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Conserved domains on  [gi|215686953|dbj|BAG89766|]
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unnamed protein product [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
118-319 5.52e-45

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


:

Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 155.19  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 118 DPVVAVLDGEGGNeYRRRLLPSYKAHRPRGPgtgAD-----SRVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQKGFR 192
Cdd:COG0258   54 THLAVAFDAKGPT-FRHELYPEYKANRPEMP---EElrpqiPLIKEVLEALGIPVLEVEGYEADDVIGTLAKQAEAEGYE 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 193 VVIGSPDKDFKQLISEDVQLVMPIPEIGRWSFYTLRHYVAQYKCDPT--AD-LSLRcfiGDEADGIPGiqhlVPGFGRKT 269
Cdd:COG0258  130 VLIVTGDKDLLQLVDDNVTVLDPMKGVSELERYDPAEVEEKYGVPPEqiIDyLALM---GDSSDNIPG----VPGIGEKT 202

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 215686953 270 AVKLLKKHGSLENLL-NTAAVRtvGKdyAQDALVKHADYLRKNYEVLSLKR 319
Cdd:COG0258  203 AAKLLQEYGSLENILaNADEIK--GK--LREKLRENKEQARLSRKLATIKT 249
 
Name Accession Description Interval E-value
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
118-319 5.52e-45

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


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 155.19  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 118 DPVVAVLDGEGGNeYRRRLLPSYKAHRPRGPgtgAD-----SRVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQKGFR 192
Cdd:COG0258   54 THLAVAFDAKGPT-FRHELYPEYKANRPEMP---EElrpqiPLIKEVLEALGIPVLEVEGYEADDVIGTLAKQAEAEGYE 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 193 VVIGSPDKDFKQLISEDVQLVMPIPEIGRWSFYTLRHYVAQYKCDPT--AD-LSLRcfiGDEADGIPGiqhlVPGFGRKT 269
Cdd:COG0258  130 VLIVTGDKDLLQLVDDNVTVLDPMKGVSELERYDPAEVEEKYGVPPEqiIDyLALM---GDSSDNIPG----VPGIGEKT 202

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 215686953 270 AVKLLKKHGSLENLL-NTAAVRtvGKdyAQDALVKHADYLRKNYEVLSLKR 319
Cdd:COG0258  203 AAKLLQEYGSLENILaNADEIK--GK--LREKLRENKEQARLSRKLATIKT 249
53EXOc smart00475
5'-3' exonuclease;
103-319 1.94e-40

5'-3' exonuclease;


Pssm-ID: 214682 [Multi-domain]  Cd Length: 259  Bit Score: 142.35  E-value: 1.94e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953   103 FARWLALFFAHVSlRDPVVAVLDGEGGNeYRRRLLPSYKAHRPRGPGTGAD--SRVIDVLRECNVPVVRVDGYEADDVVA 180
Cdd:smart00475  36 FLRMLLKLIKEEK-PTYVAVVFDAKGKT-FRHELYPEYKANRPKTPDELLEqiPLIKELLDALGIPVLEVEGYEADDVIA 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953   181 TLTEQVLQKGFRVVIGSPDKDFKQLISEDVQLVMPIPEIGRWSFYTLRHYVAQYKCDPTADLSLRCFIGDEADGIPGiqh 260
Cdd:smart00475 114 TLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPG--- 190

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953   261 lVPGFGRKTAVKLLKKHGSLENLL-NTAAVRtvGKdyAQDALVKHADYLRKNYEVLSLKR 319
Cdd:smart00475 191 -VPGIGEKTAAKLLKEFGSLENILeNLDKLK--KK--LREKLLAHKEDAKLSRKLATIET 245
PRK05755 PRK05755
DNA polymerase I; Provisional
 118-319 1.41e-35

