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Conserved domains on  [gi|1835671291|ref|XP_033806539|]
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DNA repair protein complementing XP-G cells-like isoform X2 [Geotrypetes seraphini]

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 ...
 1-930 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: 837.25  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291    1 MQNAHLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRREVAASDSKKTTKKLMKTLLKRQAIKMALTDK-SS 79
Cdd:TIGR00600   50 IKNSHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKkST 129

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291   80 GEPVLSLSQVLRKgiDDIYVLPSLEEKEKNNSEEENEREWEEKMTQKQLLQEQFFENPHSVDIESEDFSCLPPEVKHEIL 159
Cdd:TIGR00600  130 PEALPSVQQVPRP--QDLYVLPPLPEEEKHSSEEESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEIL 207

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  160 SDMKEFTKRRRTLFEPMPEESNDFSRYQLKGLLKKNSFNMHIQNVQREMNEQYSEEVQTQYEHKGSVLKDVETRRLVSEE 239
Cdd:TIGR00600  208 TDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLLKKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSED 287

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  240 ASHYILIKGVKTRKadaEEMSSISPPSRLFGDSKcteNVSKINVDGKLLSDEK-----DSKMDTTPPSPRTMLAIQEALL 314
Cdd:TIGR00600  288 TSHYILIKGIQGKT---AVKAVDSDDESLPSLSS---QLDSNSEDLKSSPWEKlkpesESIVEAEPPSPRTLLAKQAAMS 361

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  315 GDSSEEEAEEKKMKHSLNVDSSfplPNEVHSNVSPQTLQIIQQTL----------------NENNENDNCNIKRIIVS-- 376
Cdd:TIGR00600  362 ESSSEDSDESEWERQELKRNNV---AFVDDGSLSPRTLQAIGQALdddedkkvsassddqaSPSKKTKMLLISRIEVEdd 438

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  377 --------EGTNVDYSSREMLLNSSDEETQEIKCVQEP------------QPCVLSSNMHFTQIDEVCQRDTELKMII-- 434
Cdd:TIGR00600  439 dldyldqgEGIPLMAALQLSSVNSKPEAVASTKIAREVtssgheavpkavQSLLLGATNDSPIPSEFTILDRKSELSIer 518

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  435 ----------VPSEK--------CRTQDINLpVSERVDLYSTQCCLSGNDVNSLSENIISEALTDTGIISNPTASLIYTP 496
Cdd:TIGR00600  519 tvkpvssefgLPSQRedklaiptEGTQNLQG-ISDHPEQFEFQNELSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTV 597

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  497 PSGNICIATNMCTRNGDS-KFVQKTISQTKKEPFKQYHLFPGEP-EVCKMAVKYESSsDSDGSFIEVETDSTDLpRFLSE 574
Cdd:TIGR00600  598 PSEALDNYETTNPSNAKEvRNFAETGIQTTNVGESADLLLISNPmEVEPMESEKEES-ESDGSFIEVDSVSSTL-ELQVP 675

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  575 TVKTLQPTYERNitamSTNTVSVLDVVGARSNTDNTFSNTLEDVALTEQQAElgKEKDAIINEWRDIDMAELKTVESALF 654
Cdd:TIGR00600  676 SKSQPTDESEEN----AENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEEE--KDADDFKNEWQDISLEELEALEANLL 749

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  655 VQQTTLHAERQQQERIAASVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKN 734
Cdd:TIGR00600  750 AEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKN 829

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  735 FFSQNKYIEYYQSVDIKNQLGLDRYKLINLAYLMGSDYTEGIPTVGYVTAMEILNEFPGPGIEPLIKFAKWWTEAQNTKK 814
Cdd:TIGR00600  830 FFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKK 909

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  815 MKPNPHDTKVKKKLYKLELSPGFPKMAVAEAYLKPVVDDSHGIFSWGRPDLEQIKEFCESHFGWCQSKTDEVLLPVLRQL 894
Cdd:TIGR00600  910 KRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKL 989

