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Conserved domains on  [gi|1215099959|ref|WP_088979660|]
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exodeoxyribonuclease III [Micromonospora coxensis]

Protein Classification

XthA family protein( domain architecture ID 10002229)

XthA family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-255 2.11e-120

Exonuclease III [Replication, recombination and repair];


:

Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 343.98  E-value: 2.11e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGRWNGVAILSRVGLADVTVGF 80
Cdd:COG0708     1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLPPEDVRRGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  81 PGEPgfPEPEARAISATCDGVRVWSVYVPNGRAPDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDDDVWD 160
Cdd:COG0708    81 GGDE--FDAEGRYIEADFGGVRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVKN 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 161 PALFVTSTHVTPAERAALAALRDLGLSDVV----PTPmkgPHPYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAYV 236
Cdd:COG0708   159 PKANLKNAGFLPEERAWFDRLLELGLVDAFralhPDV---EGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGI 235

                         250
                  ....*....|....*....
gi 1215099959 237 DREARKGKGPSDHAPIVVD 255
Cdd:COG0708   236 DREPRGDERPSDHAPVVVE 254
 
Name Accession Description Interval E-value
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-255 2.11e-120

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 343.98  E-value: 2.11e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGRWNGVAILSRVGLADVTVGF 80
Cdd:COG0708     1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLPPEDVRRGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  81 PGEPgfPEPEARAISATCDGVRVWSVYVPNGRAPDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDDDVWD 160
Cdd:COG0708    81 GGDE--FDAEGRYIEADFGGVRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVKN 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 161 PALFVTSTHVTPAERAALAALRDLGLSDVV----PTPmkgPHPYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAYV 236
Cdd:COG0708   159 PKANLKNAGFLPEERAWFDRLLELGLVDAFralhPDV---EGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGI 235

                         250
                  ....*....|....*....
gi 1215099959 237 DREARKGKGPSDHAPIVVD 255
Cdd:COG0708   236 DREPRGDERPSDHAPVVVE 254
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-255 4.18e-118

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: 337.95  E-value: 4.18e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGRWNGVAILSRVGLADVTVGF 80
Cdd:cd09086     1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHGQKAYNGVAILSRLPLEDVRTGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  81 PGEPgfPEPEARAISATCDGVRVWSVYVPNGRAPDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDDDVWD 160
Cdd:cd09086    81 PGDP--DDDQARLIAARVGGVRVINLYVPNGGDIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDVWD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 161 PALFVTSTHVTPAERAALAALRDLGLSDVVPTPMKGPHPYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAYVDREA 240
Cdd:cd09086   159 PKQLLGKVLFTPEEREALRALLDLGFVDAFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGIDREP 238

                         250
                  ....*....|....*
gi 1215099959 241 RKGKGPSDHAPIVVD 255
Cdd:cd09086   239 RGWEKPSDHAPVVAE 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-257 3.82e-101

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: 295.34  E-value: 3.82e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRL-LDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHS-DGRWNGVAILSRVGLADVTV 78
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLfLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGaKKGYSGVAILSKVEPLDVRY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  79 GFPGEPGfpEPEARAISATCDGVRVWSVYVPNGRAPDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDDDV 158
Cdd:TIGR00633  81 GFGGEPH--DEEGRVITAEFDGFTVVNVYVPNGGSRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 159 WDPALFVTSTHVTPAERAALAALRDLGLSDVVPTPMKGPH-PYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAYVD 237
Cdd:TIGR00633 159 GNPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGdAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYID 238

                         250       260
                  ....*....|....*....|
gi 1215099959 238 REARKgkgpSDHAPIVVDAD 257
Cdd:TIGR00633 239 SEIRG----SDHCPIVLELD 254
PRK11756 PRK11756
exonuclease III; Provisional
 1-258 2.70e-39

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 137.72  E-value: 2.70e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGRWNGVAILSRVGLADVTVGF 80
Cdd:PRK11756    1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVALLSKQTPIAVRKGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  81 PGEpgFPEPEARAISATCD----GVRVWSVYVPNGRAPDDP-HYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTD 155
Cdd:PRK11756   81 PTD--DEEAQRRIIMATIPtpngNLTVINGYFPQGESRDHPtKFPAKRQFYQDLQNYLETELSPDNPLLIMGDMNISPTD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 156 DDV------------------------WDPALFvtsthvtpaeraalaalrDLGLSDVvptpMKGPHP-----YTYWDYR 206
Cdd:PRK11756  159 LDIgigeenrkrwlrtgkcsflpeereWLDRLM------------------DWGLVDT----FRQLNPdvndrFSWFDYR 216

