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Conserved domains on  [gi|1907068296|ref|XP_036019586|]
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DNA excision repair protein ERCC-5 isoform X1 [Mus musculus]

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 ...
 1-860 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: 1275.60  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296    1 MDQKQALQEEFFHNPQAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLLKKNYLNQHIE 80
Cdd:TIGR00600  171 MNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLLKKNDLNQHIE 250

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296   81 NVQKEMNQQHSGQIQRQYQDEGGFLKEVESRRVVSEDTSHYILIKGIQGKK-VMDVDS--ESLPSSSNV-HSVSSNLKSS 156
Cdd:TIGR00600  251 NVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKTaVKAVDSddESLPSLSSQlDSNSEDLKSS 330

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  157 PHEKVKPEREP--EAAPPSPRTLLAIQAAMLGSSSEDEPESREGRQSKERNSGATADAGSISPRTCAAIQKALDDDNDEK 234
Cdd:TIGR00600  331 PWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIGQALDDDEDKK 410

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  235 VSGSSDD-----LAEKMLLGSGLEQEEHADETAERGGGVPFDTAPLTPSVTEVKECVTSGSSANGQTDSAHSfttashrc 309
Cdd:TIGR00600  411 VSASSDDqaspsKKTKMLLISRIEVEDDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSGHE-------- 482

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  310 DTPKETVSLARAVKEASQISSECEVEGRPAALSPAFIGTPSSHVSGVLSEREPTLAPPTTRTHSDQGIDIHPEDPELQNG 389
Cdd:TIGR00600  483 AVPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTEGTQNLQGISDHPEQFEFQNE 562

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  390 LYPLETKCNSSRLSSDDETEGGQNPAPKACSTVHVPAEAMSNLENALPSNAEERGDFQET-IQLREVPEAAARELISAPK 468
Cdd:TIGR00600  563 LSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGESADLLLISNPM 642

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  469 PMGPMEMESEESESDGSFIEVQSVVSNSELQTESSEASTHLSEKDAEEPRETLEEGTSRDTECLLQDSSDIEAMEGHREA 548
Cdd:TIGR00600  643 EVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEE 722

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  549 DIDAEDMPNEWQDINLEELDALESNLLAEQNSLKAQKQQQDRIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAML 628
Cdd:TIGR00600  723 EKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAIL 802

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  629 DLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYSQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEI 708
Cdd:TIGR00600  803 DLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEI 882

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  709 LNEFPGRGLDPLLKFSEWWHEAQNNKKVAENPYDTKVKKKLRKLQLTPGFPNPAVADAYLRPVVDDSRGSFLWGKPDVDK 788
Cdd:TIGR00600  883 LNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGKPDLDK 962

                          810       820       830       840       850       860       870
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907068296  789 IREFCQRYFGWNRMKTDESLYPVLKHLNAHQTQLRIDSFFRLAQQEKQDAKLIKSHRLNRAVTCILRKEREE 860
Cdd:TIGR00600  963 IREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRKEKEK 1034
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-860 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: 1275.60  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296    1 MDQKQALQEEFFHNPQAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLLKKNYLNQHIE 80
Cdd:TIGR00600  171 MNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLLKKNDLNQHIE 250

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296   81 NVQKEMNQQHSGQIQRQYQDEGGFLKEVESRRVVSEDTSHYILIKGIQGKK-VMDVDS--ESLPSSSNV-HSVSSNLKSS 156
Cdd:TIGR00600  251 NVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKTaVKAVDSddESLPSLSSQlDSNSEDLKSS 330

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  157 PHEKVKPEREP--EAAPPSPRTLLAIQAAMLGSSSEDEPESREGRQSKERNSGATADAGSISPRTCAAIQKALDDDNDEK 234
Cdd:TIGR00600  331 PWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIGQALDDDEDKK 410

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  235 VSGSSDD-----LAEKMLLGSGLEQEEHADETAERGGGVPFDTAPLTPSVTEVKECVTSGSSANGQTDSAHSfttashrc 309
Cdd:TIGR00600  411 VSASSDDqaspsKKTKMLLISRIEVEDDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSGHE-------- 482

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  310 DTPKETVSLARAVKEASQISSECEVEGRPAALSPAFIGTPSSHVSGVLSEREPTLAPPTTRTHSDQGIDIHPEDPELQNG 389
Cdd:TIGR00600  483 AVPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTEGTQNLQGISDHPEQFEFQNE 562

