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Conserved domains on  [gi|170172544|ref|NP_035859|]
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DNA excision repair protein ERCC-5 [Mus musculus]

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 ...
 1-1028 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: 1583.76  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544     1 MGVQGLWKLLECSGHRVSPEALEGKVLAVDISIWLNQALKGVRDSHGNVIENAHLLTLFHRLCKLLFFRIRPIFVFDGDA 80
Cdd:TIGR00600    1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    81 PLLKKQTLAKRRQRKDSASIDSRKTTEKLLKTFLKRQALKTAFRSSR--HEAPPSLTQVQRQDDIYVLPPLPEEEKHSSE 158
Cdd:TIGR00600   81 PLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   159 EEDEKQWQARMDQKQALQEEFFHNPQAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLL 238
Cdd:TIGR00600  161 EESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   239 KKNYLNQHIENVQKEMNQQHSGQIQRQYQDEGGFLKEVESRRVVSEDTSHYILIKGIQGKK-VMDVDS--ESLPSSSNV- 314
Cdd:TIGR00600  241 KKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKTaVKAVDSddESLPSLSSQl 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   315 HSVSSNLKSSPHEKVKPEREP--EAAPPSPRTLLAIQAAMLGSSSEDEPESREGRQSKERNSGATADAGSISPRTCAAIQ 392
Cdd:TIGR00600  321 DSNSEDLKSSPWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIG 400

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   393 KALDDDNDEKVSGSSDD-----LAEKMLLGSGLEQEEHADETAERGGGVPFDTAPLTPSVTEVKECVTSGSSANGQTDSA 467
Cdd:TIGR00600  401 QALDDDEDKKVSASSDDqaspsKKTKMLLISRIEVEDDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSG 480

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   468 HSfttashrcDTPKETVSLARAVKEASQISSECEVEGRPAALSPAFIGTPSSHVSGVLSEREPTLAPPTTRTHSDQGIDI 547
Cdd:TIGR00600  481 HE--------AVPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTEGTQNLQGISD 552

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   548 HPEDPELQNGLYPLETKCNSSRLSSDDETEGGQNPAPKACSTVHVPAEAMSNLENALPSNAEERGDFQET-IQLREVPEA 626
Cdd:TIGR00600  553 HPEQFEFQNELSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGES 632

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   627 AARELISAPKPMGPMEMESEESESDGSFIEVQSVVSNSELQTESSEASTHLSEKDAEEPRETLEEGTSRDTECLLQDSSD 706
Cdd:TIGR00600  633 ADLLLISNPMEVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESE 712

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   707 IEAMEGHREADIDAEDMPNEWQDINLEELDALESNLLAEQNSLKAQKQQQDRIAASVTGQMFLESQELLRLFGVPYIQAP 786
Cdd:TIGR00600  713 EDNIVGMIEEEKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAP 792

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   787 MEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYSQLGLDRNKLINLAYLLGSDYTEGIP 866
Cdd:TIGR00600  793 MEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIP 872

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   867 TVGCVTAMEILNEFPGRGLDPLLKFSEWWHEAQNNKKVAENPYDTKVKKKLRKLQLTPGFPNPAVADAYLRPVVDDSRGS 946
Cdd:TIGR00600  873 TVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGS 952

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   947 FLWGKPDVDKIREFCQRYFGWNRMKTDESLYPVLKHLNAHQTQLRIDSFFRLAQQEKQDAKLIKSHRLNRAVTCILRKER 1026
Cdd:TIGR00600  953 FLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRKEK 1032


