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Conserved domains on  [gi|446535019|ref|WP_000612365|]
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MULTISPECIES: exodeoxyribonuclease III [Acinetobacter]

Protein Classification

exodeoxyribonuclease III( domain architecture ID 10178908)

exodeoxyribonuclease III is a Mg-dependent 3' to 5' exonuclease acting on dsDNA, which releases 5' phosphomononucleotides as degradation products

CATH:  3.60.10.10
EC:  3.1.11.2
Gene Ontology:  GO:0003677|GO:0046872|GO:0006281|GO:0008311
PubMed:  7885481|10838565
SCOP:  4002213

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 14-270 2.64e-144

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: 404.69  E-value: 2.64e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTKGLLEWLEQSDADVVCMQESRITHEQWTE-KFRPEGWHTHLFPAERAGYAGTAIYSRLPFVSIK 92
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDdFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  93 DGLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSSGEEAQARKDLFLGEYAKILKQWRDENKSIIICGDYNIVHKR 172
Cdd:cd10281   81 YGLGFEEFDDEGRYIEADFD-----NVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 173 IDIKNWSGNQKSSGCLPHERAWLDHIYDELGYVDTFRVVRTEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKARTVNA 252
Cdd:cd10281  156 IDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSA 235

                        250
                 ....*....|....*...
gi 446535019 253 WVYKDQWFSDHAPVIIDY 270
Cdd:cd10281  236 WIYREERFSDHAPLIVDY 253
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 14-270 2.64e-144

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: 404.69  E-value: 2.64e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTKGLLEWLEQSDADVVCMQESRITHEQWTE-KFRPEGWHTHLFPAERAGYAGTAIYSRLPFVSIK 92
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDdFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  93 DGLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSSGEEAQARKDLFLGEYAKILKQWRDENKSIIICGDYNIVHKR 172
Cdd:cd10281   81 YGLGFEEFDDEGRYIEADFD-----NVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 173 IDIKNWSGNQKSSGCLPHERAWLDHIYDELGYVDTFRVVRTEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKARTVNA 252
Cdd:cd10281  156 IDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSA 235

                        250
                 ....*....|....*...
gi 446535019 253 WVYKDQWFSDHAPVIIDY 270
Cdd:cd10281  236 WIYREERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
14-271 1.36e-105

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 307.00  E-value: 1.36e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTKgLLEWLEQSDADVVCMQESRITHEQWTEK-FRPEGWHTHLFPaeRAGYAGTAIYSRLPFVSIK 92
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEaFEAAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  93 DGLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSS-GEEAQARKDLFLGEYAKILKQWRDENKSIIICGDYNIVHK 171
Cdd:COG0708   78 RGLGGDEFDAEGRYIEADFG-----GVRVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPT 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 172 RIDIKNWSGNQKSSGCLPHERAWLDHIYDeLGYVDTFRVVRTEAE-LYSWWSNRGQARAKNVGWRIDYHACSPDWKARTV 250
Cdd:COG0708  153 EIDVKNPKANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPDVEgQYTWWSYRAGAFARNRGWRIDYILASPALADRLK 231

                        250       260
                 ....*....|....*....|....*
gi 446535019 251 NAWVYK----DQWFSDHAPVIIDYK 271
Cdd:COG0708  232 DAGIDReprgDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 14-271 3.38e-74

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: 227.16  E-value: 3.38e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019   14 LRVVSINVNGLRSSVTKGLLEWLEQSDADVVCMQESRITHEQWTEK-FRPEGWHTHLFPAERaGYAGTAIYSRLPFVSIK 92
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAElFEELGYHVFFHGAKK-GYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019   93 DGLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSS--GEEAQARKDLFLGEYAKILKqWRDENKSIIICGDYNIVH 170
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFD-----GFTVVNVYVPNGGSrdLERLEYKLQFWDALFQYLEK-ELDAGKPVVICGDMNVAH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  171 KRIDIKNWSGNQKSSGCLPHERAWLDHIYDElGYVDTFRVVRTEAEL-YSWWSNRGQARAKNVGWRIDYHACSPDWKART 249
Cdd:TIGR00633 154 TEIDLGNPKENKGNAGFTPEEREWFDELLEA-GFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERV 232

