPYIQAPMEA 790
Cdd:PTZ00217    88 DGKPPELKSGELEKRRERREEAEEELEK------AIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEA 161

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  791 EAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFF---NKNKFVEYYQYVDFHNQLGLDRNKLINLAYLLGSDYTEGIP 867
Cdd:PTZ00217   162 EAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNfseAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTIK 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  868 TVGCVTAMEILNEFpgHGLEPLLKfsewwheaqknpkirpnpHDTKVKKklrtlQLTPGFPNPAVAEAYLKP-VVDDSKG 946
Cdd:PTZ00217   242 GIGPKTAYKLIKKY--KSIEEILE------------------HLDKTKY-----PVPENFDYKEARELFLNPeVTPAEEI 296

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  947 SFLWGKPDLDKIREFCQRYFGWNRTKTDESLfPVLKQLDAQQTQLRIDSFF-----RLAQQEKEDAKRIKSQRLNRAVTC 1021
Cdd:PTZ00217   297 DLKWNEPDEEGLKKFLVKEKNFNEERVEKYI-ERLKKAKTKKTQTRLDSFFtatkkPIKKSNSKAKLKKKKKKAGASAVP 375

                          330
                   ....*....|..
gi 1780199937 1022 MLRKEKEAAASE 1033
Cdd:PTZ00217   376 KSETSQEAKSSG 387
PRK03980 PRK03980
flap endonuclease-1; Provisional
 711-997 7.83e-26

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 108.75  E-value: 7.83e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  711 DGEPQEAeKDAEdsLHEWQDINLEELETLEsNLLAQQNSLKAQKQQQEriAATVTGQMFLESQELLRLFGIPYIQAPMEA 790
Cdd:PRK03980    33 DGKPPEL-KAEE--IEERREVREEAEEKYE-EAKEEGDLEEARKYAQR--SSRLTDEIVEDSKKLLDLMGIPYVQAPSEG 106

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  791 EAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNF--------FNKNKFVEYY-QYVDFH---NQLGLDRNKLINLAYLL 858
Cdd:PRK03980   107 EAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLtisgkrklPGKNVYVEVKpELIELEevlKELGITREQLIDIAILV 186

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  859 GSDYTEGIPTVGCVTAMEILNEfpgHG-LEPLLKfsewwheaqknpKIRPNPHDTKVKKKLrtlqltpgFPNPavaeayl 937
Cdd:PRK03980   187 GTDYNPGIKGIGPKTALKLIKK---HGdLEKVLE------------ERGFEIENYDEIREF--------FLNP------- 236

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1780199937  938 kPVVDDSKgsFLWGKPDLDKIREF-CQRY-FGWNRTKtdeslfPVLKQLDA---QQTQLRIDSFF 997
Cdd:PRK03980   237 -PVTDDYE--LKWKEPDKEGIIEFlVEEHdFSEERVK------KALERLEKavkEKKQTTLDSWF 292
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 2-105 8.08e-25

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: 104.22  E-value: 8.08e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    2 GVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKgVRDRHGNsIENPHLLTLFHRLCKLLFFRIRPIFVFDGDAP 81
Cdd:cd09869      1 GVKGLWTILDPVKKRKPLSELRGKTLAVDLSIWICEAQT-VLALFET-VPKPHLRNLFFRTVNLLRLGIKPVFVLDGDAP 78

                           90       100
                   ....*....|....*....|....
gi 1780199937   82 LLKKQTLVKRRQRKDLASSDSRKT 105
Cdd:cd09869     79 ELKLQTIKKRNAARFGGAKKKGGS 102
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
 777-837 1.27e-24

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 98.04  E-value: 1.27e-24
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1780199937   777 RLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFFNKNK-FVEYYQY 837
Cdd:smart00484    1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKkKLEFRII 62
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 6-97 9.56e-21

