Rv0842 Resolved · high auto-curated
H37Rv Rv0842 · MTBC0 mtbc0_000897 ·
430 aa · 941263–942555 (+) ·
RefSeq NP_215357.1
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). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53854
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismG Carbohydrate transport and metabolismP Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | Major Facilitator Superfamily |
| Orthologous group | COG0477 |
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 | 0.165 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 3 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-17 | 43–261 | Major Facilitator Superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0843 (dehydrogenase), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0843 |
dehydrogenase | 887 | 887 ctx | neighborhood:882 |
Rv2209 |
integral membrane protein | 685 | 685 ctx | cooccurence:681 |
Rv3350c PPE56 |
PPE family protein PPE56 | 683 | 684 ctx | cooccurence:682 |
Rv0355c PPE8 |
PPE family protein PPE8 | 683 | 683 ctx | cooccurence:680 |
Rv3347c PPE55 |
PPE family protein PPE55 | 681 | 681 ctx | cooccurence:679 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 673 | 673 ctx | cooccurence:673 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 668 | 668 ctx | cooccurence:668 |
Rv1004c |
membrane protein | 669 | 657 ctx | cooccurence:655 |
Rv0304c PPE5 |
PPE family protein PPE5 | 652 | 652 ctx | cooccurence:648 |
Rv3343c PPE54 |
PPE family protein PPE54 | 650 | 651 ctx | cooccurence:646 |
Rv1917c PPE34 |
PPE family protein PPE34 | 639 | 639 ctx | cooccurence:637 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 636 | 636 ctx | cooccurence:636 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 608 | 608 ctx | cooccurence:608 |
Rv2636 |
O-phosphotransferase | 601 | 602 ctx | cooccurence:600 |
Rv0341 iniB |
isoniazid inducible protein IniB | 605 | 590 ctx | cooccurence:587 |
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-17)
- (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_215357.1)
- Domains: Pfam-A via hmmscan --cut_ga — MFS_1 (PF07690.22)
- 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
COG0477 - Curated reference: UniProt O53854 (TrEMBL, unreviewed; Predicted)
- 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 —
77 functional partner(s); context anchor
Rv0843 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000897|Rv0842| MRYTGPERCSGDGQVRAAGDRYSTVIWLLGGNLLVRSAGFGYPFLAYHVAGRGHGAGAVGAVVAAYGLGWAVGQLLCGWLVDRVGARVTLVSTMLVAAAVLVLMAGLHTVPGLLVGAMIAGLVCDAPRPVLGAVIAELVADPQRRAQLDGWRYGWVLNIGAAITGGVGGVVAGWLDTPVLYWINGIGCAIFAGLAGRCIPADVCRRTESGLRACTAMSKVGYRQALSDKRLVLLAVSGLATLTTLMGFFAAVPMLMSASGLGVGAYGWVQLINALAVVAVTPLLTPWLSKQLALGPRPDILAGAGVWVTLCMAAAGLARTTVGFSVAAAACSPGEIAWFVVAAGIVHRIAPPAHGGRYHGIWSMAVAASSVAAPILAAFNLANGGRLVLAATTVTVGFFGAALCLPLARVLAAASCGPLSSKEPSRDSYQ