                         250       260
                  ....*....|....*....|..
gi 446535019  250 VNAWVYKDQWFSDHAPVIIDYK 271
Cdd:TIGR00633 233 VDSYIDSEIRGSDHCPIVLELD 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 14-266 5.59e-49

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 162.56  E-value: 5.59e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTKGLLEWLEQSDADVVCMQESRITHEQWTEKFRpeGWHTHLFPAERAGYAGTAIYSRLPFVSIKD 93
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFK--GYFDFWNCAIKKGYSGVVTFTKKEPLSVSY 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  94 GLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSSGEEAQARKDLFLGEYAKILKQWrDENKSIIICGDYNIVHKRI 173
Cdd:PRK13911  79 GINIEEHDKEGRVITCEFE-----SFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKAL-ELKKPVIVCGDLNVAHNEI 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 174 DIKNWSGNQKSSGCLPHERAWLDHIYDElGYVDTFRVVRTEAE-LYSWWSNRGQARAKNVGWRIDYHACSPDWKARTVNA 252
Cdd:PRK13911 153 DLENPKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEkAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDA 231

                        250
                 ....*....|....
gi 446535019 253 WVYKDQWFSDHAPV 266
Cdd:PRK13911 232 LIYKDILGSDHCPV 245
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 17-168 2.03e-14

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: 69.95  E-value: 2.03e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019   17 VSINVNGLRSSVT------KGLLEWLEQSDADVVCMQESRITHEQWTEKFRPEGW--HTHLFPAERAGYAGTAIYSRLPF 88
Cdd:pfam03372   1 LTWNVNGGNADAAgddrklDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGgfLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019   89 VSIKDGLGFELADSQGRFISAEFDLGLSHPVHIASLYLPSGSSGEEAQARKDLFLGEYAKilkqwRDENKSIIICGDYNI 168
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALL-----APRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 14-270 2.64e-144

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: 404.69  E-value: 2.64e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTKGLLEWLEQSDADVVCMQESRITHEQWTE-KFRPEGWHTHLFPAERAGYAGTAIYSRLPFVSIK 92
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDdFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  93 DGLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSSGEEAQARKDLFLGEYAKILKQWRDENKSIIICGDYNIVHKR 172
Cdd:cd10281   81 YGLGFEEFDDEGRYIEADFD-----NVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 173 IDIKNWSGNQKSSGCLPHERAWLDHIYDELGYVDTFRVVRTEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKARTVNA 252
Cdd:cd10281  156 IDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSA 235

                        250
                 ....*....|....*...
gi 446535019 253 WVYKDQWFSDHAPVIIDY 270
Cdd:cd10281  236 WIYREERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
14-271 1.36e-105

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 307.00  E-value: 1.36e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTKgLLEWLEQSDADVVCMQESRITHEQWTEK-FRPEGWHTHLFPaeRAGYAGTAIYSRLPFVSIK 92
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEaFEAAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  93 DGLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSS-GEEAQARKDLFLGEYAKILKQWRDENKSIIICGDYNIVHK 171
Cdd:COG0708   78 RGLGGDEFDAEGRYIEADFG-----GVRVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPT 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 172 RIDIKNWSGNQKSSGCLPHERAWLDHIYDeLGYVDTFRVVRTEAE-LYSWWSNRGQARAKNVGWRIDYHACSPDWKARTV 250
Cdd:COG0708  153 EIDVKNPKANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPDVEgQYTWWSYRAGAFARNRGWRIDYILASPALADRLK 231

                        250       260
                 ....*....|....*....|....*
gi 446535019 251 NAWVYK----DQWFSDHAPVIIDYK 271
Cdd:COG0708  232 DAGIDReprgDERPSDHAPVVVELD 256
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 15-270 8.00e-88

