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Conserved domains on  [gi|1577328161|ref|WP_130110524|]
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endonuclease/exonuclease/phosphatase family protein [Leucobacter triazinivorans]

Protein Classification

exonuclease/endonuclease/phosphatase family protein( domain architecture ID 662)

exonuclease/endonuclease/phosphatase (EEP) family protein may cleave phosphodiester bonds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YafD super family cl43764
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-222 5.09e-11

Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily [General function prediction only];


The actual alignment was detected with superfamily member COG3021:

Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 61.16  E-value: 5.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161   1 MKVVSYNLR-KNRAVAEIGALADDHEVDVLCLQEAEAIALPAhLGHLSL-----VHATERNRLGLAMYVREErFRTRSAH 74
Cdd:COG3021    95 LRVLTANVLfGNADAEALAALVREEDPDVLVLQETTPAWEEA-LAALEAdypyrVLCPLDNAYGMALLSRLP-LTEAEVV 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161  75 TfqlkkslhdrlLAPAHERLLGARIhDLETeRDLVVASFHAAPLTALNSLRRYQIHTALAQLRQLGPglPALMVGDYNYP 154
Cdd:COG3021   173 Y-----------LVGDDIPSIRATV-ELPG-GPVRLVAVHPAPPVGGSAERDAELAALAKAVAALDG--PVIVAGDFNAT 237

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1577328161 155 VFKGRLDTEMRDHGYELSLSDKRTY----TRYKMFRGHFDFA-TSSGLDINRVETLQRGLSDHLPILVSASLR 222
Cdd:COG3021   238 PWSPTLRRLLRASGLRDARAGRGLGptwpANLPFLRLPIDHVlVSRGLTVVDVRVLPVIGSDHRPLLAELALP 310
 
Name Accession Description Interval E-value
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-222 5.09e-11

Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily [General function prediction only];


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 61.16  E-value: 5.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161   1 MKVVSYNLR-KNRAVAEIGALADDHEVDVLCLQEAEAIALPAhLGHLSL-----VHATERNRLGLAMYVREErFRTRSAH 74
Cdd:COG3021    95 LRVLTANVLfGNADAEALAALVREEDPDVLVLQETTPAWEEA-LAALEAdypyrVLCPLDNAYGMALLSRLP-LTEAEVV 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161  75 TfqlkkslhdrlLAPAHERLLGARIhDLETeRDLVVASFHAAPLTALNSLRRYQIHTALAQLRQLGPglPALMVGDYNYP 154
Cdd:COG3021   173 Y-----------LVGDDIPSIRATV-ELPG-GPVRLVAVHPAPPVGGSAERDAELAALAKAVAALDG--PVIVAGDFNAT 237

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1577328161 155 VFKGRLDTEMRDHGYELSLSDKRTY----TRYKMFRGHFDFA-TSSGLDINRVETLQRGLSDHLPILVSASLR 222
Cdd:COG3021   238 PWSPTLRRLLRASGLRDARAGRGLGptwpANLPFLRLPIDHVlVSRGLTVVDVRVLPVIGSDHRPLLAELALP 310
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 2-217 7.08e-07

Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.


Pssm-ID: 197317 [Multi-domain]  Cd Length: 252  Bit Score: 48.75  E-value: 7.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161   2 KVVSYNL--------------RKNRAVAEIgalaDDHEVDVLCLQEAeaiaLPAHLGHLsLVHATERNRLGL-------- 59
Cdd:cd09083     1 RVMTFNIrydnpsdgenswenRKDLVAELI----KFYDPDIIGTQEA----LPHQLADL-EELLPEYDWIGVgrddgkek 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161  60 ----AMYVREERFRTRSAHTFQLKKSlhdrllaPAHERLLG-----------ARIHDLETERDLVVASFH-------Aap 117
Cdd:cd09083    72 gefsAIFYRKDRFELLDSGTFWLSET-------PDVVGSKGwdaalprictwARFKDKKTGKEFYVFNTHldhvgeeA-- 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161 118 ltalnslRRYQIHTALAQLRQLGPGLPALMVGDYN----YPVFKGRLDTEMRDhGYELSL----SDKRTYTRYKMFRG-- 187
Cdd:cd09083   143 -------REESAKLILERIKEIAGDLPVILTGDFNaepdSEPYKTLTSGGLKD-ARDTAAttdgGPEGTFHGFKGPPGgs 214

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1577328161 188 HFDFA-TSSGLDINRVETLQRG-----LSDHLPILV 217
Cdd:cd09083   215 RIDYIfVSPGVKVLSYEILTDRydgryPSDHFPVVA 250
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-153 4.98e-05

