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Conserved domains on  [gi|1152310641|ref|WP_078193225|]
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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

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 6.59e-143

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: 401.22  E-value: 6.59e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKGIFDWMATSDADVICMQESRITHEQWTDKFK-PEGWFTHLFPAERPGYAGTAIYSRLPFVSVT 92
Cdd:cd10281     1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFePEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  93 DGLGFELADTQGRFISAEFDlglgqTAHICSLYLPSGSSGEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNIVHKR 172
Cdd:cd10281    81 YGLGFEEFDDEGRYIEADFD-----NVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTE 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 173 IDIKNWSGNQKASGCLPHERAWLDHIYDELGYVDTFREVRKEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKERTVNA 252
Cdd:cd10281   156 IDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSA 235

                         250
                  ....*....|....*...
gi 1152310641 253 WIFKDEWFSDHAPVIIDY 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 6.59e-143

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: 401.22  E-value: 6.59e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKGIFDWMATSDADVICMQESRITHEQWTDKFK-PEGWFTHLFPAERPGYAGTAIYSRLPFVSVT 92
Cdd:cd10281     1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFePEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  93 DGLGFELADTQGRFISAEFDlglgqTAHICSLYLPSGSSGEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNIVHKR 172
Cdd:cd10281    81 YGLGFEEFDDEGRYIEADFD-----NVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTE 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 173 IDIKNWSGNQKASGCLPHERAWLDHIYDELGYVDTFREVRKEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKERTVNA 252
Cdd:cd10281   156 IDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSA 235

                         250
                  ....*....|....*...
gi 1152310641 253 WIFKDEWFSDHAPVIIDY 270
Cdd:cd10281   236 WIYREERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
14-271 7.27e-105

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 305.08  E-value: 7.27e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKgIFDWMATSDADVICMQESRITHEQWTDK-FKPEGWFTHLFPaeRPGYAGTAIYSRLPFVSVT 92
Cdd:COG0708     1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEaFEAAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  93 DGLGFELADTQGRFISAEFDlGLgqtaHICSLYLPSGSS-GEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNIVHK 171
Cdd:COG0708    78 RGLGGDEFDAEGRYIEADFG-GV----RVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPT 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 172 RIDIKNWSGNQKASGCLPHERAWLDHIYDeLGYVDTFREVRKEAE-LYSWWSNRGQARAKNVGWRIDYHACSPDWKERTV 250
Cdd:COG0708   153 EIDVKNPKANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPDVEgQYTWWSYRAGAFARNRGWRIDYILASPALADRLK 231

                         250       260
                  ....*....|....*....|....*
gi 1152310641 251 NAWIFK----DEWFSDHAPVIIDYK 271
Cdd:COG0708   232 DAGIDReprgDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 14-271 2.93e-72

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: 222.15  E-value: 2.93e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKGIFDWMATSDADVICMQESRITHEQWT-DKFKPEGWFTHLFPAERpGYAGTAIYSRLPFVSVT 92
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPaELFEELGYHVFFHGAKK-GYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  93 DGLGFELADTQGRFISAEFDLglgqtAHICSLYLPSGSS-GEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNIVHK 171
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDG-----FTVVNVYVPNGGSrDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHT 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 172 RIDIKNWSGNQKASGCLPHERAWLDHIYDElGYVDTFREVRKEAEL-YSWWSNRGQARAKNVGWRIDYHACSPDWKERTV 250
Cdd:TIGR00633 155 EIDLGNPKENKGNAGFTPEEREWFDELLEA-GFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVV 233

                         250       260
                  ....*....|....*....|.
gi 1152310641 251 NAWIFKDEWFSDHAPVIIDYK 271
Cdd:TIGR00633 234 DSYIDSEIRGSDHCPIVLELD 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 14-266 6.66e-49

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 162.17  E-value: 6.66e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKGIFDWMATSDADVICMQESRITHEQWTDKFKpeGWFTHLFPAERPGYAGTAIYSRLPFVSVTD 93
Cdd:PRK13911    1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFK--GYFDFWNCAIKKGYSGVVTFTKKEPLSVSY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  94 GLGFELADTQGRFISAEFdlglgQTAHICSLYLPSGSSGEEAQARKDLFLGEYQQILKQWRAEnKSVIVCGDYNIVHKRI 173
Cdd:PRK13911   79 GINIEEHDKEGRVITCEF-----ESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELK-KPVIVCGDLNVAHNEI 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 174 DIKNWSGNQKASGCLPHERAWLDHIYDElGYVDTFREVRKEAE-LYSWWSNRGQARAKNVGWRIDYHACSPDWKERTVNA 252
Cdd:PRK13911  153 DLENPKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEkAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDA 231