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 137.15  E-value: 1.41e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 118 DPVVAVLDGEGGNeYRRRLLPSYKAHRPRGPgtgADSRV-IDVLREC----NVPVVRVDGYEADDVVATLTEQVLQKGFR 192
Cdd:PRK05755  52 THVAVAFDAKGKT-FRHELYPEYKANRPPMP---EDLREqIPLIRELlralGIPLLELEGYEADDVIGTLAKQAEAAGYE 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 193 VVIGSPDKDFKQLISEDVQLV--MPIPEIGRwsfYTLRHYVAQYKCDPT--AD-LSLrcfIGDEADGIPGiqhlVPGFGR 267
Cdd:PRK05755 128 VLIVTGDKDLLQLVDDNVTLLdtMGVSKNEE---LDPEEVVEKYGVTPEqiIDyLAL---MGDSSDNIPG----VPGIGE 197

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 215686953 268 KTAVKLLKKHGSLENLL-NTAAVRTVGKdyaqDALVKHADYLRKNYEVLSLKR 319
Cdd:PRK05755 198 KTAAKLLQEYGSLEGLYeNLDEIKGKKK----EKLRENKEQAFLSRKLATIKT 246
pola TIGR00593
DNA polymerase I; All proteins in this family for which functions are known are DNA ...
 120-319 2.12e-33

DNA polymerase I; All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. 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: 273160 [Multi-domain]  Cd Length: 887  Bit Score: 130.54  E-value: 2.12e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953  120 VVAVLDgEGGNEYRRRLLPSYKAHRPRGPgtgAD-----SRVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQKGFRVV 194
Cdd:TIGR00593  52 VAVAFD-SGTPTFRHEAYAEYKANRAPTP---EElieqiPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVR 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953  195 IGSPDKDFKQLISEDVQLVMPIpEIGRWSFYTLRHYVAQYKCDPTADLSLRCFIGDEADGIPGiqhlVPGFGRKTAVKLL 274
Cdd:TIGR00593 128 IISGDKDLLQLVSDNVKVLIPK-GKTSFTEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPG----VKGIGEKTAAKLL 202

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 215686953  275 KKHGSLENLLNTaaVRTVGKDYAQDALVKHADYLRKNYEVLSLKR 319
Cdd:TIGR00593 203 QEFGSLENIYEN--LDQIKSAKMREKLIAHKEDAFLSKELATIVT 245
PIN_53EXO cd09859
FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA ...
 118-215 1.40e-24

FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA polymerase I (Taq) and homologs; The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family. Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain 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 PIN domain cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases 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: 350209  Cd Length: 160  Bit Score: 97.44  E-value: 1.40e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 118 DPVVAVLDGEGGNeYRRRLLPSYKAHRPRGPgtgaDS------RVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQKGF 191
Cdd:cd09859   46 DYIAVAFDAKGPT-FRHELYPEYKANRPPMP----EElipqipLIKELLEALGIPVLEVEGYEADDIIGTLAKKAEKEGL 120

                         90       100
                 ....*....|....*....|....
gi 215686953 192 RVVIGSPDKDFKQLISEDVQLVMP 215
Cdd:cd09859  121 EVVIVTGDKDLLQLVDDNVKVLDP 144
5_3_exonuc_N pfam02739
5'-3' exonuclease, N-terminal resolvase-like domain;
120-215 7.18e-23

5'-3' exonuclease, N-terminal resolvase-like domain;


Pssm-ID: 460672  Cd Length: 163  Bit Score: 93.23  E-value: 7.18e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953  120 VVAVLDGEGGneYRRRLLPSYKAHRPrgpGTGAD-----SRVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQKGFRVV 194
Cdd:pfam02739  51 VAVAFDAKPT--FRHELYPEYKANRP---PMPEElrpqiPLIKELLEALGIPVLEVEGYEADDIIGTLAKRAEEEGYEVV 125

                          90       100
                  ....*....|....*....|.
gi 215686953  195 IGSPDKDFKQLISEDVQLVMP 215
Cdd:pfam02739 126 IVTGDKDLLQLVSDNVTVLDP 146
 
