Rv2235 Family assigned · medium auto-curated
H37Rv Rv2235 · MTBC0 mtbc0_002375 ·
271 aa · 2533795–2534610 (+) ·
RefSeq NP_216751.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | SURF1 family protein |
| Revised (this work) | SURF1 family protein. Pfam: SURF1 (PF02104.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGA7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized SURF1-like protein Rv2235 |
UniProt still lists this protein as Uncharacterized SURF1-like protein Rv2235; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | SURF1-like protein |
| Orthologous group | COG3346 |
| Gene Ontology (15) |
GO:0005575, GO:0005618, GO:0005623, GO:0008150, GO:0030312, GO:0040007, GO:0044110, GO:0044116, GO:0044117, GO:0044119, GO:0044403, GO:0044419 +3 more
|
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 | 0.925 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
SURF1 | PF02104.21 | 3.7e-34 | 22–226 | SURF1 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1456c (antibiotic ABC transporter permease), high confidence from genomic context alone (score 905 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1456c |
antibiotic ABC transporter permease | 927 | 905 ctx | cooccurence:495 coexpression:674 experimental:425 |
Rv2234 ptpA |
protein-tyrosine-phosphatase | 887 | 887 ctx | neighborhood:882 |
Rv2232 ptkA |
protein tyrosine kinase transcriptional regulator PtkA | 883 | 883 ctx | neighborhood:882 |
Rv2229c hyp |
hypothetical protein | 842 | 842 ctx | neighborhood:746 |
Rv2228c |
multifunctional RNASE H/alpha-ribazole phosphatase/acid phosphatase | 750 | 751 ctx | neighborhood:746 |
Rv2230c |
GTP cyclohydrolase | 749 | 750 ctx | neighborhood:746 |
Rv2231c cobC |
aminotransferase | 749 | 749 ctx | neighborhood:746 |
Rv2200c ctaC |
cytochrome C oxidase subunit II | 731 | 692 | |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 698 | 684 ctx | cooccurence:638 |
Rv1451 ctaB |
protoheme IX farnesyltransferase | 750 | 674 | coexpression:423 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 697 | 651 | coexpression:420 |
Rv0556 |
transmembrane protein | 624 | 625 ctx | cooccurence:623 |
Rv3205c hyp |
hypothetical protein | 614 | 614 ctx | cooccurence:586 |
Rv2698 |
transmembrane protein | 598 | 599 ctx | cooccurence:595 |
Rv1632c hyp |
hypothetical protein | 597 | 597 ctx | cooccurence:596 |
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
- Legacy H37Rv annotation: transmembrane protein
- MTBC0 PGAP product: SURF1 family protein
- Pfam (hmmscan --cut_ga): SURF1 PF02104.21 (E=4e-34)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
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_216751.1)
- Domains: Pfam-A via hmmscan --cut_ga — SURF1 (PF02104.21)
- 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
COG3346 - Curated reference: UniProt P9WGA7 (SwissProt, reviewed; Evidence at protein 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 —
64 functional partner(s); context anchor
Rv1456c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002375|Rv2235| MPRLAFLLRPGWLALALVVVAFTYLCFTVLAPWQLGKNAKTSRENQQIRYSLDTPPVPLKTLLPQQDSSAPDAQWRRVTATGQYLPDVQVLARLRVVEGDQAFEVLAPFVVDGGPTVLVDRGYVRPQVGSHVPPIPRLPVQTVTITARLRDSEPSVAGKDPFVRDGFQQVYSINTGQVAALTGVQLAGSYLQLIEDQPGGLGVLGVPHLDPGPFLSYGIQWISFGILAPIGLGYFAYAEIRARRREKAGSPPPDKPMTVEQKLADRYGRRR