                          970       980       990
                   ....*....|....*....|....*....|....*....
gi 1835671291  895 NAYKSQLQIDSFFRLEQHEKQ---TIKSQRLQRAVTCIL 930
Cdd:TIGR00600  990 NAQQTQLRIDSFFRLAQQEKYdakDIKSQRLKRAVTCML 1028
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-930 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: 837.25  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291    1 MQNAHLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRREVAASDSKKTTKKLMKTLLKRQAIKMALTDK-SS 79
Cdd:TIGR00600   50 IKNSHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKkST 129

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291   80 GEPVLSLSQVLRKgiDDIYVLPSLEEKEKNNSEEENEREWEEKMTQKQLLQEQFFENPHSVDIESEDFSCLPPEVKHEIL 159
Cdd:TIGR00600  130 PEALPSVQQVPRP--QDLYVLPPLPEEEKHSSEEESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEIL 207

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  160 SDMKEFTKRRRTLFEPMPEESNDFSRYQLKGLLKKNSFNMHIQNVQREMNEQYSEEVQTQYEHKGSVLKDVETRRLVSEE 239
Cdd:TIGR00600  208 TDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLLKKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSED 287

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  240 ASHYILIKGVKTRKadaEEMSSISPPSRLFGDSKcteNVSKINVDGKLLSDEK-----DSKMDTTPPSPRTMLAIQEALL 314
Cdd:TIGR00600  288 TSHYILIKGIQGKT---AVKAVDSDDESLPSLSS---QLDSNSEDLKSSPWEKlkpesESIVEAEPPSPRTLLAKQAAMS 361

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  315 GDSSEEEAEEKKMKHSLNVDSSfplPNEVHSNVSPQTLQIIQQTL----------------NENNENDNCNIKRIIVS-- 376
Cdd:TIGR00600  362 ESSSEDSDESEWERQELKRNNV---AFVDDGSLSPRTLQAIGQALdddedkkvsassddqaSPSKKTKMLLISRIEVEdd 438

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  377 --------EGTNVDYSSREMLLNSSDEETQEIKCVQEP------------QPCVLSSNMHFTQIDEVCQRDTELKMII-- 434
Cdd:TIGR00600  439 dldyldqgEGIPLMAALQLSSVNSKPEAVASTKIAREVtssgheavpkavQSLLLGATNDSPIPSEFTILDRKSELSIer 518

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  435 ----------VPSEK--------CRTQDINLpVSERVDLYSTQCCLSGNDVNSLSENIISEALTDTGIISNPTASLIYTP 496
Cdd:TIGR00600  519 tvkpvssefgLPSQRedklaiptEGTQNLQG-ISDHPEQFEFQNELSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTV 597

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  497 PSGNICIATNMCTRNGDS-KFVQKTISQTKKEPFKQYHLFPGEP-EVCKMAVKYESSsDSDGSFIEVETDSTDLpRFLSE 574
Cdd:TIGR00600  598 PSEALDNYETTNPSNAKEvRNFAETGIQTTNVGESADLLLISNPmEVEPMESEKEES-ESDGSFIEVDSVSSTL-ELQVP 675

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  575 TVKTLQPTYERNitamSTNTVSVLDVVGARSNTDNTFSNTLEDVALTEQQAElgKEKDAIINEWRDIDMAELKTVESALF 654
Cdd:TIGR00600  676 SKSQPTDESEEN----AENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEEE--KDADDFKNEWQDISLEELEALEANLL 749

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  655 VQQTTLHAERQQQERIAASVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKN 734
Cdd:TIGR00600  750 AEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKN 829

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  735 FFSQNKYIEYYQSVDIKNQLGLDRYKLINLAYLMGSDYTEGIPTVGYVTAMEILNEFPGPGIEPLIKFAKWWTEAQNTKK 814
Cdd:TIGR00600  830 FFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKK 909

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  815 MKPNPHDTKVKKKLYKLELSPGFPKMAVAEAYLKPVVDDSHGIFSWGRPDLEQIKEFCESHFGWCQSKTDEVLLPVLRQL 894
Cdd:TIGR00600  910 KRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKL 989

