Rv2120c Family assigned · medium auto-curated
H37Rv Rv2120c · MTBC0 mtbc0_002252 ·
160 aa · 2406508–2406990 (-) ·
RefSeq NP_216636.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | glycine zipper 2TM domain-containing protein |
| Revised (this work) | Glycine zipper 2TM domain-containing protein. Pfam: Rick_17kDa_Anti (PF05433.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33255
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | COG3918 |
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 | 0.397 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
Rick_17kDa_Anti | PF05433.21 | 1.2e-06 | 86–123 | Glycine zipper 2TM domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hisG (ATP phosphoribosyltransferase), high confidence from genomic context alone (score 768 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2121c hisG |
ATP phosphoribosyltransferase | 768 | 768 ctx | neighborhood:765 |
Rv2122c hisE |
phosphoribosyl-ATP pyrophosphatase | 682 | 682 ctx | neighborhood:679 |
Rv3810 pirG |
cell surface protein | 643 | 644 ctx | cooccurence:642 |
Rv3707c hyp |
hypothetical protein | 616 | 616 ctx | cooccurence:616 |
Rv0315 |
beta-1,3-glucanase | 520 | 521 ctx | cooccurence:514 |
Rv2743c hyp |
hypothetical protein | 513 | 513 ctx | cooccurence:513 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 485 | 485 ctx | cooccurence:482 |
Rv3096 hyp |
hypothetical protein | 478 | 478 ctx | cooccurence:478 |
Rv3593 lpqF |
lipoprotein LpqF | 431 | 431 ctx | cooccurence:431 |
Rv1216c |
integral membrane protein | 425 | 426 ctx | cooccurence:422 |
Rv2123 PPE37 |
PPE family protein PPE37 | 781 | 418 ctx | neighborhood:418 textmining:640 |
Rv1856c |
oxidoreductase | 405 | 406 ctx | cooccurence:405 |
Rv0256c PPE2 |
PPE family protein PPE2 | 509 | 369 | |
Rv2356c PPE40 |
Rv2356c, (MTCY98.25), len: 615 aa. PPE40, Member of Mycobacterium tuberculosis PPE_family, highly similar to others e.g. Q10778|MTCY48.17|YF | 520 | 47 | textmining:517 |
Rv0453 PPE11 |
PPE family protein PPE11 | 548 | 45 | textmining:547 |
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: glycine zipper 2TM domain-containing protein
- Pfam (hmmscan --cut_ga): Rick_17kDa_Anti PF05433.21 (E=1e-06)
- (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_216636.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rick_17kDa_Anti (PF05433.21)
- 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
COG3918 - Curated reference: UniProt O33255 (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 —
18 functional partner(s); context anchor
hisG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002252|Rv2120c| MTHVLVLLLALLIGVVAGLRSLTAPAVVSWAAFLGWINLHGTWASWMGNFVTVVIVSVLAVAELVNDKRPKTPPRTVTPVFAVRIILGAFAGAVIGTAWGYRWGGLGAGVIGAVLGTMGGYQARTRLVAARGGHDLPIALLEDSVAVLGGFAIVAAAAAL