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: 90.51  E-value: 9.56e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    6 LWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHG-NSIENPHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLK 84
Cdd:cd00128      1 LWQFIGEAKEPISIESLKGKTVAIDASIWVYQFLTAKREQGGdIGVTNSHLRGLFYRIIKLLSNGIKPIFVFDGGPPPLK 80

                           90
                   ....*....|...
gi 1780199937   85 KQTLVKRRQRKDL 97
Cdd:cd00128     81 KETITKKMYQECK 93
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 2-113 1.79e-18

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: 85.79  E-value: 1.79e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    2 GVQGLWKLLECSGRQVSPEAL--------EGK---ILAVDISIWLNQALKGVRDRHGNSIENPHLLTLFHRLCKLLFFRI 70
Cdd:cd09870      1 GIPGLWDLLEPAAESRSLAELavveefnkRGGrplRIGIDASIWLFHAQSSFGGGHIQAGENPELRTLFYRLARLLSLPI 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1780199937   71 RPIFVFDGDaplLKKQtlVKRRQRKDLASSDS-RKTTEKLLKTF 113
Cdd:cd09870     81 QPVFVFDGP---NRPP--FKRGKKVGKSTPHWlTKLFKELLDAF 119
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 711-841 4.81e-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: 4.81e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  711 DGEPQEAEKDAEDSLHEWQDinleelETLESNLLAQQNSLKAQKQQQERIAATVTGQMFLESQELLRLFGIPYIQAPMEA 790
Cdd:cd09856     73 DGEPPKLKKRTRRKRKERRQ------GAEESAKSAVEDELFEEQSKDKKRSGTVTKVMTAECKHLLSLFGIPYVDAPGEA 146

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1780199937  791 EAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFFNKNKfveyYQYVDFH 841
Cdd:cd09856    147 EAQCAYLEQQGIVDAVLTEDVDTFLFGSPVVYRNLTSEGK----KTHVELY 193
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 771-850 1.60e-17

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: 83.04  E-value: 1.60e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  771 ESQELLRLFGIPYIQAPMEAEAQCAILD---LTDqtsGTITDDSDIWLFGARHVYRNF--FNKNKFVEYYQYVDFHNQLG 845
Cdd:cd09869    116 ECEELLELLGVPVVQAPGEAEALCALLNaegLVD---GCITNDGDAFLYGARTVYRNFslNTKDGSVECYDMSDIEKRLS 192


                   ....*
gi 1780199937  846 LDRNK 850
Cdd:cd09869    193 LRWRR 197
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 763-835 1.94e-17

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: 80.88  E-value: 1.94e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1780199937  763 TVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFFNKNKFVEYY 835
Cdd:cd00128     83 TITKKMYQECKHLLSLFGIPYVVAPYEAEAQCAYLLKAGIVDAAITEDSDCLLFGAPRVIRNMTFEGPHVEEF 155
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 5-127 2.07e-16

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: 80.14  E-value: 2.07e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    5 GLWKLLEcsGRQVSPEALEGKILAVDISIWLNQALKGVR--------DRHGN--SienpHLLTLFHRLCKLLFFRIRPIF 74
Cdd:cd09867      2 NLSKLIA--IKEIELKDLSGKKIAIDASNALYQFLSAIRqpdgtpltDSKGRvtS----HLSGLFYRTINLLENGIKPVY 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1780199937   75 VFDGDAPLLKKQTLVKRRQRKDLAssdsrkttEKLLKTFLKRQAIKTAFR-SKR 127
Cdd:cd09867     76 VFDGKPPELKSGELEKRRERREEA--------EEKLEEALEEGDLEEARKyAKR 121
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 773-825 1.12e-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: 77.70  E-value: 1.12e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1780199937  773 QELLRLFGIPYIQAPMEAEAQCAILdltdQTSGTI----TDDSDIWLFGARHVYRNF 825
Cdd:cd09870    113 KELLDAFGFPWHEAPGEAEAELARL----QRLGVVdavlTDDSDALVFGATTVLRNF 165
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 1-121 2.08e-15