                          970       980       990
                   ....*....|....*....|....*....|....*....
gi 1835671291  895 NAYKSQLQIDSFFRLEQHEKQ---TIKSQRLQRAVTCIL 930
Cdd:TIGR00600  990 NAQQTQLRIDSFFRLAQQEKYdakDIKSQRLKRAVTCML 1028
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 673-892 3.29e-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: 187.72  E-value: 3.29e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  673 SVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFSQNKYIEYYQSVDIKN 752
Cdd:cd09868     92 SVTDEMYEEIQELLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSDVFLFGAKRVYKNFFNQNKYVEYYDMEDIER 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  753 QLGldryklinlaylmgsdytegiptvgyvtameilnefpgpgieplikfakwwteaqntkkmkpnphdtkvkkklykle 832
Cdd:cd09868    172 ELK----------------------------------------------------------------------------- 174

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  833 lspgfpkmavaeaylkpvvddshgiFSWGRPDLEQIKEFCESHFGWCQSKTDEVLLPVLR 892
Cdd:cd09868    175 -------------------------FSWGKPDLELLREFCLDKFGWPKEKTDELLLPVLK 209
XPG_I pfam00867
XPG I-region;
690-771 1.14e-27

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 107.22  E-value: 1.14e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  690 GIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFSQNK-----YIEYYQSVDIKNQLGLDRYKLINL 764
Cdd:pfam00867    1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKkkskvPVEEIDLEKILKELGLTREQLIDL 80


                   ....*..
gi 1835671291  765 AYLMGSD 771
Cdd:pfam00867   81 AILLGCD 87
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
 687-746 7.33e-23

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 93.03  E-value: 7.33e-23
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1835671291   687 RLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFSQNK-YIEYYQ 746
Cdd:smart00484    1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKkKLEFRI 61
PRK03980 PRK03980
flap endonuclease-1; Provisional
 663-907 1.22e-22

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 99.51  E-value: 1.22e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  663 ERQQQERIAASVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNF------- 735
Cdd:PRK03980    69 EARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLtisgkrk 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  736 -FSQNKYIEYY-QSVDIK---NQLGLDRYKLINLAYLMGSDYTEGIPTVGYVTAMEILNEFpgpgieplikfakwwteaq 810
Cdd:PRK03980   149 lPGKNVYVEVKpELIELEevlKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKH------------------- 209

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  811 ntkkmkpnphdtKVKKKLYKLELSPGFPKMAVAEAYLKPVVDDSHGIfSWGRPDLEQIKEF-CESH-FGwcqskTDEVlL 888
Cdd:PRK03980   210 ------------GDLEKVLEERGFEIENYDEIREFFLNPPVTDDYEL-KWKEPDKEGIIEFlVEEHdFS-----EERV-K 270

                          250       260
                   ....*....|....*....|..
gi 1835671291  889 PVLRQL-NAYKSQLQ--IDSFF 907
Cdd:PRK03980   271 KALERLeKAVKEKKQttLDSWF 292
 
Name Accession Description Interval E-value
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 1-930 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: 837.25  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291    1 MQNAHLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRREVAASDSKKTTKKLMKTLLKRQAIKMALTDK-SS 79
Cdd:TIGR00600   50 IKNSHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKkST 129

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291   80 GEPVLSLSQVLRKgiDDIYVLPSLEEKEKNNSEEENEREWEEKMTQKQLLQEQFFENPHSVDIESEDFSCLPPEVKHEIL 159
Cdd:TIGR00600  130 PEALPSVQQVPRP--QDLYVLPPLPEEEKHSSEEESEKEWEERMNQKQALQEEFFHNPSAIDIESEEFSSLPPEVKHEIL 207

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  160 SDMKEFTKRRRTLFEPMPEESNDFSRYQLKGLLKKNSFNMHIQNVQREMNEQYSEEVQTQYEHKGSVLKDVETRRLVSEE 239
Cdd:TIGR00600  208 TDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLLKKNDLNQHIENVTKEMNQQHSGNIQRQYRDEGGFLKEVELRRVVSED 287