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1215099959 207 AGMFHQNKGMRIDLVYASAAFARAVRSAYVDREARKGKGPSDHAPIVVDADL 258
Cdd:PRK11756  217 SKGFDDNRGLRIDLILATQPLAERCVETGIDYDIRGMEKPSDHAPIWATFKL 268
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-188 2.69e-19

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: 82.66  E-value: 2.69e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   4 ATWNVNS-------VKARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDG---RWNGVAILSRVGL 73
Cdd:pfam03372   1 LTWNVNGgnadaagDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGgggGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  74 ADVTVGFPGEPGFPEpeaRAISATCDGVRVWSVYVPNGRAPDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNvap 153
Cdd:pfam03372  81 SSVILVDLGEFGDPA---LRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN--- 154

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1215099959 154 tDDDVWdpalfvTSTHVTPAERAALAALRDLGLSD 188
Cdd:pfam03372 155 -ADYIL------VSGGLTVLSVGVLPDLGPRTGSD 182
 
Name Accession Description Interval E-value
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-255 2.11e-120

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 343.98  E-value: 2.11e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGRWNGVAILSRVGLADVTVGF 80
Cdd:COG0708     1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLPPEDVRRGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  81 PGEPgfPEPEARAISATCDGVRVWSVYVPNGRAPDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDDDVWD 160
Cdd:COG0708    81 GGDE--FDAEGRYIEADFGGVRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVKN 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 161 PALFVTSTHVTPAERAALAALRDLGLSDVV----PTPmkgPHPYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAYV 236
Cdd:COG0708   159 PKANLKNAGFLPEERAWFDRLLELGLVDAFralhPDV---EGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGI 235

                         250
                  ....*....|....*....
gi 1215099959 237 DREARKGKGPSDHAPIVVD 255
Cdd:COG0708   236 DREPRGDERPSDHAPVVVE 254
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-255 4.18e-118

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: 337.95  E-value: 4.18e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGRWNGVAILSRVGLADVTVGF 80
Cdd:cd09086     1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHGQKAYNGVAILSRLPLEDVRTGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  81 PGEPgfPEPEARAISATCDGVRVWSVYVPNGRAPDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDDDVWD 160
Cdd:cd09086    81 PGDP--DDDQARLIAARVGGVRVINLYVPNGGDIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDVWD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 161 PALFVTSTHVTPAERAALAALRDLGLSDVVPTPMKGPHPYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAYVDREA 240
Cdd:cd09086   159 PKQLLGKVLFTPEEREALRALLDLGFVDAFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGIDREP 238

                         250
                  ....*....|....*
gi 1215099959 241 RKGKGPSDHAPIVVD 255
Cdd:cd09086   239 RGWEKPSDHAPVVAE 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-257 3.82e-101

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: 295.34  E-value: 3.82e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRL-LDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHS-DGRWNGVAILSRVGLADVTV 78
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLfLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGaKKGYSGVAILSKVEPLDVRY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  79 GFPGEPGfpEPEARAISATCDGVRVWSVYVPNGRAPDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDDDV 158
Cdd:TIGR00633  81 GFGGEPH--DEEGRVITAEFDGFTVVNVYVPNGGSRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 159 WDPALFVTSTHVTPAERAALAALRDLGLSDVVPTPMKGPH-PYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAYVD 237
Cdd:TIGR00633 159 GNPKENKGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGdAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYID 238

                         250       260
                  ....*....|....*....|
gi 1215099959 238 REARKgkgpSDHAPIVVDAD 257
Cdd:TIGR00633 239 SEIRG----SDHCPIVLELD 254
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-254 1.19e-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: 1.19e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGRWNGVAILSRVGLADVTVGF 80
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQKGYSGVAIFSKEEPISVRRGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  81 PGEPgfPEPEARAISATCDGVRVWSVYVPNGRAPDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDDDVWD 160
Cdd:TIGR00195  81 GVEE--EDAEGRIIMAEFDSFLVINGYFPNGSRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDLHI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 161 PALFVTSTHVTPAERAALAALRDLGLSDVVPTPMKGPHPYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAYVDREA 240
Cdd:TIGR00195 159 PDENRNHTGFLPEEREWLDRLLEAGLVDTFRKFNPDEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDYDI 238

