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Conserved domains on  [gi|1907443944|ref|WP_190054702|]
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endonuclease/exonuclease/phosphatase family protein [Streptomyces lomondensis]

Protein Classification

endonuclease/exonuclease/phosphatase family protein( domain architecture ID 10007571)

endonuclease/exonuclease/phosphatase (EEP) family protein similar to PGAP2-interacting protein, which is involved in lipid remodeling during glycosylphosphatidylinositol (GPI)-anchor maturation

CATH:  3.60.10.10
Gene Ontology:  GO:0003824
PubMed:  10838565

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-269 7.64e-25

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


:

Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 97.29  E-value: 7.64e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   1 MRIVTWNLWWRFGPWQ-ARQKAILTALRELRPDVVGLQEvwaadgenlaewlagelglhcawaashaperwrrriddptv 79
Cdd:COG3568     8 LRVMTYNIRYGLGTDGrADLERIARVIRALDPDVVALQE----------------------------------------- 46

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  80 digNAVLSRWPVVDQDVLPLPAPADTddGRLALYARLAGPGHDVPFFTAHFASapDASAVRCGQATALAGFVARHRGGTP 159
Cdd:COG3568    47 ---NAILSRYPIVSSGTFDLPDPGGE--PRGALWADVDVPGKPLRVVNTHLDL--RSAAARRRQARALAELLAELPAGAP 119

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 160 FppVVTGDLNAwpdsdevrllggyktapaapgqvlldaweyadpaapsatwdaanpyvapthepsvrIDYIHVGPPgpdg 239
Cdd:COG3568   120 V--ILAGDFND--------------------------------------------------------IDYILVSPG---- 137

                         250       260       270
                  ....*....|....*....|....*....|
gi 1907443944 240 lGHVRSVHRACAGpvDGVWPSDHAAVVADL 269
Cdd:COG3568   138 -LRVLSAEVLDSP--LGRAASDHLPVVADL 164
 
Name Accession Description Interval E-value
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-269 7.64e-25

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 97.29  E-value: 7.64e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   1 MRIVTWNLWWRFGPWQ-ARQKAILTALRELRPDVVGLQEvwaadgenlaewlagelglhcawaashaperwrrriddptv 79
Cdd:COG3568     8 LRVMTYNIRYGLGTDGrADLERIARVIRALDPDVVALQE----------------------------------------- 46

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  80 digNAVLSRWPVVDQDVLPLPAPADTddGRLALYARLAGPGHDVPFFTAHFASapDASAVRCGQATALAGFVARHRGGTP 159
Cdd:COG3568    47 ---NAILSRYPIVSSGTFDLPDPGGE--PRGALWADVDVPGKPLRVVNTHLDL--RSAAARRRQARALAELLAELPAGAP 119

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 160 FppVVTGDLNAwpdsdevrllggyktapaapgqvlldaweyadpaapsatwdaanpyvapthepsvrIDYIHVGPPgpdg 239
Cdd:COG3568   120 V--ILAGDFND--------------------------------------------------------IDYILVSPG---- 137

                         250       260       270
                  ....*....|....*....|....*....|
gi 1907443944 240 lGHVRSVHRACAGpvDGVWPSDHAAVVADL 269
Cdd:COG3568   138 -LRVLSAEVLDSP--LGRAASDHLPVVADL 164
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 1-269 4.68e-23

Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family 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: 197314 [Multi-domain]  Cd Length: 248  Bit Score: 94.72  E-value: 4.68e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   1 MRIVTWNLWW-RFGPWQARQKAILTALRELRPDVVGLQEV----WAADGENlaEWLAGElglhcaWAASHAPERWRRRid 75
Cdd:cd09080     1 LKVLTWNVDFlDDVNLAERMRAILKLLEELDPDVIFLQEVtppfLAYLLSQ--PWVRKN------YYFSEGPPSPAVD-- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  76 dptvDIGNAVLSRWPVVdQDVLPLPApadTDDGRLALYARLAGpGHDVPF--FTAHFASAPDASAVRCGQATALAGFVAR 153
Cdd:cd09080    71 ----PYGVLILSKKSLV-VRRVPFTS---TRMGRNLLAAEINL-GSGEPLrlATTHLESLKSHSSERTAQLEEIAKKLKK 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 154 HRGgtpFPPVVT-GDLNAWPDSDEVRLL-GGYKtapaapgqvllDAWEYADPAA-PSATWDA-ANPYVAPT-HEPSVRID 228
Cdd:cd09080   142 PPG---AANVILgGDFNLRDKEDDTGGLpNGFV-----------DAWEELGPPGePGYTWDTqKNPMLRKGeAGPRKRFD 207