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  240 ASHYILIKGVKTRKadaEEMSSISPPSRLFGDSKcteNVSKINVDGKLLSDEK-----DSKMDTTPPSPRTMLAIQEALL 314
Cdd:TIGR00600  288 TSHYILIKGIQGKT---AVKAVDSDDESLPSLSS---QLDSNSEDLKSSPWEKlkpesESIVEAEPPSPRTLLAKQAAMS 361

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  315 GDSSEEEAEEKKMKHSLNVDSSfplPNEVHSNVSPQTLQIIQQTL----------------NENNENDNCNIKRIIVS-- 376
Cdd:TIGR00600  362 ESSSEDSDESEWERQELKRNNV---AFVDDGSLSPRTLQAIGQALdddedkkvsassddqaSPSKKTKMLLISRIEVEdd 438

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  377 --------EGTNVDYSSREMLLNSSDEETQEIKCVQEP------------QPCVLSSNMHFTQIDEVCQRDTELKMII-- 434
Cdd:TIGR00600  439 dldyldqgEGIPLMAALQLSSVNSKPEAVASTKIAREVtssgheavpkavQSLLLGATNDSPIPSEFTILDRKSELSIer 518

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  435 ----------VPSEK--------CRTQDINLpVSERVDLYSTQCCLSGNDVNSLSENIISEALTDTGIISNPTASLIYTP 496
Cdd:TIGR00600  519 tvkpvssefgLPSQRedklaiptEGTQNLQG-ISDHPEQFEFQNELSPLETKNNESNLSSDAETEGSPNPEMPSWSSVTV 597

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  497 PSGNICIATNMCTRNGDS-KFVQKTISQTKKEPFKQYHLFPGEP-EVCKMAVKYESSsDSDGSFIEVETDSTDLpRFLSE 574
Cdd:TIGR00600  598 PSEALDNYETTNPSNAKEvRNFAETGIQTTNVGESADLLLISNPmEVEPMESEKEES-ESDGSFIEVDSVSSTL-ELQVP 675

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  575 TVKTLQPTYERNitamSTNTVSVLDVVGARSNTDNTFSNTLEDVALTEQQAElgKEKDAIINEWRDIDMAELKTVESALF 654
Cdd:TIGR00600  676 SKSQPTDESEEN----AENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEEE--KDADDFKNEWQDISLEELEALEANLL 749

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  655 VQQTTLHAERQQQERIAASVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKN 734
Cdd:TIGR00600  750 AEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKN 829

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  735 FFSQNKYIEYYQSVDIKNQLGLDRYKLINLAYLMGSDYTEGIPTVGYVTAMEILNEFPGPGIEPLIKFAKWWTEAQNTKK 814
Cdd:TIGR00600  830 FFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKK 909

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  815 MKPNPHDTKVKKKLYKLELSPGFPKMAVAEAYLKPVVDDSHGIFSWGRPDLEQIKEFCESHFGWCQSKTDEVLLPVLRQL 894
Cdd:TIGR00600  910 KRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKL 989

                          970       980       990
                   ....*....|....*....|....*....|....*....
gi 1835671291  895 NAYKSQLQIDSFFRLEQHEKQ---TIKSQRLQRAVTCIL 930
Cdd:TIGR00600  990 NAQQTQLRIDSFFRLAQQEKYdakDIKSQRLKRAVTCML 1028
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 673-892 3.29e-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: 187.72  E-value: 3.29e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  673 SVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFSQNKYIEYYQSVDIKN 752
Cdd:cd09868     92 SVTDEMYEEIQELLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSDVFLFGAKRVYKNFFNQNKYVEYYDMEDIER 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  753 QLGldryklinlaylmgsdytegiptvgyvtameilnefpgpgieplikfakwwteaqntkkmkpnphdtkvkkklykle 832
Cdd:cd09868    172 ELK----------------------------------------------------------------------------- 174

