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Conserved domains on  [gi|1002226203|ref|XP_015625662|]
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DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic [Oryza sativa Japonica Group]

Protein Classification

SAP and Ape1-like_AP-endo domain-containing protein( domain architecture ID 10488539)

SAP and Ape1-like_AP-endo domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 239-497 1.25e-141

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: 406.94  E-value: 1.25e-141
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKALLKSrgfSIHQLAQREDFDILCLQETKMQEKDVEVIKEGLLEGYtHSFWTCSvSKLGYSGTAIISRV 318
Cdd:cd09087     1 LKIISWNVNGLRALLKK---GLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGY-HQYWNAA-EKKGYSGTAILSKK 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 319 KPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGDGLKRLtYRVTEWDPSLGNYMKDLEKSKPVILTGDLNCAHQ 398
Cdd:cd09087    76 KPLSVTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERL-DRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHE 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 399 EIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNVVG-YSYWGYRHNARKTNKGWRLDYFLVSESIAERVH 477
Cdd:cd09087   155 EIDLANPKTNKKSAGFTPEERESF-TELLEAGFVDTFRHLHPDKEGaYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVV 233

                         250       260
                  ....*....|....*....|
gi 1002226203 478 DSYIIPDISASDHSPLGLVL 497
Cdd:cd09087   234 DSFIRSDIMGSDHCPIGLEL 253
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 87-121 5.47e-07

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


:

Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 45.85  E-value: 5.47e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002226203  87 LQSMTVKELREITRMMGIPVKGNKKDLVSALMDSL 121
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERLQEYL 35
PLN03124 super family cl33640
poly [ADP-ribose] polymerase; Provisional
 29-175 3.66e-03

poly [ADP-ribose] polymerase; Provisional


The actual alignment was detected with superfamily member PLN03124:

Pssm-ID: 215591 [Multi-domain]  Cd Length: 643  Bit Score: 39.82  E-value: 3.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203  29 KLALI-RLSLMMAETRATYSRRAASKNTDIKKDDEHVLEKEDVAESKLeieqlRNDPDRLQSMTVKELREITRMMGIPVK 107
Cdd:PLN03124   25 KAALVrRLDDAIAEDAKTASKSGTKSSAGRKKRRERQDDGDDEPVSPK-----RIAIDEVKGMTVRELREAASERGLATT 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002226203 108 GNKKDLVSALMDSLgkvgtssvekigVSEVPSKRKGASVVVEQNIDSSEViSETPSKRSRAKNKGTAE 175
Cdd:PLN03124  100 GRKKDLLERLCAAL------------ESDVKVGSANGTGEDEKEKGGDEE-REKEEKIVTATKKGRAV 154
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 239-497 1.25e-141

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: 406.94  E-value: 1.25e-141
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKALLKSrgfSIHQLAQREDFDILCLQETKMQEKDVEVIKEGLLEGYtHSFWTCSvSKLGYSGTAIISRV 318
Cdd:cd09087     1 LKIISWNVNGLRALLKK---GLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGY-HQYWNAA-EKKGYSGTAILSKK 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 319 KPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGDGLKRLtYRVTEWDPSLGNYMKDLEKSKPVILTGDLNCAHQ 398
Cdd:cd09087    76 KPLSVTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERL-DRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHE 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 399 EIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNVVG-YSYWGYRHNARKTNKGWRLDYFLVSESIAERVH 477
Cdd:cd09087   155 EIDLANPKTNKKSAGFTPEERESF-TELLEAGFVDTFRHLHPDKEGaYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVV 233

                         250       260
                  ....*....|....*....|
gi 1002226203 478 DSYIIPDISASDHSPLGLVL 497
Cdd:cd09087   234 DSFIRSDIMGSDHCPIGLEL 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 239-498 1.18e-119

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: 351.20  E-value: 1.18e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKALLKsRGFSihQLAQREDFDILCLQETKMQEkDVEVIKEGLLEGYtHSFWTCSvsKLGYSGTAIISRV 318
Cdd:TIGR00633   1 MKIISWNVNGLRARLH-KLFL--DWLKEEQPDVLCLQETKVAD-EQFPAELFEELGY-HVFFHGA--KKGYSGVAILSKV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 319 KPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSG-DGLKRLTYRVTEWDPSLGNYMKDLEKSKPVILTGDLNCAH 397
Cdd:TIGR00633  74 EPLDVRYGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 398 QEIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNVVG-YSYWGYRHNARKTNKGWRLDYFLVSESIAERV 476
Cdd:TIGR00633 154 TEIDLGNPKENKGNAGFTPEEREWF-DELLEAGFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERV 232

