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Conserved domains on  [gi|658755479|ref|WP_029773434|]
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MULTISPECIES: RnfH family protein [Pseudoalteromonas]

Protein Classification

RnfH family protein( domain architecture ID 10006787)

RnfH family protein, a member of the ubiquitin superfamily, is involved in transporting electrons for various reductive reactions such as nitrogen fixation and may also play a role in the SmpB-tmRNA-based tagging and degradation system of bacteria

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PasI COG2914
Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH ...
 1-89 5.43e-45

Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH superfamily [Defense mechanisms];


:

Pssm-ID: 442158  Cd Length: 92  Bit Score: 140.25  E-value: 5.43e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658755479   1 MISVEIVFALPTKATTLTVEVAQGTTAEQAVIQSGIIEKCPEIDPTALTLGVWNRTVKAHYELKDGDRIEIYRPLIADPK 80
Cdd:COG2914    4 MIRVEVAYALPDKQVLLRLEVPEGTTVEQAIEASGILERFPEIDLAKNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPK 83


                 ....*....
gi 658755479  81 DARRKRAEK 89
Cdd:COG2914   84 EARRRRAAK 92
 
Name Accession Description Interval E-value
PasI COG2914
Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH ...
 1-89 5.43e-45

Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH superfamily [Defense mechanisms];


Pssm-ID: 442158  Cd Length: 92  Bit Score: 140.25  E-value: 5.43e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658755479   1 MISVEIVFALPTKATTLTVEVAQGTTAEQAVIQSGIIEKCPEIDPTALTLGVWNRTVKAHYELKDGDRIEIYRPLIADPK 80
Cdd:COG2914    4 MIRVEVAYALPDKQVLLRLEVPEGTTVEQAIEASGILERFPEIDLAKNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPK 83


                 ....*....
gi 658755479  81 DARRKRAEK 89
Cdd:COG2914   84 EARRRRAAK 92
Ub-RnfH pfam03658
RnfH family Ubiquitin; A member of the RnfH family of the ubiquitin superfamily. Members of ...
 2-84 3.85e-40

RnfH family Ubiquitin; A member of the RnfH family of the ubiquitin superfamily. Members of this family strongly co-occur in two distinct gene neighborhood contexts. In one it is associated with a START domain protein, a membrane protein SmpA and the transfer mRNA binding protein SmpB. This association suggests a possible role in the SmpB-tmRNA-based tagging and degadation system of bacteria, which is interesting given that other members of the ubiquitin system are analogously involved in protein-tagging and degradation across eukaryotes and various prokaryotes. The second context in which the RnfH genes are present is in a membrane associated complex involved in transporting electrons for various reductive reactions such as nitrogen fixation.


Pssm-ID: 427429  Cd Length: 83  Bit Score: 127.93  E-value: 3.85e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658755479    2 ISVEIVFALPTKATTLTVEVAQGTTAEQAVIQSGIIEKCPEIDPTALTLGVWNRTVKAHYELKDGDRIEIYRPLIADPKD 81
Cdd:pfam03658   1 IKVEVAYALPDRQVLLKLEVPEGATVEQAIEASGILERFPEIDLATNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 80


                  ...
gi 658755479   82 ARR 84
Cdd:pfam03658  81 ARR 83
PRK01777 PRK01777
RnfH family protein;
1-93 7.62e-35

RnfH family protein;


Pssm-ID: 234982  Cd Length: 95  Bit Score: 114.69  E-value: 7.62e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658755479   1 MISVEIVFALPTKATTLTVEVAQGTTAEQAVIQSGIIEKCPEIDPTALTLGVWNRTVKAHYELKDGDRIEIYRPLIADPK 80
Cdd:PRK01777   3 KIRVEVVYALPERQYLQRLTLQEGATVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEIYRPLLADPK 82

                         90
                 ....*....|...
gi 658755479  81 DARRKRAEKAKEE 93
Cdd:PRK01777  83 ELRRKRAEQAKKK 95
 
Name Accession Description Interval E-value
PasI COG2914
Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH ...
 1-89 5.43e-45

Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH superfamily [Defense mechanisms];


Pssm-ID: 442158  Cd Length: 92  Bit Score: 140.25  E-value: 5.43e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658755479   1 MISVEIVFALPTKATTLTVEVAQGTTAEQAVIQSGIIEKCPEIDPTALTLGVWNRTVKAHYELKDGDRIEIYRPLIADPK 80
Cdd:COG2914    4 MIRVEVAYALPDKQVLLRLEVPEGTTVEQAIEASGILERFPEIDLAKNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPK 83


                 ....*....
gi 658755479  81 DARRKRAEK 89
Cdd:COG2914   84 EARRRRAAK 92
Ub-RnfH pfam03658
RnfH family Ubiquitin; A member of the RnfH family of the ubiquitin superfamily. Members of ...
 2-84 3.85e-40

RnfH family Ubiquitin; A member of the RnfH family of the ubiquitin superfamily. Members of this family strongly co-occur in two distinct gene neighborhood contexts. In one it is associated with a START domain protein, a membrane protein SmpA and the transfer mRNA binding protein SmpB. This association suggests a possible role in the SmpB-tmRNA-based tagging and degadation system of bacteria, which is interesting given that other members of the ubiquitin system are analogously involved in protein-tagging and degradation across eukaryotes and various prokaryotes. The second context in which the RnfH genes are present is in a membrane associated complex involved in transporting electrons for various reductive reactions such as nitrogen fixation.


Pssm-ID: 427429  Cd Length: 83  Bit Score: 127.93  E-value: 3.85e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658755479    2 ISVEIVFALPTKATTLTVEVAQGTTAEQAVIQSGIIEKCPEIDPTALTLGVWNRTVKAHYELKDGDRIEIYRPLIADPKD 81
Cdd:pfam03658   1 IKVEVAYALPDRQVLLKLEVPEGATVEQAIEASGILERFPEIDLATNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 80


                  ...
gi 658755479   82 ARR 84
Cdd:pfam03658  81 ARR 83
PRK01777 PRK01777
RnfH family protein;
1-93 7.62e-35

RnfH family protein;


Pssm-ID: 234982  Cd Length: 95  Bit Score: 114.69  E-value: 7.62e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658755479   1 MISVEIVFALPTKATTLTVEVAQGTTAEQAVIQSGIIEKCPEIDPTALTLGVWNRTVKAHYELKDGDRIEIYRPLIADPK 80
Cdd:PRK01777   3 KIRVEVVYALPERQYLQRLTLQEGATVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEIYRPLLADPK 82

                         90
                 ....*....|...
gi 658755479  81 DARRKRAEKAKEE 93
Cdd:PRK01777  83 ELRRKRAEQAKKK 95
 
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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