                   ..
gi 170172544  1027 EE 1028
Cdd:TIGR00600 1033 EK 1034
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-1028 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: 1583.76  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544     1 MGVQGLWKLLECSGHRVSPEALEGKVLAVDISIWLNQALKGVRDSHGNVIENAHLLTLFHRLCKLLFFRIRPIFVFDGDA 80
Cdd:TIGR00600    1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    81 PLLKKQTLAKRRQRKDSASIDSRKTTEKLLKTFLKRQALKTAFRSSR--HEAPPSLTQVQRQDDIYVLPPLPEEEKHSSE 158
Cdd:TIGR00600   81 PLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   159 EEDEKQWQARMDQKQALQEEFFHNPQAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLL 238
Cdd:TIGR00600  161 EESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   239 KKNYLNQHIENVQKEMNQQHSGQIQRQYQDEGGFLKEVESRRVVSEDTSHYILIKGIQGKK-VMDVDS--ESLPSSSNV- 314
Cdd:TIGR00600  241 KKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKTaVKAVDSddESLPSLSSQl 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   315 HSVSSNLKSSPHEKVKPEREP--EAAPPSPRTLLAIQAAMLGSSSEDEPESREGRQSKERNSGATADAGSISPRTCAAIQ 392
Cdd:TIGR00600  321 DSNSEDLKSSPWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIG 400

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   393 KALDDDNDEKVSGSSDD-----LAEKMLLGSGLEQEEHADETAERGGGVPFDTAPLTPSVTEVKECVTSGSSANGQTDSA 467
Cdd:TIGR00600  401 QALDDDEDKKVSASSDDqaspsKKTKMLLISRIEVEDDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSG 480

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   468 HSfttashrcDTPKETVSLARAVKEASQISSECEVEGRPAALSPAFIGTPSSHVSGVLSEREPTLAPPTTRTHSDQGIDI 547
Cdd:TIGR00600  481 HE--------AVPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTEGTQNLQGISD 552

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   548 HPEDPELQNGLYPLETKCNSSRLSSDDETEGGQNPAPKACSTVHVPAEAMSNLENALPSNAEERGDFQET-IQLREVPEA 626
Cdd:TIGR00600  553 HPEQFEFQNELSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGES 632

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   627 AARELISAPKPMGPMEMESEESESDGSFIEVQSVVSNSELQTESSEASTHLSEKDAEEPRETLEEGTSRDTECLLQDSSD 706
Cdd:TIGR00600  633 ADLLLISNPMEVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESE 712

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   707 IEAMEGHREADIDAEDMPNEWQDINLEELDALESNLLAEQNSLKAQKQQQDRIAASVTGQMFLESQELLRLFGVPYIQAP 786
Cdd:TIGR00600  713 EDNIVGMIEEEKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAP 792

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   787 MEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYSQLGLDRNKLINLAYLLGSDYTEGIP 866
Cdd:TIGR00600  793 MEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIP 872

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   867 TVGCVTAMEILNEFPGRGLDPLLKFSEWWHEAQNNKKVAENPYDTKVKKKLRKLQLTPGFPNPAVADAYLRPVVDDSRGS 946
Cdd:TIGR00600  873 TVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGS 952

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   947 FLWGKPDVDKIREFCQRYFGWNRMKTDESLYPVLKHLNAHQTQLRIDSFFRLAQQEKQDAKLIKSHRLNRAVTCILRKER 1026
Cdd:TIGR00600  953 FLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRKEK 1032


                   ..
gi 170172544  1027 EE 1028
Cdd:TIGR00600 1033 EK 1034
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 2-113 8.39e-57

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: 195.43  E-value: 8.39e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    2 GVQGLWKLLECSGHRVSPEALEGKVLAVDISIWLNQALKGVRDSHGNVIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAP 81
Cdd:cd09868     1 GVKGLWKLLEPTGRPVSLESLEGKVLAVDASIWLHQFVKGMRDNEGNSVPNAHLLGFFRRICKLLFYGIKPVFVFDGPAP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 170172544   82 LLKKQTLAKRRQRKDSASIDSRktteKLLKTF 113
Cdd:cd09868    81 ALKRRTLARRRSVTDEMYEEIQ----ELLRLF 108
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 1-98 7.46e-41

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 145.45  E-value: 7.46e-41
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544      1 MGVQGLWKLLECSGHRVSPEALEGKVLAVDISIWLNQALKGVRDSHGNVIEN-AHLLTLFHRLCKLLFFRIRPIFVFDGD 79
Cdd:smart00485    1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKLGTPLPNsKHLMGLFYRTCRLLEFGIKPIFVFDGK 80

                            90
                    ....*....|....*....
gi 170172544     80 APLLKKQTLAKRRQRKDSA 98
Cdd:smart00485   81 PPPLKSETLAKRRERREEA 99
XPG_N pfam00752
XPG N-terminal domain;
2-98 1.86e-40