                         250       260
                  ....*....|....*....|..
gi 1002226203 477 HDSYIIPDISASDHSPLGLVLK 498
Cdd:TIGR00633 233 VDSYIDSEIRGSDHCPIVLELD 254
XthA COG0708
Exonuclease III [Replication, recombination and repair];
239-498 6.34e-96

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 290.44  E-value: 6.34e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKAllksRgfsIHQLA---QREDFDILCLQETKMQEKDVEViKEGLLEGYtHSFWtcsVSKLGYSGTAII 315
Cdd:COG0708     1 MKIASWNVNGIRA----R---LPKLLdwlAEEDPDVLCLQETKAQDEQFPL-EAFEAAGY-HVYF---HGQKGYNGVAIL 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 316 SRVKPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGD-GLKRLTYRVtEWDPSLGNYMKDLEKS-KPVILTGDL 393
Cdd:COG0708    69 SRLPPEDVRRGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSvGSEKFDYKL-RFLDALRAYLAELLAPgRPLILCGDF 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 394 NCAHQEIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNVVG-YSYWGYRHNARKTNKGWRLDYFLVSESI 472
Cdd:COG0708   148 NIAPTEIDVKNPKANLKNAGFLPEERAWF-DRLLELGLVDAFRALHPDVEGqYTWWSYRAGAFARNRGWRIDYILASPAL 226

                         250       260       270
                  ....*....|....*....|....*....|
gi 1002226203 473 AERVHDSYIIPDISA----SDHSPLGLVLK 498
Cdd:COG0708   227 ADRLKDAGIDREPRGderpSDHAPVVVELD 256
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 239-497 3.20e-76

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 239.98  E-value: 3.20e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKALLkSRGFSihQLAQREDFDILCLQETKMQEKDVEVIKEGLLEgythsFWTCSVSKlGYSGTAIISRV 318
Cdd:PRK13911    1 MKLISWNVNGLRACM-TKGFM--DFFNSVDADVFCIQESKMQQEQNTFEFKGYFD-----FWNCAIKK-GYSGVVTFTKK 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 319 KPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGDGLKRLTYRVTeWDPSLGNYMKDLEKSKPVILTGDLNCAHQ 398
Cdd:PRK13911   72 EPLSVSYGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMS-WEVEFKKFLKALELKKPVIVCGDLNVAHN 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 399 EIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNV-VGYSYWGYRHNARKTNKGWRLDYFLVSESIAERVH 477
Cdd:PRK13911  151 EIDLENPKTNRKNAGFSDEERGKF-SELLNAGFIDTFRYFYPNKeKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLK 229

                         250       260
                  ....*....|....*....|
gi 1002226203 478 DSYIIPDISASDHSPLGLVL 497
Cdd:PRK13911  230 DALIYKDILGSDHCPVGLEL 249
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 242-394 1.37e-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: 86.51  E-value: 1.37e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 242 LSWNVNGLKALLKSRGFSIHQLAQ---REDFDILCLQETKMQekDVEVIKEGLLEGYTHSFWTCSVSKLGYSGTAIISRV 318
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRKLDALAAlirAYDPDVVALQETDDD--DASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRY 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002226203 319 KPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGDGLKRLTYRVTEWDPSLGNYMKDLEKSKPVILTGDLN 394
Cdd:pfam03372  79 PLSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN 154
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 87-121 5.47e-07

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 45.85  E-value: 5.47e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002226203  87 LQSMTVKELREITRMMGIPVKGNKKDLVSALMDSL 121
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERLQEYL 35
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
87-117 2.20e-04

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 38.62  E-value: 2.20e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1002226203   87 LQSMTVKELREITRMMGIPVKGNKKDLVSAL 117
Cdd:smart00513   1 LAKLKVSELKDELKKRGLSTSGTKAELVDRL 31
PLN03124 PLN03124
poly [ADP-ribose] polymerase; Provisional
 29-175 3.66e-03

poly [ADP-ribose] polymerase; Provisional


Pssm-ID: 215591 [Multi-domain]  Cd Length: 643  Bit Score: 39.82  E-value: 3.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203  29 KLALI-RLSLMMAETRATYSRRAASKNTDIKKDDEHVLEKEDVAESKLeieqlRNDPDRLQSMTVKELREITRMMGIPVK 107
Cdd:PLN03124   25 KAALVrRLDDAIAEDAKTASKSGTKSSAGRKKRRERQDDGDDEPVSPK-----RIAIDEVKGMTVRELREAASERGLATT 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002226203 108 GNKKDLVSALMDSLgkvgtssvekigVSEVPSKRKGASVVVEQNIDSSEViSETPSKRSRAKNKGTAE 175
Cdd:PLN03124  100 GRKKDLLERLCAAL------------ESDVKVGSANGTGEDEKEKGGDEE-REKEEKIVTATKKGRAV 154
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 239-497 1.25e-141