Name Accession Description Interval E-value
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
118-319 5.52e-45

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


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 155.19  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 118 DPVVAVLDGEGGNeYRRRLLPSYKAHRPRGPgtgAD-----SRVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQKGFR 192
Cdd:COG0258   54 THLAVAFDAKGPT-FRHELYPEYKANRPEMP---EElrpqiPLIKEVLEALGIPVLEVEGYEADDVIGTLAKQAEAEGYE 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 193 VVIGSPDKDFKQLISEDVQLVMPIPEIGRWSFYTLRHYVAQYKCDPT--AD-LSLRcfiGDEADGIPGiqhlVPGFGRKT 269
Cdd:COG0258  130 VLIVTGDKDLLQLVDDNVTVLDPMKGVSELERYDPAEVEEKYGVPPEqiIDyLALM---GDSSDNIPG----VPGIGEKT 202

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 215686953 270 AVKLLKKHGSLENLL-NTAAVRtvGKdyAQDALVKHADYLRKNYEVLSLKR 319
Cdd:COG0258  203 AAKLLQEYGSLENILaNADEIK--GK--LREKLRENKEQARLSRKLATIKT 249
53EXOc smart00475
5'-3' exonuclease;
103-319 1.94e-40

5'-3' exonuclease;


Pssm-ID: 214682 [Multi-domain]  Cd Length: 259  Bit Score: 142.35  E-value: 1.94e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953   103 FARWLALFFAHVSlRDPVVAVLDGEGGNeYRRRLLPSYKAHRPRGPGTGAD--SRVIDVLRECNVPVVRVDGYEADDVVA 180
Cdd:smart00475  36 FLRMLLKLIKEEK-PTYVAVVFDAKGKT-FRHELYPEYKANRPKTPDELLEqiPLIKELLDALGIPVLEVEGYEADDVIA 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953   181 TLTEQVLQKGFRVVIGSPDKDFKQLISEDVQLVMPIPEIGRWSFYTLRHYVAQYKCDPTADLSLRCFIGDEADGIPGiqh 260
Cdd:smart00475 114 TLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPG--- 190

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953   261 lVPGFGRKTAVKLLKKHGSLENLL-NTAAVRtvGKdyAQDALVKHADYLRKNYEVLSLKR 319
Cdd:smart00475 191 -VPGIGEKTAAKLLKEFGSLENILeNLDKLK--KK--LREKLLAHKEDAKLSRKLATIET 245
PRK05755 PRK05755
DNA polymerase I; Provisional
 118-319 1.41e-35

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 137.15  E-value: 1.41e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 118 DPVVAVLDGEGGNeYRRRLLPSYKAHRPRGPgtgADSRV-IDVLREC----NVPVVRVDGYEADDVVATLTEQVLQKGFR 192
Cdd:PRK05755  52 THVAVAFDAKGKT-FRHELYPEYKANRPPMP---EDLREqIPLIRELlralGIPLLELEGYEADDVIGTLAKQAEAAGYE 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 193 VVIGSPDKDFKQLISEDVQLV--MPIPEIGRwsfYTLRHYVAQYKCDPT--AD-LSLrcfIGDEADGIPGiqhlVPGFGR 267
Cdd:PRK05755 128 VLIVTGDKDLLQLVDDNVTLLdtMGVSKNEE---LDPEEVVEKYGVTPEqiIDyLAL---MGDSSDNIPG----VPGIGE 197

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 215686953 268 KTAVKLLKKHGSLENLL-NTAAVRTVGKdyaqDALVKHADYLRKNYEVLSLKR 319
Cdd:PRK05755 198 KTAAKLLQEYGSLEGLYeNLDEIKGKKK----EKLRENKEQAFLSRKLATIKT 246
pola TIGR00593
DNA polymerase I; All proteins in this family for which functions are known are DNA ...
 120-319 2.12e-33