                         250
                  ....*....|....
gi 1215099959 241 RKGKGPSDHAPIVV 254
Cdd:TIGR00195 239 RGSEKPSDHCPVVL 252
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-254 2.62e-64

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: 201.36  E-value: 2.62e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   2 RLATWNVNSVKARLPR-LLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGR--WNGVAILSRVGLADVTV 78
Cdd:cd09073     1 KIISWNVNGLRARLKKgVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPARKkgYSGVATLSKEEPLDVSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  79 GFPGEPgfPEPEARAISATCDGVRVWSVYVPNGRaPDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDDDV 158
Cdd:cd09073    81 GIGGEE--FDSEGRVITAEFDDFYLINVYFPNGG-RGLERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEIDL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 159 WDPALFVTSTHVTPAERAALAALRDLGLSDVVPTPMKGPHPYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAYVDR 238
Cdd:cd09073   158 ARPKKNEKNAGFTPEERAWFDKLLSLGYVDTFRHFHPEPGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILS 237

                         250
                  ....*....|....*.
gi 1215099959 239 EARkgkgPSDHAPIVV 254
Cdd:cd09073   238 KVK----GSDHAPVTL 249
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-255 2.76e-43

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: 147.31  E-value: 2.76e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPR-LLDWLAGTGPDVVCLQETKCPDGAFPvAEVGEL--GYEVASHS--DGRWNGVAILSRVGLAD 75
Cdd:cd09087     1 LKIISWNVNGLRALLKKgLLDYVKKEDPDILCLQETKLQEGDVP-KELKELlkGYHQYWNAaeKKGYSGTAILSKKKPLS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  76 VTVGFPGEPgfPEPEARAISATCDGVRVWSVYVPN-GRapDDPHYAYKLSWFAALRDALEpELDSGGPVAVCGDFNVAPT 154
Cdd:cd09087    80 VTYGIGIEE--HDQEGRVITAEFENFYLVNTYVPNsGR--GLERLDRRKEWDVDFRAYLK-KLDSKKPVIWCGDLNVAHE 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 155 DDDVWDPALFVTSTHVTPAERAALAALRDLGLSDvvpT-----PMKGPHpYTYWDYRAGMFHQNKGMRIDLVYASAAFAR 229
Cdd:cd09087   155 EIDLANPKTNKKSAGFTPEERESFTELLEAGFVD---TfrhlhPDKEGA-YTFWSYRGNARAKNVGWRLDYFLVSERLKD 230

                         250       260
                  ....*....|....*....|....*.
gi 1215099959 230 AVRSAYVdreaRKGKGPSDHAPIVVD 255
Cdd:cd09087   231 RVVDSFI----RSDIMGSDHCPIGLE 252
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-255 6.32e-42

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: 143.91  E-value: 6.32e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPR-LLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHS---DGRwNGVAILSRVGLADV 76
Cdd:cd10281     1 MRVISVNVNGIRAAAKKgFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDaekKGY-AGVAIYSRTQPKAV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  77 TVGFPGEPGfpEPEARAISATCDGVRVWSVYVPNGRApDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDD 156
Cdd:cd10281    80 IYGLGFEEF--DDEGRYIEADFDNVSVASLYVPSGSS-GDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEI 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 157 DVWDPALFVTSTHVTPA-ERAALAALRDLGLSDVVPTPMKGPHPYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAY 235
Cdd:cd10281   157 DIKNWKANQKNSGFLPEeRAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAW 236

                         250       260
                  ....*....|....*....|
gi 1215099959 236 VDREARKgkgpSDHAPIVVD 255
Cdd:cd10281   237 IYREERF----SDHAPLIVD 252
PRK11756 PRK11756
exonuclease III; Provisional
 1-258 2.70e-39

