arfB Family assigned · low
H37Rv Rv0900 · MTBC0 mtbc0_000954 ·
50 aa · 1007019–1007171 (+) ·
RefSeq NP_215415.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Small membrane protein that post-transcriptionally regulates expression of the major outer-membrane porin OmpATb. RefSeq leaves it 'membrane protein'. Rv0900 lies in an operon with ompATb (Rv0899) and Rv0901; mutations in Rv0900/Rv0901 strongly alter OmpATb expression, demonstrating a regulatory role (Veyron-Churlet 2011). |
Curated reference (UniProt)
| UniProt |
P9WJG7
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Uncharacterized membrane protein ArfB |
| Curated function | Required for wild-type expression of ArfA and ammonia secretion, not however part of an ammonia transporter. |
UniProt still lists this protein as Uncharacterized membrane protein ArfB; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Preferred name | arfB |
|---|---|
| Orthologous group | 2AYBF |
| KEGG orthology |
K16192
|
| Gene Ontology (9) |
GO:0008150, GO:0040007, GO:0044110, GO:0044116, GO:0044117, GO:0044119, GO:0044403, GO:0044419, GO:0051704
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arfC (membrane protein), high confidence from genomic context alone (score 885 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0901 arfC |
membrane protein | 984 | 885 ctx | neighborhood:882 textmining:870 |
Rv0899 arfA |
peptidoglycan-binding protein ArfA | 969 | 777 ctx | neighborhood:777 textmining:870 |
Rv0898c hyp |
hypothetical protein | 570 | 570 ctx | neighborhood:570 |
Rv0897c |
oxidoreductase | 488 | 488 ctx | neighborhood:485 |
Rv1027c kdpE |
transcriptional regulator KdpE | 433 | 47 | textmining:430 |
Rv1031 kdpC |
potassium-transporting ATPase subunit C | 646 | 46 | textmining:645 |
Rv1028A kdpF |
membrane protein KdpF | 809 | 41 | textmining:809 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Small membrane protein; ompATb-Rv0900-Rv0901 operon; regulates OmpATb post-transcriptionally (Veyron-Churlet 2011, PMID 21802366)
- Curated from the literature crible (project 'Still unknown gene function', 2026-06-09)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215415.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
2AYBF - Curated reference: UniProt P9WJG7 (SwissProt, reviewed; Evidence at transcript level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
7 functional partner(s); context anchor
arfC - Primary literature: Veyron-Churlet R, Brust B, Kremer L, Blanc-Potard AB (2011). Expression of OmpATb is dependent on small membrane proteins in Mycobacterium bovis BCG Tuberculosis (Edinb) 91(6):544-8. doi:10.1016/j.tube.2011.06.008 PMID:21802366
Ancestral MTBC0 protein sequence
>mtbc0_000954|Rv0900|arfB MDFVIQWSCYLLAFLGGSAVAWVVVTLSIKRASRDEGAAEAPSAAETGAQ