DNA polymerase I; All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. 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: 273160 [Multi-domain]  Cd Length: 887  Bit Score: 130.54  E-value: 2.12e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953  120 VVAVLDgEGGNEYRRRLLPSYKAHRPRGPgtgAD-----SRVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQKGFRVV 194
Cdd:TIGR00593  52 VAVAFD-SGTPTFRHEAYAEYKANRAPTP---EElieqiPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVR 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953  195 IGSPDKDFKQLISEDVQLVMPIpEIGRWSFYTLRHYVAQYKCDPTADLSLRCFIGDEADGIPGiqhlVPGFGRKTAVKLL 274
Cdd:TIGR00593 128 IISGDKDLLQLVSDNVKVLIPK-GKTSFTEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPG----VKGIGEKTAAKLL 202

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 215686953  275 KKHGSLENLLNTaaVRTVGKDYAQDALVKHADYLRKNYEVLSLKR 319
Cdd:TIGR00593 203 QEFGSLENIYEN--LDQIKSAKMREKLIAHKEDAFLSKELATIVT 245
PIN_53EXO cd09859
FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA ...
 118-215 1.40e-24

FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA polymerase I (Taq) and homologs; The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family. Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain 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 PIN domain cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases 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: 350209  Cd Length: 160  Bit Score: 97.44  E-value: 1.40e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 118 DPVVAVLDGEGGNeYRRRLLPSYKAHRPRGPgtgaDS------RVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQKGF 191
Cdd:cd09859   46 DYIAVAFDAKGPT-FRHELYPEYKANRPPMP----EElipqipLIKELLEALGIPVLEVEGYEADDIIGTLAKKAEKEGL 120

                         90       100
                 ....*....|....*....|....
gi 215686953 192 RVVIGSPDKDFKQLISEDVQLVMP 215
Cdd:cd09859  121 EVVIVTGDKDLLQLVDDNVKVLDP 144
5_3_exonuc_N pfam02739
5'-3' exonuclease, N-terminal resolvase-like domain;
120-215 7.18e-23

5'-3' exonuclease, N-terminal resolvase-like domain;


Pssm-ID: 460672  Cd Length: 163  Bit Score: 93.23  E-value: 7.18e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953  120 VVAVLDGEGGneYRRRLLPSYKAHRPrgpGTGAD-----SRVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQKGFRVV 194
Cdd:pfam02739  51 VAVAFDAKPT--FRHELYPEYKANRP---PMPEElrpqiPLIKELLEALGIPVLEVEGYEADDIIGTLAKRAEEEGYEVV 125

                          90       100
                  ....*....|....*....|.
gi 215686953  195 IGSPDKDFKQLISEDVQLVMP 215
Cdd:pfam02739 126 IVTGDKDLLQLVSDNVTVLDP 146
PRK14976 PRK14976
5'-3' exonuclease; Provisional
 133-285 1.19e-19

5'-3' exonuclease; Provisional


Pssm-ID: 237877 [Multi-domain]  Cd Length: 281  Bit Score: 87.31  E-value: 1.19e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 133 RRRLLPSYKAHRPRGPgtgaDS------RVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQKGFRVVIGSPDKDFKQLI 206
Cdd:PRK14976  70 RHQLYDEYKQGRKKTP----ESlisqipLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLV 145

