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Conserved domains on  [gi|302900157|ref|XP_003048206|]
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uncharacterized protein NECHADRAFT_40444 [Fusarium vanettenii 77-13-4]

Protein Classification

flap endonuclease 1( domain architecture ID 11488256)

flap endonuclease 1 is a structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
1-361 0e+00

flap endonuclease-1; Provisional


:

Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 532.66  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   1 MGIKQLFQIIKEEAPDAIKEGEIKNQFGRKVAIDASMSIYSFLIAVRSDGQ--QLMNDSGETTSHLMGMFYRTLRMVDNG 78
Cdd:PTZ00217   1 MGIKGLSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQggNLTNEAGEVTSHISGLFNRTIRLLEAG 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  79 IKPLYVFDGAPPKLKSGELAKRFQRKQEATEGLEEAKETGTAEDIEKFSRRTVRVTREHNAECQRLLKLMGIPYIIAPTE 158
Cdd:PTZ00217  81 IKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 159 AEAQCAVLAQAGKVYAAASEDMDTLCFNSPILLRHLTFSEQRKEPIQEIHLEKVLEGLGMERKQFVDLCILLGCDYLDPI 238
Cdd:PTZ00217 161 AEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTI 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 239 PKVGPTTALKLIRDHGSLEKIVEAMEkdpKKKYVLPEDWPYKDARDLFFEPDVRKADdpECDVKWEKPDMEGLVQFLVTE 318
Cdd:PTZ00217 241 KGIGPKTAYKLIKKYKSIEEILEHLD---KTKYPVPENFDYKEARELFLNPEVTPAE--EIDLKWNEPDEEGLKKFLVKE 315
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|...
gi 302900157 319 KGFSEDRVRSGGARLEKNLKSSQQARLEGFFKPVPKTDAQKAA 361
Cdd:PTZ00217 316 KNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKKPIKKSNS 358
 
Name Accession Description Interval E-value
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
1-361 0e+00

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 532.66  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   1 MGIKQLFQIIKEEAPDAIKEGEIKNQFGRKVAIDASMSIYSFLIAVRSDGQ--QLMNDSGETTSHLMGMFYRTLRMVDNG 78
Cdd:PTZ00217   1 MGIKGLSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQggNLTNEAGEVTSHISGLFNRTIRLLEAG 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  79 IKPLYVFDGAPPKLKSGELAKRFQRKQEATEGLEEAKETGTAEDIEKFSRRTVRVTREHNAECQRLLKLMGIPYIIAPTE 158
Cdd:PTZ00217  81 IKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 159 AEAQCAVLAQAGKVYAAASEDMDTLCFNSPILLRHLTFSEQRKEPIQEIHLEKVLEGLGMERKQFVDLCILLGCDYLDPI 238
Cdd:PTZ00217 161 AEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTI 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 239 PKVGPTTALKLIRDHGSLEKIVEAMEkdpKKKYVLPEDWPYKDARDLFFEPDVRKADdpECDVKWEKPDMEGLVQFLVTE 318
Cdd:PTZ00217 241 KGIGPKTAYKLIKKYKSIEEILEHLD---KTKYPVPENFDYKEARELFLNPEVTPAE--EIDLKWNEPDEEGLKKFLVKE 315
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|...
gi 302900157 319 KGFSEDRVRSGGARLEKNLKSSQQARLEGFFKPVPKTDAQKAA 361
Cdd:PTZ00217 316 KNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKKPIKKSNS 358
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
4-335 3.66e-128

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: 368.65  E-value: 3.66e-128
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   4 KQLFQIIkeeapdAIKEGEIKNQFGRKVAIDASMSIYSFLIAVRS-DGQQLMNDSGETTSHLMGMFYRTLRMVDNGIKPL 82
Cdd:cd09867    1 VNLSKLI------AIKEIELKDLSGKKIAIDASNALYQFLSAIRQpDGTPLTDSKGRVTSHLSGLFYRTINLLENGIKPV 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  83 YVFDGAPPKLKSGELAKRFQRKQEATEGLEEAKETGTAEDIEKFSRRTVRVTREHNAECQRLLKLMGIPYIIAPTEAEAQ 162
Cdd:cd09867   75 YVFDGKPPELKSGELEKRRERREEAEEKLEEALEEGDLEEARKYAKRTVRVTKEMVEEAKKLLDLMGIPYVQAPSEGEAQ 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 163 CAVLAQAGKVYAAASEDMDTLCFNSPILLRHLTFSEQRK-------EPIQEIHLEKVLEGLgmerkqfvdlcillgcdyl 235
Cdd:cd09867  155 AAYLVKKGDVYAVASQDYDSLLFGAPRLVRNLTISGKRKlkgvyrkVPPEEIELEEVLEEL------------------- 215
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 236 dpipkvgpttalklirdhgslekiveamekdpkkkyvlpedwpykdardlffepdvrkaddpecDVKWEKPDMEGLVQFL 315
Cdd:cd09867  216 ----------------------------------------------------------------ELKWKEPDEEGLVKFL 231
                        330       340
                 ....*....|....*....|
gi 302900157 316 VTEKGFSEDRVRSGGARLEK 335
Cdd:cd09867  232 CEEHDFSEERVEKALERLKK 251
fen_arch TIGR03674
flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap ...
17-349 7.45e-112