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1907443944 229 YIHVGPPGPDglghVRSVHR----ACAGPVDGVWPSDHAAVVADL 269
Cdd:cd09080   208 RVLLRGSDLK----PKSIELigtePIPGDEEGLFPSDHFGLLAEL 248
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-170 1.80e-12

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: 64.55  E-value: 1.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   4 VTWNLWWRFGP---WQARQKAILTALRELRPDVVGLQEVWAADGENLAEWLAGELGLHCAWAASHAPERWrrriddptvd 80
Cdd:pfam03372   1 LTWNVNGGNADaagDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGGGGG---------- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  81 iGNAVLSRWPVVDQDVLPLPapadTDDGRLALYARLAGPGHDVPFFTAHFASAPDASAVRCGQATALAGFVARHRGGTPF 160
Cdd:pfam03372  71 -GVAILSRYPLSSVILVDLG----EFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSE 145

                         170
                  ....*....|
gi 1907443944 161 PPVVTGDLNA 170
Cdd:pfam03372 146 PVILAGDFNA 155
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-64 1.14e-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: 39.67  E-value: 1.14e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907443944   1 MRIVTWNLwwrfGPWQARQKAILTALRELRPDVVGLQEVWAADgENLAEWLAGELGLHCAWAAS 64
Cdd:TIGR00195   1 MKIISWNV----NGLRARPHKGLAWLKENQPDVLCLQETKVQD-EQFPLEPFHKEGYHVFFSGQ 59
 
Name Accession Description Interval E-value
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-269 7.64e-25

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 97.29  E-value: 7.64e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   1 MRIVTWNLWWRFGPWQ-ARQKAILTALRELRPDVVGLQEvwaadgenlaewlagelglhcawaashaperwrrriddptv 79
Cdd:COG3568     8 LRVMTYNIRYGLGTDGrADLERIARVIRALDPDVVALQE----------------------------------------- 46

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  80 digNAVLSRWPVVDQDVLPLPAPADTddGRLALYARLAGPGHDVPFFTAHFASapDASAVRCGQATALAGFVARHRGGTP 159
Cdd:COG3568    47 ---NAILSRYPIVSSGTFDLPDPGGE--PRGALWADVDVPGKPLRVVNTHLDL--RSAAARRRQARALAELLAELPAGAP 119

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 160 FppVVTGDLNAwpdsdevrllggyktapaapgqvlldaweyadpaapsatwdaanpyvapthepsvrIDYIHVGPPgpdg 239
Cdd:COG3568   120 V--ILAGDFND--------------------------------------------------------IDYILVSPG---- 137

                         250       260       270
                  ....*....|....*....|....*....|
gi 1907443944 240 lGHVRSVHRACAGpvDGVWPSDHAAVVADL 269
Cdd:COG3568   138 -LRVLSAEVLDSP--LGRAASDHLPVVADL 164
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 1-269 4.68e-23

Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family 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: 197314 [Multi-domain]  Cd Length: 248  Bit Score: 94.72  E-value: 4.68e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   1 MRIVTWNLWW-RFGPWQARQKAILTALRELRPDVVGLQEV----WAADGENlaEWLAGElglhcaWAASHAPERWRRRid 75
Cdd:cd09080     1 LKVLTWNVDFlDDVNLAERMRAILKLLEELDPDVIFLQEVtppfLAYLLSQ--PWVRKN------YYFSEGPPSPAVD-- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  76 dptvDIGNAVLSRWPVVdQDVLPLPApadTDDGRLALYARLAGpGHDVPF--FTAHFASAPDASAVRCGQATALAGFVAR 153
Cdd:cd09080    71 ----PYGVLILSKKSLV-VRRVPFTS---TRMGRNLLAAEINL-GSGEPLrlATTHLESLKSHSSERTAQLEEIAKKLKK 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 154 HRGgtpFPPVVT-GDLNAWPDSDEVRLL-GGYKtapaapgqvllDAWEYADPAA-PSATWDA-ANPYVAPT-HEPSVRID 228
Cdd:cd09080   142 PPG---AANVILgGDFNLRDKEDDTGGLpNGFV-----------DAWEELGPPGePGYTWDTqKNPMLRKGeAGPRKRFD 207

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1907443944 229 YIHVGPPGPDglghVRSVHR----ACAGPVDGVWPSDHAAVVADL 269
Cdd:cd09080   208 RVLLRGSDLK----PKSIELigtePIPGDEEGLFPSDHFGLLAEL 248
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-269 4.72e-18

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: 80.99  E-value: 4.72e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   3 IVTWNLwwrfGPWQA--RQKAILTALRELRPDVVGLQEVWAADGENLAEWLAGELGLHCAWAASHAPERwrrriddptvD 80
Cdd:cd08372     1 VASYNV----NGLNAatRASGIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGYHQYQSGPSRKEG----------Y 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  81 IGNAVLSRWPVVDQDVLPLPAPADTDDG-RLALYARLAGPGHDVPFFTAHFASAPDASAVRCGQATALAGFVARHRGGTP 159
Cdd:cd08372    67 EGVAILSKTPKFKIVEKHQYKFGEGDSGeRRAVVVKFDVHDKELCVVNAHLQAGGTRADVRDAQLKEVLEFLKRLRQPNS 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 160 FPPVVTGDLNAWPDSDEVRLLGGYKTAPAAPgqVLLDAWEYADPAapsATWDAAnpyvapTHEPSVRIDYIHVGPpgpdg 239
Cdd:cd08372   147 APVVICGDFNVRPSEVDSENPSSMLRLFVAL--NLVDSFETLPHA---YTFDTY------MHNVKSRLDYIFVSK----- 210

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1907443944 240 lGHVRSVHRAcAGPVDGVW---PSDHAAVVADL 269
Cdd:cd08372   211 -SLLPSVKSS-KILSDAARariPSDHYPIEVTL 241
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
1-180 1.55e-17

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 81.22  E-value: 1.55e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   1 MRIVTWNLWWRFGP----------------WQARQKAILTALRELRPDVVGLQEVWAADG--ENLAEWLAGELGlhcAWA 62
Cdd:COG2374    69 LRVATFNVENLFDTddddddfgrgadtpeeYERKLAKIAAAIAALDADIVGLQEVENNGSalQDLVAALNLAGG---TYA 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  63 ASHAPER-WRRRIDdptvdigNAVLSR---WPVVDQDV---LPLPAPADTDDGRLALYARL-AGPGHDVPFFTAHFAS-A 133
Cdd:COG2374   146 FVHPPDGpDGDGIR-------VALLYRpdrVTLVGSATiadLPDSPGNPDRFSRPPLAVTFeLANGEPFTVIVNHFKSkG 218

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907443944 134 PDASA--------VRCGQATALAGFVARHRGGTPFPPV-VTGDLNAWPDSDEVRLL 180
Cdd:COG2374   219 SDDPGdgqgaseaKRTAQAEALRAFVDSLLAADPDAPViVLGDFNDYPFEDPLRAL 274
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-270 9.43e-17

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 78.50  E-value: 9.43e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   1 MRIVTWNLWWRfgpwQARQKAILTALRELRPDVVGLQEVWAADGENLAEwLAGELglhcawaashaPERWRRRIDDPTvd 80
Cdd:COG3021    95 LRVLTANVLFG----NADAEALAALVREEDPDVLVLQETTPAWEEALAA-LEADY-----------PYRVLCPLDNAY-- 156