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 215686953 207 SEDVQLVMPIPEIGrWSFYTLRHYVAQYKCDPTADLSLRCFIGDEADGIPGiqhlVPGFGRKTAVKLLKKHGSLENLLN 285
Cdd:PRK14976 146 NENTDVLLKKKGTS-HFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKG----VKGIGPKTAIKLLNKYGNIENIYE 219
PRK09482 PRK09482
flap endonuclease-like protein; Provisional
 120-318 1.49e-19

flap endonuclease-like protein; Provisional


Pssm-ID: 181896 [Multi-domain]  Cd Length: 256  Bit Score: 86.51  E-value: 1.49e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 120 VVAVLDGEGGNE-YRRRLLPSYKAHRPRGPGTGADSRVI--DVLRECNVPVVRVDGYEADDVVATLTEQVLQKGFRVVIG 196
Cdd:PRK09482  50 AVAVFDGDARSSgWRHQLLPDYKAGRKPMPEALQQGLPAirAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIV 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 197 SPDKDFKQLISEDVQL-------VMPIPEIGRwSFYTLRHYVAQYkcdptadLSLrcfIGDEADGIPGiqhlVPGFGRKT 269
Cdd:PRK09482 130 STDKGYCQLLSPTIQIrdyfqkrWLDAPFIEQ-EFGVEPQQLPDY-------WGL---AGISSSKIPG----VAGIGPKS 194

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 215686953 270 AVKLLKKHGSLENLLNTAAvrTVGKDYAQDaLVKHADYLRKNYEVLSLK 318
Cdd:PRK09482 195 AAELLNQFRSLENIYESLD--ALPEKWRKK-LEEHKEMARLCRKLAQLQ 240
PIN_T4-like cd09860
FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N ...
 118-216 2.24e-19

FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N terminus) domain of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. 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. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, metal binding site 1, whereas exonuclease activity requires both, the high-affinity, metal binding site 1 and the low-affinity, metal binding site 2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors.


Pssm-ID: 350210  Cd Length: 158  Bit Score: 83.41  E-value: 2.24e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 118 DPVVAvldGEGGNEYRRRLLPSYKAHRPRGPGTGADSRVI-----DVLRECN----VPVVRVDGYEADDVVATLTEQVLQ 188
Cdd:cd09860   47 KPIVL---WDGRASWRKDLFPEYKANRKKTREEKKAWREAfeaqrPFIEEALeylgVPQIRAPGAEADDLAGVLVKRLAA 123

                         90       100
                 ....*....|....*....|....*...
gi 215686953 189 KGFRVVIGSPDKDFKQLISEDVQLVMPI 216
Cdd:cd09860  124 FGDKVLLVSGDKDWLQLVYENVSWFSPI 151
5_3_exonuc pfam01367
5'-3' exonuclease, C-terminal SAM fold;
248-319 5.31e-15

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


Pssm-ID: 460176 [Multi-domain]  Cd Length: 93  Bit Score: 69.71  E-value: 5.31e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 215686953  248 IGDEADGIPGiqhlVPGFGRKTAVKLLKKHGSLENLLNTAAVRTVGKdyAQDALVKHADYLRKNYEVLSLKR 319
Cdd:pfam01367  13 MGDSSDNIPG----VPGIGEKTAAKLLNEYGSLENILANADEIKGGK--LREKLRENKEQALLSRKLATIKT 78
H3TH_53EXO cd09898
H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; H3TH ...
 248-317 2.38e-14

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: 67.04  E-value: 2.38e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 248 IGDEADGIPGiqhlVPGFGRKTAVKLLKKHGSLENLLNTAAVRTvGKdyAQDALVKHADYLRKNYEVLSL 317
Cdd:cd09898   11 VGDSSDNIPG----VPGIGPKTAAKLLQEYGSLENILANLDELK-GK--LREKLEENKEQALLSRKLATL 73
rnh PHA02567
RnaseH; Provisional
 120-258 9.58e-13

RnaseH; Provisional


Pssm-ID: 222882 [Multi-domain]  Cd Length: 304  Bit Score: 67.78  E-value: 9.58e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 120 VVAVLDGEGGnEYRRRLLPSYKAHRP--RGPGT-------GADSRVIDVLREcNVP--VVRVDGYEADDVVATLTEQVLQ 188
Cdd:PHA02567  67 VLAFDNSKSG-YWRRDIAWYYKKNRKkdREESPwdweglfEAINKIVDEIKE-NMPykVMKIDKAEADDIIAVLTKKFSA 144