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: 261.45  E-value: 8.00e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  15 RVVSINVNGLRSSVTKGLLEWLEQSDADVVCMQESRITHEQWTEKFR-PEGWHTHLFPAERAGYAGTAIYSRLPFVSIKD 93
Cdd:cd09073    1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQhVEGYHSYWSPARKKGYSGVATLSKEEPLDVSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  94 GLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSSGEEAQARKDLFLGEYAKILKQWRDENKSIIICGDYNIVHKRI 173
Cdd:cd09073   81 GIGGEEFDSEGRVITAEFD-----DFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEI 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 174 DIKNWSGNQKSSGCLPHERAWLDHIYdELGYVDTFRVVRTEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKARTVNAW 253
Cdd:cd09073  156 DLARPKKNEKNAGFTPEERAWFDKLL-SLGYVDTFRHFHPEPGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSG 234

                        250
                 ....*....|....*..
gi 446535019 254 VYKDQWFSDHAPVIIDY 270
Cdd:cd09073  235 ILSKVKGSDHAPVTLEL 251
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 14-270 1.10e-82

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: 248.73  E-value: 1.10e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTKGLLEWLEQSDADVVCMQESRITHEQWTEKFR-PEGWHTHLFPAERAGYAGTAIYSRLPFVSIK 92
Cdd:cd09085    1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRnIEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  93 DGLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSSGEEAQARKDLFLGEYAKILKQWRDENKSIIICGDYNIVHKR 172
Cdd:cd09085   81 EGLGVEEFDNEGRILIADFD-----DFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 173 IDIKNWSGNQKSSGCLPHERAWLDHIYDElGYVDTFRVVRTEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKARTVNA 252
Cdd:cd09085  156 IDLARPKENEKVSGFLPEERAWMDKFIEN-GYVDTFRMFNKEPGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDA 234

                        250
                 ....*....|....*...
gi 446535019 253 WVYKDQWFSDHAPVIIDY 270
Cdd:cd09085  235 GILPDVMGSDHCPVSLEL 252
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 14-271 3.38e-74

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: 227.16  E-value: 3.38e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019   14 LRVVSINVNGLRSSVTKGLLEWLEQSDADVVCMQESRITHEQWTEK-FRPEGWHTHLFPAERaGYAGTAIYSRLPFVSIK 92
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAElFEELGYHVFFHGAKK-GYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019   93 DGLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSS--GEEAQARKDLFLGEYAKILKqWRDENKSIIICGDYNIVH 170
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFD-----GFTVVNVYVPNGGSrdLERLEYKLQFWDALFQYLEK-ELDAGKPVVICGDMNVAH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  171 KRIDIKNWSGNQKSSGCLPHERAWLDHIYDElGYVDTFRVVRTEAEL-YSWWSNRGQARAKNVGWRIDYHACSPDWKART 249
Cdd:TIGR00633 154 TEIDLGNPKENKGNAGFTPEEREWFDELLEA-GFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERV 232

                         250       260
                  ....*....|....*....|..
gi 446535019  250 VNAWVYKDQWFSDHAPVIIDYK 271
Cdd:TIGR00633 233 VDSYIDSEIRGSDHCPIVLELD 254
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 14-266 1.94e-70

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: 217.64  E-value: 1.94e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019   14 LRVVSINVNGLRSSVTKGLlEWLEQSDADVVCMQESRITHEQWTEKFRP-EGWHTHLFPAEraGYAGTAIYSRLPFVSIK 92
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGL-AWLKENQPDVLCLQETKVQDEQFPLEPFHkEGYHVFFSGQK--GYSGVAIFSKEEPISVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019   93 DGLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSS-GEEAQARKDLFLGEYAKILKQWRDENKSIIICGDYNIVHK 171
Cdd:TIGR00195  78 RGFGVEEEDAEGRIIMAEFD-----SFLVINGYFPNGSRdDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPT 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  172 RIDIKNWSGNQKSSGCLPHERAWLDHIYdELGYVDTFRVVRTEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKARTVN 251
Cdd:TIGR00195 153 EIDLHIPDENRNHTGFLPEEREWLDRLL-EAGLVDTFRKFNPDEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVD 231

                         250
                  ....*....|....*....
gi 446535019  252 AWVYKD----QWFSDHAPV 266
Cdd:TIGR00195 232 CGIDYDirgsEKPSDHCPV 250
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 14-269 7.06e-70

Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and 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. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197321 [Multi-domain]  Cd Length: 253  Bit Score: 215.88  E-value: 7.06e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTKGLLEWLEQSDADVVCMQESRITHEQWTEKFR--PEGWHTHLFPAERAGYAGTAIYSRLPFVSI 91
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKelLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  92 KDGLGFELADSQGRFISAEFDlglshpvhiaSLYL-----PSGSSGEEAQARKDLFLGEYAKILKqWRDENKSIIICGDY 166
Cdd:cd09087   81 TYGIGIEEHDQEGRVITAEFE----------NFYLvntyvPNSGRGLERLDRRKEWDVDFRAYLK-KLDSKKPVIWCGDL 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 167 NIVHKRIDIKNWSGNQKSSGCLPHERAWLDHIYDElGYVDTFRVVRTEAE-LYSWWSNRGQARAKNVGWRIDYHACSPDW 245
Cdd:cd09087  150 NVAHEEIDLANPKTNKKSAGFTPEERESFTELLEA-GFVDTFRHLHPDKEgAYTFWSYRGNARAKNVGWRLDYFLVSERL 228

                        250       260
                 ....*....|....*....|....
gi 446535019 246 KARTVNAWVYKDQWFSDHAPVIID 269
Cdd:cd09087  229 KDRVVDSFIRSDIMGSDHCPIGLE 252
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 14-269 9.27e-60

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: 190.03  E-value: 9.27e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVtKGLLEWLEQSDADVVCMQESRITHEQWTEK-FRPEGWHTHLFpaERAGYAGTAIYSRLPFVSIK 92
Cdd:cd09086    1 MKIATWNVNSIRARL-EQVLDWLKEEDPDVLCLQETKVEDDQFPADaFEALGYHVAVH--GQKAYNGVAILSRLPLEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  93 DGLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSS-GEEAQARKDLFLGEYAKILKQWRDENKSIIICGDYNIVHK 171
Cdd:cd09086   78 TGFPGDPDDDQARLIAARVG-----GVRVINLYVPNGGDiGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPE 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 172 RIDIKNWSGNQKSSGCLPHERAWLDHIYDeLGYVDTFRVVRTEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKARTVN 251
Cdd:cd09086  153 DIDVWDPKQLLGKVLFTPEEREALRALLD-LGFVDAFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKD 231

                        250       260
                 ....*....|....*....|..
gi 446535019 252 AWVYKDQ--WF--SDHAPVIID 269
Cdd:cd09086  232 VGIDREPrgWEkpSDHAPVVAE 253
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 14-266 5.59e-49

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 162.56  E-value: 5.59e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTKGLLEWLEQSDADVVCMQESRITHEQWTEKFRpeGWHTHLFPAERAGYAGTAIYSRLPFVSIKD 93
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFK--GYFDFWNCAIKKGYSGVVTFTKKEPLSVSY 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  94 GLGFELADSQGRFISAEFDlglshPVHIASLYLPSGSSGEEAQARKDLFLGEYAKILKQWrDENKSIIICGDYNIVHKRI 173
Cdd:PRK13911  79 GINIEEHDKEGRVITCEFE-----SFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKAL-ELKKPVIVCGDLNVAHNEI 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 174 DIKNWSGNQKSSGCLPHERAWLDHIYDElGYVDTFRVVRTEAE-LYSWWSNRGQARAKNVGWRIDYHACSPDWKARTVNA 252
Cdd:PRK13911 153 DLENPKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEkAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDA 231

                        250
                 ....*....|....
gi 446535019 253 WVYKDQWFSDHAPV 266
Cdd:PRK13911 232 LIYKDILGSDHCPV 245
PRK11756 PRK11756
exonuclease III; Provisional
 14-272 2.99e-30