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  390 LYPLETKCNSSRLSSDDETEGGQNPAPKACSTVHVPAEAMSNLENALPSNAEERGDFQET-IQLREVPEAAARELISAPK 468
Cdd:TIGR00600  563 LSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGESADLLLISNPM 642

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  469 PMGPMEMESEESESDGSFIEVQSVVSNSELQTESSEASTHLSEKDAEEPRETLEEGTSRDTECLLQDSSDIEAMEGHREA 548
Cdd:TIGR00600  643 EVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEE 722

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  549 DIDAEDMPNEWQDINLEELDALESNLLAEQNSLKAQKQQQDRIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAML 628
Cdd:TIGR00600  723 EKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAIL 802

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  629 DLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYSQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEI 708
Cdd:TIGR00600  803 DLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEI 882

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  709 LNEFPGRGLDPLLKFSEWWHEAQNNKKVAENPYDTKVKKKLRKLQLTPGFPNPAVADAYLRPVVDDSRGSFLWGKPDVDK 788
Cdd:TIGR00600  883 LNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGKPDLDK 962

                          810       820       830       840       850       860       870
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907068296  789 IREFCQRYFGWNRMKTDESLYPVLKHLNAHQTQLRIDSFFRLAQQEKQDAKLIKSHRLNRAVTCILRKEREE 860
Cdd:TIGR00600  963 IREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRKEKEK 1034
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 594-813 6.21e-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: 6.21e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  594 SVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYS 673
Cdd:cd09868     92 SVTDEMYEEIQELLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSDVFLFGAKRVYKNFFNQNKYVEYYDMEDIER 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  674 QLgldrnklinlayllgsdytegiptvgcvtameilnefpgrgldpllkfsewwheaqnnkkvaenpydtkvkkklrklq 753
Cdd:cd09868    172 EL------------------------------------------------------------------------------ 173

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  754 ltpgfpnpavadaylrpvvddsrgSFLWGKPDVDKIREFCQRYFGWNRMKTDESLYPVLK 813
Cdd:cd09868    174 ------------------------KFSWGKPDLELLREFCLDKFGWPKEKTDELLLPVLK 209
XPG_I pfam00867
XPG I-region;
611-692 8.20e-30

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 113.38  E-value: 8.20e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  611 GVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNK-----FVEYYQYVDFYSQLGLDRNKLINL 685
Cdd:pfam00867    1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKkkskvPVEEIDLEKILKELGLTREQLIDL 80


                   ....*..
gi 1907068296  686 AYLLGSD 692
Cdd:pfam00867   81 AILLGCD 87
PRK03980 PRK03980
flap endonuclease-1; Provisional
 575-792 2.95e-26

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 109.91  E-value: 2.95e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  575 LAEQNSLKAQKQQQDriAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYK 654
Cdd:PRK03980    62 KEEGDLEEARKYAQR--SSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVR 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  655 NF--------FNKNKFVEYY-QYVDF---YSQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEfpGRGLDPLLK 722
Cdd:PRK03980   140 NLtisgkrklPGKNVYVEVKpELIELeevLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKK--HGDLEKVLE 217

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  723 fsEWWHEAQNNKKVaenpydtkvkkklRKLqltpgFPNPAVADAYlrpvvddsrgSFLWGKPDVDKIREF 792
Cdd:PRK03980   218 --ERGFEIENYDEI-------------REF-----FLNPPVTDDY----------ELKWKEPDKEGIIEF 257
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
 608-677 2.87e-25

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 99.96  E-value: 2.87e-25
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907068296   608 RLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNK-FVEYYQYV--DFYSQLGL 677
Cdd:smart00484    1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKkKLEFRIIDleSVLKELGL 73
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-860 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: 1275.60  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296    1 MDQKQALQEEFFHNPQAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESNDFSQYQLKGLLKKNYLNQHIE 80
Cdd:TIGR00600  171 MNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLLKKNDLNQHIE 250

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296   81 NVQKEMNQQHSGQIQRQYQDEGGFLKEVESRRVVSEDTSHYILIKGIQGKK-VMDVDS--ESLPSSSNV-HSVSSNLKSS 156
Cdd:TIGR00600  251 NVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSEDTSHYILIKGIQGKTaVKAVDSddESLPSLSSQlDSNSEDLKSS 330

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  157 PHEKVKPEREP--EAAPPSPRTLLAIQAAMLGSSSEDEPESREGRQSKERNSGATADAGSISPRTCAAIQKALDDDNDEK 234
Cdd:TIGR00600  331 PWEKLKPESESivEAEPPSPRTLLAKQAAMSESSSEDSDESEWERQELKRNNVAFVDDGSLSPRTLQAIGQALDDDEDKK 410