XPG N-terminal domain;


Pssm-ID: 395609 [Multi-domain]  Cd Length: 100  Bit Score: 144.43  E-value: 1.86e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544     2 GVQGLWKLLECSGHR--VSPEALEGKVLAVDISIWLNQALKGVRDSHGNVIEN-AHLLTLFHRLCKLLFFRIRPIFVFDG 78
Cdd:pfam00752    1 GIKGLLPILKPVALIrpVDIEALEGKTLAIDASIWLYQFLKAVRDQLGNALQNtSHLMGFFSRLCRLKDFGIKPIFVFDG 80

                           90       100
                   ....*....|....*....|
gi 170172544    79 DAPLLKKQTLAKRRQRKDSA 98
Cdd:pfam00752   81 GPPPLKAETLQKRSARRQEA 100
PRK03980 PRK03980
flap endonuclease-1; Provisional
 743-960 2.90e-26

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 110.30  E-value: 2.90e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  743 LAEQNSLKAQKQQQDriAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYK 822
Cdd:PRK03980   62 KEEGDLEEARKYAQR--SSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVR 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  823 NF--------FNKNKFVEYY-QYVDF---YSQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEfpGRGLDPLLK 890
Cdd:PRK03980  140 NLtisgkrklPGKNVYVEVKpELIELeevLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKK--HGDLEKVLE 217

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  891 fsEWWHEAQNNKKVaenpydtkvkkklRKLqltpgFPNPAVADAYlrpvvddsrgSFLWGKPDVDKIREF 960
Cdd:PRK03980  218 --ERGFEIENYDEI-------------REF-----FLNPPVTDDY----------ELKWKEPDKEGIIEF 257
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-1028 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: 1583.76  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544     1 MGVQGLWKLLECSGHRVSPEALEGKVLAVDISIWLNQALKGVRDSHGNVIENAHLLTLFHRLCKLLFFRIRPIFVFDGDA 80
Cdd:TIGR00600    1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    81 PLLKKQTLAKRRQRKDSASIDSRKTTEKLLKTFLKRQALKTAFRSSR--HEAPPSLTQVQRQDDIYVLPPLPEEEKHSSE 158
Cdd:TIGR00600   81 PLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKstPEALPSVQQVPRPQDLYVLPPLPEEEKHSSE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   159 EEDEKQWQARMDQKQALQEEFFHNPQAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLL 238
Cdd:TIGR00600  161 EESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   239 KKNYLNQHIENVQKEMNQQHSGQIQRQYQDEGGFLKEVESRRVVSEDTSHYILIKGIQGKK-VMDVDS--ESLPSSSNV- 314
Cdd:TIGR00600  241 KKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKTaVKAVDSddESLPSLSSQl 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   315 HSVSSNLKSSPHEKVKPEREP--EAAPPSPRTLLAIQAAMLGSSSEDEPESREGRQSKERNSGATADAGSISPRTCAAIQ 392
Cdd:TIGR00600  321 DSNSEDLKSSPWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIG 400

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   393 KALDDDNDEKVSGSSDD-----LAEKMLLGSGLEQEEHADETAERGGGVPFDTAPLTPSVTEVKECVTSGSSANGQTDSA 467
Cdd:TIGR00600  401 QALDDDEDKKVSASSDDqaspsKKTKMLLISRIEVEDDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSG 480

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   468 HSfttashrcDTPKETVSLARAVKEASQISSECEVEGRPAALSPAFIGTPSSHVSGVLSEREPTLAPPTTRTHSDQGIDI 547
Cdd:TIGR00600  481 HE--------AVPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTEGTQNLQGISD 552

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   548 HPEDPELQNGLYPLETKCNSSRLSSDDETEGGQNPAPKACSTVHVPAEAMSNLENALPSNAEERGDFQET-IQLREVPEA 626
Cdd:TIGR00600  553 HPEQFEFQNELSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGES 632

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   627 AARELISAPKPMGPMEMESEESESDGSFIEVQSVVSNSELQTESSEASTHLSEKDAEEPRETLEEGTSRDTECLLQDSSD 706
Cdd:TIGR00600  633 ADLLLISNPMEVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESE 712

