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Conserved domains on  [gi|1958804942|ref|XP_038940484|]
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DNA excision repair protein ERCC-5 isoform X3 [Rattus norvegicus]

Protein Classification

Rad2 family DNA repair protein( domain architecture ID 1003537)

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

Gene Ontology:  GO:0046872|GO:0003697|GO:0006281

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
rad2 super family cl36701
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-890 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]


The actual alignment was detected with superfamily member TIGR00600:

Pssm-ID: 273166 [Multi-domain]  Cd Length: 1034  Bit Score: 1215.13  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942    1 MGVQGLWKLLECSGRPVSPEALEGKVLAVDISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDA 80
Cdd:TIGR00600    1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   81 PLLKKQTLAKRRQKKDSASIDSRKTTEKLLKTFLKRQALKTAFRSKR--NEVLPSLTQVQREDDIYVLPPLQEEEKHSSE 158
Cdd:TIGR00600   81 PLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  159 EEDEKQWQARMDQKQALQEEFFHNPHAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLL 238
Cdd:TIGR00600  161 EESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  239 KKNYLNQHIENVQKEMNQEHSGQIQRQYEDEGGFLKEVESRRVVAEDTSHYILIKGIQGK---KVVDVDLESLPSSSKE- 314
Cdd:TIGR00600  241 KKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKtavKAVDSDDESLPSLSSQl 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  315 HSVSFNLKSSPYEKVKPESEP--EATPPSPRTLHAIQVAMLGGSSEEEPESGEGGQSKERSAWATADAGSISPQTCAAIQ 392
Cdd:TIGR00600  321 DSNSEDLKSSPWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIG 400

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  393 RALDDDEEERMCASSDN-----LAVEMLLGNGLKQE-HADEVVVKGGGVPLDTASLLPSVTEVEECVASASNDKEQTAST 466
Cdd:TIGR00600  401 QALDDDEDKKVSASSDDqaspsKKTKMLLISRIEVEdDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSG 480

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  467 HASstachpgeVPKETVSPAHVVSEASQISSECEVAGRPVPLPSAFIETPCSYASGVLSERELTLAPPI-RTHSHQRTSI 545
Cdd:TIGR00600  481 HEA--------VPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTeGTQNLQGISD 552

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  546 DPEEPELQNGLCPPKNTCNSSHLSSDDETEGGQNPASKAGSTVHVPSEAVGNVENVSSSNAEEHGDFQKT-IQLWEMPEA 624
Cdd:TIGR00600  553 HPEQFEFQNELSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGES 632

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  625 AARELISAPESLGPVEMESEESESDGSFIEVQSVISNDELQIESSEISKHLSEKDAEEPKETLEEGSPRNTECLLQDSSD 704
Cdd:TIGR00600  633 ADLLLISNPMEVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESE 712

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  705 IKAMKEHRKEDRGAEDSPDEWQDVNLEELDALESNLLAEQNSLEAQKQQQDRIAASVTGQMFLESQELLRLFGIPYIQAP 784
Cdd:TIGR00600  713 EDNIVGMIEEEKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAP 792

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  785 MEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYNQLGLDRNKLINLAYLLGSDYTEGIP 864
Cdd:TIGR00600  793 MEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIP 872

                          890       900
                   ....*....|....*....|....*.
gi 1958804942  865 TVGCVTAMEILNEFPGRGLDPLLKFS 890
Cdd:TIGR00600  873 TVGPVSAMEILNEFPGDGLEPLLKFK 898
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-890 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: 1215.13  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942    1 MGVQGLWKLLECSGRPVSPEALEGKVLAVDISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDA 80
Cdd:TIGR00600    1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   81 PLLKKQTLAKRRQKKDSASIDSRKTTEKLLKTFLKRQALKTAFRSKR--NEVLPSLTQVQREDDIYVLPPLQEEEKHSSE 158
Cdd:TIGR00600   81 PLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  159 EEDEKQWQARMDQKQALQEEFFHNPHAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLL 238
Cdd:TIGR00600  161 EESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  239 KKNYLNQHIENVQKEMNQEHSGQIQRQYEDEGGFLKEVESRRVVAEDTSHYILIKGIQGK---KVVDVDLESLPSSSKE- 314
Cdd:TIGR00600  241 KKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKtavKAVDSDDESLPSLSSQl 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  315 HSVSFNLKSSPYEKVKPESEP--EATPPSPRTLHAIQVAMLGGSSEEEPESGEGGQSKERSAWATADAGSISPQTCAAIQ 392
Cdd:TIGR00600  321 DSNSEDLKSSPWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIG 400