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  235 VSGSSDD-----LAEKMLLGSGLEQEEHADETAERGGGVPFDTAPLTPSVTEVKECVTSGSSANGQTDSAHSfttashrc 309
Cdd:TIGR00600  411 VSASSDDqaspsKKTKMLLISRIEVEDDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTKIAREVTSSGHE-------- 482

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  310 DTPKETVSLARAVKEASQISSECEVEGRPAALSPAFIGTPSSHVSGVLSEREPTLAPPTTRTHSDQGIDIHPEDPELQNG 389
Cdd:TIGR00600  483 AVPKAVQSLLLGATNDSPIPSEFTILDRKSELSIERTVKPVSSEFGLPSQREDKLAIPTEGTQNLQGISDHPEQFEFQNE 562

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  390 LYPLETKCNSSRLSSDDETEGGQNPAPKACSTVHVPAEAMSNLENALPSNAEERGDFQET-IQLREVPEAAARELISAPK 468
Cdd:TIGR00600  563 LSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTVPSEALDNYETTNPSNAKEVRNFAETgIQTTNVGESADLLLISNPM 642

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  469 PMGPMEMESEESESDGSFIEVQSVVSNSELQTESSEASTHLSEKDAEEPRETLEEGTSRDTECLLQDSSDIEAMEGHREA 548
Cdd:TIGR00600  643 EVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEE 722

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  549 DIDAEDMPNEWQDINLEELDALESNLLAEQNSLKAQKQQQDRIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAML 628
Cdd:TIGR00600  723 EKDADDFKNEWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAIL 802

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  629 DLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYSQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEI 708
Cdd:TIGR00600  803 DLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEI 882

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  709 LNEFPGRGLDPLLKFSEWWHEAQNNKKVAENPYDTKVKKKLRKLQLTPGFPNPAVADAYLRPVVDDSRGSFLWGKPDVDK 788
Cdd:TIGR00600  883 LNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGKPDLDK 962

                          810       820       830       840       850       860       870
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907068296  789 IREFCQRYFGWNRMKTDESLYPVLKHLNAHQTQLRIDSFFRLAQQEKQDAKLIKSHRLNRAVTCILRKEREE 860
Cdd:TIGR00600  963 IREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCMLRKEKEK 1034
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 594-813 6.21e-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: 6.21e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  594 SVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVDFYS 673
Cdd:cd09868     92 SVTDEMYEEIQELLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSDVFLFGAKRVYKNFFNQNKYVEYYDMEDIER 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  674 QLgldrnklinlayllgsdytegiptvgcvtameilnefpgrgldpllkfsewwheaqnnkkvaenpydtkvkkklrklq 753
Cdd:cd09868    172 EL------------------------------------------------------------------------------ 173

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  754 ltpgfpnpavadaylrpvvddsrgSFLWGKPDVDKIREFCQRYFGWNRMKTDESLYPVLK 813
Cdd:cd09868    174 ------------------------KFSWGKPDLELLREFCLDKFGWPKEKTDELLLPVLK 209
H3TH_XPG cd09904
H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 680-774 7.89e-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: 7.89e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  680 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPgrGLDPLLKFSEWWHEAQNNKKVAEN----PYDTKVKKKLRKLQLT 755
Cdd:cd09904      1 DKLIRLALLLGSDYTEGVSGIGPVNAMEILSEFP--GEEDLEKFKDWWENAQPEKSEDSDndkqEFKRKHKNYLKNLILP 78

                           90
                   ....*....|....*....
gi 1907068296  756 PGFPNPAVADAYLRPVVDD 774
Cdd:cd09904     79 PGFPSPAVINAYLNPNVDD 97
XPG_I pfam00867
XPG I-region;
611-692 8.20e-30

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 113.38  E-value: 8.20e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  611 GVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNK-----FVEYYQYVDFYSQLGLDRNKLINL 685
Cdd:pfam00867    1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKkkskvPVEEIDLEKILKELGLTREQLIDL 80


                   ....*..
gi 1907068296  686 AYLLGSD 692
Cdd:pfam00867   81 AILLGCD 87
PRK03980 PRK03980
flap endonuclease-1; Provisional
 575-792 2.95e-26

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 109.91  E-value: 2.95e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  575 LAEQNSLKAQKQQQDriAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYK 654
Cdd:PRK03980    62 KEEGDLEEARKYAQR--SSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVR 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  655 NF--------FNKNKFVEYY-QYVDF---YSQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEfpGRGLDPLLK 722
Cdd:PRK03980   140 NLtisgkrklPGKNVYVEVKpELIELeevLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKK--HGDLEKVLE 217