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 114.22  E-value: 2.99e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTKgLLEWLEQSDADVVCMQESRITHEQW-TEKFRPEGWHTHlFPAERAGYaGTAIYSRLPFVSIK 92
Cdd:PRK11756   1 MKFVSFNINGLRARPHQ-LEAIIEKHQPDVIGLQETKVHDEMFpLEEVEALGYHVF-YHGQKGHY-GVALLSKQTPIAVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  93 DGLGFELADSQGRFISAEFDLGLShPVHIASLYLPSGSSGE-----EAQAR--KDLFLgeyakILKQWRDENKSIIICGD 165
Cdd:PRK11756  78 KGFPTDDEEAQRRIIMATIPTPNG-NLTVINGYFPQGESRDhptkfPAKRQfyQDLQN-----YLETELSPDNPLLIMGD 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 166 YNIVHKRIDI-------KNWSGNQKSSgCLPHERAWLDHIYDeLGYVDTFRVVRTEA-ELYSWWSNRGQARAKNVGWRID 237
Cdd:PRK11756 152 MNISPTDLDIgigeenrKRWLRTGKCS-FLPEEREWLDRLMD-WGLVDTFRQLNPDVnDRFSWFDYRSKGFDDNRGLRID 229

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 446535019 238 YHACSPDWKARTVNAWVYKD----QWFSDHAPVIIDYKI 272
Cdd:PRK11756 230 LILATQPLAERCVETGIDYDirgmEKPSDHAPIWATFKL 268
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 15-269 2.49e-25

Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and 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. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197322 [Multi-domain]  Cd Length: 309  Bit Score: 102.01  E-value: 2.49e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  15 RVVSINVNGLR-------SSVTKGLLEWLEQSDADVVCMQESRITHEQWTEKF-RPEGWHT-HLFPAERAGYAGTAIYSR 85
Cdd:cd09088    1 RIVTWNVNGIRtrlqyqpWNKENSLKSFLDSLDADIICLQETKLTRDELDEPSaIVEGYDSfFSFSRGRKGYSGVATYCR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  86 LPFV----------------------SIKDGLGF-----------ELA--DSQGRFISAEFdlglsHPVHIASLYLPSGS 130
Cdd:cd09088   81 DSAAtpvaaeegltgvlsspnqknelSENDDIGCygemleftdskELLelDSEGRCVLTDH-----GTFVLINVYCPRAD 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 131 SGEEAQAR-KDLFLGEYAKILKQWRDENKSIIICGDYNIVHKRIDIKNWSGNQKSSGCLPHE---RAWLDHIYDELG--- 203
Cdd:cd09088  156 PEKEERLEfKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLGDSGegg 235

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446535019 204 ------YVDTFRVVRTEAE-LYSWWSNRGQARAKNVGWRIDYHACSPDWKARTVNAWVYKDQWFSDHAPVIID 269
Cdd:cd09088  236 gspgglLIDSFRYFHPTRKgAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYAD 308
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 16-270 2.44e-23

Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. 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: 197310 [Multi-domain]  Cd Length: 236  Bit Score: 95.11  E-value: 2.44e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  16 VVSINVNGLRSSV-TKGLLEWLEQSDADVVCMQESRITHEQwTEKFRPEGWHTHLFPAERAGYAGTAIYSRLPFVSIKdg 94
Cdd:cd09076    1 IGTLNVRGLRSPGkRAQLLEELKRKKLDILGLQETHWTGEG-ELKKKREGGTILYSGSDSGKSRGVAILLSKTAANKL-- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  95 LGFElADSQGRFISAEFDlGLSHPVHIASLYLPSGSSGEEaqarKDLFLGEYAKILKQWRDENkSIIICGDYNIVHKRID 174
Cdd:cd09076   78 LEYT-KVVSGRIIMVRFK-IKGKRLTIINVYAPTARDEEE----KEEFYDQLQDVLDKVPRHD-TLIIGGDFNAVLGPKD 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 175 IKNWsGNQKSSGCLPHErawLDHIYDELGYVDTFRVVRTEAELYSWWSNRGQARAknvgwRIDYHACSPDWKARTVNAwV 254
Cdd:cd09076  151 DGRK-GLDKRNENGERA---LSALIEEHDLVDVWRENNPKTREYTWRSPDHGSRS-----RIDRILVSKRLRVKVKKT-K 220

                        250
                 ....*....|....*.
gi 446535019 255 YKDQWFSDHAPVIIDY 270
Cdd:cd09076  221 ITPGAGSDHRLVTLKL 236
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 16-266 1.53e-21

