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Conserved domains on  [gi|1125076517|gb|OLA39662|]
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hypothetical protein BHW35_00105 [Firmicutes bacterium CAG:176_63_11]

Protein Classification

PIN domain-containing protein( domain architecture ID 10177139)

PIN (PilT N terminus) domain-containing protein may function as a nuclease; similar to Arabidopsis thaliana 5'-3' exonuclease family protein

Gene Ontology:  GO:0004540
PubMed:  21036780

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_53EXO cd09859
FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA ...
 5-166 1.30e-84

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: 245.74  E-value: 1.30e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   5 VLDGNSIVNRAYYGIRPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKGMPEELAM 84
Cdd:cd09859     1 LIDGSSLLYRAYYALPPLTTSDGEPTNAVYGFTNMLLKLLKEEKPDYIAVAFDAKGPTFRHELYPEYKANRPPMPEELIP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  85 QMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHTKVKLVstrMGQTTTKDMTPET 164
Cdd:cd09859    81 QIPLIKELLEALGIPVLEVEGYEADDIIGTLAKKAEKEGLEVVIVTGDKDLLQLVDDNVKVLDP---KKGSKTEIYDEEE 157


                  ..
gi 1125076517 165 FQ 166
Cdd:cd09859   158 VK 159
 
Name Accession Description Interval E-value
PIN_53EXO cd09859
FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA ...
 5-166 1.30e-84

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: 245.74  E-value: 1.30e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   5 VLDGNSIVNRAYYGIRPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKGMPEELAM 84
Cdd:cd09859     1 LIDGSSLLYRAYYALPPLTTSDGEPTNAVYGFTNMLLKLLKEEKPDYIAVAFDAKGPTFRHELYPEYKANRPPMPEELIP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  85 QMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHTKVKLVstrMGQTTTKDMTPET 164
Cdd:cd09859    81 QIPLIKELLEALGIPVLEVEGYEADDIIGTLAKKAEKEGLEVVIVTGDKDLLQLVDDNVKVLDP---KKGSKTEIYDEEE 157


                  ..
gi 1125076517 165 FQ 166
Cdd:cd09859   158 VK 159
5_3_exonuc_N pfam02739
5'-3' exonuclease, N-terminal resolvase-like domain;
2-166 1.64e-83

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


Pssm-ID: 460672  Cd Length: 163  Bit Score: 243.07  E-value: 1.64e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   2 KLMVLDGNSIVNRAYYGIRPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRRePTFRHEADAAYKAQRKGMPEE 81
Cdd:pfam02739   1 KLLLIDGSSLLFRAFYALPPLTNSDGLPTNAVYGFLNMLLKLLKEEKPTHVAVAFDAK-PTFRHELYPEYKANRPPMPEE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  82 LAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHTKVKLVStrmgqTTTKDMT 161
Cdd:pfam02739  80 LRPQIPLIKELLEALGIPVLEVEGYEADDIIGTLAKRAEEEGYEVVIVTGDKDLLQLVSDNVTVLDPG-----VTTEIYD 154


                  ....*
gi 1125076517 162 PETFQ 166
Cdd:pfam02739 155 PEEVK 159
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
2-166 5.27e-83

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


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 246.09  E-value: 5.27e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   2 KLMVLDGNSIVNRAYYGIRPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKGMPEE 81
Cdd:COG0258     6 KLLLIDGSSLLFRAFYALPPLTNSDGQPTNAVYGFTNMLLKLLKEEKPTHLAVAFDAKGPTFRHELYPEYKANRPEMPEE 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  82 LAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHtkVKLVSTRMGQTTTKDMT 161
Cdd:COG0258    86 LRPQIPLIKEVLEALGIPVLEVEGYEADDVIGTLAKQAEAEGYEVLIVTGDKDLLQLVDDN--VTVLDPMKGVSELERYD 163


                  ....*
gi 1125076517 162 PETFQ 166
Cdd:COG0258   164 PAEVE 168
PRK05755 PRK05755
DNA polymerase I; Provisional
 2-163 4.86e-72

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 232.29  E-value: 4.86e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   2 KLMVLDGNSIVNRAYYGI-RPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKGMPE 80
Cdd:PRK05755    3 TLLLIDGSSLLFRAFYALlPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDAKGKTFRHELYPEYKANRPPMPE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  81 ELAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHtkVKLVSTrMGQTTTKDM 160
Cdd:PRK05755   83 DLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDN--VTLLDT-MGVSKNEEL 159


                  ...
gi 1125076517 161 TPE 163
Cdd:PRK05755  160 DPE 162
53EXOc smart00475
5'-3' exonuclease;
1-166 1.84e-62

5'-3' exonuclease;