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  393 RALDDDEEERMCASSDN-----LAVEMLLGNGLKQE-HADEVVVKGGGVPLDTASLLPSVTEVEECVASASNDKEQTAST 466
Cdd:TIGR00600  401 QALDDDEDKKVSASSDDqaspsKKTKMLLISRIEVEdDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSG 480

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  467 HASstachpgeVPKETVSPAHVVSEASQISSECEVAGRPVPLPSAFIETPCSYASGVLSERELTLAPPI-RTHSHQRTSI 545
Cdd:TIGR00600  481 HEA--------VPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTeGTQNLQGISD 552

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  546 DPEEPELQNGLCPPKNTCNSSHLSSDDETEGGQNPASKAGSTVHVPSEAVGNVENVSSSNAEEHGDFQKT-IQLWEMPEA 624
Cdd:TIGR00600  553 HPEQFEFQNELSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGES 632

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  625 AARELISAPESLGPVEMESEESESDGSFIEVQSVISNDELQIESSEISKHLSEKDAEEPKETLEEGSPRNTECLLQDSSD 704
Cdd:TIGR00600  633 ADLLLISNPMEVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESE 712

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  705 IKAMKEHRKEDRGAEDSPDEWQDVNLEELDALESNLLAEQNSLEAQKQQQDRIAASVTGQMFLESQELLRLFGIPYIQAP 784
Cdd:TIGR00600  713 EDNIVGMIEEEKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAP 792

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  785 MEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYNQLGLDRNKLINLAYLLGSDYTEGIP 864
Cdd:TIGR00600  793 MEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIP 872

                          890       900
                   ....*....|....*....|....*.
gi 1958804942  865 TVGCVTAMEILNEFPGRGLDPLLKFS 890
Cdd:TIGR00600  873 TVGPVSAMEILNEFPGDGLEPLLKFK 898
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 2-113 1.12e-58

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: 199.67  E-value: 1.12e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   2 GVQGLWKLLECSGRPVSPEALEGKVLAVDISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAP 81
Cdd:cd09868     1 GVKGLWKLLEPTGRPVSLESLEGKVLAVDASIWLHQFVKGMRDNEGNSVPNAHLLGFFRRICKLLFYGIKPVFVFDGPAP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1958804942  82 LLKKQTLAKRRQKKDSASIDSRktteKLLKTF 113
Cdd:cd09868    81 ALKRRTLARRRSVTDEMYEEIQ----ELLRLF 108
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 1-98 6.95e-43

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 150.85  E-value: 6.95e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942    1 MGVQGLWKLLECSGRPVSPEALEGKVLAVDISIWLNQALKGVRDRHGNAIEN-AHLLTLFHRLCKLLFFRIRPIFVFDGD 79
Cdd:smart00485   1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKLGTPLPNsKHLMGLFYRTCRLLEFGIKPIFVFDGK 80

                           90
                   ....*....|....*....
gi 1958804942   80 APLLKKQTLAKRRQKKDSA 98
Cdd:smart00485  81 PPPLKSETLAKRRERREEA 99
XPG_N pfam00752
XPG N-terminal domain;
2-98 9.58e-43

XPG N-terminal domain;


Pssm-ID: 395609 [Multi-domain]  Cd Length: 100  Bit Score: 150.59  E-value: 9.58e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   2 GVQGLWKLLECSG--RPVSPEALEGKVLAVDISIWLNQALKGVRDRHGNAIEN-AHLLTLFHRLCKLLFFRIRPIFVFDG 78
Cdd:pfam00752   1 GIKGLLPILKPVAliRPVDIEALEGKTLAIDASIWLYQFLKAVRDQLGNALQNtSHLMGFFSRLCRLKDFGIKPIFVFDG 80