                         250
                  ....*....|....
gi 1152310641 253 WIFKDEWFSDHAPV 266
Cdd:PRK13911  232 LIYKDILGSDHCPV 245
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 17-168 6.65e-15

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: 71.10  E-value: 6.65e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  17 VSINVNGLRS------AEKKGIFDWMATSDADVICMQESRITHEQWTDK--FKPEGWFTHLFPAERPGYAGTAIYSRLPF 88
Cdd:pfam03372   1 LTWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASRLLLalLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  89 VSVTDGLGFELADTQGRFISAEFDlglgqTAHICSLYLPSGSSGEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNI 168
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFA-----GVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 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 6.59e-143

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: 401.22  E-value: 6.59e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKGIFDWMATSDADVICMQESRITHEQWTDKFK-PEGWFTHLFPAERPGYAGTAIYSRLPFVSVT 92
Cdd:cd10281     1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFePEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  93 DGLGFELADTQGRFISAEFDlglgqTAHICSLYLPSGSSGEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNIVHKR 172
Cdd:cd10281    81 YGLGFEEFDDEGRYIEADFD-----NVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTE 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 173 IDIKNWSGNQKASGCLPHERAWLDHIYDELGYVDTFREVRKEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKERTVNA 252
Cdd:cd10281   156 IDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSA 235

                         250
                  ....*....|....*...
gi 1152310641 253 WIFKDEWFSDHAPVIIDY 270
Cdd:cd10281   236 WIYREERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
14-271 7.27e-105

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 305.08  E-value: 7.27e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKgIFDWMATSDADVICMQESRITHEQWTDK-FKPEGWFTHLFPaeRPGYAGTAIYSRLPFVSVT 92
Cdd:COG0708     1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEaFEAAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  93 DGLGFELADTQGRFISAEFDlGLgqtaHICSLYLPSGSS-GEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNIVHK 171
Cdd:COG0708    78 RGLGGDEFDAEGRYIEADFG-GV----RVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPT 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 172 RIDIKNWSGNQKASGCLPHERAWLDHIYDeLGYVDTFREVRKEAE-LYSWWSNRGQARAKNVGWRIDYHACSPDWKERTV 250
Cdd:COG0708   153 EIDVKNPKANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPDVEgQYTWWSYRAGAFARNRGWRIDYILASPALADRLK 231

                         250       260
                  ....*....|....*....|....*
gi 1152310641 251 NAWIFK----DEWFSDHAPVIIDYK 271
Cdd:COG0708   232 DAGIDReprgDERPSDHAPVVVELD 256
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 15-270 3.27e-85

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: 254.91  E-value: 3.27e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  15 RVVSINVNGLRSAEKKGIFDWMATSDADVICMQESRITHEQWTDKFK-PEGWFTHLFPAERPGYAGTAIYSRLPFVSVTD 93
Cdd:cd09073     1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQhVEGYHSYWSPARKKGYSGVATLSKEEPLDVSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  94 GLGFELADTQGRFISAEFDlglgqTAHICSLYLPSGSSGEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNIVHKRI 173
Cdd:cd09073    81 GIGGEEFDSEGRVITAEFD-----DFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEI 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 174 DIKNWSGNQKASGCLPHERAWLDHIYdELGYVDTFREVRKEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKERTVNAW 253
Cdd:cd09073   156 DLARPKKNEKNAGFTPEERAWFDKLL-SLGYVDTFRHFHPEPGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSG 234

                         250
                  ....*....|....*..
gi 1152310641 254 IFKDEWFSDHAPVIIDY 270
Cdd:cd09073   235 ILSKVKGSDHAPVTLEL 251
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 14-270 8.29e-84

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: 251.43  E-value: 8.29e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKGIFDWMATSDADVICMQESRITHEQWTDKFK-PEGWFTHLFPAERPGYAGTAIYSRLPFVSVT 92
Cdd:cd09085     1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRnIEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  93 DGLGFELADTQGRFISAEFDlglgqTAHICSLYLPSGSSGEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNIVHKR 172
Cdd:cd09085    81 EGLGVEEFDNEGRILIADFD-----DFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKE 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 173 IDIKNWSGNQKASGCLPHERAWLDHIYDElGYVDTFREVRKEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKERTVNA 252
Cdd:cd09085   156 IDLARPKENEKVSGFLPEERAWMDKFIEN-GYVDTFRMFNKEPGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDA 234