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  833 lspgfpkmavaeaylkpvvddshgiFSWGRPDLEQIKEFCESHFGWCQSKTDEVLLPVLR 892
Cdd:cd09868    175 -------------------------FSWGKPDLELLREFCLDKFGWPKEKTDELLLPVLK 209
H3TH_XPG cd09904
H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 760-853 5.37e-39

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: 140.08  E-value: 5.37e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  760 KLINLAYLMGSDYTEGIPTVGYVTAMEILNEFPGPgiEPLIKFAKWWTEAQNTKKMKPN----PHDTKVKKKLYKLELSP 835
Cdd:cd09904      2 KLIRLALLLGSDYTEGVSGIGPVNAMEILSEFPGE--EDLEKFKDWWENAQPEKSEDSDndkqEFKRKHKNYLKNLILPP 79

                           90
                   ....*....|....*...
gi 1835671291  836 GFPKMAVAEAYLKPVVDD 853
Cdd:cd09904     80 GFPSPAVINAYLNPNVDD 97
XPG_I pfam00867
XPG I-region;
690-771 1.14e-27

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 107.22  E-value: 1.14e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  690 GIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFSQNK-----YIEYYQSVDIKNQLGLDRYKLINL 764
Cdd:pfam00867    1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKkkskvPVEEIDLEKILKELGLTREQLIDL 80


                   ....*..
gi 1835671291  765 AYLMGSD 771
Cdd:pfam00867   81 AILLGCD 87
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 3-47 5.21e-23

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: 98.36  E-value: 5.21e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1835671291    3 NAHLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRRE 47
Cdd:cd09868     51 NAHLLGFFRRICKLLFYGIKPVFVFDGPAPALKRRTLARRRSVTD 95
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
 687-746 7.33e-23

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 93.03  E-value: 7.33e-23
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1835671291   687 RLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFSQNK-YIEYYQ 746
Cdd:smart00484    1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKkKLEFRI 61
PRK03980 PRK03980
flap endonuclease-1; Provisional
 663-907 1.22e-22

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 99.51  E-value: 1.22e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  663 ERQQQERIAASVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNF------- 735
Cdd:PRK03980    69 EARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLtisgkrk 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  736 -FSQNKYIEYY-QSVDIK---NQLGLDRYKLINLAYLMGSDYTEGIPTVGYVTAMEILNEFpgpgieplikfakwwteaq 810
Cdd:PRK03980   149 lPGKNVYVEVKpELIELEevlKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKH------------------- 209

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  811 ntkkmkpnphdtKVKKKLYKLELSPGFPKMAVAEAYLKPVVDDSHGIfSWGRPDLEQIKEF-CESH-FGwcqskTDEVlL 888
Cdd:PRK03980   210 ------------GDLEKVLEERGFEIENYDEIREFFLNPPVTDDYEL-KWKEPDKEGIIEFlVEEHdFS-----EERV-K 270

                          250       260
                   ....*....|....*....|..
gi 1835671291  889 PVLRQL-NAYKSQLQ--IDSFF 907
Cdd:PRK03980   271 KALERLeKAVKEKKQttLDSWF 292
fen_arch TIGR03674
flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap ...
 662-907 2.10e-20

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: 93.85  E-value: 2.10e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  662 AERQQQERIAASVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNF------ 735
Cdd:TIGR03674  115 EEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLtisgkr 194

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  736 --FSQNKYIEYYQSV----DIKNQLGLDRYKLINLAYLMGSDYTEGIPTVGYVTAMEILNEFpgpgieplikfakwwtea 809
Cdd:TIGR03674  195 klPGKNIYVEVKPELieleEVLSELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEH------------------ 256

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  810 qntkkmkpnphdTKVKKKLYKLELSPGFPKmAVAEAYLKPVVDDSHGIfSWGRPDLEQIKEF-CESHfgwcQSKTDEVLL 888
Cdd:TIGR03674  257 ------------GDLEKVLKARGEDIENYD-EIREFFLNPPVTDDYEL-EWRKPDKEGIIEFlCDEH----DFSEDRVER 318