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 189 KGFRVVIGSPDKDFKQLisedvqlvMPIPEIGRWSFYTlRHYVAQYKCDPTADLSLRCFIGDEADGIPGI 258
Cdd:PHA02567 145 EGRPVLIVSSDGDFTQL--------HKYPGVKQWSPMQ-KKWVKPKYGSPEKDLMTKIIKGDKKDGVASI 205
PHA00439 PHA00439
exonuclease
 130-276 1.45e-10

exonuclease


Pssm-ID: 222794 [Multi-domain]  Cd Length: 286  Bit Score: 60.95  E-value: 1.45e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 130 NEYRRRLLPSYKAHRP--RGPgTGADSRVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQKGF-RVVIGSPDKDFKQli 206
Cdd:PHA00439  75 VNWRKEVVPTYKANRKakRKP-VGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFkKAVLVSCDKDFKT-- 151

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 215686953 207 sedvqlvmpIPEiGRWSFYTLRHYVAQykcDP-TAD--LSLRCFIGDEADGIPGIqhlvPGFGrKTAVKLLKK 276
Cdd:PHA00439 152 ---------IPN-CDFLWCTTGNILTQ---TPeTADrwHLFQTIKGDSTDGYSGI----PGWG-DTAEAFLEN 206
PIN_53EXO-like cd00008
FEN-like PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H ...
 118-230 8.32e-10

FEN-like PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H and T5-5' nucleases, and homologs; PIN (PilT N terminus) domains of the 5'-3' exonucleases (53EXO) of multi-domain DNA polymerase I and single domain protein homologs, as well as, the PIN domains of bacteriophage T5-5'nuclease (T5FEN or 5'-3'exonuclease), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar nucleases are included in this family. The 53EXO of DNA polymerase I 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 T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. 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: 350199  Cd Length: 158  Bit Score: 56.88  E-value: 8.32e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953 118 DPVVAVLDgEGGNEYRRRLLPSYKAHR--PRGPGTGAD-------SRVIDVLRECNVPVVRVDGYEADDVVATLTEQVLQ 188
Cdd:cd00008   45 DAVIVVFD-AKKPSFRHEAYGGYKANRaeKYAEEKPTPedffeqlALIKELVKLLGLARLEIPGYEADDVLASLVKKAEK 123

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 215686953 189 KGFRVVIGSPDKDFKQLISedvqlvmpiPEIGRWSFYTLRHY 230
Cdd:cd00008  124 EGYEVRIISADGDLYQLLS---------DRVHVLSPTEGYLI 156
H3TH_T4-like cd09899
H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs; H3TH ...
 237-311 5.22e-07

H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs; H3TH (helix-3-turn-helix) domains of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. The T5-5'nuclease is a 5'-3' exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3' exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases 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. They 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 required for nuclease activity. The first metal binding site (MBS-1) is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site (MBS-2) is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, MBS-1, whereas exonuclease activity requires both, the high-affinity, MBS-1 and the low-affinity, MBS-2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors. 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: 188619 [Multi-domain]  Cd Length: 74  Bit Score: 46.72  E-value: 5.22e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 215686953 237 DPTADLSLRCFIGDEADGIPGiqhlVPGFGRKTAVKLLKKHGSLENLLNTAAvrTVGKDYAQDALVKHADYLRKN 311
Cdd:cd09899    1 DPEAYLSAKALAGDTKDNIAG----VPGIGTGRATKLLEEIGDVADIIDALL--TPGKVKNSLALEEAYERFKEN 69
H3TH_StructSpec-5'-nucleases cd00080
H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA ...
 262-316 1.55e-04