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 42.60  E-value: 4.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161   4 VSYNL--------RKNRAVAEIGALADDHEVDVLCLQEA--------EAIALPAHLGHLSLVHATERNRLGLAMYVReer 67
Cdd:pfam03372   1 LTWNVnggnadaaGDDRKLDALAALIRAYDPDVVALQETddddasrlLLALLAYGGFLSYGGPGGGGGGGGVAILSR--- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161  68 frtrsahtFQLKKSLHDRLLAPAHERLLGARIHDLETERDLVVASFHAAPLTALNSLRRYQIHTALAQLRQLGPGLPALM 147
Cdd:pfam03372  78 --------YPLSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVIL 149


                  ....*.
gi 1577328161 148 VGDYNY 153
Cdd:pfam03372 150 AGDFNA 155
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-66 2.46e-04

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.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: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 41.11  E-value: 2.46e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1577328161   1 MKVVSYNLRKNRAVAEIGALA--DDHEVDVLCLQEAEA------IALPAHLGHLSLVHATERNRLGLAMYVREE 66
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDwlKEEQPDVLCLQETKVadeqfpAELFEELGYHVFFHGAKKGYSGVAILSKVE 74
 
Name Accession Description Interval E-value
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-222 5.09e-11

Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily [General function prediction only];


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 61.16  E-value: 5.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161   1 MKVVSYNLR-KNRAVAEIGALADDHEVDVLCLQEAEAIALPAhLGHLSL-----VHATERNRLGLAMYVREErFRTRSAH 74
Cdd:COG3021    95 LRVLTANVLfGNADAEALAALVREEDPDVLVLQETTPAWEEA-LAALEAdypyrVLCPLDNAYGMALLSRLP-LTEAEVV 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161  75 TfqlkkslhdrlLAPAHERLLGARIhDLETeRDLVVASFHAAPLTALNSLRRYQIHTALAQLRQLGPglPALMVGDYNYP 154
Cdd:COG3021   173 Y-----------LVGDDIPSIRATV-ELPG-GPVRLVAVHPAPPVGGSAERDAELAALAKAVAALDG--PVIVAGDFNAT 237

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1577328161 155 VFKGRLDTEMRDHGYELSLSDKRTY----TRYKMFRGHFDFA-TSSGLDINRVETLQRGLSDHLPILVSASLR 222
Cdd:COG3021   238 PWSPTLRRLLRASGLRDARAGRGLGptwpANLPFLRLPIDHVlVSRGLTVVDVRVLPVIGSDHRPLLAELALP 310
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-217 4.43e-08

Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only];


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 51.06  E-value: 4.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161   1 MKVVSYNLRKNRA------VAEIGALADDHEVDVLCLQEaeaIALpahlghLSlvhaternrlglamyvreeRFRTRSAH 74
Cdd:COG3568     8 LRVMTYNIRYGLGtdgradLERIARVIRALDPDVVALQE---NAI------LS-------------------RYPIVSSG 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161  75 TFQLKKSlhdrllAPAHERLLGARIHDleTERDLVVASFHAAPLTAlnSLRRYQIHTALAQLRQLGPGLPALMVGDYNyp 154
Cdd:COG3568    60 TFDLPDP------GGEPRGALWADVDV--PGKPLRVVNTHLDLRSA--AARRRQARALAELLAELPAGAPVILAGDFN-- 127

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1577328161 155 vfkgrldteMRDHgyelslsdkrtytrykmfrghfdFATSSGLDINRVETLQ----RGLSDHLPILV 217
Cdd:COG3568   128 ---------DIDY-----------------------ILVSPGLRVLSAEVLDsplgRAASDHLPVVA 162
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 2-217 7.08e-07

Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.


Pssm-ID: 197317 [Multi-domain]  Cd Length: 252  Bit Score: 48.75  E-value: 7.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161   2 KVVSYNL--------------RKNRAVAEIgalaDDHEVDVLCLQEAeaiaLPAHLGHLsLVHATERNRLGL-------- 59
Cdd:cd09083     1 RVMTFNIrydnpsdgenswenRKDLVAELI----KFYDPDIIGTQEA----LPHQLADL-EELLPEYDWIGVgrddgkek 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161  60 ----AMYVREERFRTRSAHTFQLKKSlhdrllaPAHERLLG-----------ARIHDLETERDLVVASFH-------Aap 117
Cdd:cd09083    72 gefsAIFYRKDRFELLDSGTFWLSET-------PDVVGSKGwdaalprictwARFKDKKTGKEFYVFNTHldhvgeeA-- 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161 118 ltalnslRRYQIHTALAQLRQLGPGLPALMVGDYN----YPVFKGRLDTEMRDhGYELSL----SDKRTYTRYKMFRG-- 187
Cdd:cd09083   143 -------REESAKLILERIKEIAGDLPVILTGDFNaepdSEPYKTLTSGGLKD-ARDTAAttdgGPEGTFHGFKGPPGgs 214

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1577328161 188 HFDFA-TSSGLDINRVETLQRG-----LSDHLPILV 217
Cdd:cd09083   215 RIDYIfVSPGVKVLSYEILTDRydgryPSDHFPVVA 250
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-153 4.98e-05