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: 90.23  E-value: 1.53e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  16 VVSINVNGLRSSV-TKGLLEWLEQSDADVVCMQESRITHEQ--WTEKFRPEGWHTHLFPAERA-GYAGTAIYSRLPFVSI 91
Cdd:cd08372    1 VASYNVNGLNAATrASGIARWVRELDPDIVCLQEVKDSQYSavALNQLLPEGYHQYQSGPSRKeGYEGVAILSKTPKFKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  92 ---KDGLGFELADSQGRFISAEFDLGLSHpVHIASLYLPSGSSGEEAqarKDLFLGEYAKILKQWRDENKS-IIICGDYN 167
Cdd:cd08372   81 vekHQYKFGEGDSGERRAVVVKFDVHDKE-LCVVNAHLQAGGTRADV---RDAQLKEVLEFLKRLRQPNSApVVICGDFN 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 168 IVHKRIDIKNWSgnqkSSGCLPHERAwldhiydelgYVDTFrvvRTEAELYSWWSNRgqaraKNVGWRIDYHACSPDWKA 247
Cdd:cd08372  157 VRPSEVDSENPS----SMLRLFVALN----------LVDSF---ETLPHAYTFDTYM-----HNVKSRLDYIFVSKSLLP 214

                        250       260
                 ....*....|....*....|...
gi 446535019 248 RTVNAWVYKDQWF----SDHAPV 266
Cdd:cd08372  215 SVKSSKILSDAARaripSDHYPI 237
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 14-272 3.81e-20

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 87.74  E-value: 3.81e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTKgLLEWLEQSDADVVCMQEsriTHEQWTEKFRP-EGWHTHLFPAERAGYAGTAIYSRLPFVSIK 92
Cdd:COG3021   95 LRVLTANVLFGNADAEA-LAALVREEDPDVLVLQE---TTPAWEEALAAlEADYPYRVLCPLDNAYGMALLSRLPLTEAE 170

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  93 dglGFELADSQGRFISAEFDLGlSHPVHIASLYLPSGSSGEEAQARkdlflgEYAKILKQWRDENKSIIICGDYNIVHkr 172
Cdd:COG3021  171 ---VVYLVGDDIPSIRATVELP-GGPVRLVAVHPAPPVGGSAERDA------ELAALAKAVAALDGPVIVAGDFNATP-- 238

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 173 idiknWSGN----QKSSGCLPHERAWldhiydelGYVDTFrvvrteaelyswwsnrgQARAKNVGWRIDYHACSPDWkaR 248
Cdd:COG3021  239 -----WSPTlrrlLRASGLRDARAGR--------GLGPTW-----------------PANLPFLRLPIDHVLVSRGL--T 286

                        250       260
                 ....*....|....*....|....
gi 446535019 249 TVNAWVYKDQWfSDHAPVIIDYKI 272
Cdd:COG3021  287 VVDVRVLPVIG-SDHRPLLAELAL 309
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 17-168 2.03e-14

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: 69.95  E-value: 2.03e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019   17 VSINVNGLRSSVT------KGLLEWLEQSDADVVCMQESRITHEQWTEKFRPEGW--HTHLFPAERAGYAGTAIYSRLPF 88
Cdd:pfam03372   1 LTWNVNGGNADAAgddrklDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGgfLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019   89 VSIKDGLGFELADSQGRFISAEFDLGLSHPVHIASLYLPSGSSGEEAQARKDLFLGEYAKilkqwRDENKSIIICGDYNI 168
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALL-----APRSEPVILAGDFNA 155
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 16-270 9.67e-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: 68.86  E-value: 9.67e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  16 VVSINVNGLR----SSVTKGLLEWLEQSDADVVCMQESRITHEQWTEKFRP--EGW-HTHLFPAERAGYAGTAIYSRLPF 88
Cdd:cd09084    1 VMSYNVRSFNrykwKDDPDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLllKGYpYYYVVYKSDSGGTGLAIFSKYPI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  89 VSiKDGLGFElaDSQGRFISAEFDLG----------LSHPVHIASLYLPSGSSGEEAQARKDLF--LGE-------YAKI 149
Cdd:cd09084   81 LN-SGSIDFP--NTNNNAIFADIRVGgdtirvynvhLESFRITPSDKELYKEEKKAKELSRNLLrkLAEafkrraaQADL 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 150 LKQWRDENKS-IIICGDYNivhkridiknwsgNQKSSgclpherawldHIYDEL--GYVDTFRvvrtEA-ELYSwWSNRG 225
Cdd:cd09084  158 LAADIAASPYpVIVCGDFN-------------DTPAS-----------YVYRTLkkGLTDAFV----EAgSGFG-YTFNG 208