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   707 IEAMEGHREADIDAEDMPNEWQDINLEELDALESNLLAEQNSLKAQKQQQDRIAASVTGQMFLESQELLRLFGVPYIQAP 786
Cdd:TIGR00600  713 EDNIVGMIEEEKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAP 792

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   787 MEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYSQLGLDRNKLINLAYLLGSDYTEGIP 866
Cdd:TIGR00600  793 MEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIP 872

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   867 TVGCVTAMEILNEFPGRGLDPLLKFSEWWHEAQNNKKVAENPYDTKVKKKLRKLQLTPGFPNPAVADAYLRPVVDDSRGS 946
Cdd:TIGR00600  873 TVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGS 952

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   947 FLWGKPDVDKIREFCQRYFGWNRMKTDESLYPVLKHLNAHQTQLRIDSFFRLAQQEKQDAKLIKSHRLNRAVTCILRKER 1026
Cdd:TIGR00600  953 FLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRKEK 1032


                   ..
gi 170172544  1027 EE 1028
Cdd:TIGR00600 1033 EK 1034
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 2-113 8.39e-57

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: 195.43  E-value: 8.39e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    2 GVQGLWKLLECSGHRVSPEALEGKVLAVDISIWLNQALKGVRDSHGNVIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAP 81
Cdd:cd09868     1 GVKGLWKLLEPTGRPVSLESLEGKVLAVDASIWLHQFVKGMRDNEGNSVPNAHLLGFFRRICKLLFYGIKPVFVFDGPAP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 170172544   82 LLKKQTLAKRRQRKDSASIDSRktteKLLKTF 113
Cdd:cd09868    81 ALKRRTLARRRSVTDEMYEEIQ----ELLRLF 108
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 762-981 8.54e-54

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


Pssm-ID: 350216 [Multi-domain]  Cd Length: 209  Bit Score: 186.95  E-value: 8.54e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  762 SVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYS 841
Cdd:cd09868    92 SVTDEMYEEIQELLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSDVFLFGAKRVYKNFFNQNKYVEYYDMEDIER 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  842 QLgldrnklinlayllgsdytegiptvgcvtameilnefpgrgldpllkfsewwheaqnnkkvaenpydtkvkkklrklq 921
Cdd:cd09868   172 EL------------------------------------------------------------------------------ 173

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  922 ltpgfpnpavadaylrpvvddsrgSFLWGKPDVDKIREFCQRYFGWNRMKTDESLYPVLK 981
Cdd:cd09868   174 ------------------------KFSWGKPDLELLREFCLDKFGWPKEKTDELLLPVLK 209
H3TH_XPG cd09904
H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 848-942 9.29e-42

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: 9.29e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  848 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPgrGLDPLLKFSEWWHEAQNNKKVAEN----PYDTKVKKKLRKLQLT 923
Cdd:cd09904     1 DKLIRLALLLGSDYTEGVSGIGPVNAMEILSEFP--GEEDLEKFKDWWENAQPEKSEDSDndkqEFKRKHKNYLKNLILP 78

                          90
                  ....*....|....*....
gi 170172544  924 PGFPNPAVADAYLRPVVDD 942
Cdd:cd09904    79 PGFPSPAVINAYLNPNVDD 97
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 1-98 7.46e-41

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 145.45  E-value: 7.46e-41
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544      1 MGVQGLWKLLECSGHRVSPEALEGKVLAVDISIWLNQALKGVRDSHGNVIEN-AHLLTLFHRLCKLLFFRIRPIFVFDGD 79
Cdd:smart00485    1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKLGTPLPNsKHLMGLFYRTCRLLEFGIKPIFVFDGK 80

                            90
                    ....*....|....*....
gi 170172544     80 APLLKKQTLAKRRQRKDSA 98
Cdd:smart00485   81 PPPLKSETLAKRRERREEA 99
XPG_N pfam00752
XPG N-terminal domain;
2-98 1.86e-40

XPG N-terminal domain;