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: 330.75  E-value: 7.45e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   17 AIKEGEIKNQFGRKVAIDASMSIYSFLIAVR-SDGQQLMNDSGETTSHLMGMFYRTLRMVDNGIKPLYVFDGAPPKLKSG 95
Cdd:TIGR03674  10 AKEEIELEDLSGKVVAVDAFNALYQFLSSIRqPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKPVYVFDGKPPELKAE 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   96 ELAKRFQRKQEATEGLEEAKETGTAEDIEKFSRRTVRVTREHNAECQRLLKLMGIPYIIAPTEAEAQCAVLAQAGKVYAA 175
Cdd:TIGR03674  90 TLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYV 169
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  176 ASEDMDTLCFNSPILLRHLTFSEQRKEPIQE---------IHLEKVLEGLGMERKQFVDLCILLGCDYLDPIPKVGPTTA 246
Cdd:TIGR03674 170 GSQDYDSLLFGAPRLVRNLTISGKRKLPGKNiyvevkpelIELEEVLSELGITREQLIDIAILVGTDYNEGVKGIGPKTA 249
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  247 LKLIRDHGSLEKIVEAMEKDPKkkyvlpedwPYKDARDLFFEPDVrkADDPEcdVKWEKPDMEGLVQFLVTEKGFSEDRV 326
Cdd:TIGR03674 250 LKLIKEHGDLEKVLKARGEDIE---------NYDEIREFFLNPPV--TDDYE--LEWRKPDKEGIIEFLCDEHDFSEDRV 316
                         330       340
                  ....*....|....*....|...
gi 302900157  327 RSGGARLEKNLKSSqQARLEGFF 349
Cdd:TIGR03674 317 ERALERLEAAYKSK-QKTLDRWF 338
XPG_I pfam00867
XPG I-region;
149-233 1.60e-40

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 138.42  E-value: 1.60e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  149 GIPYIIAPTEAEAQCAVLAQAGKVYAAASEDMDTLCFNSPILLRHLTFSEQ--RKEPIQEIHLEKVLEGLGMERKQFVDL 226
Cdd:pfam00867   1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKkkSKVPVEEIDLEKILKELGLTREQLIDL 80

                  ....*..
gi 302900157  227 CILLGCD 233
Cdd:pfam00867  81 AILLGCD 87
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
1-107 1.69e-35

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 125.81  E-value: 1.69e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157     1 MGIKQLFQIIKEeapdAIKEGEIKNQFGRKVAIDASMSIYSFLIAVRS-DGQQLMNDSgettsHLMGMFYRTLRMVDNGI 79
Cdd:smart00485   1 MGIKGLWPLLKP----VVREVPLEALRGKTLAIDASIWLYQFLTACREkLGTPLPNSK-----HLMGLFYRTCRLLEFGI 71
                           90       100
                   ....*....|....*....|....*...
gi 302900157    80 KPLYVFDGAPPKLKSGELAKRFQRKQEA 107
Cdd:smart00485  72 KPIFVFDGKPPPLKSETLAKRRERREEA 99
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
141-269 2.07e-06

5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 48.87  E-value: 2.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 141 CQRLLKLMGIPYIIAPT-EAEAQCAVLAQAgkvyaAASEDMDTLcfnspI---------LLRHLTF---SEQRKEPIQEI 207
Cdd:COG0258   93 IKEVLEALGIPVLEVEGyEADDVIGTLAKQ-----AEAEGYEVL-----IvtgdkdllqLVDDNVTvldPMKGVSELERY 162
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 302900157 208 HLEKVLEGLGMERKQFVDLCILLGcdylDP------IPKVGPTTALKLIRDHGSLEKIVEAMEKDPKK 269
Cdd:COG0258  163 DPAEVEEKYGVPPEQIIDYLALMG----DSsdnipgVPGIGEKTAAKLLQEYGSLENILANADEIKGK 226
 
Name Accession Description Interval E-value
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
1-361 0e+00

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 532.66  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   1 MGIKQLFQIIKEEAPDAIKEGEIKNQFGRKVAIDASMSIYSFLIAVRSDGQ--QLMNDSGETTSHLMGMFYRTLRMVDNG 78
Cdd:PTZ00217   1 MGIKGLSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQggNLTNEAGEVTSHISGLFNRTIRLLEAG 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  79 IKPLYVFDGAPPKLKSGELAKRFQRKQEATEGLEEAKETGTAEDIEKFSRRTVRVTREHNAECQRLLKLMGIPYIIAPTE 158
Cdd:PTZ00217  81 IKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 159 AEAQCAVLAQAGKVYAAASEDMDTLCFNSPILLRHLTFSEQRKEPIQEIHLEKVLEGLGMERKQFVDLCILLGCDYLDPI 238
Cdd:PTZ00217 161 AEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTI 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 239 PKVGPTTALKLIRDHGSLEKIVEAMEkdpKKKYVLPEDWPYKDARDLFFEPDVRKADdpECDVKWEKPDMEGLVQFLVTE 318
Cdd:PTZ00217 241 KGIGPKTAYKLIKKYKSIEEILEHLD---KTKYPVPENFDYKEARELFLNPEVTPAE--EIDLKWNEPDEEGLKKFLVKE 315
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|...
gi 302900157 319 KGFSEDRVRSGGARLEKNLKSSQQARLEGFFKPVPKTDAQKAA 361
Cdd:PTZ00217 316 KNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKKPIKKSNS 358
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
4-335 3.66e-128