                         250
                  ....*....|....*...
gi 1152310641 253 WIFKDEWFSDHAPVIIDY 270
Cdd:cd09085   235 GILPDVMGSDHCPVSLEL 252
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 14-271 2.93e-72

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: 222.15  E-value: 2.93e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKGIFDWMATSDADVICMQESRITHEQWT-DKFKPEGWFTHLFPAERpGYAGTAIYSRLPFVSVT 92
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPaELFEELGYHVFFHGAKK-GYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  93 DGLGFELADTQGRFISAEFDLglgqtAHICSLYLPSGSS-GEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNIVHK 171
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDG-----FTVVNVYVPNGGSrDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHT 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 172 RIDIKNWSGNQKASGCLPHERAWLDHIYDElGYVDTFREVRKEAEL-YSWWSNRGQARAKNVGWRIDYHACSPDWKERTV 250
Cdd:TIGR00633 155 EIDLGNPKENKGNAGFTPEEREWFDELLEA-GFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVV 233

                         250       260
                  ....*....|....*....|.
gi 1152310641 251 NAWIFKDEWFSDHAPVIIDYK 271
Cdd:TIGR00633 234 DSYIDSEIRGSDHCPIVLELD 254
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 14-269 7.99e-72

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: 220.89  E-value: 7.99e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKGIFDWMATSDADVICMQESRITHEQWTD--KFKPEGWFTHLFPAERPGYAGTAIYSRLPFVSV 91
Cdd:cd09087     1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKelKELLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  92 TDGLGFELADTQGRFISAEFDlglgqtahicSLYL-----PSGSSGEEAQARKDLFLGEYQQILKQWRAEnKSVIVCGDY 166
Cdd:cd09087    81 TYGIGIEEHDQEGRVITAEFE----------NFYLvntyvPNSGRGLERLDRRKEWDVDFRAYLKKLDSK-KPVIWCGDL 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 167 NIVHKRIDIKNWSGNQKASGCLPHERAWLDHIYDElGYVDTFREVRKEAE-LYSWWSNRGQARAKNVGWRIDYHACSPDW 245
Cdd:cd09087   150 NVAHEEIDLANPKTNKKSAGFTPEERESFTELLEA-GFVDTFRHLHPDKEgAYTFWSYRGNARAKNVGWRLDYFLVSERL 228

                         250       260
                  ....*....|....*....|....
gi 1152310641 246 KERTVNAWIFKDEWFSDHAPVIID 269
Cdd:cd09087   229 KDRVVDSFIRSDIMGSDHCPIGLE 252
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 14-266 5.72e-71

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: 218.79  E-value: 5.72e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKGIfDWMATSDADVICMQESRITHEQWT-DKFKPEGWFTHLFPAErpGYAGTAIYSRLPFVSVT 92
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGL-AWLKENQPDVLCLQETKVQDEQFPlEPFHKEGYHVFFSGQK--GYSGVAIFSKEEPISVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  93 DGLGFELADTQGRFISAEFDlglgqTAHICSLYLPSGSS-GEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNIVHK 171
Cdd:TIGR00195  78 RGFGVEEEDAEGRIIMAEFD-----SFLVINGYFPNGSRdDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPT 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 172 RIDIKNWSGNQKASGCLPHERAWLDHIYdELGYVDTFREVRKEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKERTVN 251
Cdd:TIGR00195 153 EIDLHIPDENRNHTGFLPEEREWLDRLL-EAGLVDTFRKFNPDEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVD 231

                         250
                  ....*....|....*....
gi 1152310641 252 AWIFKD----EWFSDHAPV 266
Cdd:TIGR00195 232 CGIDYDirgsEKPSDHCPV 250
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 14-269 1.13e-56