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 446535019 226 QARaknvGWRIDYHACSPDWkaRTVNAWVYKDQWfSDHAPVIIDY 270
Cdd:cd09084  209 LFF----PLRIDYILTSKGF--KVLRYRVDPGKY-SDHYPIVATL 246
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 14-263 4.31e-12

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: 64.29  E-value: 4.31e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSV----TKGLLEWLEQSDADVVCMQE------SRITHEQWTEKfrpeGWH-THLFPAERAGYAGTAI 82
Cdd:cd09080    1 LKVLTWNVDFLDDVNlaerMRAILKLLEELDPDVIFLQEvtppflAYLLSQPWVRK----NYYfSEGPPSPAVDPYGVLI 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  83 YSR-------LPFVSIKDGLGfeladsqgrFISAEFDLGLSHPVHIASLYLPSGSSGEEAQARKdlfLGEYAKILKQWRD 155
Cdd:cd09080   77 LSKkslvvrrVPFTSTRMGRN---------LLAAEINLGSGEPLRLATTHLESLKSHSSERTAQ---LEEIAKKLKKPPG 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 156 ENKsIIICGDYNIVHKRIdiknwsgnqkssgclpherawlDHIYDELGYVDTFRVVRTEAEL-YSW------WSNRGQAR 228
Cdd:cd09080  145 AAN-VILGGDFNLRDKED----------------------DTGGLPNGFVDAWEELGPPGEPgYTWdtqknpMLRKGEAG 201

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 446535019 229 AKNvgwRID--YhACSPDWKARTVN-------AWVYKDQWFSDH 263
Cdd:cd09080  202 PRK---RFDrvL-LRGSDLKPKSIEligtepiPGDEEGLFPSDH 241
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 14-272 1.87e-07

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 49.91  E-value: 1.87e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSVTK----GLLEWLEQSDADVVCMQEsritheqwtekfrpegwhthlfpaeragyagTAIYSRLPFV 89
Cdd:COG3568    8 LRVMTYNIRYGLGTDGRadleRIARVIRALDPDVVALQE-------------------------------NAILSRYPIV 56

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  90 SIKDgLGFELADSQGR-FISAEFDLGlSHPVHIASLYLPSGSSGE-EAQARkdlFLgeyAKILKQwRDENKSIIICGDYN 167
Cdd:COG3568   57 SSGT-FDLPDPGGEPRgALWADVDVP-GKPLRVVNTHLDLRSAAArRRQAR---AL---AELLAE-LPAGAPVILAGDFN 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 168 IvhkridiknwsgnqkssgclpherawLDHIYdelgyvdtfrvvrteaelyswwsnrgqaraknvgwridyhaCSPDWKA 247
Cdd:COG3568  128 D--------------------------IDYIL-----------------------------------------VSPGLRV 140

                        250       260
                 ....*....|....*....|....*...
gi 446535019 248 rtVNAWVYKD---QWFSDHAPVIIDYKI 272
Cdd:COG3568  141 --LSAEVLDSplgRAASDHLPVVADLEL 166
nSMase cd09078
Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological ...
 42-266 8.14e-06

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: 46.18  E-value: 8.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  42 DVVCMQE-------SRITHEQWTEKF--------RPEGWHTHLFPAeragyaGTAIYSRLPFVSI-----KDGLGFELAD 101
Cdd:cd09078   38 DVVVLQEvfdararKRLLNGLKKEYPyqtdvvgrSPSGWSSKLVDG------GVVILSRYPIVEKdqyifPNGCGADCLA 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 102 SQGrFISAEFDLGLSHPVHIASLYLPSGSSGEEAQA-RKDLFlGEYAK-ILKQWRDENKSIIICGDYNIvhkridikNWs 179
Cdd:cd09078  112 AKG-VLYAKINKGGTKVYHVFGTHLQASDGSCLDRAvRQKQL-DELRAfIEEKNIPDNEPVIIAGDFNV--------DK- 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 180 gnqkssgclpheRAWLDHIYDELGYVDTFRVV--RTEAEL-YSW----WSNRGQARAKNVGWRIDY------HACSPDWK 246
Cdd:cd09078  181 ------------RSSRDEYDDMLEQLHDYNAPepITAGETpLTWdpgtNLLAKYNYPGGGGERLDYilysndHLQPSSWS 248