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  81 iGNAVLSRWPVVDQDVLPLpapadTDDGRLALYARLAGPGHDVPFFTAHFASAPDASAVRCGQATALAGFVARHRGGTpf 160
Cdd:COG3021   157 -GMALLSRLPLTEAEVVYL-----VGDDIPSIRATVELPGGPVRLVAVHPAPPVGGSAERDAELAALAKAVAALDGPV-- 228

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 161 ppVVTGDLNAWPDSDEVRLlggyktapaapgqvLLDAWEYADPAA---PSATWDAANPYvapthePSVRIDYIHVGPpgp 237
Cdd:COG3021   229 --IVAGDFNATPWSPTLRR--------------LLRASGLRDARAgrgLGPTWPANLPF------LRLPIDHVLVSR--- 283

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1907443944 238 dglgHVRsVHRACAGPVDGvwpSDHAAVVADLA 270
Cdd:COG3021   284 ----GLT-VVDVRVLPVIG---SDHRPLLAELA 308
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 3-269 2.17e-14

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; 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: 197318 [Multi-domain]  Cd Length: 246  Bit Score: 70.79  E-value: 2.17e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   3 IVTWNL-WWRFGPWQARQKAILTALRELRPDVVGLQEVWAADGENLAEWLAGELGLhcawaashapERWRRRIDDPTVDI 81
Cdd:cd09084     1 VMSYNVrSFNRYKWKDDPDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLLLKGY----------PYYYVVYKSDSGGT 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  82 GNAVLSRWPVVDQDVLPLPapadtDDGRLALYARLAGPGHDVPFFTAHFASA---------------------------P 134
Cdd:cd09084    71 GLAIFSKYPILNSGSIDFP-----NTNNNAIFADIRVGGDTIRVYNVHLESFritpsdkelykeekkakelsrnllrklA 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 135 DASAVRCGQATALAGFVARhrggTPFPPVVTGDLNAWPDSDEVRLLGGyktapaapgqVLLDAWEYADPaAPSATWDAAN 214
Cdd:cd09084   146 EAFKRRAAQADLLAADIAA----SPYPVIVCGDFNDTPASYVYRTLKK----------GLTDAFVEAGS-GFGYTFNGLF 210

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907443944 215 PYvapthepsVRIDYIHVGPPgpdglghvRSVHRACAGPVDGvwpSDHAAVVADL 269
Cdd:cd09084   211 FP--------LRIDYILTSKG--------FKVLRYRVDPGKY---SDHYPIVATL 246
nSMase cd09078
Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological ...
 2-269 7.69e-14

Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine; Sphingomyelinases (SMase) are phosphodiesterases that catalyze the hydrolysis of sphingomyelin to ceramide and phosphorylcholine. Eukaryotic SMases have been classified according to their pH optima and are known as acid SMase, alkaline SMase, and neutral SMase (nSMase). Eukaryotic proteins in this family are nSMases, and are activated by a variety of stress-inducing agents such as cytokines or UV radiation. Ceramides and other metabolic derivatives, including sphingosine, are lipid "second messenger" molecules that participate in the regulation of stress-induced cellular responses, including cell death, adhesion, differentiation, and proliferation. Bacterial neutral SMases, which also belong to this domain family, are secreted proteins that act as membrane-damaging virulence factors. They promote colonization of the host tissue. This family 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: 197312 [Multi-domain]  Cd Length: 280  Bit Score: 69.68  E-value: 7.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   2 RIVTWNLWWR------FGPWQARQKAILTALRELRPDVVGLQEVWAADGEN-LAEWLAGELGLHCAwAASHAPERWRRRI 74
Cdd:cd09078     2 KVLTYNVFLLppllynNGDDGQDERLDLIPKALLQYDVVVLQEVFDARARKrLLNGLKKEYPYQTD-VVGRSPSGWSSKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  75 ddptVDIGNAVLSRWPVVDQDVLPLPAPADTDdgRLA----LYARLAGPGhDVPF--FTAH---FASAPDASAVRCGQAT 145
Cdd:cd09078    81 ----VDGGVVILSRYPIVEKDQYIFPNGCGAD--CLAakgvLYAKINKGG-TKVYhvFGTHlqaSDGSCLDRAVRQKQLD 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 146 ALAGFVARHRGGTPFPPVVTGDLN----AWPDS--DEVRLLGGYK-TAPAAPGQvlldaweyadpaaPSATWDAANPYVA 218
Cdd:cd09078   154 ELRAFIEEKNIPDNEPVIIAGDFNvdkrSSRDEydDMLEQLHDYNaPEPITAGE-------------TPLTWDPGTNLLA 220