Pssm-ID: 395609 [Multi-domain]  Cd Length: 100  Bit Score: 144.43  E-value: 1.86e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544     2 GVQGLWKLLECSGHR--VSPEALEGKVLAVDISIWLNQALKGVRDSHGNVIEN-AHLLTLFHRLCKLLFFRIRPIFVFDG 78
Cdd:pfam00752    1 GIKGLLPILKPVALIrpVDIEALEGKTLAIDASIWLYQFLKAVRDQLGNALQNtSHLMGFFSRLCRLKDFGIKPIFVFDG 80

                           90       100
                   ....*....|....*....|
gi 170172544    79 DAPLLKKQTLAKRRQRKDSA 98
Cdd:pfam00752   81 GPPPLKAETLQKRSARRQEA 100
XPG_I pfam00867
XPG I-region;
779-860 9.62e-30

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 113.38  E-value: 9.62e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   779 GVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNK-----FVEYYQYVDFYSQLGLDRNKLINL 853
Cdd:pfam00867    1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKkkskvPVEEIDLEKILKELGLTREQLIDL 80


                   ....*..
gi 170172544   854 AYLLGSD 860
Cdd:pfam00867   81 AILLGCD 87
PRK03980 PRK03980
flap endonuclease-1; Provisional
 743-960 2.90e-26

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 110.30  E-value: 2.90e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  743 LAEQNSLKAQKQQQDriAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYK 822
Cdd:PRK03980   62 KEEGDLEEARKYAQR--SSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVR 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  823 NF--------FNKNKFVEYY-QYVDF---YSQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEfpGRGLDPLLK 890
Cdd:PRK03980  140 NLtisgkrklPGKNVYVEVKpELIELeevLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKK--HGDLEKVLE 217

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  891 fsEWWHEAQNNKKVaenpydtkvkkklRKLqltpgFPNPAVADAYlrpvvddsrgSFLWGKPDVDKIREF 960
Cdd:PRK03980  218 --ERGFEIENYDEI-------------REF-----FLNPPVTDDY----------ELKWKEPDKEGIIEF 257
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 744-1032 5.51e-26

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 111.64  E-value: 5.51e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  744 AEQNSLKAQKQ-------QQDRIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFG 816
Cdd:PTZ00217  109 AEEELEKAIEEgddeeikKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFG 188

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  817 ARHVYKNFFN----KNKFVEyYQYVDFYSQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFpgRGLDPLLKfs 892
Cdd:PTZ00217  189 TPVLLRNLNFseakKRPIQE-INLSTVLEELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKY--KSIEEILE-- 263

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  893 ewwHEAQNNKKVAEN-PYdtkvkKKLRKLqltpgFPNPAVADAylrpvvddSRGSFLWGKPDVDKIREFCQRYFGWNRMK 971
Cdd:PTZ00217  264 ---HLDKTKYPVPENfDY-----KEAREL-----FLNPEVTPA--------EEIDLKWNEPDEEGLKKFLVKEKNFNEER 322

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 170172544  972 TDESLYPVLKHLNaHQTQLRIDSFF----RLAQQEKQDAKLIKSHRLNRAvTCILRKEREEKAPE 1032
Cdd:PTZ00217  323 VEKYIERLKKAKT-KKTQTRLDSFFtatkKPIKKSNSKAKLKKKKKKAGA-SAVPKSETSQEAKS 385
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 5-128 5.57e-26

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: 107.62  E-value: 5.57e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    5 GLWKLLECSGHRVSPEALEGKVLAVDISIWLNQALKGVRDSHGNVIENAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLK 84
Cdd:cd09856     1 GFWKIIGPSKRRISLESLRGKRVAIDASIWIYQFLTAVRGQGGNGVSNSHIRGLFYRIIRLLENGIKPVFVFDGEPPKLK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 170172544   85 KQTLAKRRQRKDSASIDSRKTTEKLlktfLKRQALKTAFRSSRH 128
Cdd:cd09856    81 KRTRRKRKERRQGAEESAKSAVEDE----LFEEQSKDKKRSGTV 120
fen_arch TIGR03674
flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap ...
 733-996 1.27e-25

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: 109.65  E-value: 1.27e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   733 EELDALESNLLAEQNSLKAQKQQQdrIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDI 812
Cdd:TIGR03674   99 EEAEEKWEEALEKGDLEEARKYAQ--RSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYDS 176

