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Conserved domains on  [gi|42572315|ref|NP_974253|]
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DNA glycosylase superfamily protein [Arabidopsis thaliana]

Protein Classification

endonuclease III domain-containing protein( domain architecture ID 1903256)

endonuclease III domain-containing protein such as endonuclease III, a DNA repair enzyme that has both DNA N-glycosylase and AP-lyase activities

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nth super family cl43050
Endonuclease III [Replication, recombination and repair];
319-407 1.29e-04

Endonuclease III [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0177:

Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 42.78  E-value: 1.29e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572315 319 EDHWHDPWRVLVICMLLNKTSGAQTRGVISDLFGLCTDAKTATEVKEEEIENLIKPLGLQKKRTKMIQRLS--------- 389
Cdd:COG0177  14 ELDYRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALArilvekygg 93

                        90       100
                ....*....|....*....|...
gi 42572315 390 -----LEYLqeswthvTQLHGVG 407
Cdd:COG0177  94 evpetREEL-------ESLPGVG 109
 
Name Accession Description Interval E-value
Nth COG0177
Endonuclease III [Replication, recombination and repair];
319-407 1.29e-04

Endonuclease III [Replication, recombination and repair];


Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 42.78  E-value: 1.29e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572315 319 EDHWHDPWRVLVICMLLNKTSGAQTRGVISDLFGLCTDAKTATEVKEEEIENLIKPLGLQKKRTKMIQRLS--------- 389
Cdd:COG0177  14 ELDYRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALArilvekygg 93

                        90       100
                ....*....|....*....|...
gi 42572315 390 -----LEYLqeswthvTQLHGVG 407
Cdd:COG0177  94 evpetREEL-------ESLPGVG 109
ENDO3c cd00056
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
 326-418 1.12e-03

endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases


Pssm-ID: 238013 [Multi-domain]  Cd Length: 158  Bit Score: 39.53  E-value: 1.12e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572315 326 WRVLVICMLLNKTSGAQTRGVISDLFGLCT-DAKTATEVKEEEIENLIKPLGLQKKRTKMI---QRLSLEYLQESWTH-- 399
Cdd:cd00056   1 FEVLVSEILSQQTTDKAVNKAYERLFERYGpTPEALAAADEEELRELIRSLGYRRKAKYLKelaRAIVEGFGGLVLDDpd 80

                        90       100
                ....*....|....*....|...
gi 42572315 400 ----VTQLHGVGKYAADAYAIFC 418
Cdd:cd00056  81 areeLLALPGVGRKTANVVLLFA 103
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
 332-427 8.83e-03

HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.


Pssm-ID: 425841 [Multi-domain]  Cd Length: 141  Bit Score: 36.49  E-value: 8.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572315   332 CMLLNKTSGAQTRGVISDLFGLC-TDAKTATEVKEEEIENLIKPLGLQKKRTKMIQRLS----LEYLQESW----THVTQ 402
Cdd:pfam00730   3 AILSQQTSDKAVNKITERLFEKFfPTPEDLADADEEELRELIRGLGFYRRKAKYLKELArilvEGYGGEVPldeeELEAL 82

                          90       100
                  ....*....|....*....|....*
gi 42572315   403 LHGVGKYAADAYAIFCngnWDRVKP 427
Cdd:pfam00730  83 LKGVGRWTAEAVLIFA---LGRPDP 104
 
Name Accession Description Interval E-value
Nth COG0177
Endonuclease III [Replication, recombination and repair];
319-407 1.29e-04

Endonuclease III [Replication, recombination and repair];


Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 42.78  E-value: 1.29e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572315 319 EDHWHDPWRVLVICMLLNKTSGAQTRGVISDLFGLCTDAKTATEVKEEEIENLIKPLGLQKKRTKMIQRLS--------- 389
Cdd:COG0177  14 ELDYRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALArilvekygg 93

                        90       100
                ....*....|....*....|...
gi 42572315 390 -----LEYLqeswthvTQLHGVG 407
Cdd:COG0177  94 evpetREEL-------ESLPGVG 109
ENDO3c cd00056
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
 326-418 1.12e-03

endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases


Pssm-ID: 238013 [Multi-domain]  Cd Length: 158  Bit Score: 39.53  E-value: 1.12e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572315 326 WRVLVICMLLNKTSGAQTRGVISDLFGLCT-DAKTATEVKEEEIENLIKPLGLQKKRTKMI---QRLSLEYLQESWTH-- 399
Cdd:cd00056   1 FEVLVSEILSQQTTDKAVNKAYERLFERYGpTPEALAAADEEELRELIRSLGYRRKAKYLKelaRAIVEGFGGLVLDDpd 80

                        90       100
                ....*....|....*....|...
gi 42572315 400 ----VTQLHGVGKYAADAYAIFC 418
Cdd:cd00056  81 areeLLALPGVGRKTANVVLLFA 103
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
 332-427 8.83e-03

HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.


Pssm-ID: 425841 [Multi-domain]  Cd Length: 141  Bit Score: 36.49  E-value: 8.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572315   332 CMLLNKTSGAQTRGVISDLFGLC-TDAKTATEVKEEEIENLIKPLGLQKKRTKMIQRLS----LEYLQESW----THVTQ 402
Cdd:pfam00730   3 AILSQQTSDKAVNKITERLFEKFfPTPEDLADADEEELRELIRGLGFYRRKAKYLKELArilvEGYGGEVPldeeELEAL 82

                          90       100
                  ....*....|....*....|....*
gi 42572315   403 LHGVGKYAADAYAIFCngnWDRVKP 427
Cdd:pfam00730  83 LKGVGRWTAEAVLIFA---LGRPDP 104
 
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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