Pssm-ID: 214682 [Multi-domain]  Cd Length: 259  Bit Score: 192.81  E-value: 1.84e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517    1 MKLMVLDGNSIVNRAYYGIRPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKGMPE 80
Cdd:smart00475   1 KKLLLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKGKTFRHELYPEYKANRPKTPD 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   81 ELAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHTKVkLVSTRmGQTTTKDM 160
Cdd:smart00475  81 ELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSV-LDPTK-GIKEFELY 158


                   ....*.
gi 1125076517  161 TPETFQ 166
Cdd:smart00475 159 TPENVI 164
pola TIGR00593
DNA polymerase I; All proteins in this family for which functions are known are DNA ...
 3-163 2.88e-55

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: 186.39  E-value: 2.88e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   3 LMVLDGNSIVNRAYYGIR--PLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKGMPE 80
Cdd:TIGR00593   1 LLLIDGHSLAFRAYFALKnkPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSGTPTFRHEAYAEYKANRAPTPE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  81 ELAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHTKVKLVStrmGQTTTKDM 160
Cdd:TIGR00593  81 ELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLIPK---GKTSFTEI 157


                  ...
gi 1125076517 161 TPE 163
Cdd:TIGR00593 158 TPE 160
 
Name Accession Description Interval E-value
PIN_53EXO cd09859
FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA ...
 5-166 1.30e-84

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: 245.74  E-value: 1.30e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   5 VLDGNSIVNRAYYGIRPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKGMPEELAM 84
Cdd:cd09859     1 LIDGSSLLYRAYYALPPLTTSDGEPTNAVYGFTNMLLKLLKEEKPDYIAVAFDAKGPTFRHELYPEYKANRPPMPEELIP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  85 QMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHTKVKLVstrMGQTTTKDMTPET 164
Cdd:cd09859    81 QIPLIKELLEALGIPVLEVEGYEADDIIGTLAKKAEKEGLEVVIVTGDKDLLQLVDDNVKVLDP---KKGSKTEIYDEEE 157


                  ..
gi 1125076517 165 FQ 166
Cdd:cd09859   158 VK 159
5_3_exonuc_N pfam02739
5'-3' exonuclease, N-terminal resolvase-like domain;
2-166 1.64e-83

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


Pssm-ID: 460672  Cd Length: 163  Bit Score: 243.07  E-value: 1.64e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   2 KLMVLDGNSIVNRAYYGIRPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRRePTFRHEADAAYKAQRKGMPEE 81
Cdd:pfam02739   1 KLLLIDGSSLLFRAFYALPPLTNSDGLPTNAVYGFLNMLLKLLKEEKPTHVAVAFDAK-PTFRHELYPEYKANRPPMPEE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  82 LAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHTKVKLVStrmgqTTTKDMT 161
Cdd:pfam02739  80 LRPQIPLIKELLEALGIPVLEVEGYEADDIIGTLAKRAEEEGYEVVIVTGDKDLLQLVSDNVTVLDPG-----VTTEIYD 154


                  ....*
gi 1125076517 162 PETFQ 166
Cdd:pfam02739 155 PEEVK 159
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
2-166 5.27e-83

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


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 246.09  E-value: 5.27e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   2 KLMVLDGNSIVNRAYYGIRPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKGMPEE 81
Cdd:COG0258     6 KLLLIDGSSLLFRAFYALPPLTNSDGQPTNAVYGFTNMLLKLLKEEKPTHLAVAFDAKGPTFRHELYPEYKANRPEMPEE 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  82 LAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHtkVKLVSTRMGQTTTKDMT 161
Cdd:COG0258    86 LRPQIPLIKEVLEALGIPVLEVEGYEADDVIGTLAKQAEAEGYEVLIVTGDKDLLQLVDDN--VTVLDPMKGVSELERYD 163


                  ....*
gi 1125076517 162 PETFQ 166
Cdd:COG0258   164 PAEVE 168
PRK05755 PRK05755
DNA polymerase I; Provisional
 2-163 4.86e-72

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 232.29  E-value: 4.86e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   2 KLMVLDGNSIVNRAYYGI-RPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKGMPE 80
Cdd:PRK05755    3 TLLLIDGSSLLFRAFYALlPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDAKGKTFRHELYPEYKANRPPMPE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  81 ELAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHtkVKLVSTrMGQTTTKDM 160
Cdd:PRK05755   83 DLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDN--VTLLDT-MGVSKNEEL 159


                  ...
gi 1125076517 161 TPE 163
Cdd:PRK05755  160 DPE 162
53EXOc smart00475
5'-3' exonuclease;
1-166 1.84e-62

5'-3' exonuclease;