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 137.72  E-value: 2.70e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGRWNGVAILSRVGLADVTVGF 80
Cdd:PRK11756    1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVALLSKQTPIAVRKGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  81 PGEpgFPEPEARAISATCD----GVRVWSVYVPNGRAPDDP-HYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTD 155
Cdd:PRK11756   81 PTD--DEEAQRRIIMATIPtpngNLTVINGYFPQGESRDHPtKFPAKRQFYQDLQNYLETELSPDNPLLIMGDMNISPTD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 156 DDV------------------------WDPALFvtsthvtpaeraalaalrDLGLSDVvptpMKGPHP-----YTYWDYR 206
Cdd:PRK11756  159 LDIgigeenrkrwlrtgkcsflpeereWLDRLM------------------DWGLVDT----FRQLNPdvndrFSWFDYR 216

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1215099959 207 AGMFHQNKGMRIDLVYASAAFARAVRSAYVDREARKGKGPSDHAPIVVDADL 258
Cdd:PRK11756  217 SKGFDDNRGLRIDLILATQPLAERCVETGIDYDIRGMEKPSDHAPIWATFKL 268
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-255 4.60e-32

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: 118.15  E-value: 4.60e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARL-PRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGR--WNGVAILSRVGLADVT 77
Cdd:cd09085     1 MKIISWNVNGLRAVHkKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAERkgYSGVALYSKIEPDSVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  78 VGFpGEPGFPEpEARAISATCDGVRVWSVYVPNGRApDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDDD 157
Cdd:cd09085    81 EGL-GVEEFDN-EGRILIADFDDFTLFNIYFPNGQM-SEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEID 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 158 VWDPALFVTSTHVTPAERAALAALRDLGLSDVVPTPMKGPHPYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAYVD 237
Cdd:cd09085   158 LARPKENEKVSGFLPEERAWMDKFIENGYVDTFRMFNKEPGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGIL 237

                         250
                  ....*....|....*...
gi 1215099959 238 REARKgkgpSDHAPIVVD 255
Cdd:cd09085   238 PDVMG----SDHCPVSLE 251
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-254 1.20e-24

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: 98.32  E-value: 1.20e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   3 LATWNVNSVKA--RLPRLLDWLAGTGPDVVCLQETKCPDgAFPVAEVGEL-----GYEVASHSDGRWNGVAILSRVGLAD 75
Cdd:cd08372     1 VASYNVNGLNAatRASGIARWVRELDPDIVCLQEVKDSQ-YSAVALNQLLpegyhQYQSGPSRKEGYEGVAILSKTPKFK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  76 VTVGFPGEPGFPEPEARAISATCDGVRVWSVYVPNGRAP-DDPHYAYKLSWFAALRDALEPELD-SGGPVAVCGDFNVAP 153
Cdd:cd08372    80 IVEKHQYKFGEGDSGERRAVVVKFDVHDKELCVVNAHLQaGGTRADVRDAQLKEVLEFLKRLRQpNSAPVVICGDFNVRP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 154 TDDDVWDPALFVTSTHvtpaeraalaalrDLGLSDVVPTpmkGPHPYTYWDYRAgmfhqNKGMRIDLVYASAAFARAVRS 233
Cdd:cd08372   160 SEVDSENPSSMLRLFV-------------ALNLVDSFET---LPHAYTFDTYMH-----NVKSRLDYIFVSKSLLPSVKS 218

                         250       260
                  ....*....|....*....|.
gi 1215099959 234 AYVDREARKGKGPSDHAPIVV 254
Cdd:cd08372   219 SKILSDAARARIPSDHYPIEV 239
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-188 2.69e-19

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: 82.66  E-value: 2.69e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   4 ATWNVNS-------VKARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDG---RWNGVAILSRVGL 73
Cdd:pfam03372   1 LTWNVNGgnadaagDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGgggGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  74 ADVTVGFPGEPGFPEpeaRAISATCDGVRVWSVYVPNGRAPDDPHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNvap 153
Cdd:pfam03372  81 SSVILVDLGEFGDPA---LRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN--- 154

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1215099959 154 tDDDVWdpalfvTSTHVTPAERAALAALRDLGLSD 188
Cdd:pfam03372 155 -ADYIL------VSGGLTVLSVGVLPDLGPRTGSD 182
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-255 1.37e-17