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: 406.94  E-value: 1.25e-141
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKALLKSrgfSIHQLAQREDFDILCLQETKMQEKDVEVIKEGLLEGYtHSFWTCSvSKLGYSGTAIISRV 318
Cdd:cd09087     1 LKIISWNVNGLRALLKK---GLLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGY-HQYWNAA-EKKGYSGTAILSKK 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 319 KPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGDGLKRLtYRVTEWDPSLGNYMKDLEKSKPVILTGDLNCAHQ 398
Cdd:cd09087    76 KPLSVTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERL-DRRKEWDVDFRAYLKKLDSKKPVIWCGDLNVAHE 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 399 EIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNVVG-YSYWGYRHNARKTNKGWRLDYFLVSESIAERVH 477
Cdd:cd09087   155 EIDLANPKTNKKSAGFTPEERESF-TELLEAGFVDTFRHLHPDKEGaYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVV 233

                         250       260
                  ....*....|....*....|
gi 1002226203 478 DSYIIPDISASDHSPLGLVL 497
Cdd:cd09087   234 DSFIRSDIMGSDHCPIGLEL 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 239-498 1.18e-119

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: 351.20  E-value: 1.18e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKALLKsRGFSihQLAQREDFDILCLQETKMQEkDVEVIKEGLLEGYtHSFWTCSvsKLGYSGTAIISRV 318
Cdd:TIGR00633   1 MKIISWNVNGLRARLH-KLFL--DWLKEEQPDVLCLQETKVAD-EQFPAELFEELGY-HVFFHGA--KKGYSGVAILSKV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 319 KPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSG-DGLKRLTYRVTEWDPSLGNYMKDLEKSKPVILTGDLNCAH 397
Cdd:TIGR00633  74 EPLDVRYGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 398 QEIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNVVG-YSYWGYRHNARKTNKGWRLDYFLVSESIAERV 476
Cdd:TIGR00633 154 TEIDLGNPKENKGNAGFTPEEREWF-DELLEAGFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERV 232

                         250       260
                  ....*....|....*....|..
gi 1002226203 477 HDSYIIPDISASDHSPLGLVLK 498
Cdd:TIGR00633 233 VDSYIDSEIRGSDHCPIVLELD 254
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 240-497 6.00e-104

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: 311.14  E-value: 6.00e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 240 KILSWNVNGLKALLKSRGFSIhqLAQrEDFDILCLQETKMQEKDVeVIKEGLLEGYtHSFWTCSVSKlGYSGTAIISRVK 319
Cdd:cd09073     1 KIISWNVNGLRARLKKGVLKW--LKE-EKPDILCLQETKADEDKL-PEELQHVEGY-HSYWSPARKK-GYSGVATLSKEE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 320 PLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGDGLKRLTYRVtEWDPSLGNYMKDL-EKSKPVILTGDLNCAHQ 398
Cdd:cd09073    75 PLDVSYGIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKL-RFYEAFLEFLEKLrKRGKPVVICGDFNVAHE 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 399 EIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNVVGYSYWGYRHNARKTNKGWRLDYFLVSESIAERVHD 478
Cdd:cd09073   154 EIDLARPKKNEKNAGFTPEERAWF-DKLLSLGYVDTFRHFHPEPGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKD 232

                         250
                  ....*....|....*....
gi 1002226203 479 SYIIPDISASDHSPLGLVL 497
Cdd:cd09073   233 SGILSKVKGSDHAPVTLEL 251
XthA COG0708
Exonuclease III [Replication, recombination and repair];
239-498 6.34e-96

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 290.44  E-value: 6.34e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKAllksRgfsIHQLA---QREDFDILCLQETKMQEKDVEViKEGLLEGYtHSFWtcsVSKLGYSGTAII 315
Cdd:COG0708     1 MKIASWNVNGIRA----R---LPKLLdwlAEEDPDVLCLQETKAQDEQFPL-EAFEAAGY-HVYF---HGQKGYNGVAIL 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 316 SRVKPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGD-GLKRLTYRVtEWDPSLGNYMKDLEKS-KPVILTGDL 393
Cdd:COG0708    69 SRLPPEDVRRGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSvGSEKFDYKL-RFLDALRAYLAELLAPgRPLILCGDF 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 394 NCAHQEIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNVVG-YSYWGYRHNARKTNKGWRLDYFLVSESI 472
Cdd:COG0708   148 NIAPTEIDVKNPKANLKNAGFLPEERAWF-DRLLELGLVDAFRALHPDVEGqYTWWSYRAGAFARNRGWRIDYILASPAL 226