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: 368.65  E-value: 3.66e-128
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   4 KQLFQIIkeeapdAIKEGEIKNQFGRKVAIDASMSIYSFLIAVRS-DGQQLMNDSGETTSHLMGMFYRTLRMVDNGIKPL 82
Cdd:cd09867    1 VNLSKLI------AIKEIELKDLSGKKIAIDASNALYQFLSAIRQpDGTPLTDSKGRVTSHLSGLFYRTINLLENGIKPV 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  83 YVFDGAPPKLKSGELAKRFQRKQEATEGLEEAKETGTAEDIEKFSRRTVRVTREHNAECQRLLKLMGIPYIIAPTEAEAQ 162
Cdd:cd09867   75 YVFDGKPPELKSGELEKRRERREEAEEKLEEALEEGDLEEARKYAKRTVRVTKEMVEEAKKLLDLMGIPYVQAPSEGEAQ 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 163 CAVLAQAGKVYAAASEDMDTLCFNSPILLRHLTFSEQRK-------EPIQEIHLEKVLEGLgmerkqfvdlcillgcdyl 235
Cdd:cd09867  155 AAYLVKKGDVYAVASQDYDSLLFGAPRLVRNLTISGKRKlkgvyrkVPPEEIELEEVLEEL------------------- 215
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 236 dpipkvgpttalklirdhgslekiveamekdpkkkyvlpedwpykdardlffepdvrkaddpecDVKWEKPDMEGLVQFL 315
Cdd:cd09867  216 ----------------------------------------------------------------ELKWKEPDEEGLVKFL 231
                        330       340
                 ....*....|....*....|
gi 302900157 316 VTEKGFSEDRVRSGGARLEK 335
Cdd:cd09867  232 CEEHDFSEERVEKALERLKK 251
fen_arch TIGR03674
flap structure-specific endonuclease; Endonuclease that cleaves the 5'-overhanging flap ...
17-349 7.45e-112

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: 330.75  E-value: 7.45e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   17 AIKEGEIKNQFGRKVAIDASMSIYSFLIAVR-SDGQQLMNDSGETTSHLMGMFYRTLRMVDNGIKPLYVFDGAPPKLKSG 95
Cdd:TIGR03674  10 AKEEIELEDLSGKVVAVDAFNALYQFLSSIRqPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKPVYVFDGKPPELKAE 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   96 ELAKRFQRKQEATEGLEEAKETGTAEDIEKFSRRTVRVTREHNAECQRLLKLMGIPYIIAPTEAEAQCAVLAQAGKVYAA 175
Cdd:TIGR03674  90 TLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYV 169
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  176 ASEDMDTLCFNSPILLRHLTFSEQRKEPIQE---------IHLEKVLEGLGMERKQFVDLCILLGCDYLDPIPKVGPTTA 246
Cdd:TIGR03674 170 GSQDYDSLLFGAPRLVRNLTISGKRKLPGKNiyvevkpelIELEEVLSELGITREQLIDIAILVGTDYNEGVKGIGPKTA 249
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  247 LKLIRDHGSLEKIVEAMEKDPKkkyvlpedwPYKDARDLFFEPDVrkADDPEcdVKWEKPDMEGLVQFLVTEKGFSEDRV 326
Cdd:TIGR03674 250 LKLIKEHGDLEKVLKARGEDIE---------NYDEIREFFLNPPV--TDDYE--LEWRKPDKEGIIEFLCDEHDFSEDRV 316
                         330       340
                  ....*....|....*....|...
gi 302900157  327 RSGGARLEKNLKSSqQARLEGFF 349
Cdd:TIGR03674 317 ERALERLEAAYKSK-QKTLDRWF 338
PRK03980 PRK03980
flap endonuclease-1; Provisional
54-349 1.32e-104

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 310.60  E-value: 1.32e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  54 MNDSGETTSHLMGMFYRTLRMVDNGIKPLYVFDGAPPKLKSGELAKRFQRKQEATEGLEEAKETGTAEDIEKFSRRTVRV 133
Cdd:PRK03980   1 MDSKGRITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 134 TREHNAECQRLLKLMGIPYIIAPTEAEAQCAVLAQAGKVYAAASEDMDTLCFNSPILLRHLTFSEQRKEPIQE------- 206
Cdd:PRK03980  81 TDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNvyvevkp 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 207 --IHLEKVLEGLGMERKQFVDLCILLGCDYLDPIPKVGPTTALKLIRDHGSLEKIVEAMEKDPKkkyvlpedwPYKDARD 284
Cdd:PRK03980 161 elIELEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERGFEIE---------NYDEIRE 231
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 302900157 285 LFFEPDVrkADDPEcdVKWEKPDMEGLVQFLVTEKGFSEDRVRSGGARLEKNLKSSQQARLEGFF 349
Cdd:PRK03980 232 FFLNPPV--TDDYE--LKWKEPDKEGIIEFLVEEHDFSEERVKKALERLEKAVKEKKQTTLDSWF 292
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
12-216 1.62e-75