                          90       100
                  ....*....|....*....|
gi 1958804942  79 DAPLLKKQTLAKRRQKKDSA 98
Cdd:pfam00752  81 GPPPLKAETLQKRSARRQEA 100
PRK03980 PRK03980
flap endonuclease-1; Provisional
 710-917 4.94e-22

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 97.58  E-value: 4.94e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 710 EHRKEDRgaEDSPDEWqdvnleeLDALEsnllaEQNSLEAQKQQQDriAASVTGQMFLESQELLRLFGIPYIQAPMEAEA 789
Cdd:PRK03980   45 EERREVR--EEAEEKY-------EEAKE-----EGDLEEARKYAQR--SSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEA 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 790 QCAILDLTDQTSGTITDDSDIWLFGARHVYKNF--------FNKNKFVEYY-QYVDF---YNQLGLDRNKLINLAYLLGS 857
Cdd:PRK03980  109 QAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLtisgkrklPGKNVYVEVKpELIELeevLKELGITREQLIDIAILVGT 188

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 858 DYTEGIPTVGCVTAMEILNEfpGRGLDPLLKFSAPSIISYLAlndvytkttnIFLIFLDP 917
Cdd:PRK03980  189 DYNPGIKGIGPKTALKLIKK--HGDLEKVLEERGFEIENYDE----------IREFFLNP 236
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-890 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: 1215.13  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942    1 MGVQGLWKLLECSGRPVSPEALEGKVLAVDISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDA 80
Cdd:TIGR00600    1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   81 PLLKKQTLAKRRQKKDSASIDSRKTTEKLLKTFLKRQALKTAFRSKR--NEVLPSLTQVQREDDIYVLPPLQEEEKHSSE 158
Cdd:TIGR00600   81 PLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  159 EEDEKQWQARMDQKQALQEEFFHNPHAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLL 238
Cdd:TIGR00600  161 EESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  239 KKNYLNQHIENVQKEMNQEHSGQIQRQYEDEGGFLKEVESRRVVAEDTSHYILIKGIQGK---KVVDVDLESLPSSSKE- 314
Cdd:TIGR00600  241 KKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKtavKAVDSDDESLPSLSSQl 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  315 HSVSFNLKSSPYEKVKPESEP--EATPPSPRTLHAIQVAMLGGSSEEEPESGEGGQSKERSAWATADAGSISPQTCAAIQ 392
Cdd:TIGR00600  321 DSNSEDLKSSPWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIG 400

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  393 RALDDDEEERMCASSDN-----LAVEMLLGNGLKQE-HADEVVVKGGGVPLDTASLLPSVTEVEECVASASNDKEQTAST 466
Cdd:TIGR00600  401 QALDDDEDKKVSASSDDqaspsKKTKMLLISRIEVEdDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSG 480

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  467 HASstachpgeVPKETVSPAHVVSEASQISSECEVAGRPVPLPSAFIETPCSYASGVLSERELTLAPPI-RTHSHQRTSI 545
Cdd:TIGR00600  481 HEA--------VPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTeGTQNLQGISD 552

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  546 DPEEPELQNGLCPPKNTCNSSHLSSDDETEGGQNPASKAGSTVHVPSEAVGNVENVSSSNAEEHGDFQKT-IQLWEMPEA 624
Cdd:TIGR00600  553 HPEQFEFQNELSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGES 632

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  625 AARELISAPESLGPVEMESEESESDGSFIEVQSVISNDELQIESSEISKHLSEKDAEEPKETLEEGSPRNTECLLQDSSD 704
Cdd:TIGR00600  633 ADLLLISNPMEVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESE 712

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  705 IKAMKEHRKEDRGAEDSPDEWQDVNLEELDALESNLLAEQNSLEAQKQQQDRIAASVTGQMFLESQELLRLFGIPYIQAP 784
Cdd:TIGR00600  713 EDNIVGMIEEEKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAP 792

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942  785 MEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYNQLGLDRNKLINLAYLLGSDYTEGIP 864
Cdd:TIGR00600  793 MEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIP 872

                          890       900
                   ....*....|....*....|....*.
gi 1958804942  865 TVGCVTAMEILNEFPGRGLDPLLKFS 890
Cdd:TIGR00600  873 TVGPVSAMEILNEFPGDGLEPLLKFK 898
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 2-113 1.12e-58