                         250       260       270
                  ....*....|....*....|....*....|
gi 1002226203 473 AERVHDSYIIPDISA----SDHSPLGLVLK 498
Cdd:COG0708   227 ADRLKDAGIDREPRGderpSDHAPVVVELD 256
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 239-497 1.83e-89

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: 273.77  E-value: 1.83e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKALLKsRGFSihQLAQREDFDILCLQETKMQEkdvEVIKEGL--LEGYtHSFWTcSVSKLGYSGTAIIS 316
Cdd:cd09085     1 MKIISWNVNGLRAVHK-KGFL--DWFKEEKPDILCLQETKAQP---EQLPEDLrnIEGY-HSYFN-SAERKGYSGVALYS 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 317 RVKPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGDGLKRLTYRVTEWDPSLgNYMKDLEKS-KPVILTGDLNC 395
Cdd:cd09085    73 KIEPDSVREGLGVEEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFL-EYLNELRDSgKNVIICGDFNT 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 396 AHQEIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNVVGYSYWGYRHNARKTNKGWRLDYFLVSESIAER 475
Cdd:cd09085   152 AHKEIDLARPKENEKVSGFLPEERAWM-DKFIENGYVDTFRMFNKEPGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPK 230

                         250       260
                  ....*....|....*....|..
gi 1002226203 476 VHDSYIIPDISASDHSPLGLVL 497
Cdd:cd09085   231 VKDAGILPDVMGSDHCPVSLEL 252
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 239-497 6.94e-89

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: 272.72  E-value: 6.94e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKALLKsRGFSIhqlAQREDFDILCLQETKMQEKDVEvIKEGLLEGYtHSFWTCSVsklGYSGTAIISRV 318
Cdd:TIGR00195   1 MKIISWNVNGLRARPH-KGLAW---LKENQPDVLCLQETKVQDEQFP-LEPFHKEGY-HVFFSGQK---GYSGVAIFSKE 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 319 KPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPN-SGDGLKRLTYRVtEWDPSLGNYMKDLE-KSKPVILTGDLNCA 396
Cdd:TIGR00195  72 EPISVRRGFGVEEEDAEGRIIMAEFDSFLVINGYFPNgSRDDSEKLPYKL-QWLEALQNYLEKLVdKDKPVLICGDMNIA 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 397 HQEIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNVVGYSYWGYRHNARKTNKGWRLDYFLVSESIAERV 476
Cdd:TIGR00195 151 PTEIDLHIPDENRNHTGFLPEEREWL-DRLLEAGLVDTFRKFNPDEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERC 229

                         250       260
                  ....*....|....*....|....*
gi 1002226203 477 HDSYIIPDISA----SDHSPLGLVL 497
Cdd:TIGR00195 230 VDCGIDYDIRGsekpSDHCPVVLEF 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 239-497 3.20e-76

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 239.98  E-value: 3.20e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKALLkSRGFSihQLAQREDFDILCLQETKMQEKDVEVIKEGLLEgythsFWTCSVSKlGYSGTAIISRV 318
Cdd:PRK13911    1 MKLISWNVNGLRACM-TKGFM--DFFNSVDADVFCIQESKMQQEQNTFEFKGYFD-----FWNCAIKK-GYSGVVTFTKK 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 319 KPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGDGLKRLTYRVTeWDPSLGNYMKDLEKSKPVILTGDLNCAHQ 398
Cdd:PRK13911   72 EPLSVSYGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMS-WEVEFKKFLKALELKKPVIVCGDLNVAHN 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 399 EIDIHDPAGNRRSAGFTIEERESFeTNFLSKGFVDTFRKQHPNV-VGYSYWGYRHNARKTNKGWRLDYFLVSESIAERVH 477
Cdd:PRK13911  151 EIDLENPKTNRKNAGFSDEERGKF-SELLNAGFIDTFRYFYPNKeKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLK 229

                         250       260
                  ....*....|....*....|
gi 1002226203 478 DSYIIPDISASDHSPLGLVL 497
Cdd:PRK13911  230 DALIYKDILGSDHCPVGLEL 249
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 239-493 3.68e-70

