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Conserved domains on  [gi|1195164469|gb|OUG06285|]
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DNA repair protein RadA [Escherichia coli]

Protein Classification

DNA repair protein RadA( domain architecture ID 1003483)

DNA repair protein RadA is responsible for the stabilization or processing of branched DNA molecules

EC:  3.6.4.-
Gene Ontology:  GO:0046872|GO:0005524|GO:0016887|GO:0003684|GO:0140664|GO:0006281

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
sms super family cl36645
DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved ...
 1-101 3.44e-52

DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus (SP:P45266) and in Listeria monocytogenes (SP:Q48761) . for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)). [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR00416:

Pssm-ID: 273067 [Multi-domain]  Cd Length: 454  Bit Score: 169.21  E-value: 3.44e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195164469   1 MAKApKRAFVCNECGADYPRWQGQCSACHAWNTITEVRLAASPTVARNERLSGYAGSAGVAKVQKLSDISLEELPRFSTG 80
Cdd:TIGR00416   1 MAKA-KSKFVCQHCGADSPKWQGKCPACHAWNTITEERLHRSLGAQKNRRNSGKAGIPQAQKSQTISAIELEEVPRFSSG 79

                          90       100
                  ....*....|....*....|.
gi 1195164469  81 FKEFDRVLGGGVVPGlSLIHI 101
Cdd:TIGR00416  80 FGELDRVLGGGIVPG-SLILI 99
 
Name Accession Description Interval E-value
sms TIGR00416
DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved ...
 1-101 3.44e-52

DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus (SP:P45266) and in Listeria monocytogenes (SP:Q48761) . for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273067 [Multi-domain]  Cd Length: 454  Bit Score: 169.21  E-value: 3.44e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195164469   1 MAKApKRAFVCNECGADYPRWQGQCSACHAWNTITEVRLAASPTVARNERLSGYAGSAGVAKVQKLSDISLEELPRFSTG 80
Cdd:TIGR00416   1 MAKA-KSKFVCQHCGADSPKWQGKCPACHAWNTITEERLHRSLGAQKNRRNSGKAGIPQAQKSQTISAIELEEVPRFSSG 79

                          90       100
                  ....*....|....*....|.
gi 1195164469  81 FKEFDRVLGGGVVPGlSLIHI 101
Cdd:TIGR00416  80 FGELDRVLGGGIVPG-SLILI 99
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 1-99 2.88e-42

DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and repair];


Pssm-ID: 440685 [Multi-domain]  Cd Length: 453  Bit Score: 143.27  E-value: 2.88e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195164469   1 MAKApKRAFVCNECGADYPRWQGQCSACHAWNTITEVRLAASPTVARNerlSGYAGSAgvAKVQKLSDISLEELPRFSTG 80
Cdd:COG1066     1 MAKT-KTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGRAA---SGAAGRA--SKPVPLSEVEAEEEPRISTG 74

                          90
                  ....*....|....*....
gi 1195164469  81 FKEFDRVLGGGVVPGlSLI 99
Cdd:COG1066    75 IGELDRVLGGGLVPG-SVV 92
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 9-99 8.47e-38

bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a role in recombination and recombinational repair of DNA damaged by UV radiation, X-rays, and chemical agent and is responsible for the stabilization or processing of branched DNA molecules.


Pssm-ID: 410866 [Multi-domain]  Cd Length: 268  Bit Score: 127.26  E-value: 8.47e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195164469   9 FVCNECGADYPRWQGQCSACHAWNTITEVRLAASPTVARNErlsgyAGSAGVAKVQKLSDISLEELPRFSTGFKEFDRVL 88
Cdd:cd01121     1 YVCQECGYESPKWLGRCPSCGEWNTFVEEVVSASSSASRRA-----SASPSPSKPLPLSDVEAEEEERISTGIGELDRVL 75

                          90
                  ....*....|.
gi 1195164469  89 GGGVVPGlSLI 99
Cdd:cd01121    76 GGGLVPG-SVV 85
Rubredoxin_2 pfam18073
Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found ...
 9-36 2.61e-11

Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found in Interest in lipopolysaccharide (LPS) assembly protein B (LapB). Rubredoxin proteins form small non-heme iron binding sites that use four cysteine residues to coordinate a single metal ion in a tetrahedral environment. Rubredoxins are most commonly found in bacterial systems, but have also been found in eukaryotes. The key features of these rubredoxin-like domains are the extended loops or 'knuckles' and the tetracysteine mode of iron binding. Structural analysis of LapB from Escherichia coli show that the rubredoxin metal binding domain is intimately bound to the TPR motifs and that this association to the TPR motifs is essential to LPS regulation and growth in vivo. Other family members include RadA proteins which play a role in DNA damage repair. In E. coli, a protein known as RadA (or Sms) participates in the recombinational repair of radiation-damaged DNA in a process that uses an undamaged DNA strand in one DNA duplex to fill a DNA strand gap in a homologous sister DNA duplex. RadA carries a zinc finger at the N-terminal domain.