Pssm-ID: 214682 [Multi-domain]  Cd Length: 259  Bit Score: 192.81  E-value: 1.84e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517    1 MKLMVLDGNSIVNRAYYGIRPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKGMPE 80
Cdd:smart00475   1 KKLLLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKGKTFRHELYPEYKANRPKTPD 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   81 ELAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHTKVkLVSTRmGQTTTKDM 160
Cdd:smart00475  81 ELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSV-LDPTK-GIKEFELY 158


                   ....*.
gi 1125076517  161 TPETFQ 166
Cdd:smart00475 159 TPENVI 164
pola TIGR00593
DNA polymerase I; All proteins in this family for which functions are known are DNA ...
 3-163 2.88e-55

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: 186.39  E-value: 2.88e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   3 LMVLDGNSIVNRAYYGIR--PLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKGMPE 80
Cdd:TIGR00593   1 LLLIDGHSLAFRAYFALKnkPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSGTPTFRHEAYAEYKANRAPTPE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  81 ELAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHTKVKLVStrmGQTTTKDM 160
Cdd:TIGR00593  81 ELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLIPK---GKTSFTEI 157


                  ...
gi 1125076517 161 TPE 163
Cdd:TIGR00593 158 TPE 160
PRK14976 PRK14976
5'-3' exonuclease; Provisional
 2-166 5.25e-46

5'-3' exonuclease; Provisional


Pssm-ID: 237877 [Multi-domain]  Cd Length: 281  Bit Score: 151.64  E-value: 5.25e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   2 KLMVLDGNSIVNRAYYG-IRP---LTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQRKG 77
Cdd:PRK14976    4 KALLIDGNSLIFRSYYAtLKQgpkLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQGRKK 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  78 MPEELAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHTKVKLVSTrmgQTTT 157
Cdd:PRK14976   84 TPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLKKK---GTSH 160


                  ....*....
gi 1125076517 158 KDMTPETFQ 166
Cdd:PRK14976  161 FILNTNNFF 169
PIN_T4-like cd09860
FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N ...
 3-151 1.11e-21

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: 85.72  E-value: 1.11e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   3 LMVLDGNSIVNRAYYGirPLTTRQGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRRePTFRHEADAAYKAQRKGMPEEL 82
Cdd:cd09860     1 LLLIDGNSIGFAAQHS--AKLTAGGMEVQARFGFLRSIRSYLKRYKYAKPIVLWDGR-ASWRKDLFPEYKANRKKTREEK 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1125076517  83 AM-------QMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDhtKVKLVSTR 151
Cdd:cd09860    78 KAwreafeaQRPFIEEALEYLGVPQIRAPGAEADDLAGVLVKRLAAFGDKVLLVSGDKDWLQLVYE--NVSWFSPI 151
PIN_53EXO-like cd00008
FEN-like PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H ...
 5-145 1.66e-21

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: 85.00  E-value: 1.66e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517   5 VLDGNSIVNRAYYGIRPLTTRqGLYTNAIYGFITTLQRLLDEEKPEALCVTFDRREPTFRHEADAAYKAQR-------KG 77
Cdd:cd00008     1 LVDGHHLAYRTFHANKGLTTS-GEPVQAVYGFAKSILKALKEDSGDAVIVVFDAKKPSFRHEAYGGYKANRaekyaeeKP 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1125076517  78 MPEELAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQLITDHTKV 145
Cdd:cd00008    80 TPEDFFEQLALIKELVKLLGLARLEIPGYEADDVLASLVKKAEKEGYEVRIISADGDLYQLLSDRVHV 147
PRK09482 PRK09482
flap endonuclease-like protein; Provisional
 39-145 4.29e-16

flap endonuclease-like protein; Provisional


Pssm-ID: 181896 [Multi-domain]  Cd Length: 256  Bit Score: 73.02  E-value: 4.29e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125076517  39 TLQRLLDEEKPEALCVTFD--RREPTFRHEADAAYKAQRKGMPEELAMQMLPLKQVLTAMSIPRYELTGYEADDLIGTIS 116
Cdd:PRK09482   37 ALDKLIRHSQPTHAVAVFDgdARSSGWRHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLA 116

                          90       100
                  ....*....|....*....|....*....
gi 1125076517 117 RKCEAAGWDCVIVTGDKDSLQLITDHTKV 145
Cdd:PRK09482  117 VKVAQAGHQATIVSTDKGYCQLLSPTIQI 145
rnh PHA02567
RnaseH; Provisional
 102-138 4.08e-03

RnaseH; Provisional


Pssm-ID: 222882 [Multi-domain]  Cd Length: 304  Bit Score: 36.57  E-value: 4.08e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1125076517 102 ELTGYEADDLIGTISRKCEAAGWDCVIVTGDKDSLQL 138
Cdd:PHA02567  125 KIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQL 161
 
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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