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: 224.03  E-value: 3.68e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKALLKsRGFSihQLAQREDFDILCLQETKMQEKDVEvIKEGLLEGYtHSFWTCSvSKLGYSGTAIISRV 318
Cdd:cd10281     1 MRVISVNVNGIRAAAK-KGFL--EWLAAQDADVVCLQEVRAQEEQLD-DDFFEPEGY-NAYFFDA-EKKGYAGVAIYSRT 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 319 KPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGDGLKRLTYRVtEWDPSLGNYMKDLEKSKP-VILTGDLNCAH 397
Cdd:cd10281    75 QPKAVIYGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKM-AFLDAFLEHLKELRRKRReFIVCGDFNIAH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 398 QEIDIHDPAGNRRSAGFTIEERESFETNFLSKGFVDTFRKQHPNVVGYSYWGYRHNARKTNKGWRLDYFLVSESIAERVH 477
Cdd:cd10281   154 TEIDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVV 233

                         250
                  ....*....|....*.
gi 1002226203 478 DSYIIPDISASDHSPL 493
Cdd:cd10281   234 SAWIYREERFSDHAPL 249
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 239-493 9.51e-65

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: 210.06  E-value: 9.51e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKAllksRgfsIHQLAQ---REDFDILCLQETKMQEKD--VEVIKEGlleGYtHSFWTCSvsKlGYSGTA 313
Cdd:cd09086     1 MKIATWNVNSIRA----R---LEQVLDwlkEEDPDVLCLQETKVEDDQfpADAFEAL---GY-HVAVHGQ--K-AYNGVA 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 314 IISRVKPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGD-GLKRLTYRVtEWDPSLGNYMKD-LEKSKPVILTG 391
Cdd:cd09086    67 ILSRLPLEDVRTGFPGDPDDDQARLIAARVGGVRVINLYVPNGGDiGSPKFAYKL-DWLDRLIRYLQKlLKPDDPLVLVG 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 392 DLNCAHQEIDIHDPAGNRRSAGFTIEERESFEtNFLSKGFVDTFRKQHPNVVGYSYWGYRHNARKTNKGWRLDYFLVSES 471
Cdd:cd09086   146 DFNIAPEDIDVWDPKQLLGKVLFTPEEREALR-ALLDLGFVDAFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILASPA 224

                         250       260
                  ....*....|....*....|....*.
gi 1002226203 472 IAERVHDSYIIPDI----SASDHSPL 493
Cdd:cd09086   225 LADRLKDVGIDREPrgweKPSDHAPV 250
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 240-497 1.11e-42

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: 153.63  E-value: 1.11e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 240 KILSWNVNGLKALLKSRGF----SIHQLAQREDFDILCLQETKMQeKDVEVIKEGLLEGYtHSFWTCSVSKLGYSGTAI- 314
Cdd:cd09088     1 RIVTWNVNGIRTRLQYQPWnkenSLKSFLDSLDADIICLQETKLT-RDELDEPSAIVEGY-DSFFSFSRGRKGYSGVATy 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 315 --ISRVKPLSIKYGL-GV----------PDH---------------------DTEGRVVTVEFNDFYLLTAYVP-NSGDG 359
Cdd:cd09088    79 crDSAATPVAAEEGLtGVlsspnqknelSENddigcygemleftdskellelDSEGRCVLTDHGTFVLINVYCPrADPEK 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 360 LKRLTYRVTewdpslgnYMKDLEK--------SKPVILTGDLNCAHQEIDIHDPagnRRSAGFTIEERESFET-----NF 426
Cdd:cd09088   159 EERLEFKLD--------FYRLLEErveallkaGRRVILVGDVNVSHRPIDHCDP---DDSEDFGGESFEDNPSrqwldQL 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 427 LSKG----------FVDTFRKQHPNVVG-YSYWGYRHNARKTNKGWRLDYFLVSESIAERVHDSYIIPDISASDHSPLGL 495
Cdd:cd09088   228 LGDSgegggspgglLIDSFRYFHPTRKGaYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYA 307


                  ..
gi 1002226203 496 VL 497
Cdd:cd09088   308 DL 309
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 241-497 3.69e-36