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: 39.67  E-value: 1.55e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 215686953 262 VPGFGRKTAVKLLKKHGSLENLL-NTAAVrtvgKDYAQDALVKHADYLRKNYEVLS 316
Cdd:cd00080   20 VPGIGPKTAAKLALKYGSLEGILeNLDEL----KGKKREKLEEPKEYAFLSRKLAT 71
H3TH_FEN1-XPG-like cd09897
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases; The 5' ...
 262-317 3.05e-04

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: 38.73  E-value: 3.05e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 215686953 262 VPGFGRKTAVKLLKKHGSLENLLNtaAVRTVGKDYAQDalvkhaDYLRKNYEVLSL 317
Cdd:cd09897   18 LPGIGPKTALKLIKEYGSLEKVLK--ALRDDKKDKVPV------PYDFPYKKAREL 65
H3TH_FEN1-Euk cd09907
H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 241-284 9.12e-04

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: 37.14  E-value: 9.12e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 215686953 241 DLSLRCfiG-DEADGIPGIqhlvpgfGRKTAVKLLKKHGSLENLL 284
Cdd:cd09907    5 DLCILL--GcDYCESIKGI-------GPKTALKLIKKHKSIEKIL 40
H3TH_FEN1-like cd09901
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 ...
 262-294 1.19e-03

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: 37.13  E-value: 1.19e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 215686953 262 VPGFGRKTAVKLLKKHGSLENLLntAAVRTVGK 294
Cdd:cd09901   18 IPGIGPKTAYKLIKKHKSIEKVL--KALRSNKK 48
PIN_asteroid-like cd18676
FEN-like PIN domain of Drosophila melanogaster asteroid and related proteins; This subfamily ...
 87-202 1.20e-03

FEN-like PIN domain of Drosophila melanogaster asteroid and related proteins; This subfamily includes Drosophila melanogaster asteroid protein which may function in EGF receptor signaling, and may play a role in compound eye morphogenesis. This subfamily belongs 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), the helical arch/clamp region is 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: 350243 [Multi-domain]  Cd Length: 164  Bit Score: 39.16  E-value: 1.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215686953  87 DVNPLC---FRGSQRSLGAFARWLALFFAHVS-----LRD----PVVaVLDGegGNEYR------RRLLPSYKAHRPRGP 148
Cdd:cd18676    4 DGNNLCyqlYFDSNLDNSAFGGDYDKYARVVReffelLSKcnvtPYV-ILDG--GYEDRklktvtSRLRAKIKIAKAKTP 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 215686953 149 GTGADSRVI---------DVLRECNVPVVRVDgYEADDVVATLTEQ----VLqkgfrvvigSPDKDF 202
Cdd:cd18676   81 STGGSGSILplllkevfvDVLKELNVKVVQCD-FEADDEIAALARKlncpVL---------SYDSDF 137
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 250-285 2.84e-03

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 39.22  E-value: 2.84e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 215686953 250 DEADGIPGIqhlvpgfGRKTAVKLLKKHGSLENLLN 285
Cdd:PTZ00217 235 DYCDTIKGI-------GPKTAYKLIKKYKSIEEILE 263
PRK03980 PRK03980
flap endonuclease-1; Provisional
 262-284 2.97e-03

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 39.03  E-value: 2.97e-03
                         10        20
                 ....*....|....*....|...
gi 215686953 262 VPGFGRKTAVKLLKKHGSLENLL 284
Cdd:PRK03980 194 IKGIGPKTALKLIKKHGDLEKVL 216
HhH2 smart00279
Helix-hairpin-helix class 2 (Pol1 family) motifs;
238-277 6.73e-03

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


Pssm-ID: 197623 [Multi-domain]  Cd Length: 36  Bit Score: 33.96  E-value: 6.73e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 215686953   238 PTADLSLRCFIGDEADGIPGiqhlVPGFGRKTAVKLLKKH 277
Cdd:smart00279   1 PEQFIDYAILVGDYSDNIPG----VKGIGPKTALKLLREF 36
 
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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