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: 199.67  E-value: 1.12e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   2 GVQGLWKLLECSGRPVSPEALEGKVLAVDISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAP 81
Cdd:cd09868     1 GVKGLWKLLEPTGRPVSLESLEGKVLAVDASIWLHQFVKGMRDNEGNSVPNAHLLGFFRRICKLLFYGIKPVFVFDGPAP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1958804942  82 LLKKQTLAKRRQKKDSASIDSRktteKLLKTF 113
Cdd:cd09868    81 ALKRRTLARRRSVTDEMYEEIQ----ELLRLF 108
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 760-841 1.06e-47

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: 168.85  E-value: 1.06e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 760 SVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYN 839
Cdd:cd09868    92 SVTDEMYEEIQELLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSDVFLFGAKRVYKNFFNQNKYVEYYDMEDIER 171


                  ..
gi 1958804942 840 QL 841
Cdd:cd09868   172 EL 173
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 1-98 6.95e-43

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 150.85  E-value: 6.95e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942    1 MGVQGLWKLLECSGRPVSPEALEGKVLAVDISIWLNQALKGVRDRHGNAIEN-AHLLTLFHRLCKLLFFRIRPIFVFDGD 79
Cdd:smart00485   1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKLGTPLPNsKHLMGLFYRTCRLLEFGIKPIFVFDGK 80

                           90
                   ....*....|....*....
gi 1958804942   80 APLLKKQTLAKRRQKKDSA 98
Cdd:smart00485  81 PPPLKSETLAKRRERREEA 99
XPG_N pfam00752
XPG N-terminal domain;
2-98 9.58e-43

XPG N-terminal domain;


Pssm-ID: 395609 [Multi-domain]  Cd Length: 100  Bit Score: 150.59  E-value: 9.58e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   2 GVQGLWKLLECSG--RPVSPEALEGKVLAVDISIWLNQALKGVRDRHGNAIEN-AHLLTLFHRLCKLLFFRIRPIFVFDG 78
Cdd:pfam00752   1 GIKGLLPILKPVAliRPVDIEALEGKTLAIDASIWLYQFLKAVRDQLGNALQNtSHLMGFFSRLCRLKDFGIKPIFVFDG 80

                          90       100
                  ....*....|....*....|
gi 1958804942  79 DAPLLKKQTLAKRRQKKDSA 98
Cdd:pfam00752  81 GPPPLKAETLQKRSARRQEA 100
XPG_I pfam00867
XPG I-region;
777-858 1.90e-29

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 112.22  E-value: 1.90e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 777 GIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNK-----FVEYYQYVDFYNQLGLDRNKLINL 851
Cdd:pfam00867   1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKkkskvPVEEIDLEKILKELGLTREQLIDL 80


                  ....*..
gi 1958804942 852 AYLLGSD 858
Cdd:pfam00867  81 AILLGCD 87
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 5-108 1.62e-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: 111.86  E-value: 1.62e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   5 GLWKLLECSGRPVSPEALEGKVLAVDISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLK 84
Cdd:cd09856     1 GFWKIIGPSKRRISLESLRGKRVAIDASIWIYQFLTAVRGQGGNGVSNSHIRGLFYRIIRLLENGIKPVFVFDGEPPKLK 80

                          90       100
                  ....*....|....*....|....
gi 1958804942  85 KQTLAKRRQKKDSASIDSRKTTEK 108
Cdd:cd09856    81 KRTRRKRKERRQGAEESAKSAVED 104
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
 774-843 7.56e-25

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 98.42  E-value: 7.56e-25
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958804942  774 RLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNK-FVEYYQYV--DFYNQLGL 843
Cdd:smart00484   1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKkKLEFRIIDleSVLKELGL 73
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 2-93 3.10e-23

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: 99.22  E-value: 3.10e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   2 GVQGLWKLLECSGRPVSPEALEGKVLAVDISIWLNQALKgVRDRHGNaIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAP 81
Cdd:cd09869     1 GVKGLWTILDPVKKRKPLSELRGKTLAVDLSIWICEAQT-VLALFET-VPKPHLRNLFFRTVNLLRLGIKPVFVLDGDAP 78