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: 182.33  E-value: 1.13e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRsAEKKGIFDWMATSDADVICMQESRITheqwTDKFkPEGWFT----HLFPAERPGYAGTAIYSRLPFV 89
Cdd:cd09086     1 MKIATWNVNSIR-ARLEQVLDWLKEEDPDVLCLQETKVE----DDQF-PADAFEalgyHVAVHGQKAYNGVAILSRLPLE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  90 SVTDGLGFELADTQGRFISAEFDlGLgqtaHICSLYLPSGSS-GEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNI 168
Cdd:cd09086    75 DVRTGFPGDPDDDQARLIAARVG-GV----RVINLYVPNGGDiGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNI 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 169 VHKRIDIKNWSGNQKASGCLPHERAWLDHIYDeLGYVDTFREVRKEAELYSWWSNRGQARAKNVGWRIDYHACSPDWKER 248
Cdd:cd09086   150 APEDIDVWDPKQLLGKVLFTPEEREALRALLD-LGFVDAFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILASPALADR 228

                         250       260
                  ....*....|....*....|....*
gi 1152310641 249 TVNAWIFKDE--WF--SDHAPVIID 269
Cdd:cd09086   229 LKDVGIDREPrgWEkpSDHAPVVAE 253
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 14-266 6.66e-49

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 162.17  E-value: 6.66e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAEKKGIFDWMATSDADVICMQESRITHEQWTDKFKpeGWFTHLFPAERPGYAGTAIYSRLPFVSVTD 93
Cdd:PRK13911    1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFK--GYFDFWNCAIKKGYSGVVTFTKKEPLSVSY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  94 GLGFELADTQGRFISAEFdlglgQTAHICSLYLPSGSSGEEAQARKDLFLGEYQQILKQWRAEnKSVIVCGDYNIVHKRI 173
Cdd:PRK13911   79 GINIEEHDKEGRVITCEF-----ESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELK-KPVIVCGDLNVAHNEI 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 174 DIKNWSGNQKASGCLPHERAWLDHIYDElGYVDTFREVRKEAE-LYSWWSNRGQARAKNVGWRIDYHACSPDWKERTVNA 252
Cdd:PRK13911  153 DLENPKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKEkAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDA 231

                         250
                  ....*....|....
gi 1152310641 253 WIFKDEWFSDHAPV 266
Cdd:PRK13911  232 LIYKDILGSDHCPV 245
PRK11756 PRK11756
exonuclease III; Provisional
 14-272 3.44e-31

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 116.53  E-value: 3.44e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSA--EKKGIFDwmaTSDADVICMQESRITHEQwtdkfkpegwfthlFPAE-------------RPGYA 78
Cdd:PRK11756    1 MKFVSFNINGLRARphQLEAIIE---KHQPDVIGLQETKVHDEM--------------FPLEevealgyhvfyhgQKGHY 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  79 GTAIYSRLPFVSVTDGLGFELADTQGRFISAEFDLGLGQTAhICSLYLPSGSSGE-----EAQAR--KDLflgeyQQILK 151
Cdd:PRK11756   64 GVALLSKQTPIAVRKGFPTDDEEAQRRIIMATIPTPNGNLT-VINGYFPQGESRDhptkfPAKRQfyQDL-----QNYLE 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 152 QWRAENKSVIVCGDYNIVHKRIDI-------KNWSGNQKASgCLPHERAWLDHIYDeLGYVDTFREVRKEA-ELYSWWSN 223
Cdd:PRK11756  138 TELSPDNPLLIMGDMNISPTDLDIgigeenrKRWLRTGKCS-FLPEEREWLDRLMD-WGLVDTFRQLNPDVnDRFSWFDY 215

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1152310641 224 RGQARAKNVGWRIDYHACSPDWKERTVNAWIFKD----EWFSDHAPVIIDYKI 272
Cdd:PRK11756  216 RSKGFDDNRGLRIDLILATQPLAERCVETGIDYDirgmEKPSDHAPIWATFKL 268
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 16-270 1.09e-26

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: 103.97  E-value: 1.09e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  16 VVSINVNGLRSAEK-KGIFDWMATSDADVICMQESRITHEQwTDKFKPEGWFTHLFPAERPGYAGTAI----YSRLPFVS 90
Cdd:cd09076     1 IGTLNVRGLRSPGKrAQLLEELKRKKLDILGLQETHWTGEG-ELKKKREGGTILYSGSDSGKSRGVAIllskTAANKLLE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  91 VTdglgfelADTQGRFISAEFDlGLGQTAHICSLYLPSGSSGEEaqarKDLFLGEYQQILKQWRAENkSVIVCGDYN-IV 169
Cdd:cd09076    80 YT-------KVVSGRIIMVRFK-IKGKRLTIINVYAPTARDEEE----KEEFYDQLQDVLDKVPRHD-TLIIGGDFNaVL 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 170 HKRIDIKNWSGNQKASGclphERAwLDHIYDELGYVDTFREVRKEAELYSWWSNRGQARAknvgwRIDYHACSPDWKERT 249
Cdd:cd09076   147 GPKDDGRKGLDKRNENG----ERA-LSALIEEHDLVDVWRENNPKTREYTWRSPDHGSRS-----RIDRILVSKRLRVKV 216

