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Conserved domains on  [gi|1798023961|emb|CAA6604063|]
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Protein RnfH [Rhodospirillaceae bacterium LM-1]

Protein Classification

RnfH family protein( domain architecture ID 10508429)

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
Ub-RnfH pfam03658
RnfH family Ubiquitin; A member of the RnfH family of the ubiquitin superfamily. Members of ...
 1-83 2.50e-47

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: 145.65  E-value: 2.50e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798023961  1 MKVGVAYATPAKQVWLTVDMPEGACVKDAIEKSGILKQFPEIDLNTQKVGIYGKASTLEAVLEEGARVEIYRPMTADPKT 80
Cdd:pfam03658  1 IKVEVAYALPDRQVLLKLEVPEGATVEQAIEASGILERFPEIDLATNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 80


                 ...
gi 1798023961 81 VPR 83
Cdd:pfam03658 81 ARR 83
 
Name Accession Description Interval E-value
Ub-RnfH pfam03658
RnfH family Ubiquitin; A member of the RnfH family of the ubiquitin superfamily. Members of ...
 1-83 2.50e-47

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: 145.65  E-value: 2.50e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798023961  1 MKVGVAYATPAKQVWLTVDMPEGACVKDAIEKSGILKQFPEIDLNTQKVGIYGKASTLEAVLEEGARVEIYRPMTADPKT 80
Cdd:pfam03658  1 IKVEVAYALPDRQVLLKLEVPEGATVEQAIEASGILERFPEIDLATNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 80


                 ...
gi 1798023961 81 VPR 83
Cdd:pfam03658 81 ARR 83
PasI COG2914
Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH ...
 1-84 4.92e-47

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


Pssm-ID: 442158  Cd Length: 92  Bit Score: 144.88  E-value: 4.92e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798023961  1 MKVGVAYATPAKQVWLTVDMPEGACVKDAIEKSGILKQFPEIDLNTQKVGIYGKASTLEAVLEEGARVEIYRPMTADPKT 80
Cdd:COG2914    5 IRVEVAYALPDKQVLLRLEVPEGTTVEQAIEASGILERFPEIDLAKNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 84


                 ....
gi 1798023961 81 VPRR 84
Cdd:COG2914   85 ARRR 88
PRK01777 PRK01777
RnfH family protein;
1-92 1.79e-29

RnfH family protein;


Pssm-ID: 234982  Cd Length: 95  Bit Score: 100.82  E-value: 1.79e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798023961  1 MKVGVAYATPAKQVWLTVDMPEGACVKDAIEKSGILKQFPEIDLNTQKVGIYGKASTLEAVLEEGARVEIYRPMTADPKT 80
Cdd:PRK01777   4 IRVEVVYALPERQYLQRLTLQEGATVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEIYRPLLADPKE 83

                         90
                 ....*....|..
gi 1798023961 81 VPRRAKAGGEAA 92
Cdd:PRK01777  84 LRRKRAEQAKKK 95
 
Name Accession Description Interval E-value
Ub-RnfH pfam03658
RnfH family Ubiquitin; A member of the RnfH family of the ubiquitin superfamily. Members of ...
 1-83 2.50e-47

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: 145.65  E-value: 2.50e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798023961  1 MKVGVAYATPAKQVWLTVDMPEGACVKDAIEKSGILKQFPEIDLNTQKVGIYGKASTLEAVLEEGARVEIYRPMTADPKT 80
Cdd:pfam03658  1 IKVEVAYALPDRQVLLKLEVPEGATVEQAIEASGILERFPEIDLATNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 80


                 ...
gi 1798023961 81 VPR 83
Cdd:pfam03658 81 ARR 83
PasI COG2914
Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH ...
 1-84 4.92e-47

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


Pssm-ID: 442158  Cd Length: 92  Bit Score: 144.88  E-value: 4.92e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798023961  1 MKVGVAYATPAKQVWLTVDMPEGACVKDAIEKSGILKQFPEIDLNTQKVGIYGKASTLEAVLEEGARVEIYRPMTADPKT 80
Cdd:COG2914    5 IRVEVAYALPDKQVLLRLEVPEGTTVEQAIEASGILERFPEIDLAKNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 84


                 ....
gi 1798023961 81 VPRR 84
Cdd:COG2914   85 ARRR 88
PRK01777 PRK01777
RnfH family protein;
1-92 1.79e-29

RnfH family protein;


Pssm-ID: 234982  Cd Length: 95  Bit Score: 100.82  E-value: 1.79e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798023961  1 MKVGVAYATPAKQVWLTVDMPEGACVKDAIEKSGILKQFPEIDLNTQKVGIYGKASTLEAVLEEGARVEIYRPMTADPKT 80
Cdd:PRK01777   4 IRVEVVYALPERQYLQRLTLQEGATVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEIYRPLLADPKE 83

                         90
                 ....*....|..
gi 1798023961 81 VPRRAKAGGEAA 92
Cdd:PRK01777  84 LRRKRAEQAKKK 95
Ub-Mut7C pfam14451
Mut7-C ubiquitin; This member of the ubiquitin superfamily is found at the N-terminus of ...
 10-74 3.32e-03

Mut7-C ubiquitin; This member of the ubiquitin superfamily is found at the N-terminus of Mut7-C like RNAses, suggestive of an RNA-binding role.


Pssm-ID: 433962  Cd Length: 81  Bit Score: 33.47  E-value: 3.32e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1798023961 10 PAKQVWLTVDMPEGACVKDAIEKSGIlkQFPEIDLntqkVGIYGKASTLEAVLEEGARVEIYrPM 74
Cdd:pfam14451 19 ARRQRTAARAFDGGATVKHMIEALGV--PHTEVGL----ILVNGESVPFSHIPADGDRVAVY-PV 76
 
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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