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   813 WLFGARHVYKNF--FNKNKFVEYYQYVDFY----------SQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEF 880
Cdd:TIGR03674  177 LLFGAPRLVRNLtiSGKRKLPGKNIYVEVKpelieleevlSELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEH 256

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   881 PgrglDPLLKFSEWWHEAQNnkkvaenpYDtkvkkKLRKLqltpgFPNPAVADAYlrpvvddsrgSFLWGKPDVDKIREF 960
Cdd:TIGR03674  257 G----DLEKVLKARGEDIEN--------YD-----EIREF-----FLNPPVTDDY----------ELEWRKPDKEGIIEF 304

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 170172544   961 -CQRY-FGWNRMKtdeslyPVLKHLNA--HQTQLRIDSFF 996
Cdd:TIGR03674  305 lCDEHdFSEDRVE------RALERLEAayKSKQKTLDRWF 338
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
 776-845 3.36e-25

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 99.96  E-value: 3.36e-25
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 170172544    776 RLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNK-FVEYYQYV--DFYSQLGL 845
Cdd:smart00484    1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKkKLEFRIIDleSVLKELGL 73
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 2-94 1.66e-24

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: 103.07  E-value: 1.66e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    2 GVQGLWKLLECSGHRVSPEALEGKVLAVDISIWLNQALKgVRDSHGNViENAHLLTLFHRLCKLLFFRIRPIFVFDGDAP 81
Cdd:cd09869     1 GVKGLWTILDPVKKRKPLSELRGKTLAVDLSIWICEAQT-VLALFETV-PKPHLRNLFFRTVNLLRLGIKPVFVLDGDAP 78

                          90
                  ....*....|...
gi 170172544   82 LLKKQTLAKRRQR 94
Cdd:cd09869    79 ELKLQTIKKRNAA 91
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 6-96 5.92e-19

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: 85.12  E-value: 5.92e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    6 LWKLLECSGHRVSPEALEGKVLAVDISIWLNQALKGVRDSHGNVIE-NAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLK 84
Cdd:cd00128     1 LWQFIGEAKEPISIESLKGKTVAIDASIWVYQFLTAKREQGGDIGVtNSHLRGLFYRIIKLLSNGIKPIFVFDGGPPPLK 80

                          90
                  ....*....|..
gi 170172544   85 KQTLAKRRQRKD 96
Cdd:cd00128    81 KETITKKMYQEC 92
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 5-127 1.17e-18

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: 86.68  E-value: 1.17e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    5 GLWKLLEcsGHRVSPEALEGKVLAVDISIWLNQALKGVR--------DSHGNVIenAHLLTLFHRLCKLLFFRIRPIFVF 76
Cdd:cd09867     2 NLSKLIA--IKEIELKDLSGKKIAIDASNALYQFLSAIRqpdgtpltDSKGRVT--SHLSGLFYRTINLLENGIKPVYVF 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 170172544   77 DGDAPLLKKQTLAKRRQRKDSAsidsrkttEKLLKTFLKRQALKTAF----RSSR 127
Cdd:cd09867    78 DGKPPELKSGELEKRRERREEA--------EEKLEEALEEGDLEEARkyakRTVR 124
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 2-131 2.39e-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: 85.40  E-value: 2.39e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    2 GVQGLWKLLECSGHRVSPEAL--------EGK---VLAVDISIWLNQALKGVRDSHGNVIENAHLLTLFHRLCKLLFFRI 70
Cdd:cd09870     1 GIPGLWDLLEPAAESRSLAELavveefnkRGGrplRIGIDASIWLFHAQSSFGGGHIQAGENPELRTLFYRLARLLSLPI 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 170172544   71 RPIFVFDGDA-PLLKkqtlakrRQRKDSASIDSRKTteKLLKTFLKrqalktAFRSSRHEAP 131
Cdd:cd09870    81 QPVFVFDGPNrPPFK-------RGKKVGKSTPHWLT--KLFKELLD------AFGFPWHEAP 127
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 770-849 5.87e-18

