Rv0811c Family assigned · low auto-curated
H37Rv Rv0811c · MTBC0 mtbc0_000860 ·
368 aa · 908301–909407 (-) ·
RefSeq NP_215326.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | folate-binding protein YgfZ |
| Revised (this work) | Folate-binding protein YgfZ. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X9V3
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | Belongs to the GcvT family |
| Orthologous group | COG0404 |
| KEGG orthology |
K06980
|
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 | 0.381 · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0812 (4-amino-4-deoxychorismate lyase), high confidence from genomic context alone (score 784 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0812 |
4-amino-4-deoxychorismate lyase | 783 | 784 ctx | neighborhood:783 |
Rv0810c hyp |
hypothetical protein | 755 | 755 ctx | neighborhood:752 |
Rv2256c hyp |
hypothetical protein | 638 | 639 ctx | cooccurence:635 |
Rv3683 hyp |
hypothetical protein | 583 | 584 ctx | cooccurence:574 |
Rv2204c hyp |
hypothetical protein | 679 | 581 | experimental:412 |
Rv2146c |
transmembrane protein | 529 | 530 ctx | cooccurence:527 |
Rv2676c hemQ hyp |
hypothetical protein | 525 | 526 ctx | cooccurence:512 |
Rv0528 |
transmembrane protein | 517 | 517 ctx | cooccurence:514 |
Rv2680 hyp |
hypothetical protein | 473 | 474 ctx | cooccurence:471 |
Rv2413c hyp |
hypothetical protein | 469 | 457 ctx | cooccurence:426 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 452 | 452 ctx | cooccurence:449 |
Rv0004 hyp |
hypothetical protein | 452 | 452 ctx | cooccurence:449 |
Rv3644c |
DNA polymerase | 449 | 449 ctx | cooccurence:446 |
Rv1086 |
(2Z,6E)-farnesyl diphosphate synthase | 457 | 437 | coexpression:437 |
Rv3245c mtrB |
two component sensory histidine kinase MtrB | 427 | 428 ctx | cooccurence:424 |
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: hypothetical protein
- MTBC0 PGAP product: folate-binding protein YgfZ
- (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_215326.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG0404 - Curated reference: UniProt I6X9V3 (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 —
20 functional partner(s); context anchor
Rv0812 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000860|Rv0811c| MAAVPAPDPGPDAGAIWHYGDPLGEQRAGQADAVLVDRSHRAVLTLDGGDRQTWLHSISTQHVSDLPEGASTQNLSLDGQGRVEDHWIQTELGGTTYLDTEPWRGEPLLAYLRKMVFWSMVTPRAADMAVLSLLGPRLAEERVLDALGLDVLPAEWLAVPLAGGGIVRRMPDGLAGQIELDVVVKRGDRADWQRRLTQAGVRPAGIWAYEAHRVAHRVPARRPRLGVDTDERTIPHEVGWIGGPGAGAVHLNKGCYRGQETVARVHNLGRPPRMLVLLHLDESVQRPSTGDAVLAGGRTVGRLGTVVEHVELGPVALALLKRGLPGDTALVTGPEAEVAAVIDVDSLPPADDVGAGRRAVERLRGGIR