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Conserved domains on  [gi|1836840727|ref|WP_169198973|]
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RnfH family protein [Aromatoleum buckelii]

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 1.31e-45

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: 141.03  E-value: 1.31e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836840727  1 MKIGIAYAIPVRQVWLTLDLPEGITVGEAILSSGITGQFPEIDLARQKVGIFGKLVALDRVLEDGDRVEIYRPVTRDPKT 80
Cdd:pfam03658  1 IKVEVAYALPDRQVLLKLEVPEGATVEQAIEASGILERFPEIDLATNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 80


                 ...
gi 1836840727 81 VRK 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 1.31e-45

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: 141.03  E-value: 1.31e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836840727  1 MKIGIAYAIPVRQVWLTLDLPEGITVGEAILSSGITGQFPEIDLARQKVGIFGKLVALDRVLEDGDRVEIYRPVTRDPKT 80
Cdd:pfam03658  1 IKVEVAYALPDRQVLLKLEVPEGATVEQAIEASGILERFPEIDLATNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 80


                 ...
gi 1836840727 81 VRK 83
Cdd:pfam03658 81 ARR 83
PasI COG2914
Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH ...
 1-84 1.74e-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: 141.02  E-value: 1.74e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836840727  1 MKIGIAYAIPVRQVWLTLDLPEGITVGEAILSSGITGQFPEIDLARQKVGIFGKLVALDRVLEDGDRVEIYRPVTRDPKT 80
Cdd:COG2914    5 IRVEVAYALPDKQVLLRLEVPEGTTVEQAIEASGILERFPEIDLAKNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 84


                 ....
gi 1836840727 81 VRKR 84
Cdd:COG2914   85 ARRR 88
PRK01777 PRK01777
RnfH family protein;
1-88 3.39e-33

RnfH family protein;


Pssm-ID: 234982  Cd Length: 95  Bit Score: 110.07  E-value: 3.39e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836840727  1 MKIGIAYAIPVRQVWLTLDLPEGITVGEAILSSGITGQFPEIDLARQKVGIFGKLVALDRVLEDGDRVEIYRPVTRDPKT 80
Cdd:PRK01777   4 IRVEVVYALPERQYLQRLTLQEGATVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEIYRPLLADPKE 83


                 ....*....
gi 1836840727 81 V-RKRAKPA 88
Cdd:PRK01777  84 LrRKRAEQA 92
 
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 1.31e-45

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: 141.03  E-value: 1.31e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836840727  1 MKIGIAYAIPVRQVWLTLDLPEGITVGEAILSSGITGQFPEIDLARQKVGIFGKLVALDRVLEDGDRVEIYRPVTRDPKT 80
Cdd:pfam03658  1 IKVEVAYALPDRQVLLKLEVPEGATVEQAIEASGILERFPEIDLATNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 80


                 ...
gi 1836840727 81 VRK 83
Cdd:pfam03658 81 ARR 83
PasI COG2914
Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH ...
 1-84 1.74e-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: 141.02  E-value: 1.74e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836840727  1 MKIGIAYAIPVRQVWLTLDLPEGITVGEAILSSGITGQFPEIDLARQKVGIFGKLVALDRVLEDGDRVEIYRPVTRDPKT 80
Cdd:COG2914    5 IRVEVAYALPDKQVLLRLEVPEGTTVEQAIEASGILERFPEIDLAKNKVGIFGKLVKLDTVLRDGDRVEIYRPLIADPKE 84


                 ....
gi 1836840727 81 VRKR 84
Cdd:COG2914   85 ARRR 88
PRK01777 PRK01777
RnfH family protein;
1-88 3.39e-33

RnfH family protein;


Pssm-ID: 234982  Cd Length: 95  Bit Score: 110.07  E-value: 3.39e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836840727  1 MKIGIAYAIPVRQVWLTLDLPEGITVGEAILSSGITGQFPEIDLARQKVGIFGKLVALDRVLEDGDRVEIYRPVTRDPKT 80
Cdd:PRK01777   4 IRVEVVYALPERQYLQRLTLQEGATVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEIYRPLLADPKE 83


                 ....*....
gi 1836840727 81 V-RKRAKPA 88
Cdd:PRK01777  84 LrRKRAEQA 92
MoaD COG1977
Molybdopterin synthase sulfur carrier subunit MoaD [Coenzyme transport and metabolism]; ...
 16-75 2.06e-06

Molybdopterin synthase sulfur carrier subunit MoaD [Coenzyme transport and metabolism]; Molybdopterin synthase sulfur carrier subunit MoaD is part of the Pathway/BioSystem: Molybdopterin biosynthesis


Pssm-ID: 441580 [Multi-domain]  Cd Length: 82  Bit Score: 41.73  E-value: 2.06e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1836840727 16 LTLDLPEGITVGEAILSsgITGQFPEID--LARQKVGIF--GKLVALDRVLEDGDRVEIYRPVT 75
Cdd:COG1977   19 EEVELPEGATVGDLLEA--LAARYPGLAerLLRRRVRVAvnGEDVRLDTPLKDGDEVALFPPVA 80
TGS pfam02824
TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain ...
 18-70 1.41e-03

TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organizm, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.


Pssm-ID: 427005 [Multi-domain]  Cd Length: 60  Bit Score: 33.67  E-value: 1.41e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1836840727 18 LDLPEGITVGEA--ILSSgitgqfpeiDLARQKVG--IFGKLVALDRVLEDGDRVEI 70
Cdd:pfam02824 11 PDLPRGATPEDFayAIHT---------SLAKKFIYakVNGQLVGLDHPLEDGDVVEI 58
 
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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