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Conserved domains on  [gi|501200052|ref|WP_012243070|]
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DNA alkylation repair protein [Acholeplasma laidlawii]

Protein Classification

DNA alkylation repair protein( domain architecture ID 10008930)

DNA alkylation repair protein similar to Bacillus cereus AlkD which is composed of helical HEAT-like repeats with excision and DNA binding activities

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
AlkD COG4912
3-methyladenine DNA glycosylase AlkD [Replication, recombination and repair];
1-214 1.88e-27

3-methyladenine DNA glycosylase AlkD [Replication, recombination and repair];


:

Pssm-ID: 443940 [Multi-domain]  Cd Length: 216  Bit Score: 103.82  E-value: 1.88e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052   1 MTLEQVMNDLKLNSNASRKKSLLKAGAS-ENTYGVLLGYLRAYAKKIGTH--HDLAFKLMHTLNTDAMLLAVMLFDVSKL 77
Cdd:COG4912    2 STLEEIRAELEALADPERAAFMARYGKEgDPFLGVRVPDLRKLAKRIKKEldHELAEELWASGYHEARLLALLILDPKKK 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052  78 SAKEAYDVLG--IITFD--QVLDDFMFRVVTLIEEVDVLYDMLK---DSDSDMLKRALWAINVERVRLKiiDDNEVLYLL 150
Cdd:COG4912   82 RDEETLELLEawVPTIDnwDLVDSLAPKVVGKLLLDPEALELLLewaKSDNEWVRRAAIVLLLAFARKG--DDTDFELLL 159
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501200052 151 DNIQRNLVDETPKAQWMMNRCFAQIGITYEAYRTKVLnlseelgvYKDMKVAPGCTSAYVPNWI 214
Cdd:COG4912  160 EIIERLLHDEEDFVQKAIGWALREIGKRDPELVEAFL--------EKHDARLPRLTLRYAIEKL 215
 
Name Accession Description Interval E-value
AlkD COG4912
3-methyladenine DNA glycosylase AlkD [Replication, recombination and repair];
1-214 1.88e-27

3-methyladenine DNA glycosylase AlkD [Replication, recombination and repair];


Pssm-ID: 443940 [Multi-domain]  Cd Length: 216  Bit Score: 103.82  E-value: 1.88e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052   1 MTLEQVMNDLKLNSNASRKKSLLKAGAS-ENTYGVLLGYLRAYAKKIGTH--HDLAFKLMHTLNTDAMLLAVMLFDVSKL 77
Cdd:COG4912    2 STLEEIRAELEALADPERAAFMARYGKEgDPFLGVRVPDLRKLAKRIKKEldHELAEELWASGYHEARLLALLILDPKKK 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052  78 SAKEAYDVLG--IITFD--QVLDDFMFRVVTLIEEVDVLYDMLK---DSDSDMLKRALWAINVERVRLKiiDDNEVLYLL 150
Cdd:COG4912   82 RDEETLELLEawVPTIDnwDLVDSLAPKVVGKLLLDPEALELLLewaKSDNEWVRRAAIVLLLAFARKG--DDTDFELLL 159
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501200052 151 DNIQRNLVDETPKAQWMMNRCFAQIGITYEAYRTKVLnlseelgvYKDMKVAPGCTSAYVPNWI 214
Cdd:COG4912  160 EIIERLLHDEEDFVQKAIGWALREIGKRDPELVEAFL--------EKHDARLPRLTLRYAIEKL 215
AlkD_like cd06561
A new structural DNA glycosylase; This domain represents a new and uncharacterized structural ...
19-209 5.71e-08

A new structural DNA glycosylase; This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity.


Pssm-ID: 132880 [Multi-domain]  Cd Length: 197  Bit Score: 51.16  E-value: 5.71e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052  19 KKSLLKAGASENTYGVLLGYLRAYAKKIGTH------HDLAFKLMHTLNTDAMLLAVMLFDVSKLSAKEAYDVLGIITFD 92
Cdd:cd06561    4 KKFMKNLGPGDPFLGVRTPDLRKIAKEFKKEdkleedHELAEALWHEEIREAQYLALDLLDKKELKEEDLERFEPWIEYI 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052  93 Q---VLDDFMFRVV-TLIEEVDVLYDMLK--DSDSDMLKRALWAINVERvrlkIIDDNEVLYLLDNIQRNLVDETPKAQW 166
Cdd:cd06561   84 DnwdLVDSLCANLLgKLLYAEPELDLLEEwaKSENEWVRRAAIVLLLRL----IKKETDFDLLLEIIERLLHDEEYFVQK 159
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 501200052 167 MMNRCFAQIGITYEAyrtKVLNLSEELGvykdmKVAPGCTSAY 209
Cdd:cd06561  160 AVGWALREYGKKDPE---RVIAFLEKNG-----LSMPRLTLRY 194
DNA_alkylation pfam08713
DNA alkylation repair enzyme; Proteins in this family are predicted to be DNA alkylation ...
6-181 3.96e-03

DNA alkylation repair enzyme; Proteins in this family are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein in this family shows it to adopt a supercoiled alpha helical structure.