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: 234.36  E-value: 1.62e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  12 EEAPDAIKEGEIKNQFGRKVAIDASMSIYSFLIAVRsdgqqLMNDSGETTSHLMGMFYRTLRMVDNGIKPLYVFDGAPPK 91
Cdd:cd09856    4 KIIGPSKRRISLESLRGKRVAIDASIWIYQFLTAVR-----GQGGNGVSNSHIRGLFYRIIRLLENGIKPVFVFDGEPPK 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  92 LKSGELAKRFQRKQEATEGLEEAKETGTAEDIEKFSRRTVRVTREHNAECQRLLKLMGIPYIIAPTEAEAQCAVLAQAGK 171
Cdd:cd09856   79 LKKRTRRKRKERRQGAEESAKSAVEDELFEEQSKDKKRSGTVTKVMTAECKHLLSLFGIPYVDAPGEAEAQCAYLEQQGI 158
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 302900157 172 VYAAASEDMDTLCFNSPILLRHLTfSEQRKEPIQEIHLEKVLEGL 216
Cdd:cd09856  159 VDAVLTEDVDTFLFGSPVVYRNLT-SEGKKTHVELYDASSILEGL 202
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
6-214 1.54e-51

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: 169.86  E-value: 1.54e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   6 LFQIIKEeapdAIKEGEIKNQFGRKVAIDASMSIYSFLIAVRSDGqqlmNDSGETTSHLMGMFYRTLRMVDNGIKPLYVF 85
Cdd:cd00128    1 LWQFIGE----AKEPISIESLKGKTVAIDASIWVYQFLTAKREQG----GDIGVTNSHLRGLFYRIIKLLSNGIKPIFVF 72
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  86 DGAPPKLKSGElakrfqrkqeategleeaketgtaediekfsrrtvrVTREHNAECQRLLKLMGIPYIIAPTEAEAQCAV 165
Cdd:cd00128   73 DGGPPPLKKET------------------------------------ITKKMYQECKHLLSLFGIPYVVAPYEAEAQCAY 116
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 302900157 166 LAQAGKVYAAASEDMDTLCFNSPILLRHLTFSeqrKEPIQEIHLEKVLE 214
Cdd:cd00128  117 LLKAGIVDAAITEDSDCLLFGAPRVIRNMTFE---GPHVEEFDASSILE 162
XPG_I pfam00867
XPG I-region;
149-233 1.60e-40

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 138.42  E-value: 1.60e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  149 GIPYIIAPTEAEAQCAVLAQAGKVYAAASEDMDTLCFNSPILLRHLTFSEQ--RKEPIQEIHLEKVLEGLGMERKQFVDL 226
Cdd:pfam00867   1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSKkkSKVPVEEIDLEKILKELGLTREQLIDL 80

                  ....*..
gi 302900157  227 CILLGCD 233
Cdd:pfam00867  81 AILLGCD 87
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
28-200 3.51e-36

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: 131.10  E-value: 3.51e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  28 GRKVAIDASMSIYSFLIAVR-SDGQQLMNDsgettsHLMGMFYRTLRMVDNGIKPLYVFDGAPPKLKSGELAKRfqrkqe 106
Cdd:cd09868   23 GKVLAVDASIWLHQFVKGMRdNEGNSVPNA------HLLGFFRRICKLLFYGIKPVFVFDGPAPALKRRTLARR------ 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 107 ategleeaketgtaediekfsrRTVrvTREHNAECQRLLKLMGIPYIIAPTEAEAQCAVLAQAGKVYAAASEDMDTLCFN 186
Cdd:cd09868   91 ----------------------RSV--TDEMYEEIQELLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSDVFLFG 146
                        170
                 ....*....|....
gi 302900157 187 SPILLRHLtFSEQR 200
Cdd:cd09868  147 AKRVYKNF-FNQNK 159
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
1-107 1.69e-35

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 125.81  E-value: 1.69e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157     1 MGIKQLFQIIKEeapdAIKEGEIKNQFGRKVAIDASMSIYSFLIAVRS-DGQQLMNDSgettsHLMGMFYRTLRMVDNGI 79
Cdd:smart00485   1 MGIKGLWPLLKP----VVREVPLEALRGKTLAIDASIWLYQFLTACREkLGTPLPNSK-----HLMGLFYRTCRLLEFGI 71
                           90       100
                   ....*....|....*....|....*...
gi 302900157    80 KPLYVFDGAPPKLKSGELAKRFQRKQEA 107
Cdd:smart00485  72 KPIFVFDGKPPPLKSETLAKRRERREEA 99
H3TH_FEN1-Euk cd09907
H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
221-293 2.43e-35

H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Eukaryotic homologs; Members of this subgroup include the H3TH (helix-3-turn-helix) domains of eukaryotic Flap endonuclease-1 (FEN1), 5' nucleases. 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. 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. The nucleases within this subfamily 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. Also, 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: 188627 [Multi-domain]  Cd Length: 70  Bit Score: 124.20  E-value: 2.43e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 302900157 221 KQFVDLCILLGCDYLDPIPKVGPTTALKLIRDHGSLEKIVEAMEkdpKKKYVLPEDWPYKDARDLFFEPDVRK 293
Cdd:cd09907    1 EQFIDLCILLGCDYCESIKGIGPKTALKLIKKHKSIEKILENID---KSKYPVPEDWPYKEARELFLNPEVTD 70
XPG_N pfam00752
XPG N-terminal domain;
2-107 2.87e-35