                          90
                  ....*....|..
gi 1958804942  82 LLKKQTLAKRRQ 93
Cdd:cd09869    79 ELKLQTIKKRNA 90
PRK03980 PRK03980
flap endonuclease-1; Provisional
 710-917 4.94e-22

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 97.58  E-value: 4.94e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 710 EHRKEDRgaEDSPDEWqdvnleeLDALEsnllaEQNSLEAQKQQQDriAASVTGQMFLESQELLRLFGIPYIQAPMEAEA 789
Cdd:PRK03980   45 EERREVR--EEAEEKY-------EEAKE-----EGDLEEARKYAQR--SSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEA 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 790 QCAILDLTDQTSGTITDDSDIWLFGARHVYKNF--------FNKNKFVEYY-QYVDF---YNQLGLDRNKLINLAYLLGS 857
Cdd:PRK03980  109 QAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLtisgkrklPGKNVYVEVKpELIELeevLKELGITREQLIDIAILVGT 188

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 858 DYTEGIPTVGCVTAMEILNEfpGRGLDPLLKFSAPSIISYLAlndvytkttnIFLIFLDP 917
Cdd:PRK03980  189 DYNPGIKGIGPKTALKLIKK--HGDLEKVLEERGFEIENYDE----------IREFFLNP 236
fen_arch TIGR03674
flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap ...
 710-878 8.14e-22

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: 97.71  E-value: 8.14e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 710 EHRKEDRgaEDSPDEWQDvnleeldALESNLLAEQNSLEAQkqqqdriAASVTGQMFLESQELLRLFGIPYIQAPMEAEA 789
Cdd:TIGR03674  92 EERREIR--EEAEEKWEE-------ALEKGDLEEARKYAQR-------SSRLTSEIVESSKKLLDLMGIPYVQAPSEGEA 155

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 790 QCAILDLTDQTSGTITDDSDIWLFGARHVYKNF--FNKNKFVEYYQYVDFY----------NQLGLDRNKLINLAYLLGS 857
Cdd:TIGR03674 156 QAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLtiSGKRKLPGKNIYVEVKpelieleevlSELGITREQLIDIAILVGT 235

                         170       180
                  ....*....|....*....|.
gi 1958804942 858 DYTEGIPTVGCVTAMEILNEF 878
Cdd:TIGR03674 236 DYNEGVKGIGPKTALKLIKEH 256
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 6-96 8.37e-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: 90.13  E-value: 8.37e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   6 LWKLLECSGRPVSPEALEGKVLAVDISIWLNQALKGVRDRHG-NAIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLK 84
Cdd:cd00128     1 LWQFIGEAKEPISIESLKGKTVAIDASIWVYQFLTAKREQGGdIGVTNSHLRGLFYRIIKLLSNGIKPIFVFDGGPPPLK 80

                          90
                  ....*....|..
gi 1958804942  85 KQTLAKRRQKKD 96
Cdd:cd00128    81 KETITKKMYQEC 92
H3TH_XPG cd09904
H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 846-889 7.48e-19

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: 82.30  E-value: 7.48e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1958804942 846 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPgrGLDPLLKF 889
Cdd:cd09904     1 DKLIRLALLLGSDYTEGVSGIGPVNAMEILSEFP--GEEDLEKF 42
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 743-878 2.23e-18

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 88.53  E-value: 2.23e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 743 EQNSLEAQKQQQDRiAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNF 822
Cdd:PTZ00217  118 EEGDDEEIKKQSKR-TVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNL 196

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 823 FN----KNKFVEyYQYVDFYNQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEF 878
Cdd:PTZ00217  197 NFseakKRPIQE-INLSTVLEELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKY 255
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 768-847 4.28e-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: 4.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 768 ESQELLRLFGIPYIQAPMEAEAQCAILD---LTDqtsGTITDDSDIWLFGARHVYKNF--FNKNKFVEYYQYVDFYNQLG 842
Cdd:cd09869   116 ECEELLELLGVPVVQAPGEAEALCALLNaegLVD---GCITNDGDAFLYGARTVYRNFslNTKDGSVECYDMSDIEKRLS 192