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


Pssm-ID: 350217 [Multi-domain]  Cd Length: 227  Bit Score: 84.19  E-value: 5.87e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  770 ESQELLRLFGVPYIQAPMEAEAQCAMLD---LTDqtsGTITDDSDIWLFGARHVYKNF--FNKNKFVEYYQYVDFYSQLG 844
Cdd:cd09869   116 ECEELLELLGVPVVQAPGEAEALCALLNaegLVD---GCITNDGDAFLYGARTVYRNFslNTKDGSVECYDMSDIEKRLS 192


                  ....*
gi 170172544  845 LDRNK 849
Cdd:cd09869   193 LRWRR 197
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 737-840 1.26e-16

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: 80.66  E-value: 1.26e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  737 ALESNLLAEQNSLKAQKQQQDRIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFG 816
Cdd:cd09856    94 AEESAKSAVEDELFEEQSKDKKRSGTVTKVMTAECKHLLSLFGIPYVDAPGEAEAQCAYLEQQGIVDAVLTEDVDTFLFG 173

                          90       100
                  ....*....|....*....|....
gi 170172544  817 ARHVYKNFFNKNKfveyYQYVDFY 840
Cdd:cd09856   174 SPVVYRNLTSEGK----KTHVELY 193
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 1-116 1.43e-16

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 83.13  E-value: 1.43e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    1 MGVQGLWKLLE----CSGHRVSPEALEGKVLAVDISIWLNQALKGVRDS--HGNVIENA-----HLLTLFHRLCKLLFFR 69
Cdd:PTZ00217    1 MGIKGLSKFLAdkapNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDsqGGNLTNEAgevtsHISGLFNRTIRLLEAG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 170172544   70 IRPIFVFDGDAPLLKKQTLAKRRQRKDSASIDSRKTTEK----LLKTFLKR 116
Cdd:PTZ00217   81 IKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEgddeEIKKQSKR 131
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 762-834 2.37e-16

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


Pssm-ID: 350200 [Multi-domain]  Cd Length: 162  Bit Score: 77.80  E-value: 2.37e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 170172544  762 SVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYY 834
Cdd:cd00128    83 TITKKMYQECKHLLSLFGIPYVVAPYEAEAQCAYLLKAGIVDAAITEDSDCLLFGAPRVIRNMTFEGPHVEEF 155
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 758-824 1.13e-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: 1.13e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 170172544  758 RIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLdltdQTSGTI----TDDSDIWLFGARHVYKNF 824
Cdd:cd09870    99 KVGKSTPHWLTKLFKELLDAFGFPWHEAPGEAEAELARL----QRLGVVdavlTDDSDALVFGATTVLRNF 165
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 1-126 3.09e-15

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: 75.52  E-value: 3.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544    1 MGVQGLWKLLECSGHRVSPEALEGKVLAVDISIWLNQALKG-VRDSHGNVIENAHLLTLFHRLCKLLFFRIRPIFVFDGD 79
Cdd:cd09857     1 MGIQGLLPFLKPIQRPVHISEYAGKTVAVDAYCWLHRGAYScAEELALGKPTDKYIDYCMKRVNMLLHHGITPILVFDGA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 170172544   80 APLLKKQTLAKRRQRKDSAsidsRKTTEKLLKTFLKRQALKtAFRSS 126
Cdd:cd09857    81 PLPSKAGTEEERRERREEA----LEKALELLREGKKSEARE-CFQRA 122
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 743-838 2.57e-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: 73.97  E-value: 2.57e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  743 LAEQNSLKAQKQQQdrIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYK 822
Cdd:cd09867   107 LEEGDLEEARKYAK--RTVRVTKEMVEEAKKLLDLMGIPYVQAPSEGEAQAAYLVKKGDVYAVASQDYDSLLFGAPRLVR 184

                          90
                  ....*....|....*.
gi 170172544  823 NFFNKNKFVEYYQYVD 838
Cdd:cd09867   185 NLTISGKRKLKGVYRK 200
H3TH_XPG-like cd09900
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 ...
 848-881 2.66e-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: 62.50  E-value: 2.66e-12
                          10        20        30
                  ....*....|....*....|....*....|....
gi 170172544  848 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFP 881
Cdd:cd09900     1 EQLILLALLLGTDYNPGVPGIGPKTALELLKEFG 34
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 731-840 1.81e-10