XPG N-terminal domain;


Pssm-ID: 395609 [Multi-domain]  Cd Length: 100  Bit Score: 125.17  E-value: 2.87e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157    2 GIKQLFQIIKEEApdAIKEGEIKNQFGRKVAIDASMSIYSFLIAVRS-DGQQLMNdsgetTSHLMGMFYRTLRMVDNGIK 80
Cdd:pfam00752   1 GIKGLLPILKPVA--LIRPVDIEALEGKTLAIDASIWLYQFLKAVRDqLGNALQN-----TSHLMGFFSRLCRLKDFGIK 73
                          90       100
                  ....*....|....*....|....*..
gi 302900157   81 PLYVFDGAPPKLKSGELAKRFQRKQEA 107
Cdd:pfam00752  74 PIFVFDGGPPPLKAETLQKRSARRQEA 100
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
32-209 2.23e-32

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: 119.90  E-value: 2.23e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  32 AIDASMSIYSFLIAVRsdgqqlmNDSGETTSHLMGMFYRTLRMVDN---GIKPLYVFDGAPPKLKSGELAKRFQRKQEat 108
Cdd:cd09853    1 VIDGMNIAFNFAHPVR-------NLKEEEGSDFQGYFSAVDDLVKKlkpGIKPILLFDGGKPKAKKGNRDKRRERRAR-- 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 109 eglEEAKETGTAEDIEKFSRRTVRVTREHNAECQRLLKL-MGIPYIIAPTEAEAQCAVLAQAGK----VYAAASEDMDTL 183
Cdd:cd09853   72 ---EEDRKKGQLKEHKEFDKRLIELGPEYLIRLFELLKHfMGIPVMDAPGEAEDEIAYLVKKHKhlgtVHLIISTDGDFL 148
                        170       180
                 ....*....|....*....|....*...
gi 302900157 184 CFNS--PILLRHLTfsEQRKEPIQEIHL 209
Cdd:cd09853  149 LLGTdhPYIPRNLL--TVKEETFQEFHL 174
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
146-218 7.06e-31

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 112.68  E-value: 7.06e-31
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 302900157   146 KLMGIPYIIAPTEAEAQCAVLAQAGKVYAAASEDMDTLCFNSPILLRHLTFSEQRKEPIQEIHLEKVLEGLGM 218
Cdd:smart00484   1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKELGL 73
H3TH_FEN1-like cd09901
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 ...
222-291 5.92e-30

H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (eukaryotic) and EXO1; 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 eukaryotic Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), and other eukaryotic 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. 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: 188621 [Multi-domain]  Cd Length: 73  Bit Score: 110.32  E-value: 5.92e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 222 QFVDLCILLGCDYLDPIPKVGPTTALKLIRDHGSLEKIVEAMEKDPKKKYVLPEDWPYKDARDLFFEPDV 291
Cdd:cd09901    2 QFIDLCILSGCDYLPSIPGIGPKTAYKLIKKHKSIEKVLKALRSNKKKKVPVPYEEPFKEARLTFLHQRV 71
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
2-231 6.47e-29

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: 112.31  E-value: 6.47e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   2 GIKQLFQIIKEEAPDAIKEgeikNQFGRKVAIDASMSIysfliaVRSDGQQLMNdSGETTSHLMGMFYRTLRMVDNGIKP 81
Cdd:cd09869    1 GVKGLWTILDPVKKRKPLS----ELRGKTLAVDLSIWI------CEAQTVLALF-ETVPKPHLRNLFFRTVNLLRLGIKP 69
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  82 LYVFDGAPPKLKSGELAKRFQRKQEATEGLEEAKETGTAEdiekFSRrTVRvtrehnaECQRLLKLMGIPYIIAPTEAEA 161
Cdd:cd09869   70 VFVLDGDAPELKLQTIKKRNAARFGGAKKKGGSKKRGRSR----FSR-VLK-------ECEELLELLGVPVVQAPGEAEA 137
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 302900157 162 QCAVLAQAGKVYAAASEDMDTLCFNSPILLRHLTfSEQRKEPIQEIHLEKVLEGLGMERKQ-----FVDLCILLG 231
Cdd:cd09869  138 LCALLNAEGLVDGCITNDGDAFLYGARTVYRNFS-LNTKDGSVECYDMSDIEKRLSLRWRRpdldlLQDFLLKKL 211
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
1-185 2.02e-28

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: 110.19  E-value: 2.02e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   1 MGIKQLFQIIKEeapdAIKEGEIKNQFGRKVAIDAsmsiYSFL-IAVRSDGQQLMNDsGETTSHL---MGMfyrtLRMV- 75
Cdd:cd09857    1 MGIQGLLPFLKP----IQRPVHISEYAGKTVAVDA----YCWLhRGAYSCAEELALG-KPTDKYIdycMKR----VNMLl 67
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  76 DNGIKPLYVFDGAPPKLKSGELAKRFQRKQEAtegLEEAKET---GTAEDIEKFSRRTVRVTREHNAECQRLLKLMGIPY 152
Cdd:cd09857   68 HHGITPILVFDGAPLPSKAGTEEERRERREEA---LEKALELlreGKKSEARECFQRAVDITPEMAHELIKALRKENVEY 144
                        170       180       190
                 ....*....|....*....|....*....|...
gi 302900157 153 IIAPTEAEAQCAVLAQAGKVYAAASEDMDTLCF 185
Cdd:cd09857  145 IVAPYEADAQLAYLAKTGYVDAVITEDSDLLAF 177
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
96-350 6.78e-25

