Rv1722 Resolved · medium auto-curated
H37Rv Rv1722 · MTBC0 mtbc0_001834 ·
494 aa · 1959876–1961360 (+) ·
RefSeq NP_216238.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | carboxylase |
|---|---|
| MTBC0 PGAP re-annotation | biotin carboxylase |
| Revised (this work) | Biotin carboxylase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71980
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible carboxylase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | An AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism |
| Orthologous group | COG0439 |
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 | 0.392 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 6 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.24% of strains (355) · clonal |
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: Rv1723 (hydrolase), high confidence from genomic context alone (score 957 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0904c accD3 |
acetyl-CoAcarboxylase carboxyl transferase subunit beta | 995 | 986 | coexpression:843 experimental:874 textmining:688 |
Rv1723 |
hydrolase | 957 | 957 ctx | neighborhood:882 cooccurence:634 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 897 | 898 | experimental:883 |
Rv3279c birA |
bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase | 954 | 884 | database:844 textmining:626 |
Rv2531c |
amino acid decarboxylase | 777 | 777 ctx | cooccurence:758 |
Rv2524c fas |
fatty acid synthase | 871 | 749 | coexpression:694 textmining:511 |
Rv1307 atpH |
ATP synthase subunit b/delta | 712 | 705 | coexpression:671 |
Rv1527c pks5 |
polyketide synthase | 707 | 515 | coexpression:418 textmining:422 |
Rv1721c vapB12 |
antitoxin VapB12 | 515 | 515 ctx | neighborhood:512 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 705 | 511 | coexpression:414 textmining:422 |
Rv2048c pks12 |
polyketide synthase | 705 | 511 | coexpression:414 textmining:422 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 704 | 511 | coexpression:413 textmining:422 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 704 | 510 | coexpression:412 textmining:422 |
Rv1310 atpD |
ATP synthase subunit beta | 509 | 501 | coexpression:436 |
Rv1720c vapC12 |
ribonuclease VapC12 | 499 | 500 ctx | neighborhood:498 |
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: carboxylase
- MTBC0 PGAP product: biotin carboxylase
- (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_216238.1)
- 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
COG0439 - Curated reference: UniProt P71980 (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 —
69 functional partner(s); context anchor
Rv1723 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001834|Rv1722| MIVPAREPEPQPRRVLNGLSDVRAFFHNNTVPLYFISPTPFNLLGIYRWIRNFFYLTYYDSFEGEHSRVFVPRRRDRRDFDGMGDVCNHLLRDPETLEFIKNRGPGGKACFVMLDEETQALARQAGLEVMHPPAELRHRLESKIVMTRLADEAGVPSVPHVIGRVSSYDELSALAHGAGLGDDLVVEAAYGNAGSATFFVRGLRDWDQCAGGIVGQPEIKVMKRIRNVEVCIEATVTRHGTVIGPAMTSLVGYPELTPYRGAWCGNDVWRGALPPAQTRAAREMVAKLGDVLSREGYRGYFEVDLLHDLDADELYLGEVNPRLSGASPMTNLTTEAYADMPLFLFHLLEYMDVDYELDIEAINSRWERGYGEDEVWGQLIMSETSPDLELFTATPRTGMWRLNHDGRVSFARQGNDWATMLDESEAFYMRVAAPGDLRCEGAQLGVLVTRGHLQTDDYQLTERGRRWIDGLKAQFASTPLTPAAPIVSRLVARA