Rv1226c Family assigned · medium auto-curated
H37Rv Rv1226c · MTBC0 mtbc0_001314 ·
487 aa · 1377276–1378739 (-) ·
RefSeq NP_215742.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | PH domain-containing protein |
| Revised (this work) | PH domain-containing protein. Pfam: bPH_2 (PF03703.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33222
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Bacterial PH domain |
| Orthologous group | COG3428 |
| KEGG orthology |
K08981
|
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 | 0.708 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 7 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 |
|---|---|---|---|---|
bPH_2 | PF03703.21 | 7.8e-15 | 62–141 | Bacterial PH domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1227c (transmembrane protein), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1227c |
transmembrane protein | 989 | 988 ctx | neighborhood:882 cooccurence:772 coexpression:580 |
Rv1225c hyp |
hypothetical protein | 641 | 642 ctx | neighborhood:577 |
Rv3365c hyp |
hypothetical protein | 601 | 601 ctx | cooccurence:587 |
Rv1228 lpqX |
lipoprotein LpqX | 549 | 549 ctx | neighborhood:547 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 533 | 533 ctx | cooccurence:532 |
Rv1234 |
transmembrane protein | 529 | 528 | coexpression:501 |
Rv0901 arfC |
membrane protein | 528 | 528 ctx | cooccurence:526 |
Rv3201c adnB |
ATP-dependent DNA helicase | 527 | 527 ctx | cooccurence:511 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 517 | 517 ctx | cooccurence:517 |
Rv0438c moeA2 |
molybdopterin molybdenumtransferase | 501 | 502 ctx | neighborhood:499 |
Rv3662c hyp |
hypothetical protein | 493 | 493 ctx | cooccurence:480 |
Rv1157c hyp |
hypothetical protein | 484 | 485 ctx | cooccurence:480 |
Rv3737 |
transmembrane protein | 482 | 482 ctx | cooccurence:463 |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 479 | 479 ctx | cooccurence:479 |
Rv2416c eis |
enhanced intracellular survival protein | 471 | 472 ctx | cooccurence:470 |
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: PH domain-containing protein
- Pfam (hmmscan --cut_ga): bPH_2 PF03703.21 (E=8e-15)
- (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_215742.1)
- Domains: Pfam-A via hmmscan --cut_ga — bPH_2 (PF03703.21)
- 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
COG3428 - Curated reference: UniProt O33222 (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 —
34 functional partner(s); context anchor
Rv1227c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001314|Rv1226c| MTDRPHDWHRLSPRMLLVHPVHEMLRQLPVLIGSVVLGSATGNPVWPLAALGVTVVFGVLRWFFTTYRIDDENVSLRTGILSRRAVSVPRNRIRSVQTEARLLHRLLGLTVLRVGTGQEARGEAAFELDAVDSARVPRLRALLLAESLAPVEPTGRVLARWQSSWLRYAPLSFSGLVMIGAVIGLGYQTGLAVRLPESGFARSAVDAAQRAGVVLVVAVTVLLVVGVSALLAVLFSWLTYGNLLLRRGGSGQEGVLHLRHGLLRVREHTYDMRRLRGATLREPLLVRLLRGARLDAVMTGVHGEGQSSMLLPPCPFETATAVLTDLIDNTDAAAGPLRRHGPAAARRRWTRALLVPTLAGVALIAAAPILGVPGWAWTLWAVLTAGCAGLAVDRVRSLGHRVADGWLVARAGSLQRRRDCIACTGIIGWTVRQTLFQRRAGVATLVAATAAGRKGYQVLDVPAELAWSVAGAASPWVADSVWLRHGS