                          250       260
                   ....*....|....*....|
gi 1835671291  889 PVLRQLNAYKS-QLQIDSFF 907
Cdd:TIGR03674  319 ALERLEAAYKSkQKTLDRWF 338
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 665-920 2.77e-20

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 94.30  E-value: 2.77e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  665 QQQERIAASVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFF---SQNKY 741
Cdd:PTZ00217   126 KKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNfseAKKRP 205

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  742 IEYYQSVDIKNQLGLDRYKLINLAYLMGSDYTEGIPTVGYVTAMEILNEFpgPGIEPLIKFakwwteAQNTKKMKPnphd 821
Cdd:PTZ00217   206 IQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKY--KSIEEILEH------LDKTKYPVP---- 273

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  822 tkvkkklyklelsPGFPKMAVAEAYLKPVVDDSHGI-FSWGRPDLEQIKEFC--ESHFgwcqSKtDEVLLPVLRQLNAY- 897
Cdd:PTZ00217   274 -------------ENFDYKEARELFLNPEVTPAEEIdLKWNEPDEEGLKKFLvkEKNF----NE-ERVEKYIERLKKAKt 335

                          250       260
                   ....*....|....*....|....
gi 1835671291  898 -KSQLQIDSFFRLEQHEKQTIKSQ 920
Cdd:PTZ00217   336 kKTQTRLDSFFTATKKPIKKSNSK 359
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 681-760 3.83e-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: 84.58  E-value: 3.83e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  681 ESQELLRLFGIPYIISPMEAEAQCAILD---LTDqtsGTITDDSDIWLFGARHVYKNFFSQNK--YIEYYQSVDIKNQLG 755
Cdd:cd09869    116 ECEELLELLGVPVVQAPGEAEALCALLNaegLVD---GCITNDGDAFLYGARTVYRNFSLNTKdgSVECYDMSDIEKRLS 192


                   ....*
gi 1835671291  756 LDRYK 760
Cdd:cd09869    193 LRWRR 197
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 650-767 5.21e-18

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


Pssm-ID: 350206 [Multi-domain]  Cd Length: 235  Bit Score: 84.51  E-value: 5.21e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  650 ESALFVQQTTLHAERQQQERIAASVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGAR 729
Cdd:cd09856     96 ESAKSAVEDELFEEQSKDKKRSGTVTKVMTAECKHLLSLFGIPYVDAPGEAEAQCAYLEQQGIVDAVLTEDVDTFLFGSP 175

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1835671291  730 HVYKNFFSQNK--YIEYYQSVDIKNQLGLdRYKLINLAYL 767
Cdd:cd09856    176 VVYRNLTSEGKktHVELYDASSILEGLFL-PWSTPDLEGL 214
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 1-47 1.98e-17

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 78.43  E-value: 1.98e-17
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1835671291     1 MQNAHLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRRE 47
Cdd:smart00485   51 PNSKHLMGLFYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRERRE 97
XPG_N pfam00752
XPG N-terminal domain;
5-46 4.43e-17

XPG N-terminal domain;


Pssm-ID: 395609 [Multi-domain]  Cd Length: 100  Bit Score: 77.40  E-value: 4.43e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1835671291    5 HLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRR 46
Cdd:pfam00752   56 HLMGFFSRLCRLKDFGIKPIFVFDGGPPPLKAETLQKRSARR 97
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 673-751 9.00e-17

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


Pssm-ID: 350200 [Multi-domain]  Cd Length: 162  Bit Score: 78.96  E-value: 9.00e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1835671291  673 SVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFSQNKYIEYYQSVDIK 751
Cdd:cd00128     83 TITKKMYQECKHLLSLFGIPYVVAPYEAEAQCAYLLKAGIVDAAITEDSDCLLFGAPRVIRNMTFEGPHVEEFDASSIL 161
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 683-761 1.11e-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: 1.11e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  683 QELLRLFGIPYIISPMEAEAQCAILdltdQTSGTI----TDDSDIWLFGARHVYKNF--FSQNKYIEYYQSVDIKNQLGL 756
Cdd:cd09870    113 KELLDAFGFPWHEAPGEAEAELARL----QRLGVVdavlTDDSDALVFGATTVLRNFskKLSDDDVKVYTASAIKDKADL 188