Pssm-ID: 436248 [Multi-domain]  Cd Length: 28  Bit Score: 53.32  E-value: 2.61e-11
                          10        20
                  ....*....|....*....|....*...
gi 1195164469   9 FVCNECGADYPRWQGQCSACHAWNTITE 36
Cdd:pfam18073   1 YRCSQCGFESPQWFGRCPSCGSWGTLVE 28
 
Name Accession Description Interval E-value
sms TIGR00416
DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved ...
 1-101 3.44e-52

DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus (SP:P45266) and in Listeria monocytogenes (SP:Q48761) . for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273067 [Multi-domain]  Cd Length: 454  Bit Score: 169.21  E-value: 3.44e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195164469   1 MAKApKRAFVCNECGADYPRWQGQCSACHAWNTITEVRLAASPTVARNERLSGYAGSAGVAKVQKLSDISLEELPRFSTG 80
Cdd:TIGR00416   1 MAKA-KSKFVCQHCGADSPKWQGKCPACHAWNTITEERLHRSLGAQKNRRNSGKAGIPQAQKSQTISAIELEEVPRFSSG 79

                          90       100
                  ....*....|....*....|.
gi 1195164469  81 FKEFDRVLGGGVVPGlSLIHI 101
Cdd:TIGR00416  80 FGELDRVLGGGIVPG-SLILI 99
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 1-99 2.88e-42

DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and repair];


Pssm-ID: 440685 [Multi-domain]  Cd Length: 453  Bit Score: 143.27  E-value: 2.88e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195164469   1 MAKApKRAFVCNECGADYPRWQGQCSACHAWNTITEVRLAASPTVARNerlSGYAGSAgvAKVQKLSDISLEELPRFSTG 80
Cdd:COG1066     1 MAKT-KTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGRAA---SGAAGRA--SKPVPLSEVEAEEEPRISTG 74

                          90
                  ....*....|....*....
gi 1195164469  81 FKEFDRVLGGGVVPGlSLI 99
Cdd:COG1066    75 IGELDRVLGGGLVPG-SVV 92
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 9-99 8.47e-38

bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a role in recombination and recombinational repair of DNA damaged by UV radiation, X-rays, and chemical agent and is responsible for the stabilization or processing of branched DNA molecules.


Pssm-ID: 410866 [Multi-domain]  Cd Length: 268  Bit Score: 127.26  E-value: 8.47e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1195164469   9 FVCNECGADYPRWQGQCSACHAWNTITEVRLAASPTVARNErlsgyAGSAGVAKVQKLSDISLEELPRFSTGFKEFDRVL 88
Cdd:cd01121     1 YVCQECGYESPKWLGRCPSCGEWNTFVEEVVSASSSASRRA-----SASPSPSKPLPLSDVEAEEEERISTGIGELDRVL 75

                          90
                  ....*....|.
gi 1195164469  89 GGGVVPGlSLI 99
Cdd:cd01121    76 GGGLVPG-SVV 85
Rubredoxin_2 pfam18073
Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found ...
 9-36 2.61e-11

Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found in Interest in lipopolysaccharide (LPS) assembly protein B (LapB). Rubredoxin proteins form small non-heme iron binding sites that use four cysteine residues to coordinate a single metal ion in a tetrahedral environment. Rubredoxins are most commonly found in bacterial systems, but have also been found in eukaryotes. The key features of these rubredoxin-like domains are the extended loops or 'knuckles' and the tetracysteine mode of iron binding. Structural analysis of LapB from Escherichia coli show that the rubredoxin metal binding domain is intimately bound to the TPR motifs and that this association to the TPR motifs is essential to LPS regulation and growth in vivo. Other family members include RadA proteins which play a role in DNA damage repair. In E. coli, a protein known as RadA (or Sms) participates in the recombinational repair of radiation-damaged DNA in a process that uses an undamaged DNA strand in one DNA duplex to fill a DNA strand gap in a homologous sister DNA duplex. RadA carries a zinc finger at the N-terminal domain.


Pssm-ID: 436248 [Multi-domain]  Cd Length: 28  Bit Score: 53.32  E-value: 2.61e-11
                          10        20
                  ....*....|....*....|....*...
gi 1195164469   9 FVCNECGADYPRWQGQCSACHAWNTITE 36
Cdd:pfam18073   1 YRCSQCGFESPQWFGRCPSCGSWGTLVE 28
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
76-101 9.81e-03

RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 33.74  E-value: 9.81e-03
                          10        20
                  ....*....|....*....|....*.
gi 1195164469  76 RFSTGFKEFDRVLGGGVVPGlSLIHI 101
Cdd:COG0467     1 RVPTGIPGLDELLGGGLPRG-SSTLL 25
 
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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