Rv3075c Resolved · high auto-curated
H37Rv Rv3075c · MTBC0 mtbc0_003269 ·
307 aa · 3459414–3460337 (-) ·
RefSeq NP_217591.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | CoA ester lyase |
| Revised (this work) | CoA ester lyase. Pfam: HpcH_HpaI (PF03328.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YF40
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 |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | citE_2 |
| eggNOG description | Belongs to the HpcH HpaI aldolase family |
| Orthologous group | COG2301 |
| EC number |
EC 4.1.3.34
|
| KEGG orthology |
K01644
|
| KEGG pathways |
map02020
|
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 | 0.664 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
HpcH_HpaI | PF03328.21 | 5.0e-26 | 27–228 | HpcH/HpaI aldolase/citrate lyase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hab (hydroxylaminobenzene mutase), medium confidence from genomic context alone (score 597 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) |
|---|---|---|---|---|
Rv2498c citE |
citrate (pro-3S)-lyase subunit beta | 949 | 926 | database:900 |
Rv0727c fucA |
L-fuculose phosphate aldolase FucA | 730 | 730 | coexpression:730 |
Rv3076 hyp |
hypothetical protein | 602 | 602 ctx | neighborhood:602 |
Rv3078 hab |
hydroxylaminobenzene mutase | 597 | 597 ctx | neighborhood:596 |
Rv2286c hyp |
hypothetical protein | 549 | 549 ctx | neighborhood:544 |
Rv3073c hyp |
hypothetical protein | 545 | 545 ctx | neighborhood:544 |
Rv3077 |
hydrolase | 545 | 545 ctx | neighborhood:545 |
Rv2499c |
oxidase regulatory-like protein | 504 | 481 | |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 455 | 448 | |
Rv2332 mez |
malate oxidoreductase | 467 | 440 | coexpression:408 |
Rv2753c dapA |
4-hydroxy-tetrahydrodipicolinate synthase | 408 | 409 | coexpression:408 |
Rv1493 mutB |
methylmalonyl-CoA mutase large subunit | 409 | 185 | |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 532 | 85 | textmining:511 |
Rv0772 purD |
phosphoribosylamine--glycine ligase | 607 | 68 | textmining:596 |
Rv1480 hyp |
hypothetical protein | 623 | 50 | textmining:620 |
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: CoA ester lyase
- Pfam (hmmscan --cut_ga): HpcH_HpaI PF03328.21 (E=5e-26)
- (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_217591.1)
- Domains: Pfam-A via hmmscan --cut_ga — HpcH_HpaI (PF03328.21)
- 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
COG2301 - Curated reference: UniProt I6YF40 (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 —
17 functional partner(s); context anchor
hab - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003269|Rv3075c| MTSMYEQVDTNTADPVAGSRIDPVLARSWLLVNGAHGDRFESAAHSRADIVVLDIEDAVAPKDKHAARDNAVRWFGDGNADWVRINGFGTPWWADDLAMLADSPVGGVMLAMVESVDHVTETAKRLPNVPIVALVETARGLERINEIAAAKGTFRLAFGIGDFRRDTGFGEDPATLAYARSRFTIAARAAGLPSAIDGPTIGSNALKLIEATAVSAEFGMTGKICLSPDQCPVVNEGLSPSQDEIVWAKEFFAEFARDGGEIRNGSDLPRIARATKILDLARAYGIEVSDFEDEPVHMPAPTDTYHY