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: 80.44  E-value: 1.37e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   2 RLATWNVNSVKARLPR--------LLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEvASHS----DGRWNGVAILS 69
Cdd:cd09088     1 RIVTWNVNGIRTRLQYqpwnkensLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYD-SFFSfsrgRKGYSGVATYC 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  70 RVGLADV---TVGFPG---EPGFPEP---------------------------EARAISATCDGVRVWSVYVPNGRAPDD 116
Cdd:cd09088    80 RDSAATPvaaEEGLTGvlsSPNQKNElsenddigcygemleftdskelleldsEGRCVLTDHGTFVLINVYCPRADPEKE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 117 PHYAYKLSWFAALRDALEPELDSGGPVAVCGDFNVAPTDDDVWDP----ALFVTSTHVTPAERAALAALRDLGLSDVVPT 192
Cdd:cd09088   160 ERLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPddseDFGGESFEDNPSRQWLDQLLGDSGEGGGSPG 239

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1215099959 193 PM-----KGPHP-----YTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAYVDREaRKGkgpSDHAPIVVD 255
Cdd:cd09088   240 GLlidsfRYFHPtrkgaYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPE-VEG---SDHCPVYAD 308
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-255 4.05e-17

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: 78.16  E-value: 4.05e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   3 LATWNVNSV--KARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGRWNGVAILSRVGLADVTVGF 80
Cdd:cd09076     1 IGTLNVRGLrsPGKRAQLLEELKRKKLDILGLQETHWTGEGELKKKREGGTILYSGSDSGKSRGVAILLSKTAANKLLEY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  81 PgepgfPEPEARAISATCDG----VRVWSVYVPNGRAPDDphyayKLSWFAALRDALEpELDSGGPVAVCGDFNvAPTDD 156
Cdd:cd09076    81 T-----KVVSGRIIMVRFKIkgkrLTIINVYAPTARDEEE-----KEEFYDQLQDVLD-KVPRHDTLIIGGDFN-AVLGP 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 157 DVWDPALFVTSTHVTPaeRAALAALRDLGLSDVVPTPMKGPHPYTYwdYRAGMFHQNkgmRIDLVYasaafaraVRSAYV 236
Cdd:cd09076   149 KDDGRKGLDKRNENGE--RALSALIEEHDLVDVWRENNPKTREYTW--RSPDHGSRS---RIDRIL--------VSKRLR 213

                         250       260
                  ....*....|....*....|..
gi 1215099959 237 DREARKGKGP---SDHAPIVVD 255
Cdd:cd09076   214 VKVKKTKITPgagSDHRLVTLK 235
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-252 1.93e-14

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 70.88  E-value: 1.93e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPR-LLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGYEVASHSDGrWNGVAILSRVGLADVTVG 79
Cdd:PRK13911    1 MKLISWNVNGLRACMTKgFMDFFNSVDADVFCIQESKMQQEQNTFEFKGYFDFWNCAIKKG-YSGVVTFTKKEPLSVSYG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  80 FPGEPGfpEPEARAISATCDGVRVWSVYVPNGRAPDDpHYAYKLSWFAALRDALEPeLDSGGPVAVCGDFNVAPTDDDVW 159
Cdd:PRK13911   80 INIEEH--DKEGRVITCEFESFYLVNVYTPNSQQALS-RLSYRMSWEVEFKKFLKA-LELKKPVIVCGDLNVAHNEIDLE 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 160 DPALFVTSTHVTPAERAALAALRDLGLSDVV----PTPMKGphpYTYWDYRAGMFHQNKGMRIDLVYASAAFARAVRSAY 235
Cdd:PRK13911  156 NPKTNRKNAGFSDEERGKFSELLNAGFIDTFryfyPNKEKA---YTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDAL 232

                         250
                  ....*....|....*..
gi 1215099959 236 VDREARKgkgpSDHAPI 252
Cdd:PRK13911  233 IYKDILG----SDHCPV 245
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-255 7.03e-14