                   ....*
gi 1835671291  757 DRYKL 761
Cdd:cd09870    189 TRTSL 193
H3TH_XPG-like cd09900
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 ...
 760-804 1.68e-12

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


Pssm-ID: 188620 [Multi-domain]  Cd Length: 52  Bit Score: 62.89  E-value: 1.68e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1835671291  760 KLINLAYLMGSDYTEGIPTVGYVTAMEILNEFPgpgiEPLIKFAK 804
Cdd:cd09900      2 QLILLALLLGTDYNPGVPGIGPKTALELLKEFG----EDLEKFLE 42
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 5-49 2.37e-12

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


Pssm-ID: 350215 [Multi-domain]  Cd Length: 251  Bit Score: 68.19  E-value: 2.37e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1835671291    5 HLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRREVA 49
Cdd:cd09867     55 HLSGLFYRTINLLENGIKPVYVFDGKPPELKSGELEKRRERREEA 99
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 671-751 7.07e-12

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


Pssm-ID: 350215 [Multi-domain]  Cd Length: 251  Bit Score: 66.65  E-value: 7.07e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  671 AASVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYKNFFSQNKYIEYYQSVDI 750
Cdd:cd09867    122 TVRVTKEMVEEAKKLLDLMGIPYVQAPSEGEAQAAYLVKKGDVYAVASQDYDSLLFGAPRLVRNLTISGKRKLKGVYRKV 201


                   .
gi 1835671291  751 K 751
Cdd:cd09867    202 P 202
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 5-46 7.58e-12

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


Pssm-ID: 350217 [Multi-domain]  Cd Length: 227  Bit Score: 66.09  E-value: 7.58e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1835671291    5 HLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRR 46
Cdd:cd09869     51 HLRNLFFRTVNLLRLGIKPVFVLDGDAPELKLQTIKKRNAAR 92
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 3-49 1.15e-10

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: 62.94  E-value: 1.15e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1835671291    3 NAHLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRREVA 49
Cdd:cd09856     48 NSHIRGLFYRIIRLLENGIKPVFVFDGEPPKLKKRTRRKRKERRQGA 94
H3TH_FEN1-XPG-like cd09897
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases; The 5' ...
 760-821 3.77e-10

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


Pssm-ID: 188617 [Multi-domain]  Cd Length: 68  Bit Score: 56.84  E-value: 3.77e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1835671291  760 KLINLAYLMGSDYTEGIPTVGYVTAMEILNEFPgpgiePLIKFAKWWTEAQntKKMKPNPHD 821
Cdd:cd09897      2 QFIDLCILSGCDYLPGLPGIGPKTALKLIKEYG-----SLEKVLKALRDDK--KDKVPVPYD 56
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 5-52 1.07e-09

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 61.95  E-value: 1.07e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1835671291    5 HLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRREVAASD 52
Cdd:PTZ00217    65 HISGLFNRTIRLLEAGIKPVYVFDGKPPELKSGELEKRRERREEAEEE 112
PRK03980 PRK03980
flap endonuclease-1; Provisional
 4-50 7.89e-09

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 58.29  E-value: 7.89e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1835671291    4 AHLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRREVAA 50
Cdd:PRK03980     9 SHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAE 55
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 671-733 1.52e-08

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: 55.87  E-value: 1.52e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1835671291  671 AASVTGQMCLESQELLRLFGIPYIISPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHV-YK 733
Cdd:cd09857    122 AVDITPEMAHELIKALRKENVEYIVAPYEADAQLAYLAKTGYVDAVITEDSDLLAFGCPKVlFK 185
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 3-47 4.96e-07