                         250       260
                  ....*....|....*....|.
gi 1152310641 250 VNAWIFkDEWFSDHAPVIIDY 270
Cdd:cd09076   217 KKTKIT-PGAGSDHRLVTLKL 236
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 15-269 6.63e-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: 100.85  E-value: 6.63e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  15 RVVSINVNGLR-------SAEKKGIFDWMATSDADVICMQESRITHEQWTDKFK-PEGW---FThlFPAERPGYAGTAIY 83
Cdd:cd09088     1 RIVTWNVNGIRtrlqyqpWNKENSLKSFLDSLDADIICLQETKLTRDELDEPSAiVEGYdsfFS--FSRGRKGYSGVATY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  84 SRLPFVSV----------------------TDGLGF-----------ELA--DTQGRFISAEFdlglgQTAHICSLYLPS 128
Cdd:cd09088    79 CRDSAATPvaaeegltgvlsspnqknelseNDDIGCygemleftdskELLelDSEGRCVLTDH-----GTFVLINVYCPR 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 129 GSSGEEAQAR-KDLFLGEYQQILKQWRAENKSVIVCGDYNIVHKRIDIKNWSGNQKASGCLPHE---RAWLDHIYDELG- 203
Cdd:cd09088   154 ADPEKEERLEfKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLGDSGe 233

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1152310641 204 --------YVDTFREV---RKEAelYSWWSNRGQARAKNVGWRIDYHACSPDWKERTVNAWIFKDEWFSDHAPVIID 269
Cdd:cd09088   234 gggspgglLIDSFRYFhptRKGA--YTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYAD 308
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 8-272 3.89e-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: 3.89e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641   8 PSDQKILRVVSINVNGlRSAEKKGIFDWMATSDADVICMQEsriTHEQWTDKFKP-EGWFTHLFPAERPGYAGTAIYSRL 86
Cdd:COG3021    89 PAGGPDLRVLTANVLF-GNADAEALAALVREEDPDVLVLQE---TTPAWEEALAAlEADYPYRVLCPLDNAYGMALLSRL 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  87 PFVSVTdglGFELADTQGRFISAEFDLGlGQTAHICSLYLPSGSSGEEAQARkdlflgEYQQILKQWRAENKSVIVCGDY 166
Cdd:COG3021   165 PLTEAE---VVYLVGDDIPSIRATVELP-GGPVRLVAVHPAPPVGGSAERDA------ELAALAKAVAALDGPVIVAGDF 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 167 NIVHkridiknWSGN----QKASGCLPHERAWldhiydelGYVDTFrevrkeaelyswwsnrgQARAKNVGWRIDYHACS 242
Cdd:COG3021   235 NATP-------WSPTlrrlLRASGLRDARAGR--------GLGPTW-----------------PANLPFLRLPIDHVLVS 282

                         250       260       270
                  ....*....|....*....|....*....|
gi 1152310641 243 PDWkeRTVNAWIFKDEWfSDHAPVIIDYKI 272
Cdd:COG3021   283 RGL--TVVDVRVLPVIG-SDHRPLLAELAL 309
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 16-266 6.03e-20

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: 86.00  E-value: 6.03e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  16 VVSINVNGLRSAEK-KGIFDWMATSDADVICMQESRITHEQ--WTDKFKPEGWFTHLFPAER-PGYAGTAIYSR---LPF 88
Cdd:cd08372     1 VASYNVNGLNAATRaSGIARWVRELDPDIVCLQEVKDSQYSavALNQLLPEGYHQYQSGPSRkEGYEGVAILSKtpkFKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  89 VSVTDGLGFELADTQGRFISAEFDLGlGQTAHICSLYLPS-GSSGEEAQARKDLFLGEYQQILkqwRAENKSVIVCGDYN 167
Cdd:cd08372    81 VEKHQYKFGEGDSGERRAVVVKFDVH-DKELCVVNAHLQAgGTRADVRDAQLKEVLEFLKRLR---QPNSAPVVICGDFN 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 168 IVHKRIDIKNWSGnqkaSGCLPHERAWLDHIYDELGyvdtfrevrkeaeLYSWWSNRgqaraKNVGWRIDYHACSPDWKE 247
Cdd:cd08372   157 VRPSEVDSENPSS----MLRLFVALNLVDSFETLPH-------------AYTFDTYM-----HNVKSRLDYIFVSKSLLP 214