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: 134.15  E-value: 3.69e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 241 ILSWNVNGLKALLKSRGfsIHQLAQREDFDILCLQETK-MQEKDVevIKEGLLEGYTHSFWTCSVSKLGYSGTAIISR-- 317
Cdd:cd08372     1 VASYNVNGLNAATRASG--IARWVRELDPDIVCLQEVKdSQYSAV--ALNQLLPEGYHQYQSGPSRKEGYEGVAILSKtp 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 318 -VKPLSIKYGLGVPDHDTEGRVVTVEF----NDFYLLTAYVPNSGdglKRLTYRVtEWDPSLGNYMKDLEK--SKPVILT 390
Cdd:cd08372    77 kFKIVEKHQYKFGEGDSGERRAVVVKFdvhdKELCVVNAHLQAGG---TRADVRD-AQLKEVLEFLKRLRQpnSAPVVIC 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 391 GDLNCAHQEIDIhdpagnrrsagftiEERESFETNFLSKGFVDTFRKQHPNvvgYSYWGYRHNarktnKGWRLDYFLVSE 470
Cdd:cd08372   153 GDFNVRPSEVDS--------------ENPSSMLRLFVALNLVDSFETLPHA---YTFDTYMHN-----VKSRLDYIFVSK 210

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1002226203 471 SIAERVHDSYIIPDISA----SDHSPLGLVL 497
Cdd:cd08372   211 SLLPSVKSSKILSDAARaripSDHYPIEVTL 241
PRK11756 PRK11756
exonuclease III; Provisional
 239-499 1.03e-28

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 114.61  E-value: 1.03e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKALLksrgfsiHQLA---QREDFDILCLQETKMQEKD--VEVIkEGLleGYtHSFWTcsvSKLGYSGTA 313
Cdd:PRK11756    1 MKFVSFNINGLRARP-------HQLEaiiEKHQPDVIGLQETKVHDEMfpLEEV-EAL--GY-HVFYH---GQKGHYGVA 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 314 IISRVKPLSIKYGLGVPDHDTEGRVVTVEFND----FYLLTAYVPNsGDGL--------KRLTYRvtewdpSLGNYM-KD 380
Cdd:PRK11756   67 LLSKQTPIAVRKGFPTDDEEAQRRIIMATIPTpngnLTVINGYFPQ-GESRdhptkfpaKRQFYQ------DLQNYLeTE 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 381 LEKSKPVILTGDLNCAHQEIDIHDPAGNRR---SAG---FTIEERESFETnFLSKGFVDTFRKQHPNVVG-YSYWGYRHN 453
Cdd:PRK11756  140 LSPDNPLLIMGDMNISPTDLDIGIGEENRKrwlRTGkcsFLPEEREWLDR-LMDWGLVDTFRQLNPDVNDrFSWFDYRSK 218

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1002226203 454 ARKTNKGWRLDYFLVSESIAERVHDSYIIPDISA----SDHSPLGLVLKL 499
Cdd:PRK11756  219 GFDDNRGLRIDLILATQPLAERCVETGIDYDIRGmekpSDHAPIWATFKL 268
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 241-493 1.32e-23

Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197310 [Multi-domain]  Cd Length: 236  Bit Score: 99.35  E-value: 1.32e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 241 ILSWNVNGLKALLKSRgfSIHQLAQREDFDILCLQETKmqEKDVEVIKEGLLEGYThsFWTCSVSKLGySGTAII--SRV 318
Cdd:cd09076     1 IGTLNVRGLRSPGKRA--QLLEELKRKKLDILGLQETH--WTGEGELKKKREGGTI--LYSGSDSGKS-RGVAILlsKTA 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 319 KPLSIKYglgvpDHDTEGRVVTVEFN----DFYLLTAYVPNSGDGLKRLTYrvteWDpSLGNYMKDLEKSKPVILTGDLN 394
Cdd:cd09076    74 ANKLLEY-----TKVVSGRIIMVRFKikgkRLTIINVYAPTARDEEEKEEF----YD-QLQDVLDKVPRHDTLIIGGDFN 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 395 CahqeidihdPAGNRRSAGFTIEERESFETNFLSK-----GFVDTFRKQHPNVVGYSYwgyRHNARKTNKgwRLDYFLVS 469
Cdd:cd09076   144 A---------VLGPKDDGRKGLDKRNENGERALSAlieehDLVDVWRENNPKTREYTW---RSPDHGSRS--RIDRILVS 209

                         250       260
                  ....*....|....*....|....
gi 1002226203 470 ESIAERVHDSYIIPDISaSDHSPL 493
Cdd:cd09076   210 KRLRVKVKKTKITPGAG-SDHRLV 232
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 242-394 1.37e-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: 86.51  E-value: 1.37e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 242 LSWNVNGLKALLKSRGFSIHQLAQ---REDFDILCLQETKMQekDVEVIKEGLLEGYTHSFWTCSVSKLGYSGTAIISRV 318
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRKLDALAAlirAYDPDVVALQETDDD--DASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRY 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002226203 319 KPLSIKYGLGVPDHDTEGRVVTVEFNDFYLLTAYVPNSGDGLKRLTYRVTEWDPSLGNYMKDLEKSKPVILTGDLN 394
Cdd:pfam03372  79 PLSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN 154
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 241-493 1.93e-12