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: 106.91  E-value: 6.78e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157    96 ELAKRFQRKQEATEGLEEAKETGTAEDIEKFSRRTVRVTREHNAECQRLLKLMGIPYIIAPTEAEAQCAVLAQAGKVYAA 175
Cdd:TIGR00600  732 EWQDISLEELEALEANLLAEQNSLKAQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGT 811
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   176 ASEDMDTLCFNSPILLRHLtFSEqrKEPIQEIHLEKVLEGLGMERKQFVDLCILLGCDYLDPIPKVGPTTALKLIRD--- 252
Cdd:TIGR00600  812 ITDDSDIWLFGARHVYKNF-FNQ--NKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEfpg 888
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   253 --------------HGSLEKIVEAMEKDPKKKYV-----LPEDWPYKDARDLFFEPDVrkaDDPECDVKWEKPDMEGLVQ 313
Cdd:TIGR00600  889 dglepllkfkewwhEAQKDKKKRENPNDTKVKKKlrllqLTPGFPNPAVADAYLRPVV---DDSKGSFLWGKPDLDKIRE 965
                          250       260       270
                   ....*....|....*....|....*....|....*...
gi 302900157   314 FLVTEKGFSEDRVRSGGARLEKNLKSSQ-QARLEGFFK 350
Cdd:TIGR00600  966 FCQRYFGWNREKTDEVLLPVLKKLNAQQtQLRIDSFFR 1003
H3TH_FEN1-XPG-like cd09897
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases; The 5' ...
222-288 8.00e-25

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: 96.13  E-value: 8.00e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 302900157 222 QFVDLCILLGCDYLDPIPKVGPTTALKLIRDHGSLEKIVEAMEKDPKKKYVLPEDWPYKDARDLFFE 288
Cdd:cd09897    2 QFIDLCILSGCDYLPGLPGIGPKTALKLIKEYGSLEKVLKALRDDKKDKVPVPYDFPYKKARELFLH 68
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
2-192 2.83e-19

FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium thermophilum junction-resolving enzyme GEN1, and fungal homologs; Fungal Endonuclease 1 (YEN1 and GEN1, GEN1 is known as YEN1 in Saccharomyces cerevisiae) is a four-way (Holliday) junction resolvase. Members of this subgroup belong to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350218 [Multi-domain]  Cd Length: 229  Bit Score: 85.79  E-value: 2.83e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   2 GIKQLFQIIKEEAPD------AIKEGEIKNQfGR--KVAIDASMSIYSFLIAVRSDGQQLMNDSGETTshlmgMFYRTLR 73
Cdd:cd09870    1 GIPGLWDLLEPAAESrslaelAVVEEFNKRG-GRplRIGIDASIWLFHAQSSFGGGHIQAGENPELRT-----LFYRLAR 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  74 MVDNGIKPLYVFDGA--PPKlksgelaKRfqrkqeategleeaketgtaediekfsRRTVRVTREH--NAECQRLLKLMG 149
Cdd:cd09870   75 LLSLPIQPVFVFDGPnrPPF-------KR---------------------------GKKVGKSTPHwlTKLFKELLDAFG 120
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 302900157 150 IPYIIAPTEAEAQCAVLAQAGKVYAAASEDMDTLCFNSPILLR 192
Cdd:cd09870  121 FPWHEAPGEAEAELARLQRLGVVDAVLTDDSDALVFGATTVLR 163
PIN_SF cd09852
PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large ...
32-185 4.62e-17

PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site 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. The PIN domain superfamily includes: the FEN-like PIN domain family such as the PIN domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. It also includes the Mut7-C PIN domain family, which is not represented here as it is a shortened version of the PIN fold and lacks a core strand and helix (H3 and S3). The Mut7-C PIN domain family includes the C-terminus of Caenorhabditis elegans exonuclease Mut-7.


Pssm-ID: 350203  Cd Length: 114  Bit Score: 76.51  E-value: 4.62e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  32 AIDASMSIYSFLIAVRsdgqqlmndsgeTTSHLMGMFYRTLRMvDNGIKPLYVFDGAPPKLKsgelakrfqrkqeategl 111
Cdd:cd09852    1 LVDGSNMIYTCREAVR------------TYRLNFDMAQRQYVA-KEGVSPIVVFDASPVQLK------------------ 49
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 302900157 112 eeaketgtaediekfsrrtVRVTREHNAECQRLlkLMGIPYIIAP--TEAEAQCAVLAQAGKVYAAASEDMDTLCF 185
Cdd:cd09852   50 -------------------VKVTKNDRKQLQFH--GVGFAV*LTPpiSDADVGIAALAIAIDRVALATGDGDFLAI 104
H3TH_StructSpec-5'-nucleases cd00080
H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA ...
221-284 2.58e-14

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: 67.40  E-value: 2.58e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 302900157 221 KQFVDLCILLGCDYLDP--IPKVGPTTALKLIRDHGSLEKIVEAMEKDPKKKYVL-----PEDWPYKDARD 284
Cdd:cd00080    1 EQFIDLCALVGCDYSDNpgVPGIGPKTAAKLALKYGSLEGILENLDELKGKKREKleepkEYAFLSRKLAT 71
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
28-109 8.12e-14