                         250       260
                  ....*....|....*....|...
gi 1152310641 248 RTVNAWIFKDEWF----SDHAPV 266
Cdd:cd08372   215 SVKSSKILSDAARaripSDHYPI 237
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 16-270 6.61e-17

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: 77.72  E-value: 6.61e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  16 VVSINVNGLR----SAEKKGIFDWMATSDADVICMQESRITHEQWTDKFKP--EGW-FTHLFPAERPGYAGTAIYSRLPF 88
Cdd:cd09084     1 VMSYNVRSFNrykwKDDPDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLllKGYpYYYVVYKSDSGGTGLAIFSKYPI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  89 VSVtDGLGFElaDTQGRFISAEFDLGlGQTAHICSLYLPS----------GSSGEEAQARKDLFLGEYQQ---------- 148
Cdd:cd09084    81 LNS-GSIDFP--NTNNNAIFADIRVG-GDTIRVYNVHLESfritpsdkelYKEEKKAKELSRNLLRKLAEafkrraaqad 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 149 ILKQWRAENKS-VIVCGDYNivhkridiknwsgNQKASgclpherawldHIYDEL--GYVDTFREVrkeAELYSwWSNRG 225
Cdd:cd09084   157 LLAADIAASPYpVIVCGDFN-------------DTPAS-----------YVYRTLkkGLTDAFVEA---GSGFG-YTFNG 208

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1152310641 226 QARaknvGWRIDYHACSPDWkeRTVNAWIFKDEWfSDHAPVIIDY 270
Cdd:cd09084   209 LFF----PLRIDYILTSKGF--KVLRYRVDPGKY-SDHYPIVATL 246
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 17-168 6.65e-15

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: 71.10  E-value: 6.65e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  17 VSINVNGLRS------AEKKGIFDWMATSDADVICMQESRITHEQWTDK--FKPEGWFTHLFPAERPGYAGTAIYSRLPF 88
Cdd:pfam03372   1 LTWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDDDASRLLLalLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  89 VSVTDGLGFELADTQGRFISAEFDlglgqTAHICSLYLPSGSSGEEAQARKDLFLGEYQQILKQWRAENKSVIVCGDYNI 168
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFA-----GVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 14-220 9.25e-10

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: 57.74  E-value: 9.25e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGL---RSAEK-KGIFDWMATSDADVICMQE------SRITHEQWT-DKFKpegwFTHLFPAERPGYAGTAI 82
Cdd:cd09080     1 LKVLTWNVDFLddvNLAERmRAILKLLEELDPDVIFLQEvtppflAYLLSQPWVrKNYY----FSEGPPSPAVDPYGVLI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  83 YSR-------LPFVSVTDGLGfeladtqgrFISAEFDLGLGQTAHICSLYLPSGSSGEEAQARKdlfLGEYQQILKQWRA 155
Cdd:cd09080    77 LSKkslvvrrVPFTSTRMGRN---------LLAAEINLGSGEPLRLATTHLESLKSHSSERTAQ---LEEIAKKLKKPPG 144

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1152310641 156 ENKsVIVCGDYNIVHKRIdiknwsgnqkasgclpherawlDHIYDELGYVDTFREVRKEAEL-YSW 220
Cdd:cd09080   145 AAN-VILGGDFNLRDKED----------------------DTGGLPNGFVDAWEELGPPGEPgYTW 187
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 8-272 1.10e-08

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 53.37  E-value: 1.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641   8 PSDQKILRVVSINVNGLRSAEKKGIFDWMA----TSDADVICMQEsritheqwtdkfkpegwfthlfpaerpgyagTAIY 83
Cdd:COG3568     2 AAAAATLRVMTYNIRYGLGTDGRADLERIArvirALDPDVVALQE-------------------------------NAIL 50