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: 51.64  E-value: 4.96e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1835671291    3 NAHLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRRE 47
Cdd:cd09857     53 DKYIDYCMKRVNMLLHHGITPILVFDGAPLPSKAGTEEERRERRE 97
H3TH_GEN1 cd09905
H3TH domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' ...
 758-849 2.83e-06

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: 46.96  E-value: 2.83e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  758 RYKLINLAYLMGSDYTE-GIPTVGYVTAMEILNEFPGPGIepLIKFAKWWTEAQNTK----KMKPNPHDT----KVKKKL 828
Cdd:cd09905      1 REKLIALALLCGCDYNPkGVPGVGKERALRLVNIVSSDEV--LDRLRNWRATSDPSSpqelKKKDKNHCSncghLGKKQE 78

                           90       100       110
                   ....*....|....*....|....*....|
gi 1835671291  829 Y---------KLELSPGFPKMAVAEAYLKP 849
Cdd:cd09905     79 HiksgcedcdKALLDPGFPNEEIIEEFLSR 108
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 3-41 4.89e-06

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: 47.75  E-value: 4.89e-06
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1835671291    3 NAHLLVLFHRLCKLLFFRIKPVFVFDGDAPLLKKQTLAK 41
Cdd:cd00128     48 NSHLRGLFYRIIKLLSNGIKPIFVFDGGPPPLKKETITK 86
HhH2 smart00279
Helix-hairpin-helix class 2 (Pol1 family) motifs;
758-791 2.45e-05

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


Pssm-ID: 197623 [Multi-domain]  Cd Length: 36  Bit Score: 42.05  E-value: 2.45e-05
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 1835671291   758 RYKLINLAYLMG--SDYTEGIPTVGYVTAMEILNEF 791
Cdd:smart00279    1 PEQFIDYAILVGdySDNIPGVKGIGPKTALKLLREF 36
H3TH_YEN1 cd09906
H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' ...
 758-852 1.31e-03

H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease; Yeast Endonuclease 1 (YEN1): Holliday junction resolvase which promotes reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. YEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of YEN1 and other similar fungal 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.


Pssm-ID: 188626  Cd Length: 105  Bit Score: 39.21  E-value: 1.31e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835671291  758 RYKLINLAYLMGSDY-TEGIPTVGYVTA------------MEILNEFPGPGIEPliKFAKWWTEAQNTKKMkpNPHDT-K 823
Cdd:cd09906      1 RGGMVLFALLSGGDYdTVGLPGCGKKTAlelaklgfgdslLEAAEDLSEEELES--FLEEWRERLLEELRT--NGRGLfG 76

                           90       100
                   ....*....|....*....|....*....
gi 1835671291  824 VKKKLYKLELSPGFPKMAVAEAYLKPVVD 852
Cdd:cd09906     77 RNYPALSLSIPEGFPDPDVLLYYTHPVVS 105
H3TH_StructSpec-5'-nucleases cd00080
H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA ...
 760-819 1.51e-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: 38.12  E-value: 1.51e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1835671291  760 KLINLAYLMGSDYTE--GIPTVGYVTAMEILNEFpgPGIEPLIKFAKWWTEAQNTKKMKPNP 819
Cdd:cd00080      2 QFIDLCALVGCDYSDnpGVPGIGPKTAAKLALKY--GSLEGILENLDELKGKKREKLEEPKE 61
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 12-51 1.62e-03

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


Pssm-ID: 350204 [Multi-domain]  Cd Length: 174  Bit Score: 40.55  E-value: 1.62e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1835671291   12 RLCKLLFFRIKPVFVFDGDAPLLKKQTLAKRRQRREVAAS 51
Cdd:cd09853     35 DLVKKLKPGIKPILLFDGGKPKAKKGNRDKRRERRAREED 74
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 2-30 1.65e-03

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: 41.10  E-value: 1.65e-03
                           10        20
                   ....*....|....*....|....*....
gi 1835671291    2 QNAHLLVLFHRLCKLLFFRIKPVFVFDGD 30
Cdd:cd09870     61 ENPELRTLFYRLARLLSLPIQPVFVFDGP 89
 
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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