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: 73.39  E-value: 8.12e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157    28 GRKVAIDASMSIYSFLIAVR-SDGQQLMNdsgettSHLMGMFYRTLRMVDNGIKPLYVFDGAPPKLKSGELAKRFQRKQE 106
Cdd:TIGR00600   24 GKRLAVDISIWLNQALKGVRdREGNAIKN------SHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDG 97

                   ...
gi 302900157   107 ATE 109
Cdd:TIGR00600   98 ASE 100
H3TH_EXO1 cd09908
H3TH domain of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease; ...
222-295 6.16e-12

H3TH domain of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease; 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. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of EXO1 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. EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively.


Pssm-ID: 188628 [Multi-domain]  Cd Length: 73  Bit Score: 60.67  E-value: 6.16e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 302900157 222 QFVDLCILLGCDYLDPIPKVGPTTALKLIRDHGSLEKIVEAMEKDPKKKyvLPEDwpykdardlfFEPDVRKAD 295
Cdd:cd09908    2 KFRHMCILSGCDYLPSLPGIGLKKAYKLVRRHRTIEKVIKALRFDGKKE--VPPD----------YEEGFQKAL 63
H3TH_FEN1-Arc cd09903
H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
222-291 2.28e-09

H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Archaeal homologs; Members of this subgroup include the H3TH (helix-3-turn-helix) domains of archaeal Flap endonuclease-1 (FEN1), 5' nucleases. 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. 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. The nucleases within this subfamily 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. Also, 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: 188623 [Multi-domain]  Cd Length: 65  Bit Score: 52.98  E-value: 2.28e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 302900157 222 QFVDLCILLGCDY-LDPIPKVGPTTALKLIRDHGSLEKIVEamekdpkkkYVLPEDWPYKDARDLFFEPDV 291
Cdd:cd09903    2 QLIDIAILVGTDYnPGGVKGIGPKTALKLVKEYGDLEKVLR---------SVEDEIVDPEEIREIFLNPPV 63
H3TH_XPG-like cd09900
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 ...
221-264 2.09e-08

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: 50.18  E-value: 2.09e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 302900157 221 KQFVDLCILLGCDYLDPIPKVGPTTALKLIRDHGS-LEKIVEAME 264
Cdd:cd09900    1 EQLILLALLLGTDYNPGVPGIGPKTALELLKEFGEdLEKFLESEE 45
PIN_MKT1 cd09858
FEN-like PIN domains of Mkt1, a global regulator of mRNAs encoding mitochondrial proteins and ...
76-200 1.83e-07

FEN-like PIN domains of Mkt1, a global regulator of mRNAs encoding mitochondrial proteins and eukaryotic homologs; The Mkt1 gene product interacts with the Poly(A)-binding protein associated factor, Pbp1, and is present at the 3' end of RNA transcripts during translation. The Mkt1-Pbp1 complex is involved in the post-transcriptional regulation of HO endonuclease expression. Mkt1 and eukaryotic homologs are atypical members of the structure-specific, 5' nuclease family (FEN-like). 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. Although Mkt1 appears to possess both a PIN and H3TH domain, the Mkt1 PIN domain lacks several of the active site residues necessary to bind essential divalent metal ion cofactors (Mg2+/Mn2+) required for nuclease activity in this family. Also, Mkt1 lacks the glycine-rich loop in the H3TH domain which is proposed to facilitate duplex DNA binding.


Pssm-ID: 350208 [Multi-domain]  Cd Length: 206  Bit Score: 51.38  E-value: 1.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157  76 DNGIKPLYVFDGAPPKLK---SGELAKRFQRKQEATEGLEEAKETGTaedIEKFSRRTVRVTREHNAECQRLLKLMGIPY 152
Cdd:cd09858   71 KLNITPVFVFNGLSLKGQdepSSQSEQAAQKREEAWDLYEKGQADQA---VKAFGESGSYRLEDLYRLLQRILKERGVEF 147
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 302900157 153 IIAPTEAEAQCAVLAQAGKVYAAA---SEDMdtLCFNSPILLRHLTFSEQR 200
Cdd:cd09858  148 LVAPYSAWAQLAYLEKHGKQYIDAiygSTEL--LLFGVDKVITSIDFEKGT 196
53EXOc smart00475
5'-3' exonuclease;
144-271 2.17e-07

5'-3' exonuclease;


Pssm-ID: 214682 [Multi-domain]  Cd Length: 259  Bit Score: 51.83  E-value: 2.17e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157   144 LLKLMGIPYIIAP-TEAEAQCAVLA-QAGKVYAAA---SEDMDTLCFNSP-ILLRHLTFSEQRKEPIQEihlEKVLEGLG 217
Cdd:smart00475  92 LLDALGIPVLEVEgYEADDVIATLAkKAEAEGYEVrivSGDKDLLQLVSDkVSVLDPTKGIKEFELYTP---ENVIEKYG 168
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 302900157   218 MERKQFVDLCILLGcDYLDPIP---KVGPTTALKLIRDHGSLEKIVEAMEKDPKKKY 271
Cdd:smart00475 169 LTPEQIIDYKALMG-DSSDNIPgvpGIGEKTAAKLLKEFGSLENILENLDKLKKKLR 224
H3TH_XPG cd09904
H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
221-293 3.76e-07