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: 66.94  E-value: 1.93e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 241 ILSWNVNGLKALLKSRGF-SIHQLAQREDFDILCLQETKMQEKDVEVIKEGLLEGYTHSFWTCSvSKLGYSGTAIISR-- 317
Cdd:cd09084     1 VMSYNVRSFNRYKWKDDPdKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLLLKGYPYYYVVYK-SDSGGTGLAIFSKyp 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 318 -VKPLSIKYGLGVP-----DHDTEGRVVTVeFN--------DFYLLTAYvpNSGDGLKRLTYRVTEwdpSLGNYMK---- 379
Cdd:cd09084    80 iLNSGSIDFPNTNNnaifaDIRVGGDTIRV-YNvhlesfriTPSDKELY--KEEKKAKELSRNLLR---KLAEAFKrraa 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 380 -------DLEKSK-PVILTGDLNcahqeidihDPAgnrrsagftieerESFETNFLSKGFVDTFRKQHpNVVGYSYWGYR 451
Cdd:cd09084   154 qadllaaDIAASPyPVIVCGDFN---------DTP-------------ASYVYRTLKKGLTDAFVEAG-SGFGYTFNGLF 210

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1002226203 452 HnarktnkGWRLDYFLVSESIaeRVHdSYIIPDISASDHSPL 493
Cdd:cd09084   211 F-------PLRIDYILTSKGF--KVL-RYRVDPGKYSDHYPI 242
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 218-493 2.31e-09

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 58.47  E-value: 2.31e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 218 AWI-PYNPKVMRSPSlsKDTKALKILSWNVNG----LKALLksrgfsihQLAQREDFDILCLQE-TKMQEKDVEVIKegl 291
Cdd:COG3021    75 ALIlPYTLPAPKSAP--AGGPDLRVLTANVLFgnadAEALA--------ALVREEDPDVLVLQEtTPAWEEALAALE--- 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 292 lEGYTHSFwtcSVSKLGYSGTAIISRVkPLSikyGLGVPDHDTEGR---VVTVEFND----FYLLTAYVPnsgdglkrlT 364
Cdd:COG3021   142 -ADYPYRV---LCPLDNAYGMALLSRL-PLT---EAEVVYLVGDDIpsiRATVELPGgpvrLVAVHPAPP---------V 204

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 365 YRVTEWDPSLGNYMKDLEKSK-PVILTGDLNcahqeidihDPAGNRRSAGFTieeRESfetnflskGFVDTFRKQHPnvv 443
Cdd:COG3021   205 GGSAERDAELAALAKAVAALDgPVIVAGDFN---------ATPWSPTLRRLL---RAS--------GLRDARAGRGL--- 261

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1002226203 444 gYSYWgyrhNARKTNKGWRLDYFLVSESIaeRVHDSYIIPDIsASDHSPL 493
Cdd:COG3021   262 -GPTW----PANLPFLRLPIDHVLVSRGL--TVVDVRVLPVI-GSDHRPL 303
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 87-121 5.47e-07

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 45.85  E-value: 5.47e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002226203  87 LQSMTVKELREITRMMGIPVKGNKKDLVSALMDSL 121
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERLQEYL 35
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 239-490 7.54e-07

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: 49.98  E-value: 7.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKA---LLksrgfsiHQLAQREDFDILCLQETkmQEKDVEVIKegllegythsfWTCSVSKlgysGTAII 315
Cdd:cd09077     1 LRILQINLNRCKAaqdLL-------LQTAREEGADIALIQEP--YLVPVNNPN-----------WVTDESG----RAAIV 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 316 --SRVKPLSIKYGLGVPDhdtegrVVTVEFNDFYLLTAYVPNSGDglkrltyrVTEWDPSLGNYMKDLEK-SKPVILTGD 392
Cdd:cd09077    57 vsDRLPRKPIQRLSLGLG------IVAARVGGITVVSCYAPPSES--------LEEFEEYLENLVRIVRGlSRPVIIGGD 122

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 393 LNCAHQEIdiHDPAGNRRsaGFTIEEreSFET---NFLSKGFVDTFrkQHPNvvGYSYwgyrhnarktnkgwrLDYFLVS 469
Cdd:cd09077   123 FNAWSPAW--GSKRTDRR--GRLLED--WIANlglVLLNDGNSPTF--VRPR--GTSI---------------IDVTFCS 177