                  ....*
gi 1958804942 843 LDRNK 847
Cdd:cd09869   193 LRWRR 197
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 735-838 6.20e-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: 84.13  E-value: 6.20e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 735 ALESNLLAEQNSLEAQKQQQDRIAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFG 814
Cdd:cd09856    94 AEESAKSAVEDELFEEQSKDKKRSGTVTKVMTAECKHLLSLFGIPYVDAPGEAEAQCAYLEQQGIVDAVLTEDVDTFLFG 173

                          90       100
                  ....*....|....*....|....
gi 1958804942 815 ARHVYKNFFNKNKfveyYQYVDFY 838
Cdd:cd09856   174 SPVVYRNLTSEGK----KTHVELY 193
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 2-115 7.54e-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: 83.47  E-value: 7.54e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   2 GVQGLWKLLECSGRPVSPEAL--------EGK---VLAVDISIWLNQALKGVRDRHGNAIENAHLLTLFHRLCKLLFFRI 70
Cdd:cd09870     1 GIPGLWDLLEPAAESRSLAELavveefnkRGGrplRIGIDASIWLFHAQSSFGGGHIQAGENPELRTLFYRLARLLSLPI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1958804942  71 RPIFVFDGDA-PLLKkqtlakrRQKKDSASIDSRKTteKLLKTFLK 115
Cdd:cd09870    81 QPVFVFDGPNrPPFK-------RGKKVGKSTPHWLT--KLFKELLD 117
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 5-127 1.22e-17

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: 83.60  E-value: 1.22e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   5 GLWKLLEcsGRPVSPEALEGKVLAVDISIWLNQALKGVRDRHGNAIENA------HLLTLFHRLCKLLFFRIRPIFVFDG 78
Cdd:cd09867     2 NLSKLIA--IKEIELKDLSGKKIAIDASNALYQFLSAIRQPDGTPLTDSkgrvtsHLSGLFYRTINLLENGIKPVYVFDG 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958804942  79 DAPLLKKQTLAKRRQKKDSAsidsrkttEKLLKTFLKRQALKTAFR-SKR 127
Cdd:cd09867    80 KPPELKSGELEKRRERREEA--------EEKLEEALEEGDLEEARKyAKR 121
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 760-832 8.58e-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: 78.57  E-value: 8.58e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958804942 760 SVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYY 832
Cdd:cd00128    83 TITKKMYQECKHLLSLFGIPYVVAPYEAEAQCAYLLKAGIVDAAITEDSDCLLFGAPRVIRNMTFEGPHVEEF 155
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 1-146 1.82e-16

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 82.36  E-value: 1.82e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   1 MGVQGLWKLLE----CSGRPVSPEALEGKVLAVDISIWLNQALKGVRD--RHGNAIENA-----HLLTLFHRLCKLLFFR 69
Cdd:PTZ00217    1 MGIKGLSKFLAdkapNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDdsQGGNLTNEAgevtsHISGLFNRTIRLLEAG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958804942  70 IRPIFVFDGDAPLLKKQTLAKRRQKKDSASIDSRKTTEKllktFLKRQALKTAFRSKRnevlpsLTQVQREDDIYVL 146
Cdd:PTZ00217   81 IKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEE----GDDEEIKKQSKRTVR------VTKEQNEDAKKLL 147
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 1-120 9.24e-16

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: 76.67  E-value: 9.24e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942   1 MGVQGLWKLLECSGRPVSPEALEGKVLAVDISIWLNQALkgvrdrHGNAIE-------NAHLLTLFHRLCKLLFFRIRPI 73
Cdd:cd09857     1 MGIQGLLPFLKPIQRPVHISEYAGKTVAVDAYCWLHRGA------YSCAEElalgkptDKYIDYCMKRVNMLLHHGITPI 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1958804942  74 FVFDGDAPLLKKQTLAKRRQKKDSAsidsRKTTEKLLKTFLKRQALK 120
Cdd:cd09857    75 LVFDGAPLPSKAGTEEERRERREEA----LEKALELLREGKKSEARE 117
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 756-822 2.95e-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: 2.95e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958804942 756 RIAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILdltdQTSGTI----TDDSDIWLFGARHVYKNF 822
Cdd:cd09870    99 KVGKSTPHWLTKLFKELLDAFGFPWHEAPGEAEAELARL----QRLGVVdavlTDDSDALVFGATTVLRNF 165
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 741-836 7.03e-15