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  84 SRLPFVSVTDgLGFELADTQGR-FISAEFDLGlGQTAHICSLYLPSGSSGE-EAQARkdlflgeyqQILKQWRAENKS-- 159
Cdd:COG3568    51 SRYPIVSSGT-FDLPDPGGEPRgALWADVDVP-GKPLRVVNTHLDLRSAAArRRQAR---------ALAELLAELPAGap 119

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 160 VIVCGDYNIvhkridiknwsgnqkasgclpherawLDHIYdelgyvdtfreVRKEAELYSWWSNRgqaraknvgwridyh 239
Cdd:COG3568   120 VILAGDFND--------------------------IDYIL-----------VSPGLRVLSAEVLD--------------- 147

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1152310641 240 acSPDWKertvnawifkdeWFSDHAPVIIDYKI 272
Cdd:COG3568   148 --SPLGR------------AASDHLPVVADLEL 166
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 14-269 2.62e-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: 44.20  E-value: 2.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  14 LRVVSINVNGLRSAeKKGIFDWMATSDADVICMQESRITHEQwtdkfkPEGWFTHLFPaerpgyaGTAIY--SRLPFVSV 91
Cdd:cd09077     1 LRILQINLNRCKAA-QDLLLQTAREEGADIALIQEPYLVPVN------NPNWVTDESG-------RAAIVvsDRLPRKPI 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  92 TDGLGFEladtqgRFISAEfdlgLGQTaHICSLYLPSGSSGEEaqarkdlFLGEYQQILKQWRAENKSVIVCGDYNIVHK 171
Cdd:cd09077    67 QRLSLGL------GIVAAR----VGGI-TVVSCYAPPSESLEE-------FEEYLENLVRIVRGLSRPVIIGGDFNAWSP 128

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 172 RidiknWSGN-QKASGclpheRAWLDHIyDELGYVdtfreVRKEAELYSWWSNRGQAraknvgwRIDYHACSPDWKERtV 250
Cdd:cd09077   129 A-----WGSKrTDRRG-----RLLEDWI-ANLGLV-----LLNDGNSPTFVRPRGTS-------IIDVTFCSPSLARR-I 184

                         250       260
                  ....*....|....*....|
gi 1152310641 251 NAW-IFKDEWFSDHAPVIID 269
Cdd:cd09077   185 SNWrVLEDETLSDHRYIRFT 204
nSMase cd09078
Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological ...
 42-266 1.17e-04

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: 42.71  E-value: 1.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641  42 DVICMQE-------SRITHE-------QwTDK--FKPEGWFTHLFPAerpgyaGTAIYSRLPFVSV-----TDGLGFELA 100
Cdd:cd09078    38 DVVVLQEvfdararKRLLNGlkkeypyQ-TDVvgRSPSGWSSKLVDG------GVVILSRYPIVEKdqyifPNGCGADCL 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 101 DTQGrFISAEFDLGLGQTAHICSLYLPSGSSGEEAQA-RKDLFlGEYQQ-ILKQWRAENKSVIVCGDYNIvhkridikNW 178
Cdd:cd09078   111 AAKG-VLYAKINKGGTKVYHVFGTHLQASDGSCLDRAvRQKQL-DELRAfIEEKNIPDNEPVIIAGDFNV--------DK 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 179 sgnqkasgclpheRAWLDHIYDELGYVDTF--REVRKEAEL-YSW----WSNRGQARAKNVGWRIDY------HACSPDW 245
Cdd:cd09078   181 -------------RSSRDEYDDMLEQLHDYnaPEPITAGETpLTWdpgtNLLAKYNYPGGGGERLDYilysndHLQPSSW 247

                         250       260
                  ....*....|....*....|....*....
gi 1152310641 246 KER----TVNAWIFKDEW----FSDHAPV 266
Cdd:cd09078   248 SNEvevpKSPTWSVTNGYtfadLSDHYPV 276
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 147-270 1.94e-03

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: 38.74  E-value: 1.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1152310641 147 QQILK--QWRAENKSVIVCGDYNivhkridiknwsgnqkasgCLPHERAwldhiYDEL---GYVDTFREV--RKEAELYS 219
Cdd:cd09083   148 KLILEriKEIAGDLPVILTGDFN-------------------AEPDSEP-----YKTLtsgGLKDARDTAatTDGGPEGT 203

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1152310641 220 WWSNRGQARAKnvgwRIDYHACSPDWK--ERTVNAWIFKDEWFSDHAPVIIDY 270
Cdd:cd09083   204 FHGFKGPPGGS----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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