                         250       260
                  ....*....|....*....|.
gi 1002226203 470 ESIAERVHDSYIIPDISASDH 490
Cdd:cd09077   178 PSLARRISNWRVLEDETLSDH 198
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 233-401 1.66e-06

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 47.98  E-value: 1.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 233 SKDTKALKILSWNVngLKALLKSRGFSIHQLAQ---REDFDILCLQEtkmqekdvevikegllegythsfwtcsvsklgy 309
Cdd:COG3568     2 AAAAATLRVMTYNI--RYGLGTDGRADLERIARvirALDPDVVALQE--------------------------------- 46

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 310 sgTAIISRVKPLSIKYgLGVPDHDTEGR-----VVTVEFNDFYLLTAYVpnsgdGLKRLTYRVTEWDpSLGNYMKDLEKS 384
Cdd:COG3568    47 --NAILSRYPIVSSGT-FDLPDPGGEPRgalwaDVDVPGKPLRVVNTHL-----DLRSAAARRRQAR-ALAELLAELPAG 117

                         170
                  ....*....|....*..
gi 1002226203 385 KPVILTGDLNCahqeID 401
Cdd:COG3568   118 APVILAGDFND----ID 130
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 376-493 5.16e-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: 47.98  E-value: 5.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 376 NYMKDLEKSKPVILTGDLNCAHQEidihdpagnrrsagftieerESFETnFLSKGFVDTFR--KQHPNVVGYSYwgyrHN 453
Cdd:cd09083   152 ERIKEIAGDLPVILTGDFNAEPDS--------------------EPYKT-LTSGGLKDARDtaATTDGGPEGTF----HG 206

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1002226203 454 ARKTNKGWRLDYFLVSESIaeRVHDSYIIPD----ISASDHSPL 493
Cdd:cd09083   207 FKGPPGGSRIDYIFVSPGV--KVLSYEILTDrydgRYPSDHFPV 248
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 239-468 1.44e-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: 43.49  E-value: 1.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 239 LKILSWNVNGLKAL-LKSRGFSIHQLAQREDFDILCLQEtkMQEKDVEVI--KEGLLEGYTHSfwTCSVSKLGYS-GTAI 314
Cdd:cd09080     1 LKVLTWNVDFLDDVnLAERMRAILKLLEELDPDVIFLQE--VTPPFLAYLlsQPWVRKNYYFS--EGPPSPAVDPyGVLI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 315 ISRVKPL-------SIKYGLGVP------DHDTEGRVVTVEfndfylLTAYVPNSGdglkrltYRVTEWDpSLGNYMKDL 381
Cdd:cd09080    77 LSKKSLVvrrvpftSTRMGRNLLaaeinlGSGEPLRLATTH------LESLKSHSS-------ERTAQLE-EIAKKLKKP 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203 382 EKSKPVILTGDLNcahqeidIHDPagnrrsagftiEEresfETNFLSKGFVDTFRKQHPNV-VGYSyWGYRHN--ARKTN 458
Cdd:cd09080   143 PGAANVILGGDFN-------LRDK-----------ED----DTGGLPNGFVDAWEELGPPGePGYT-WDTQKNpmLRKGE 199

                         250
                  ....*....|..
gi 1002226203 459 KGW--RLDYFLV 468
Cdd:cd09080   200 AGPrkRFDRVLL 211
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
87-117 2.20e-04

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 38.62  E-value: 2.20e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1002226203   87 LQSMTVKELREITRMMGIPVKGNKKDLVSAL 117
Cdd:smart00513   1 LAKLKVSELKDELKKRGLSTSGTKAELVDRL 31
PLN03124 PLN03124
poly [ADP-ribose] polymerase; Provisional
 29-175 3.66e-03

poly [ADP-ribose] polymerase; Provisional


Pssm-ID: 215591 [Multi-domain]  Cd Length: 643  Bit Score: 39.82  E-value: 3.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002226203  29 KLALI-RLSLMMAETRATYSRRAASKNTDIKKDDEHVLEKEDVAESKLeieqlRNDPDRLQSMTVKELREITRMMGIPVK 107
Cdd:PLN03124   25 KAALVrRLDDAIAEDAKTASKSGTKSSAGRKKRRERQDDGDDEPVSPK-----RIAIDEVKGMTVRELREAASERGLATT 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002226203 108 GNKKDLVSALMDSLgkvgtssvekigVSEVPSKRKGASVVVEQNIDSSEViSETPSKRSRAKNKGTAE 175
Cdd:PLN03124  100 GRKKDLLERLCAAL------------ESDVKVGSANGTGEDEKEKGGDEE-REKEEKIVTATKKGRAV 154
 
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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