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907443944 219 PTHEPS---VRIDYI-----HVGPPGpdglGHVRSVHRACAGPVDGVWP-----SDHAAVVADL 269
Cdd:cd09078   221 KYNYPGgggERLDYIlysndHLQPSS----WSNEVEVPKSPTWSVTNGYtfadlSDHYPVSATF 280
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 2-269 8.94e-14

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: 69.17  E-value: 8.94e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   2 RIVTWNLwwRFG-------PWQARQKAILTALRELRPDVVGLQEVWA---AD-GENLAEWlagelglhcAWAAshaperw 70
Cdd:cd09083     1 RVMTFNI--RYDnpsdgenSWENRKDLVAELIKFYDPDIIGTQEALPhqlADlEELLPEY---------DWIG------- 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  71 RRRIDDPTVDIGNAVL---SRWPVVDQDVL-----PLPAPADTDDG---RLALYARL---AGpGHDVPFFTAHFasaPDA 136
Cdd:cd09083    63 VGRDDGKEKGEFSAIFyrkDRFELLDSGTFwlsetPDVVGSKGWDAalpRICTWARFkdkKT-GKEFYVFNTHL---DHV 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 137 SAV-RCGQATALAGFVARHRGGTPFppVVTGDLNAWPDSDEVRLLggyktapaaPGQVLLDAWEYAD--PAAPSATWDAA 213
Cdd:cd09083   139 GEEaREESAKLILERIKEIAGDLPV--ILTGDFNAEPDSEPYKTL---------TSGGLKDARDTAAttDGGPEGTFHGF 207

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907443944 214 NPYvapthEPSVRIDYIHVGPPGpdglgHVRSvHRACAGPVDGVWPSDHAAVVADL 269
Cdd:cd09083   208 KGP-----PGGSRIDYIFVSPGV-----KVLS-YEILTDRYDGRYPSDHFPVVADL 252
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-170 1.80e-12

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: 64.55  E-value: 1.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   4 VTWNLWWRFGP---WQARQKAILTALRELRPDVVGLQEVWAADGENLAEWLAGELGLHCAWAASHAPERWrrriddptvd 80
Cdd:pfam03372   1 LTWNVNGGNADaagDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGGGGG---------- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  81 iGNAVLSRWPVVDQDVLPLPapadTDDGRLALYARLAGPGHDVPFFTAHFASAPDASAVRCGQATALAGFVARHRGGTPF 160
Cdd:pfam03372  71 -GVAILSRYPLSSVILVDLG----EFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSE 145

                         170
                  ....*....|
gi 1907443944 161 PPVVTGDLNA 170
Cdd:pfam03372 146 PVILAGDFNA 155
RgfB-like cd09079
Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, ...
 5-269 7.91e-09

Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, and related proteins; This family includes Streptococcus agalactiae RgfB (for regulator of fibrinogen binding) and related proteins. The function of RgfB is unknown. It is part of a putative two component signal transduction system designated rgfBDAC (the rgf locus was identified in a screen for mutants of Streptococcus agalactiae with altered binding to fibrinogen). RgfA,-C,and -D do not belong to this superfamily: rgfA encodes a putative response regulator, and rgfC, a putative histidine kinase. All four genes are co-transcribed, and may be involved in regulating expression of bacterial cell surface components. This family 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: 197313 [Multi-domain]  Cd Length: 259  Bit Score: 54.96  E-value: 7.91e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   5 TWNLW-WRFGPWQARQKAILTALRELRPDVVGLQEVW----AADG------ENLAEWLAG---ELGLHCAWAA--SHAPe 68
Cdd:cd09079     3 TLNTHsWLEENQKEKLERLAKIIAEEDYDVIALQEVNqsidAPVSqvpikeDNFALLLYEklrELGATYYWTWilSHIG- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  69 rwrrrIDdpTVDIGNAVLSRWPVVD-QDVLPLPAPADTDDG-RLALYARLAGPGHDVPFFTAHFaSAPDASavRCGQATA 146
Cdd:cd09079    82 -----YD--KYDEGLAILSKRPIAEvEDFYVSKSQDYTDYKsRKILGATIEINGQPIDVYSCHL-GWWYDE--EEPFAYE 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 147 LAGFVAR--HRGGtpfPPVVTGDLNAWPDSDEVrllgGYKTAPAAPgqvLLDAWEYAD-----PAAPSA--TWDAanpyv 217
Cdd:cd09079   152 WSKLEKAlaEAGR---PVLLMGDFNNPAGSRGE----GYDLISSLG---LQDTYDLAEekdggVTVEKAidGWRG----- 216

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1907443944 218 aptHEPSVRIDYIHVGPPgpdglGHVRSVHRACAGPVDGVWpSDHAAVVADL 269
Cdd:cd09079   217 ---NKEAKRIDYIFVNRK-----VKVKSSRVIFNGKNPPIV-SDHFGVEVEL 259
Deadenylase_nocturnin cd09096
C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the ...
 15-270 2.08e-06

C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the C-terminal catalytic domain of the deadenylase, nocturnin, and related domains. Nocturnin is a poly(A)-specific 3' exonuclease that specifically degrades the 3' poly(A) tail of RNA in a process known as deadenylation. This nuclease activity is manganese dependent. Nocturnin is expressed in the cytoplasm of Xenopus laevis retinal photoreceptor cells in a rhythmic fashion, and it has been proposed that it participates in posttranscriptional regulation of the circadian clock or its outputs, and that the mRNA target(s) of this deadenylase are circadian clock-related. In mouse, the nocturnin gene, mNoc, is expressed in a circadian pattern in a range of tissues including retina, spleen, heart, kidney, and liver. It is highly expressed in bone-marrow stromal cells, adipocytes and hepatocytes. In mammals, nocturnin plays a role in regulating mesenchymal stem-cell lineage allocation, perhaps through regulating PPAR-gamma (peroxisome proliferator-activated receptor-gamma) nuclear translocation. 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: 197330 [Multi-domain]  Cd Length: 280  Bit Score: 48.19  E-value: 2.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  15 WQARQKAILTALRELRPDVVGLQEVwaaDG-ENLAEWLAGELGLHCAWAAshaperwrrRIDDPTVDI-------GNAVL 86
Cdd:cd09096    29 WEERKYLILEEILTYDPDILCLQEV---DHyKDTLQPLLSRLGYQGTFFP---------KPDSPCLYIennngpdGCALF 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  87 ---SRWPVVDQDVLPLPAPAdTDDGRLALYARL--AGPGHDVPFFTAHFASAPDASAVRCGQATALAGFVARHRGGTPFP 161
Cdd:cd09096    97 frkDRFELVNTEKIRLSAMT-LKTNQVAIACTLrcKETGREICLAVTHLKARTGWERLRSEQGKDLLQNLQSFIEGAKIP 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 162 PVVTGDLNAWPDSDEVRLLGGYKTAPAAPGQVLLDAWEYaDPaaPSATWDaanpyVAPTHEPSVRIDYIHVGppgpdglG 241
Cdd:cd09096   176 LIICGDFNAEPTEPVYKTFSNSSLNLNSAYKLLSADGQS-EP--PYTTWK-----IRTSGECRHTLDYIFYS-------K 240