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  723 fsEWWHEAQNNKKVaenpydtkvkkklRKLqltpgFPNPAVADAYlrpvvddsrgSFLWGKPDVDKIREF 792
Cdd:PRK03980   218 --ERGFEIENYDEI-------------REF-----FLNPPVTDDY----------ELKWKEPDKEGIIEF 257
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 576-864 6.51e-26

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 111.25  E-value: 6.51e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  576 AEQNSLKAQKQ-------QQDRIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFG 648
Cdd:PTZ00217   109 AEEELEKAIEEgddeeikKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFG 188

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  649 ARHVYKNFFN----KNKFVEyYQYVDFYSQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFpgRGLDPLLKfs 724
Cdd:PTZ00217   189 TPVLLRNLNFseakKRPIQE-INLSTVLEELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKY--KSIEEILE-- 263

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  725 ewwHEAQNNKKVAEN-PYdtkvkKKLRKLqltpgFPNPAVADAylrpvvddSRGSFLWGKPDVDKIREFCQRYFGWNRMK 803
Cdd:PTZ00217   264 ---HLDKTKYPVPENfDY-----KEAREL-----FLNPEVTPA--------EEIDLKWNEPDEEGLKKFLVKEKNFNEER 322

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907068296  804 TDESLYPVLKHLNaHQTQLRIDSFF----RLAQQEKQDAKLIKSHRLNRAvTCILRKEREEKAPE 864
Cdd:PTZ00217   323 VEKYIERLKKAKT-KKTQTRLDSFFtatkKPIKKSNSKAKLKKKKKKAGA-SAVPKSETSQEAKS 385
fen_arch TIGR03674
flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap ...
 565-828 1.16e-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: 109.26  E-value: 1.16e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  565 EELDALESNLLAEQNSLKAQKQQQdrIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDI 644
Cdd:TIGR03674   99 EEAEEKWEEALEKGDLEEARKYAQ--RSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYDS 176

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  645 WLFGARHVYKNF--FNKNKFVEYYQYVDFY----------SQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEF 712
Cdd:TIGR03674  177 LLFGAPRLVRNLtiSGKRKLPGKNIYVEVKpelieleevlSELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEH 256

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  713 PgrglDPLLKFSEWWHEAQNnkkvaenpYDtkvkkKLRKLqltpgFPNPAVADAYlrpvvddsrgSFLWGKPDVDKIREF 792
Cdd:TIGR03674  257 G----DLEKVLKARGEDIEN--------YD-----EIREF-----FLNPPVTDDY----------ELEWRKPDKEGIIEF 304

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 1907068296  793 -CQRY-FGWNRMKtdeslyPVLKHLNA--HQTQLRIDSFF 828
Cdd:TIGR03674  305 lCDEHdFSEDRVE------RALERLEAayKSKQKTLDRWF 338
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
 608-677 2.87e-25

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 99.96  E-value: 2.87e-25
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907068296   608 RLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNK-FVEYYQYV--DFYSQLGL 677
Cdd:smart00484    1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKkKLEFRIIDleSVLKELGL 73
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 602-681 4.90e-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: 4.90e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  602 ESQELLRLFGVPYIQAPMEAEAQCAMLD---LTDqtsGTITDDSDIWLFGARHVYKNF--FNKNKFVEYYQYVDFYSQLG 676
Cdd:cd09869    116 ECEELLELLGVPVVQAPGEAEALCALLNaegLVD---GCITNDGDAFLYGARTVYRNFslNTKDGSVECYDMSDIEKRLS 192


                   ....*
gi 1907068296  677 LDRNK 681
Cdd:cd09869    193 LRWRR 197
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 569-672 1.01e-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: 1.01e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  569 ALESNLLAEQNSLKAQKQQQDRIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFG 648
Cdd:cd09856     94 AEESAKSAVEDELFEEQSKDKKRSGTVTKVMTAECKHLLSLFGIPYVDAPGEAEAQCAYLEQQGIVDAVLTEDVDTFLFG 173

                           90       100
                   ....*....|....*....|....
gi 1907068296  649 ARHVYKNFFNKNKfveyYQYVDFY 672
Cdd:cd09856    174 SPVVYRNLTSEGK----KTHVELY 193
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 594-666 1.99e-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: 1.99e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907068296  594 SVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYY 666
Cdd:cd00128     83 TITKKMYQECKHLLSLFGIPYVVAPYEAEAQCAYLLKAGIVDAAITEDSDCLLFGAPRVIRNMTFEGPHVEEF 155
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 590-656 9.41e-16