Pssm-ID: 378033  Cd Length: 212  Bit Score: 37.22  E-value: 3.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052    6 VMNDLKLNSNASRKKSLLKAGASE-NTYGVLLGYLRAYAKKIGTHH------DLAFKLMHTLNTDAMLLAVMLFD-VSKL 77
Cdd:pfam08713   1 IQAELEALADPEKAAEMQRYFKEGfPFLGVRTPERRKIAKDFFKELkledrlELAEELWQSPYREERYLALDLLTqARKK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052   78 SAKEAYDVLG--IITFD--QVLDDFMFRVVTLI-----EEVDVLYDMLKdSDSDMLKRALWAINVERVRLKIIDDnevly 148
Cdd:pfam08713  81 LTEADLDLYEswVETINnwDTVDGLAPHIVGRYladrpERLDLLEEWAK-SENLWLRRAAIVSTLPFKKKTDFEL----- 154
                         170       180       190
                  ....*....|....*....|....*....|...
gi 501200052  149 LLDNIQRNLVDETPKAQWMMNRCFAQIGITYEA 181
Cdd:pfam08713 155 LLEIAELLLGDKEFFIQKAIGWALREYSKTDPD 187
 
Name Accession Description Interval E-value
AlkD COG4912
3-methyladenine DNA glycosylase AlkD [Replication, recombination and repair];
1-214 1.88e-27

3-methyladenine DNA glycosylase AlkD [Replication, recombination and repair];


Pssm-ID: 443940 [Multi-domain]  Cd Length: 216  Bit Score: 103.82  E-value: 1.88e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052   1 MTLEQVMNDLKLNSNASRKKSLLKAGAS-ENTYGVLLGYLRAYAKKIGTH--HDLAFKLMHTLNTDAMLLAVMLFDVSKL 77
Cdd:COG4912    2 STLEEIRAELEALADPERAAFMARYGKEgDPFLGVRVPDLRKLAKRIKKEldHELAEELWASGYHEARLLALLILDPKKK 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052  78 SAKEAYDVLG--IITFD--QVLDDFMFRVVTLIEEVDVLYDMLK---DSDSDMLKRALWAINVERVRLKiiDDNEVLYLL 150
Cdd:COG4912   82 RDEETLELLEawVPTIDnwDLVDSLAPKVVGKLLLDPEALELLLewaKSDNEWVRRAAIVLLLAFARKG--DDTDFELLL 159
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501200052 151 DNIQRNLVDETPKAQWMMNRCFAQIGITYEAYRTKVLnlseelgvYKDMKVAPGCTSAYVPNWI 214
Cdd:COG4912  160 EIIERLLHDEEDFVQKAIGWALREIGKRDPELVEAFL--------EKHDARLPRLTLRYAIEKL 215
AlkD_like cd06561
A new structural DNA glycosylase; This domain represents a new and uncharacterized structural ...
19-209 5.71e-08

A new structural DNA glycosylase; This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity.


Pssm-ID: 132880 [Multi-domain]  Cd Length: 197  Bit Score: 51.16  E-value: 5.71e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052  19 KKSLLKAGASENTYGVLLGYLRAYAKKIGTH------HDLAFKLMHTLNTDAMLLAVMLFDVSKLSAKEAYDVLGIITFD 92
Cdd:cd06561    4 KKFMKNLGPGDPFLGVRTPDLRKIAKEFKKEdkleedHELAEALWHEEIREAQYLALDLLDKKELKEEDLERFEPWIEYI 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052  93 Q---VLDDFMFRVV-TLIEEVDVLYDMLK--DSDSDMLKRALWAINVERvrlkIIDDNEVLYLLDNIQRNLVDETPKAQW 166
Cdd:cd06561   84 DnwdLVDSLCANLLgKLLYAEPELDLLEEwaKSENEWVRRAAIVLLLRL----IKKETDFDLLLEIIERLLHDEEYFVQK 159
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 501200052 167 MMNRCFAQIGITYEAyrtKVLNLSEELGvykdmKVAPGCTSAY 209
Cdd:cd06561  160 AVGWALREYGKKDPE---RVIAFLEKNG-----LSMPRLTLRY 194
DNA_alkylation pfam08713
DNA alkylation repair enzyme; Proteins in this family are predicted to be DNA alkylation ...
6-181 3.96e-03

DNA alkylation repair enzyme; Proteins in this family are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein in this family shows it to adopt a supercoiled alpha helical structure.


Pssm-ID: 378033  Cd Length: 212  Bit Score: 37.22  E-value: 3.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052    6 VMNDLKLNSNASRKKSLLKAGASE-NTYGVLLGYLRAYAKKIGTHH------DLAFKLMHTLNTDAMLLAVMLFD-VSKL 77
Cdd:pfam08713   1 IQAELEALADPEKAAEMQRYFKEGfPFLGVRTPERRKIAKDFFKELkledrlELAEELWQSPYREERYLALDLLTqARKK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501200052   78 SAKEAYDVLG--IITFD--QVLDDFMFRVVTLI-----EEVDVLYDMLKdSDSDMLKRALWAINVERVRLKIIDDnevly 148
Cdd:pfam08713  81 LTEADLDLYEswVETINnwDTVDGLAPHIVGRYladrpERLDLLEEWAK-SENLWLRRAAIVSTLPFKKKTDFEL----- 154
                         170       180       190
                  ....*....|....*....|....*....|...
gi 501200052  149 LLDNIQRNLVDETPKAQWMMNRCFAQIGITYEA 181
Cdd:pfam08713 155 LLEIAELLLGDKEFFIQKAIGWALREYSKTDPD 187
 
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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