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: 48.02  E-value: 3.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 221 KQFVDLCILLGCDYLDPIPKVGPTTALKLIR---DHGSLEKIVE-AMEKDP--------------------KKKYVLPED 276
Cdd:cd09904    1 DKLIRLALLLGSDYTEGVSGIGPVNAMEILSefpGEEDLEKFKDwWENAQPeksedsdndkqefkrkhknyLKNLILPPG 80
                         90
                 ....*....|....*..
gi 302900157 277 WPYKDARDLFFEPDVRK 293
Cdd:cd09904   81 FPSPAVINAYLNPNVDD 97
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
141-269 2.07e-06

5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 48.87  E-value: 2.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302900157 141 CQRLLKLMGIPYIIAPT-EAEAQCAVLAQAgkvyaAASEDMDTLcfnspI---------LLRHLTF---SEQRKEPIQEI 207
Cdd:COG0258   93 IKEVLEALGIPVLEVEGyEADDVIGTLAKQ-----AEAEGYEVL-----IvtgdkdllqLVDDNVTvldPMKGVSELERY 162
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 302900157 208 HLEKVLEGLGMERKQFVDLCILLGcdylDP------IPKVGPTTALKLIRDHGSLEKIVEAMEKDPKK 269
Cdd:COG0258  163 DPAEVEEKYGVPPEQIIDYLALMG----DSsdnipgVPGIGEKTAAKLLQEYGSLENILANADEIKGK 226
5_3_exonuc pfam01367
5'-3' exonuclease, C-terminal SAM fold;
221-270 2.81e-06

5'-3' exonuclease, C-terminal SAM fold;


Pssm-ID: 460176 [Multi-domain]  Cd Length: 93  Bit Score: 45.05  E-value: 2.81e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 302900157  221 KQFVDLCILLGcdylDP------IPKVGPTTALKLIRDHGSLEKIVEAMEKDPKKK 270
Cdd:pfam01367   4 EQIIDYLALMG----DSsdnipgVPGIGEKTAAKLLNEYGSLENILANADEIKGGK 55
H3TH_53EXO cd09898
H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; H3TH ...
221-269 3.41e-06

H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; H3TH (helix-3-turn-helix) domains of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs are included in this family. Taq DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. 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. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+ or Mn2+ or Zn2+) 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 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: 188618 [Multi-domain]  Cd Length: 73  Bit Score: 44.31  E-value: 3.41e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 302900157 221 KQFVDLCILLGcdylDP------IPKVGPTTALKLIRDHGSLEKIVEAMEKDPKK 269
Cdd:cd09898    2 EQIIDYLALVG----DSsdnipgVPGIGPKTAAKLLQEYGSLENILANLDELKGK 52
PRK05755 PRK05755
DNA polymerase I; Provisional
210-270 1.13e-05

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 47.39  E-value: 1.13e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 302900157 210 EKVLEGLGMERKQFVDLCILLGcdylDP------IPKVGPTTALKLIRDHGSLEKIVEAMEKDPKKK 270
Cdd:PRK05755 162 EEVVEKYGVTPEQIIDYLALMG----DSsdnipgVPGIGEKTAAKLLQEYGSLEGLYENLDEIKGKK 224
HhH2 smart00279
Helix-hairpin-helix class 2 (Pol1 family) motifs;
220-251 2.21e-05

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


Pssm-ID: 197623 [Multi-domain]  Cd Length: 36  Bit Score: 40.89  E-value: 2.21e-05
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 302900157   220 RKQFVDLCILLGcDYLDPIP---KVGPTTALKLIR 251
Cdd:smart00279   1 PEQFIDYAILVG-DYSDNIPgvkGIGPKTALKLLR 34
H3TH_MKT1 cd09902
H3TH domain of Mkt1: A global regulator of mRNAs encoding mitochondrial proteins and ...
222-272 2.72e-03

H3TH domain of Mkt1: A global regulator of mRNAs encoding mitochondrial proteins and eukaryotic homologs; The Mkt1 gene product interacts with the Poly(A)-binding protein associated factor, Pbp1, and is present at the 3' end of RNA transcripts during translation. The Mkt1-Pbp1 complex is involved in the post-transcriptional regulation of HO endonuclease expression. Mkt1 and eukaryotic homologs are atypical members of the structure-specific, 5' nuclease family. Conical members of this family possess 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 (helix-3-turn-helix) 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. Although Mkt1 appears to possess both a PIN and H3TH domain, the Mkt1 PIN domain lacks several of the active site residues necessary to bind essential divalent metal ion cofactors (Mg2+/Mn2+) required for nuclease activity in this family. Also, Mkt1 lacks the glycine-rich loop in the H3TH domain which is proposed to facilitate duplex DNA binding.


Pssm-ID: 188622  Cd Length: 81  Bit Score: 36.50  E-value: 2.72e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 302900157 222 QFVDLCILLGCDYLDPIP---------KVGPTTALKLIRDHGSLEKIVEAMEKDPK---KKYV 272
Cdd:cd09902    2 QFLDACLLAGTELCPTFPplqdspfpkPQNFRDALDMVKQARSGISVCQQFPDTPSvndKNYL 64
 
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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