Rv2508c Resolved · high auto-curated
H37Rv Rv2508c · MTBC0 mtbc0_002670 ·
445 aa · 2846146–2847483 (-) ·
RefSeq NP_217024.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | MFS transporter |
| Revised (this work) | MFS transporter. Pfam: MFS_1 (PF07690.22), ATG22 (PF11700.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06171
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved integral membrane leucine and alanine rich protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Major facilitator superfamily |
| Orthologous group | COG2270 |
| KEGG orthology |
K06902
|
| KEGG pathways |
map04138
|
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 | 3.492 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 9 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 |
|---|---|---|---|---|
MFS_1 | PF07690.22 | 3.0e-16 | 35–396 | Major Facilitator Superfamily |
ATG22 | PF11700.15 | 3.5e-24 | 149–434 | Vacuole effluxer Atg22 like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cmrA (short-chain type dehydrogenase/reductase), high confidence from genomic context alone (score 784 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2509 cmrA |
short-chain type dehydrogenase/reductase | 784 | 784 ctx | neighborhood:783 |
Rv0317c glpQ2 |
glycerophosphoryl diester phosphodiesterase GlpQ | 401 | 402 |
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: integral membrane protein
- MTBC0 PGAP product: MFS transporter
- Pfam (hmmscan --cut_ga): MFS_1 PF07690.22 (E=3e-16), ATG22 PF11700.15 (E=3e-24)
- (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_217024.1)
- Domains: Pfam-A via hmmscan --cut_ga — MFS_1 (PF07690.22), ATG22 (PF11700.15)
- 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
COG2270 - Curated reference: UniProt O06171 (TrEMBL, unreviewed; 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 —
2 functional partner(s); context anchor
cmrA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002670|Rv2508c| MNNPGSRAGTLLHFRVVAWAMWDCGSTGLNAIVTTFVFSVYLTSAVGQGLPGGTSPASWLGRAGAVAGLTIGVLAPVVGVWVESPHRRRVALSVLTGTAVALTCAMFLIRDDPRYLWAGLVLLAATAASSDLSSVPYNAMLRQLSTPSTAGRISGFGWASGYVGSVALLLVIYLGFMSGSGSQRGLLQLPVANGLNVRMAMLVAAAWLALLGLPLLLVAHRLPDSGAASHPSTGLLGGYRKLWTEISAEWRRDRNLVYFLVASAIFRDGLAAIFAFGAVLGVNAYGLTQADVLIFGAAASVVAAVGAVLGGFVDHRIGSKPVIVGSLAAIIAAALTLLTLSGPTAFWACGLLLCVFIGPAQSSARALLLHMAQHGKEGVAFGLYTMTGRAVSFLGPWLFSVFVDVFHTVRAGLGGVCLVLTTGLLLMLRVQVSRHGGALTTAQSS