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


Pssm-ID: 350207 [Multi-domain]  Cd Length: 202  Bit Score: 61.65  E-value: 1.81e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  731 NLEEldALEsnLLAEQNSLKAQKQ-QQdriAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDD 809
Cdd:cd09857    99 ALEK--ALE--LLREGKKSEARECfQR---AVDITPEMAHELIKALRKENVEYIVAPYEADAQLAYLAKTGYVDAVITED 171

                          90       100       110
                  ....*....|....*....|....*....|..
gi 170172544  810 SDIWLFGARHV-YKnfFNKNKFVEYYQYVDFY 840
Cdd:cd09857   172 SDLLAFGCPKVlFK--LDKDGNGQEIDRDDLG 201
H3TH_FEN1-XPG-like cd09897
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases; The 5' ...
 848-936 2.74e-10

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


Pssm-ID: 188617 [Multi-domain]  Cd Length: 68  Bit Score: 57.22  E-value: 2.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  848 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPgrgldPLLKFSEWWHeaQNNKKVAENPYDtkvkkklrklqltpgFP 927
Cdd:cd09897     1 EQFIDLCILSGCDYLPGLPGIGPKTALKLIKEYG-----SLEKVLKALR--DDKKDKVPVPYD---------------FP 58


                  ....*....
gi 170172544  928 NPAVADAYL 936
Cdd:cd09897    59 YKKARELFL 67
PRK03980 PRK03980
flap endonuclease-1; Provisional
 43-98 2.79e-09

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 59.83  E-value: 2.79e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 170172544   43 RDSHGNVIenAHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQRKDSA 98
Cdd:PRK03980    1 MDSKGRIT--SHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEA 54
H3TH_GEN1 cd09905
H3TH domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' ...
 847-938 5.72e-08

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: 51.97  E-value: 5.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544  847 RNKLINLAYLLGSDYTE-GIPTVGCVTAMEILNEFPGRGLdpLLKFSEWWHEAQNNKKVAE------------NPYDTKV 913
Cdd:cd09905     1 REKLIALALLCGCDYNPkGVPGVGKERALRLVNIVSSDEV--LDRLRNWRATSDPSSPQELkkkdknhcsncgHLGKKQE 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 170172544  914 KKKL-----RKLQLTPGFPNPAVADAYLRP 938
Cdd:cd09905    79 HIKSgcedcDKALLDPGFPNEEIIEEFLSR 108
HhH2 smart00279
Helix-hairpin-helix class 2 (Pol1 family) motifs;
847-880 8.19e-06

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


Pssm-ID: 197623 [Multi-domain]  Cd Length: 36  Bit Score: 43.59  E-value: 8.19e-06
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 170172544    847 RNKLINLAYLLG--SDYTEGIPTVGCVTAMEILNEF 880
Cdd:smart00279    1 PEQFIDYAILVGdySDNIPGVKGIGPKTALKLLREF 36
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 61-142 4.27e-04

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: 42.47  E-value: 4.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170172544   61 RLCKLLFFRIRPIFVFDGDAPLLKKQTLAKRRQRKDSAsIDSRKTTEKLLKTFLKR------QALKTAFRSSRHEAP-PS 133
Cdd:cd09853    35 DLVKKLKPGIKPILLFDGGKPKAKKGNRDKRRERRARE-EDRKKGQLKEHKEFDKRlielgpEYLIRLFELLKHFMGiPV 113


                  ....*....
gi 170172544  134 LTQVQRQDD 142
Cdd:cd09853   114 MDAPGEAED 122
H3TH_StructSpec-5'-nucleases cd00080
H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA ...
 848-910 1.23e-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: 38.51  E-value: 1.23e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 170172544  848 NKLINLAYLLGSDYTE--GIPTVGCVTAMEILNEFpGRgLDPLLKFSEWWHEAQNNKKVAENPYD 910
Cdd:cd00080     1 EQFIDLCALVGCDYSDnpGVPGIGPKTAAKLALKY-GS-LEGILENLDELKGKKREKLEEPKEYA 63
 
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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