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1907443944 242 HVRSVHRACA-------GPvDGV----WPSDHAAVVADLA 270
Cdd:cd09096   241 DALSVEQLLDlpteeqiGP-NRLpsfnYPSDHLSLVCDFS 279
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-109 1.06e-04

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 42.76  E-value: 1.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   1 MRIVTWN---LwwRfgpwqARQKAILTALRELRPDVVGLQEVWAADgENLAEWLAGELGLHCAWAA--SHAperwrrrid 75
Cdd:COG0708     1 MKIASWNvngI--R-----ARLPKLLDWLAEEDPDVLCLQETKAQD-EQFPLEAFEAAGYHVYFHGqkGYN--------- 63

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1907443944  76 dptvdiGNAVLSRWPVVDQDVlPLPAPADTDDGR 109
Cdd:COG0708    64 ------GVAILSRLPPEDVRR-GLGGDEFDAEGR 90
MnuA_DNase1-like cd10283
Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a ...
 2-269 2.44e-04

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: 41.61  E-value: 2.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   2 RIVTWNLWwRFGPWQARQKAILTA--LRELRPDVVGLQEVWAADGENLA-EWLAGELGLHCA-WAA---------SHAPE 68
Cdd:cd10283     2 RIASWNIL-NFGNSKGKEKNPAIAeiISAFDLDLIALQEVMDNGGGLDAlAKLVNELNKPGGtWKYivsdktggsSGDKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944  69 R----WRRRIDDPtvdIGNAVLSrwpvvdqdvlplpapadtDDGRLALYARL--------AGPGHDVPFFTAHF----AS 132
Cdd:cd10283    81 RyaflYKSSKVRK---VGKAVLE------------------KDSNTDGFARPpyaakfksGGTGFDFTLVNVHLksggSS 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944 133 APDASAVRCGQATALAGFVARHRGGTPFPPVV-TGDLNAWPDSDEVRLLG--GYKTAPAAPGQVLLDAWEYADP-----A 204
Cdd:cd10283   140 KSGQGAKRVAEAQALAEYLKELADEDPDDDVIlLGDFNIPADEDAFKALTkaGFKSLLPDSTNLSTSFKGYANSydnifV 219

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907443944 205 APSATWDAANPYVAPTHEPSVRIDYIHvgppgpDGLGHVRSVHracagpvdgvwpSDHAAVVADL 269
Cdd:cd10283   220 SGNLKEKFSNSGVFDFNILVDEAGEED------LDYSKWRKQI------------SDHDPVWVEF 266
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-118 3.48e-04

Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family 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 efficiencies. 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, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and 3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197320 [Multi-domain]  Cd Length: 254  Bit Score: 40.96  E-value: 3.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907443944   1 MRIVTWN---LwwrfgpwQARQKAILTALRELRPDVVGLQEVWAADGENLAEWLAgELGLHCAWAA--SHAperwrrrid 75
Cdd:cd09086     1 MKIATWNvnsI-------RARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFE-ALGYHVAVHGqkAYN--------- 63

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1907443944  76 dptvdiGNAVLSRWPVVDqDVLPLPAPADTDDGRLaLYARLAG 118
Cdd:cd09086    64 ------GVAILSRLPLED-VRTGFPGDPDDDQARL-IAARVGG 98
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-64 1.14e-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: 39.67  E-value: 1.14e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907443944   1 MRIVTWNLwwrfGPWQARQKAILTALRELRPDVVGLQEVWAADgENLAEWLAGELGLHCAWAAS 64
Cdd:TIGR00195   1 MKIISWNV----NGLRARPHKGLAWLKENQPDVLCLQETKVQD-EQFPLEPFHKEGYHVFFSGQ 59
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-64 7.96e-03

Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases 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, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range 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 functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197307 [Multi-domain]  Cd Length: 251  Bit Score: 36.88  E-value: 7.96e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907443944   2 RIVTWNLwwrFGPWQARQKAILTALRELRPDVVGLQEVWAADGENLAEWLAgELGLHCAWAAS 64
Cdd:cd09073     1 KIISWNV---NGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQH-VEGYHSYWSPA 59
 
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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