                        250       260
                 ....*....|....*....|....*...
gi 446535019 247 AR----TVNAWVYKDQW----FSDHAPV 266
Cdd:cd09078  249 NEvevpKSPTWSVTNGYtfadLSDHYPV 276
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 14-269 9.93e-05

Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. 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: 197311 [Multi-domain]  Cd Length: 205  Bit Score: 42.28  E-value: 9.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  14 LRVVSINVNGLRSSvTKGLLEWLEQSDADVVCMQEsritheQWTEKFRPEGWHTHLFPaeragyaGTAIY--SRLPFVSI 91
Cdd:cd09077    1 LRILQINLNRCKAA-QDLLLQTAREEGADIALIQE------PYLVPVNNPNWVTDESG-------RAAIVvsDRLPRKPI 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019  92 KDGLGFEladsqgRFISAefDLGlshPVHIASLYLPSGSSGEEaqarkdlFLGEYAKILKQWRDENKSIIICGDYNIVHK 171
Cdd:cd09077   67 QRLSLGL------GIVAA--RVG---GITVVSCYAPPSESLEE-------FEEYLENLVRIVRGLSRPVIIGGDFNAWSP 128

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 172 RidiknWSGN-QKSSGclpheRAWLDHIyDELGYvdtfrVVRTEAELYSWWSNRGQAraknvgwRIDYHACSPDWkARTV 250
Cdd:cd09077  129 A-----WGSKrTDRRG-----RLLEDWI-ANLGL-----VLLNDGNSPTFVRPRGTS-------IIDVTFCSPSL-ARRI 184

                        250       260
                 ....*....|....*....|
gi 446535019 251 NAW-VYKDQWFSDHAPVIID 269
Cdd:cd09077  185 SNWrVLEDETLSDHRYIRFT 204
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
109-274 5.14e-04

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 40.77  E-value: 5.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 109 AEFDLGLSHPVHIASLYLPSGSSGEEA--QARKDLFLGEYAKILKQW------RDENKSIIICGDYNivhkridiknwsg 180
Cdd:COG2374  197 VTFELANGEPFTVIVNHFKSKGSDDPGdgQGASEAKRTAQAEALRAFvdsllaADPDAPVIVLGDFN------------- 263

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 181 nqkssgCLPHERAwLDHIYDELGYVDTFRVVRtEAELYS-------------WWSNRGQARAKNVG-WRIDYHACSPDWK 246
Cdd:COG2374  264 ------DYPFEDP-LRALLGAGGLTNLAEKLP-AAERYSyvydgnsglldhiLVSPALAARVTGADiWHINADIYNDDFK 335

                        170       180       190
                 ....*....|....*....|....*....|
gi 446535019 247 --ARTVNAWVYkdqWFSDHAPVIIDYKIQE 274
Cdd:COG2374  336 pdFRTYADDPG---RASDHDPVVVGLRLPP 362
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 132-270 6.17e-04

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: 40.28  E-value: 6.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446535019 132 GEEAQArkdlflgEYAKILKQW---RDENKSIIICGDYNivhkridiknwsgnqkssgCLPHERAwldhiYDEL---GYV 205
Cdd:cd09083  139 GEEARE-------ESAKLILERikeIAGDLPVILTGDFN-------------------AEPDSEP-----YKTLtsgGLK 187

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446535019 206 DTFRVVRT--EAELYSWWSNRGQARAKnvgwRIDYHACSPDWKART--VNAWVYKDQWFSDHAPVIIDY 270
Cdd:cd09083  188 DARDTAATtdGGPEGTFHGFKGPPGGS----RIDYIFVSPGVKVLSyeILTDRYDGRYPSDHFPVVADL 252
 
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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