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 70.02  E-value: 7.03e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRLLDWLAGTGPDVVCLQETKcPDGAFPVAEVGE-LGYEVASHSDGRWnGVAILSRVGLADVTVG 79
Cdd:COG3021    95 LRVLTANVLFGNADAEALAALVREEDPDVLVLQETT-PAWEEALAALEAdYPYRVLCPLDNAY-GMALLSRLPLTEAEVV 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  80 FPGEPGFPEPEARaISATCDGVRVWSV--YVPNGRAPDdphyayklsW---FAALRDALEpelDSGGPVAVCGDFNVAPt 154
Cdd:COG3021   173 YLVGDDIPSIRAT-VELPGGPVRLVAVhpAPPVGGSAE---------RdaeLAALAKAVA---ALDGPVIVAGDFNATP- 238

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 155 dddvWDPA--LFVTSThvtpaeraalaalrdlGLSDvvptPMKGPHPYTYWDYRAGMFhqnkGMRIDLVYASAAFarAVR 232
Cdd:COG3021   239 ----WSPTlrRLLRAS----------------GLRD----ARAGRGLGPTWPANLPFL----RLPIDHVLVSRGL--TVV 288

                         250       260
                  ....*....|....*....|...
gi 1215099959 233 SAYVDREARkgkgpSDHAPIVVD 255
Cdd:COG3021   289 DVRVLPVIG-----SDHRPLLAE 306
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-170 2.43e-09

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 54.91  E-value: 2.43e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNV-----NSVKARLPRLLDWLAGTGPDVVCLQEtkcpdgafpvaevgelgyevashsdgrwngVAILSRVGLAD 75
Cdd:COG3568     8 LRVMTYNIryglgTDGRADLERIARVIRALDPDVVALQE------------------------------NAILSRYPIVS 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  76 V-TVGFPGepgfPEPEAR-AISATCDG----VRVWSVyvpngrapddpHYAYKLSW-----FAALRDALEpELDSGGPVA 144
Cdd:COG3568    58 SgTFDLPD----PGGEPRgALWADVDVpgkpLRVVNT-----------HLDLRSAAarrrqARALAELLA-ELPAGAPVI 121

                         170       180
                  ....*....|....*....|....*..
gi 1215099959 145 VCGDFNVAptdDDVW-DPALFVTSTHV 170
Cdd:COG3568   122 LAGDFNDI---DYILvSPGLRVLSAEV 145
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
1-260 2.77e-07

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 50.79  E-value: 2.77e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNV----------------NSVKARLPRLLDWLA----GTGPDVVCLQETKCPDGAF------PVAEVGElgYEV 54
Cdd:COG2374    69 LRVATFNVenlfdtddddddfgrgADTPEEYERKLAKIAaaiaALDADIVGLQEVENNGSALqdlvaaLNLAGGT--YAF 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  55 ASHSDGRWNG---VAILSR---VGLAD--VTVGFPGEPGFPEPEARAISA----TCDGVRVWsVYV--PNGRAPDDPHYA 120
Cdd:COG2374   147 VHPPDGPDGDgirVALLYRpdrVTLVGsaTIADLPDSPGNPDRFSRPPLAvtfeLANGEPFT-VIVnhFKSKGSDDPGDG 225

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 121 YKLSWF------AALRDALE--PELDSGGPVAVCGDFNVAPTDDDVwdpalfvtsTHVTpaeraalaalRDLGLSDVVPT 192
Cdd:COG2374   226 QGASEAkrtaqaEALRAFVDslLAADPDAPVIVLGDFNDYPFEDPL---------RALL----------GAGGLTNLAEK 286

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 193 pMKGPHPYTYwdyragmFHQNKGMRIDLVYASAAFARAVRSAYV----------------DREARKGKGPSDHAPIVVDA 256
Cdd:COG2374   287 -LPAAERYSY-------VYDGNSGLLDHILVSPALAARVTGADIwhinadiynddfkpdfRTYADDPGRASDHDPVVVGL 358


                  ....
gi 1215099959 257 DLVP 260
Cdd:COG2374   359 RLPP 362
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 136-255 2.60e-06

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: 47.21  E-value: 2.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 136 ELDSGGPVAVCGDFNVAPtDDDVWDpalFVTSThvtpaeraalaalrdlGLSD--VVPTPMKGPHPYTYWDYRAGmfhqN 213
Cdd:cd09083   156 EIAGDLPVILTGDFNAEP-DSEPYK---TLTSG----------------GLKDarDTAATTDGGPEGTFHGFKGP----P 211