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: 9.41e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907068296  590 RIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLdltdQTSGTI----TDDSDIWLFGARHVYKNF 656
Cdd:cd09870     99 KVGKSTPHWLTKLFKELLDAFGFPWHEAPGEAEAELARL----QRLGVVdavlTDDSDALVFGATTVLRNF 165
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 575-670 1.97e-14

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


Pssm-ID: 350215 [Multi-domain]  Cd Length: 251  Bit Score: 74.36  E-value: 1.97e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  575 LAEQNSLKAQKQQQdrIAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDDSDIWLFGARHVYK 654
Cdd:cd09867    107 LEEGDLEEARKYAK--RTVRVTKEMVEEAKKLLDLMGIPYVQAPSEGEAQAAYLVKKGDVYAVASQDYDSLLFGAPRLVR 184

                           90
                   ....*....|....*.
gi 1907068296  655 NFFNKNKFVEYYQYVD 670
Cdd:cd09867    185 NLTISGKRKLKGVYRK 200
H3TH_XPG-like cd09900
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 ...
 680-713 2.28e-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: 2.28e-12
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1907068296  680 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFP 713
Cdd:cd09900      1 EQLILLALLLGTDYNPGVPGIGPKTALELLKEFG 34
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 563-672 1.52e-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: 1.52e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  563 NLEEldALEsnLLAEQNSLKAQKQ-QQdriAASVTGQMFLESQELLRLFGVPYIQAPMEAEAQCAMLDLTDQTSGTITDD 641
Cdd:cd09857     99 ALEK--ALE--LLREGKKSEARECfQR---AVDITPEMAHELIKALRKENVEYIVAPYEADAQLAYLAKTGYVDAVITED 171

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1907068296  642 SDIWLFGARHV-YKnfFNKNKFVEYYQYVDFY 672
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' ...
 680-768 2.34e-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: 2.34e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  680 NKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPgrgldPLLKFSEWWHeaQNNKKVAENPYDtkvkkklrklqltpgFP 759
Cdd:cd09897      1 EQFIDLCILSGCDYLPGLPGIGPKTALKLIKEYG-----SLEKVLKALR--DDKKDKVPVPYD---------------FP 58


                   ....*....
gi 1907068296  760 NPAVADAYL 768
Cdd:cd09897     59 YKKARELFL 67
H3TH_GEN1 cd09905
H3TH domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' ...
 679-770 4.77e-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: 4.77e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907068296  679 RNKLINLAYLLGSDYTE-GIPTVGCVTAMEILNEFPGRGLdpLLKFSEWWHEAQNNKKVAE------------NPYDTKV 745
Cdd:cd09905      1 REKLIALALLCGCDYNPkGVPGVGKERALRLVNIVSSDEV--LDRLRNWRATSDPSSPQELkkkdknhcsncgHLGKKQE 78

                           90       100       110
                   ....*....|....*....|....*....|
gi 1907068296  746 KKKL-----RKLQLTPGFPNPAVADAYLRP 770
Cdd:cd09905     79 HIKSgcedcDKALLDPGFPNEEIIEEFLSR 108
HhH2 smart00279
Helix-hairpin-helix class 2 (Pol1 family) motifs;
679-712 7.02e-06

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


Pssm-ID: 197623 [Multi-domain]  Cd Length: 36  Bit Score: 43.59  E-value: 7.02e-06
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 1907068296   679 RNKLINLAYLLG--SDYTEGIPTVGCVTAMEILNEF 712
Cdd:smart00279    1 PEQFIDYAILVGdySDNIPGVKGIGPKTALKLLREF 36
H3TH_StructSpec-5'-nucleases cd00080
H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA ...
 680-742 1.05e-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: 1.05e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907068296  680 NKLINLAYLLGSDYTE--GIPTVGCVTAMEILNEFpGRgLDPLLKFSEWWHEAQNNKKVAENPYD 742
Cdd:cd00080      1 EQFIDLCALVGCDYSDnpGVPGIGPKTAAKLALKY-GS-LEGILENLDELKGKKREKLEEPKEYA 63
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 604-653 8.65e-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: 38.23  E-value: 8.65e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1907068296  604 QELLRLF-GVPYIQAPMEAEAQCAMLDLTDQTSGT----ITDDSDIWLFGARHVY 653
Cdd:cd09853    102 FELLKHFmGIPVMDAPGEAEDEIAYLVKKHKHLGTvhliISTDGDFLLLGTDHPY 156
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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