Rv0373c Family assigned · medium auto-curated
H37Rv Rv0373c · MTBC0 mtbc0_000393 ·
799 aa · 452766–455165 (-) ·
RefSeq NP_214887.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | carbon monoxyde dehydrogenase large subunit |
|---|---|
| MTBC0 PGAP re-annotation | aerobic carbon-monoxide dehydrogenase large subunit |
| Revised (this work) | Aerobic carbon-monoxide dehydrogenase large subunit. Pfam: Ald_Xan_dh_C (PF01315.28), MoCoBD_1 (PF02738.24), MoCoBD_2 (PF20256.4). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53708
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable carbon monoxyde dehydrogenase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | coxL |
| eggNOG description | aldehyde oxidase and xanthine dehydrogenase, a b hammerhead |
| Orthologous group | COG1529 |
| EC number |
EC 1.2.5.3
|
| KEGG orthology |
K03520
|
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 | 0.331 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 17 synonymous, 17 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 |
|---|---|---|---|---|
Ald_Xan_dh_C | PF01315.28 | 1.7e-36 | 38–145 | Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain |
MoCoBD_1 | PF02738.24 | 1.7e-73 | 169–415 | Molybdopterin cofactor-binding domain |
MoCoBD_2 | PF20256.4 | 2.3e-87 | 442–729 | Molybdopterin cofactor-binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0374c (carbon monoxyde dehydrogenase small subunit), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0374c |
carbon monoxyde dehydrogenase small subunit | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:773 coexpression:577 experimental:928 textmining:895 |
Rv0375c |
carbon monoxyde dehydrogenase medium subunit | 999 | 999 ctx | neighborhood:860 cooccurence:774 coexpression:436 experimental:928 textmining:934 |
Rv0372c hyp |
hypothetical protein | 980 | 978 ctx | neighborhood:852 cooccurence:773 |
Rv0370c |
oxidoreductase | 957 | 956 ctx | neighborhood:861 cooccurence:690 |
Rv0371c hyp |
hypothetical protein | 948 | 943 ctx | neighborhood:798 cooccurence:714 |
Rv0368c hyp |
hypothetical protein | 942 | 942 ctx | neighborhood:748 cooccurence:770 |
Rv0369c |
membrane oxidoreductase | 954 | 936 ctx | neighborhood:760 cooccurence:735 |
Rv0376c hyp |
hypothetical protein | 929 | 922 ctx | neighborhood:619 cooccurence:752 |
Rv3621c PPE65 |
PPE family protein PPE65 | 730 | 730 | coexpression:730 |
Rv0377 |
HTH-type transcriptional regulator | 715 | 708 ctx | neighborhood:442 cooccurence:471 |
Rv0345 hyp |
hypothetical protein | 660 | 620 ctx | neighborhood:544 |
Rv2426c hyp |
hypothetical protein | 621 | 604 ctx | cooccurence:553 |
Rv0887c hyp |
hypothetical protein | 580 | 581 | coexpression:580 |
Rv0344c lpqJ |
lipoprotein LpqJ | 482 | 483 ctx | neighborhood:480 |
Rv0367c hyp |
hypothetical protein | 410 | 411 ctx | neighborhood:409 |
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: carbon monoxyde dehydrogenase large subunit
- MTBC0 PGAP product: aerobic carbon-monoxide dehydrogenase large subunit
- Pfam (hmmscan --cut_ga): Ald_Xan_dh_C PF01315.28 (E=2e-36), MoCoBD_1 PF02738.24 (E=2e-73), MoCoBD_2 PF20256.4 (E=2e-87)
- (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_214887.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ald_Xan_dh_C (PF01315.28), MoCoBD_1 (PF02738.24), MoCoBD_2 (PF20256.4)
- 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
COG1529 - Curated reference: UniProt O53708 (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 —
25 functional partner(s); context anchor
Rv0374c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000393|Rv0373c| MTTIESRPPSPEDLADNAQQPCGHGRMMRKEDPRFIRGRGTYVDDVALPGMLHLAILRSPYAHARIVRIDVTAAQAHPKVKAVVTGADLAAKGLAWMPTLANDVQAVLATDKTRFQGQEVAFVVAEDRYSARDACELVDVDYEPRDPVVDARTALDPSAPVIRTDLEGKSDNHIFDWETGDAAATEAVFAKADVVVQQEIVYPRVHPAPMETCGAVADLDPVTGKLTLWTTSQAPHAHRTLYALVAGLPEHKIRVISPDIGGGFGNKVPIYPGYVCAIVASLLLDKPVKWMEDRSENLTSTGFARDYIMVGEIAANRDGKILAIRSNVLADHGAFNAQAAPAKYPAGFFGVFTGSYDIEAAYCHMTAVYTNKAPGGVAYACSFRITEAVYFVERLVDCLAFELKMDPAELRLRNLLRPNQFPYQSKTGWVYDSGDYETTMRKAMNMIGYEALRAEQKQRRARGELMGIGMSFFTEAVGAGPRKDMDILGLGMADGCELRVHPTGKAVLRLSVQTQGQGHETTFAQIVAEELGIAPDDIEVVHGDTDQTPFGLGTYGSRSTPVSGGAAALVARKVRDKAKIIASGMLEVSVADLQWEKGKFHVKGDPSAAVTIADIAMRAHGAGDLPEGIEGGLDAEVCYNPSNLTYPYGAYFCVVDIDPGTAVVKVRRFLAVDDCGTRINPMIIEGQVHGGIVDGIGMALMEMIAFDEDGNCLGGSLMDYLIPTALEVPHLETGHTVTPSPHHPIGAKGIGESATVGSPPAVVNAVVDALAPFGVRHADMPLTPSRVWEAMQGRATPPI