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: 75.51  E-value: 7.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 741 LAEQNSLEAQKQQQdrIAASVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYK 820
Cdd:cd09867   107 LEEGDLEEARKYAK--RTVRVTKEMVEEAKKLLDLMGIPYVQAPSEGEAQAAYLVKKGDVYAVASQDYDSLLFGAPRLVR 184

                          90
                  ....*....|....*.
gi 1958804942 821 NFFNKNKFVEYYQYVD 836
Cdd:cd09867   185 NLTISGKRKLKGVYRK 200
H3TH_XPG-like cd09900
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 ...
 846-897 1.83e-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: 1.83e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958804942 846 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPgrglDPLLKF-SAPSIISY 897
Cdd:cd09900     1 EQLILLALLLGTDYNPGVPGIGPKTALELLKEFG----EDLEKFlESEEILEA 49
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 708-839 8.87e-11

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: 8.87e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958804942 708 MKEH----RKEDRgaedspdewqDVNLEEldALEsnLLAEQNSLEAQKQ-QQdriAASVTGQMFLESQELLRLFGIPYIQ 782
Cdd:cd09857    84 SKAGteeeRRERR----------EEALEK--ALE--LLREGKKSEARECfQR---AVDITPEMAHELIKALRKENVEYIV 146

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958804942 783 APMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHV-YKnfFNKNKFVEYYQYVDFYN 839
Cdd:cd09857   147 APYEADAQLAYLAKTGYVDAVITEDSDLLAFGCPKVlFK--LDKDGNGQEIDRDDLGK 202
H3TH_FEN1-XPG-like cd09897
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases; The 5' ...
 846-879 7.80e-09

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: 52.98  E-value: 7.80e-09
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1958804942 846 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFP 879
Cdd:cd09897     1 EQFIDLCILSGCDYLPGLPGIGPKTALKLIKEYG 34
PRK03980 PRK03980
flap endonuclease-1; Provisional
 43-98 2.16e-08

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 56.75  E-value: 2.16e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958804942  43 RDRHGNaiENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSA 98
Cdd:PRK03980    1 MDSKGR--ITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEA 54
HhH2 smart00279
Helix-hairpin-helix class 2 (Pol1 family) motifs;
845-878 6.47e-06

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


Pssm-ID: 197623 [Multi-domain]  Cd Length: 36  Bit Score: 43.59  E-value: 6.47e-06
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1958804942  845 RNKLINLAYLLG--SDYTEGIPTVGCVTAMEILNEF 878
Cdd:smart00279   1 PEQFIDYAILVGdySDNIPGVKGIGPKTALKLLREF 36
H3TH_GEN1 cd09905
H3TH domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' ...
 845-881 1.81e-04

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: 41.57  E-value: 1.81e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1958804942 845 RNKLINLAYLLGSDYTE-GIPTVGCVTAMEILNEFPGR 881
Cdd:cd09905     1 REKLIALALLCGCDYNPkGVPGVGKERALRLVNIVSSD 38
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 61-116 3.54e-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: 3.54e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958804942  61 RLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQKKDSAsIDSRKTTEKLLKTFLKR 116
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 ...
 770-819 5.24e-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: 5.24e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958804942 770 QELLRLF-GIPYIQAPMEAEAQCAILDLTDQTSGT----ITDDSDIWLFGARHVY 819
Cdd:cd09853   102 FELLKHFmGIPVMDAPGEAEDEIAYLVKKHKHLGTvhliISTDGDFLLLGTDHPY 156
H3TH_StructSpec-5'-nucleases cd00080
H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA ...
 846-878 6.58e-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: 36.20  E-value: 6.58e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958804942 846 NKLINLAYLLGSDYTE--GIPTVGCVTAMEILNEF 878
Cdd:cd00080     1 EQFIDLCALVGCDYSDnpGVPGIGPKTAAKLALKY 35
 
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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