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1215099959 214 KGMRIDLVYASAAFarAVRSAYVDREARKGKGPSDHAPIVVD 255
Cdd:cd09083   212 GGSRIDYIFVSPGV--KVLSYEILTDRYDGRYPSDHFPVVAD 251
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 3-255 7.45e-06

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: 46.14  E-value: 7.45e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   3 LATWNVNS-----VKARLPRLLDWLAGTGPDVVCLQETKcPDGAFPVAEVGEL--GYE-VASHSDGRW--NGVAILSRvg 72
Cdd:cd09084     1 VMSYNVRSfnrykWKDDPDKILDFIKKQDPDILCLQEYY-GSEGDKDDDLRLLlkGYPyYYVVYKSDSggTGLAIFSK-- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  73 ladvtvgFP----GEPGFPEPEARAISATC----DGVRVWSVYVP-NGRAPDDPHYAYKLSW--------FAALRDAL-- 133
Cdd:cd09084    78 -------YPilnsGSIDFPNTNNNAIFADIrvggDTIRVYNVHLEsFRITPSDKELYKEEKKakelsrnlLRKLAEAFkr 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 134 -EPELD--------SGGPVAVCGDFNvaptddDVwdPALFVTSThVTPaeraalaalrdlGLSDVVPTPMKGPhPYTYWD 204
Cdd:cd09084   151 rAAQADllaadiaaSPYPVIVCGDFN------DT--PASYVYRT-LKK------------GLTDAFVEAGSGF-GYTFNG 208

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1215099959 205 YRagmfhqnKGMRIDLVYASAAF----ARAVRSAYvdrearkgkgpSDHAPIVVD 255
Cdd:cd09084   209 LF-------FPLRIDYILTSKGFkvlrYRVDPGKY-----------SDHYPIVAT 245
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 1-249 1.57e-04

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: 41.95  E-value: 1.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNS-----VKARLPRLLDWLAGTGPDVVCLQETkCPD------------GAFPVAEVGElgyevaSHSDGRWn 63
Cdd:cd09080     1 LKVLTWNVDFlddvnLAERMRAILKLLEELDPDVIFLQEV-TPPflayllsqpwvrKNYYFSEGPP------SPAVDPY- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959  64 GVAILSRVGLADVTVGFP---GEPGFPEPEARAISATCdgVRVWSVYVPNGRApddpHYAYKLSWFAALRDALEPELDSG 140
Cdd:cd09080    73 GVLILSKKSLVVRRVPFTstrMGRNLLAAEINLGSGEP--LRLATTHLESLKS----HSSERTAQLEEIAKKLKKPPGAA 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959 141 GpVAVCGDFNvaptdddvWDPAlFVTSTHvtpaeraalaalRDLGLSDVVPTPMKGPHP-YTyWDYR----AGMFHQNKG 215
Cdd:cd09080   147 N-VILGGDFN--------LRDK-EDDTGG------------LPNGFVDAWEELGPPGEPgYT-WDTQknpmLRKGEAGPR 203

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1215099959 216 MRIDLVYA--SAAFARAVRSAYVDREARKGKG--PSDH 249
Cdd:cd09080   204 KRFDRVLLrgSDLKPKSIELIGTEPIPGDEEGlfPSDH 241
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 1-150 4.30e-03

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: 37.27  E-value: 4.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215099959   1 MRLATWNVNSVKARLPRLLDWLAGTGPDVVCLQETKCPDGAFPVAEVGELGyevashsdgrwnGVAILSRVGLADVTVgf 80
Cdd:cd09077     1 LRILQINLNRCKAAQDLLLQTAREEGADIALIQEPYLVPVNNPNWVTDESG------------RAAIVVSDRLPRKPI-- 66

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1215099959  81 pgEPGFPEPEARAISATcdGVRVWSVYVPNGRAPDDphyayklswFAALRDALEPELDSGG-PVAVCGDFN 150
Cdd:cd09077    67 --QRLSLGLGIVAARVG--GITVVSCYAPPSESLEE---------FEEYLENLVRIVRGLSrPVIIGGDFN 124
 
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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