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 79.67  E-value: 2.08e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    1 MGVQGLWKLLE----CSGRQVSPEALEGKILAVDISIWLNQALKGVRDrhGNSIEN---------PHLLTLFHRLCKLLF 67
Cdd:PTZ00217     1 MGIKGLSKFLAdkapNAIKEQELKNYFGRVIAIDASMALYQFLIAIRD--DSQGGNltneagevtSHISGLFNRTIRLLE 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1780199937   68 FRIRPIFVFDGDAPLLKKQTLVKRRQRKDLASSDSRKTTEKLLKTFLKRQAIKT 121
Cdd:PTZ00217    79 AGIKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRT 132
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 751-839 1.86e-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: 74.36  E-value: 1.86e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  751 KAQKQQQerIAATVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFFNKNK 830
Cdd:cd09867    114 EARKYAK--RTVRVTKEMVEEAKKLLDLMGIPYVQAPSEGEAQAAYLVKKGDVYAVASQDYDSLLFGAPRLVRNLTISGK 191


                   ....*....
gi 1780199937  831 FVEYYQYVD 839
Cdd:cd09867    192 RKLKGVYRK 200
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 1-120 3.85e-14

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: 72.44  E-value: 3.85e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937    1 MGVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIE-NPHLLTLFHRLCKLLFFRIRPIFVFDGD 79
Cdd:cd09857      1 MGIQGLLPFLKPIQRPVHISEYAGKTVAVDAYCWLHRGAYSCAEELALGKPtDKYIDYCMKRVNMLLHHGITPILVFDGA 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1780199937   80 APLLKKQTLVKRRQRKDLAssdsRKTTEKLLKTFLKRQAIK 120
Cdd:cd09857     81 PLPSKAGTEEERRERREEA----LEKALELLREGKKSEARE 117
H3TH_XPG-like cd09900
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 ...
 849-906 1.66e-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: 62.89  E-value: 1.66e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1780199937  849 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPghglEPLLKFsewwheaQKNPKIR 906
Cdd:cd09900      1 EQLILLALLLGTDYNPGVPGIGPKTALELLKEFG----EDLEKF-------LESEEIL 47
H3TH_FEN1-XPG-like cd09897
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases; The 5' ...
 849-937 9.58e-11

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: 58.38  E-value: 9.58e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  849 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPghglePLLKFSEWWHEAQKNPKIRPnphdtkvkkklrtlqltPGFP 928
Cdd:cd09897      1 EQFIDLCILSGCDYLPGLPGIGPKTALKLIKEYG-----SLEKVLKALRDDKKDKVPVP-----------------YDFP 58


                   ....*....
gi 1780199937  929 NPAVAEAYL 937
Cdd:cd09897     59 YKKARELFL 67
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 711-842 1.92e-09

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: 58.57  E-value: 1.92e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  711 DGEPQEAEKDAEDSLHEWQDINLEELETLesnlLAQQNSLKAQKQQQEriAATVTGQMFLESQELLRLFGIPYIQAPMEA 790
Cdd:cd09857     78 DGAPLPSKAGTEEERRERREEALEKALEL----LREGKKSEARECFQR--AVDITPEMAHELIKALRKENVEYIVAPYEA 151

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1780199937  791 EAQCAILDLTDQTSGTITDDSDIWLFGARHVyrnFF--NKNKFVEYYQYVDFHN 842
Cdd:cd09857    152 DAQLAYLAKTGYVDAVITEDSDLLAFGCPKV---LFklDKDGNGQEIDRDDLGK 202
H3TH_GEN1 cd09905
H3TH domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' ...
 848-939 1.94e-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: 50.43  E-value: 1.94e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  848 RNKLINLAYLLGSDYTE-GIPTVGCVTAMEILNEFpgHGLEPLLKFSEWWHEAQKNP----KIRPNPH--------DTKV 914
Cdd:cd09905      1 REKLIALALLCGCDYNPkGVPGVGKERALRLVNIV--SSDEVLDRLRNWRATSDPSSpqelKKKDKNHcsncghlgKKQE 78