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 42.60  E-value: 4.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161   4 VSYNL--------RKNRAVAEIGALADDHEVDVLCLQEA--------EAIALPAHLGHLSLVHATERNRLGLAMYVReer 67
Cdd:pfam03372   1 LTWNVnggnadaaGDDRKLDALAALIRAYDPDVVALQETddddasrlLLALLAYGGFLSYGGPGGGGGGGGVAILSR--- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161  68 frtrsahtFQLKKSLHDRLLAPAHERLLGARIHDLETERDLVVASFHAAPLTALNSLRRYQIHTALAQLRQLGPGLPALM 147
Cdd:pfam03372  78 --------YPLSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVIL 149


                  ....*.
gi 1577328161 148 VGDYNY 153
Cdd:pfam03372 150 AGDFNA 155
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-66 2.46e-04

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.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: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 41.11  E-value: 2.46e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1577328161   1 MKVVSYNLRKNRAVAEIGALA--DDHEVDVLCLQEAEA------IALPAHLGHLSLVHATERNRLGLAMYVREE 66
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDwlKEEQPDVLCLQETKVadeqfpAELFEELGYHVFFHGAKKGYSGVAILSKVE 74
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-154 3.61e-04

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


Pssm-ID: 197306 [Multi-domain]  Cd Length: 241  Bit Score: 40.54  E-value: 3.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161   3 VVSYNLRKNRAVA---EIGALADDHEVDVLCLQEAE-----AIALPAHLGHLSLVHATERNRL----GLAMYVREERFRT 70
Cdd:cd08372     1 VASYNVNGLNAATrasGIARWVRELDPDIVCLQEVKdsqysAVALNQLLPEGYHQYQSGPSRKegyeGVAILSKTPKFKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161  71 RSAHTFQLKKS-LHDRllapaheRLLGARI--HDleteRDLVVASFHAAPLTALNSLRRYQIHTALAQLRQLGP--GLPA 145
Cdd:cd08372    81 VEKHQYKFGEGdSGER-------RAVVVKFdvHD----KELCVVNAHLQAGGTRADVRDAQLKEVLEFLKRLRQpnSAPV 149


                  ....*....
gi 1577328161 146 LMVGDYNYP 154
Cdd:cd08372   150 VICGDFNVR 158
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-66 6.22e-04

Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.


Pssm-ID: 197319 [Multi-domain]  Cd Length: 252  Bit Score: 39.95  E-value: 6.22e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1577328161   1 MKVVSYNLRKNRAVAEIGALA--DDHEVDVLCLQE--AEAIALPAHL----GHLSLVHATERNRL-GLAMYVREE 66
Cdd:cd09085     1 MKIISWNVNGLRAVHKKGFLDwfKEEKPDILCLQEtkAQPEQLPEDLrnieGYHSYFNSAERKGYsGVALYSKIE 75
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-66 8.13e-04

Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.


Pssm-ID: 197336 [Multi-domain]  Cd Length: 253  Bit Score: 39.52  E-value: 8.13e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1577328161   1 MKVVSYNLRKNRAVAEIGAL--ADDHEVDVLCLQEAEA-------IALPAHLGHLSLVHATERNRLGLAMYVREE 66
Cdd:cd10281     1 MRVISVNVNGIRAAAKKGFLewLAAQDADVVCLQEVRAqeeqlddDFFEPEGYNAYFFDAEKKGYAGVAIYSRTQ 75
MnuA_DNase1-like cd10283
Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a ...
 95-217 1.51e-03

Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a membrane-associated nuclease related to Deoxyribonuclease 1 (DNase1 or DNase I, EC 3.1.21.1). The in vivo role of MnuA is as yet undetermined. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197338 [Multi-domain]  Cd Length: 266  Bit Score: 38.92  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1577328161  95 LGARIHDLETERDLVVASFHA----APLTALNSLRRYQIHtALAQ----LRQLGPGLPALMVGDYNYP----VFKgrldt 162
Cdd:cd10283   113 YAAKFKSGGTGFDFTLVNVHLksggSSKSGQGAKRVAEAQ-ALAEylkeLADEDPDDDVILLGDFNIPadedAFK----- 186

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1577328161 163 EMRDHGYELSLSDKRTYT-RYKMFRGHFD----------FATSSG-LDINRV-----------ETLQRGLSDHLPILV 217
Cdd:cd10283   187 ALTKAGFKSLLPDSTNLStSFKGYANSYDnifvsgnlkeKFSNSGvFDFNILvdeageedldySKWRKQISDHDPVWV 264
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-66 2.73e-03

exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 272954 [Multi-domain]  Cd Length: 254  Bit Score: 38.13  E-value: 2.73e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1577328161   1 MKVVSYNLRKNRAVAEIG-ALADDHEVDVLCLQEAEAI--ALPAHLGHLS---LVHATERNRLGLAMYVREE 66
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGlAWLKENQPDVLCLQETKVQdeQFPLEPFHKEgyhVFFSGQKGYSGVAIFSKEE 72
 
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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