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Conserved domains on  [gi|133738485|emb|CAL61530|]
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conserved hypothetical protein [Herminiimonas arsenicoxydans]

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 ...
 8-98 1.89e-46

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


:

Pssm-ID: 442158  Cd Length: 92  Bit Score: 144.11  E-value: 1.89e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133738485   8 APAAIHIQICYAREDKQFLLDQTVPPGTTIQQAIQGSGIIQLAPEIDVSVWRVGIYSKLKTLDTVLREHDRVEIYRPLIA 87
Cdd:COG2914    1 MMEMIRVEVAYALPDKQVLLRLEVPEGTTVEQAIEASGILERFPEIDLAKNKVGIFGKLVKLDTVLRDGDRVEIYRPLIA 80

                         90
                 ....*....|.
gi 133738485  88 DPKDSRRKRAE 98
Cdd:COG2914   81 DPKEARRRRAA 91
 
Name Accession Description Interval E-value
PasI COG2914
Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH ...
 8-98 1.89e-46

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


Pssm-ID: 442158  Cd Length: 92  Bit Score: 144.11  E-value: 1.89e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133738485   8 APAAIHIQICYAREDKQFLLDQTVPPGTTIQQAIQGSGIIQLAPEIDVSVWRVGIYSKLKTLDTVLREHDRVEIYRPLIA 87
Cdd:COG2914    1 MMEMIRVEVAYALPDKQVLLRLEVPEGTTVEQAIEASGILERFPEIDLAKNKVGIFGKLVKLDTVLRDGDRVEIYRPLIA 80

                         90
                 ....*....|.
gi 133738485  88 DPKDSRRKRAE 98
Cdd:COG2914   81 DPKEARRRRAA 91
Ub-RnfH pfam03658
RnfH family Ubiquitin; A member of the RnfH family of the ubiquitin superfamily. Members of ...
 12-94 7.32e-42

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: 132.17  E-value: 7.32e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133738485   12 IHIQICYAREDKQFLLDQTVPPGTTIQQAIQGSGIIQLAPEIDVSVWRVGIYSKLKTLDTVLREHDRVEIYRPLIADPKD 91
Cdd:pfam03658   1 IKVEVAYALPDRQVLLKLEVPEGATVEQAIEASGILERFPEIDLATNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 80


                  ...
gi 133738485   92 SRR 94
Cdd:pfam03658  81 ARR 83
PRK01777 PRK01777
RnfH family protein;
9-98 3.69e-32

RnfH family protein;


Pssm-ID: 234982  Cd Length: 95  Bit Score: 108.14  E-value: 3.69e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133738485   9 PAAIHIQICYAREDKQFLLDQTVPPGTTIQQAIQGSGIIQLAPEIDVSVWRVGIYSKLKTLDTVLREHDRVEIYRPLIAD 88
Cdd:PRK01777   1 MGKIRVEVVYALPERQYLQRLTLQEGATVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEIYRPLLAD 80

                         90
                 ....*....|
gi 133738485  89 PKDSRRKRAE 98
Cdd:PRK01777  81 PKELRRKRAE 90
 
Name Accession Description Interval E-value
PasI COG2914
Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH ...
 8-98 1.89e-46

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


Pssm-ID: 442158  Cd Length: 92  Bit Score: 144.11  E-value: 1.89e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133738485   8 APAAIHIQICYAREDKQFLLDQTVPPGTTIQQAIQGSGIIQLAPEIDVSVWRVGIYSKLKTLDTVLREHDRVEIYRPLIA 87
Cdd:COG2914    1 MMEMIRVEVAYALPDKQVLLRLEVPEGTTVEQAIEASGILERFPEIDLAKNKVGIFGKLVKLDTVLRDGDRVEIYRPLIA 80

                         90
                 ....*....|.
gi 133738485  88 DPKDSRRKRAE 98
Cdd:COG2914   81 DPKEARRRRAA 91
Ub-RnfH pfam03658
RnfH family Ubiquitin; A member of the RnfH family of the ubiquitin superfamily. Members of ...
 12-94 7.32e-42

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: 132.17  E-value: 7.32e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133738485   12 IHIQICYAREDKQFLLDQTVPPGTTIQQAIQGSGIIQLAPEIDVSVWRVGIYSKLKTLDTVLREHDRVEIYRPLIADPKD 91
Cdd:pfam03658   1 IKVEVAYALPDRQVLLKLEVPEGATVEQAIEASGILERFPEIDLATNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 80


                  ...
gi 133738485   92 SRR 94
Cdd:pfam03658  81 ARR 83
PRK01777 PRK01777
RnfH family protein;
9-98 3.69e-32

RnfH family protein;


Pssm-ID: 234982  Cd Length: 95  Bit Score: 108.14  E-value: 3.69e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133738485   9 PAAIHIQICYAREDKQFLLDQTVPPGTTIQQAIQGSGIIQLAPEIDVSVWRVGIYSKLKTLDTVLREHDRVEIYRPLIAD 88
Cdd:PRK01777   1 MGKIRVEVVYALPERQYLQRLTLQEGATVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEIYRPLLAD 80

                         90
                 ....*....|
gi 133738485  89 PKDSRRKRAE 98
Cdd:PRK01777  81 PKELRRKRAE 90
 
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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