                           90       100       110
                   ....*....|....*....|....*....|
gi 1780199937  915 KKKL-----RTLQLTPGFPNPAVAEAYLKP 939
Cdd:cd09905     79 HIKSgcedcDKALLDPGFPNEEIIEEFLSR 108
PRK03980 PRK03980
flap endonuclease-1; Provisional
 43-95 1.95e-06

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 50.97  E-value: 1.95e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1780199937   43 RDRHGNsiENPHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLVKRRQRK 95
Cdd:PRK03980     1 MDSKGR--ITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVR 51
HhH2 smart00279
Helix-hairpin-helix class 2 (Pol1 family) motifs;
848-881 8.30e-06

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


Pssm-ID: 197623 [Multi-domain]  Cd Length: 36  Bit Score: 43.59  E-value: 8.30e-06
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 1780199937   848 RNKLINLAYLLG--SDYTEGIPTVGCVTAMEILNEF 881
Cdd:smart00279    1 PEQFIDYAILVGdySDNIPGVKGIGPKTALKLLREF 36
H3TH_YEN1 cd09906
H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' ...
 848-942 6.49e-05

H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease; Yeast Endonuclease 1 (YEN1): Holliday junction resolvase which promotes reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. YEN1 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 YEN1 and other similar fungal 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: 188626  Cd Length: 105  Bit Score: 43.06  E-value: 6.49e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  848 RNKLINLAYLLGSDY-TEGIPTVGCVTA------------MEILNEFPGHGLEPLLkfSEWWHEAQKnpKIRPNPHDT-K 913
Cdd:cd09906      1 RGGMVLFALLSGGDYdTVGLPGCGKKTAlelaklgfgdslLEAAEDLSEEELESFL--EEWRERLLE--ELRTNGRGLfG 76

                           90       100
                   ....*....|....*....|....*....
gi 1780199937  914 VKKKLRTLQLTPGFPNPAVAEAYLKPVVD 942
Cdd:cd09906     77 RNYPALSLSIPEGFPDPDVLLYYTHPVVS 105
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 710-823 1.49e-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: 40.93  E-value: 1.49e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  710 VDGEPQEAEKDAEDSLHEWQdiNLEELEtlesnllaQQNSLKAQKQQQERIAaTVTGQMFLESQELLRLF-GIPYIQAPM 788
Cdd:cd09853     50 FDGGKPKAKKGNRDKRRERR--AREEDR--------KKGQLKEHKEFDKRLI-ELGPEYLIRLFELLKHFmGIPVMDAPG 118

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1780199937  789 EAEAQCAILDLTDQTSGT----ITDDSDIWLFGARHVYR 823
Cdd:cd09853    119 EAEDEIAYLVKKHKHLGTvhliISTDGDFLLLGTDHPYI 157
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 61-116 1.67e-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: 40.55  E-value: 1.67e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1780199937   61 RLCKLLFFRIRPIFVFDGDAPLLKKQTLVKRRQRKDLAsSDSRKTTEKLLKTFLKR 116
Cdd:cd09853     35 DLVKKLKPGIKPILLFDGGKPKAKKGNRDKRRERRARE-EDRKKGQLKEHKEFDKR 89
H3TH_StructSpec-5'-nucleases cd00080
H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA ...
 849-904 3.12e-03

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: 37.35  E-value: 3.12e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780199937  849 NKLINLAYLLGSDYTE--GIPTVGCVTAMEILNEFP--GHGLEPLLKFSEWWHEAQKNPK 904
Cdd:cd00080      1 EQFIDLCALVGCDYSDnpGVPGIGPKTAAKLALKYGslEGILENLDELKGKKREKLEEPK 60
 
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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