argF Resolved · high auto-curated
H37Rv Rv1656 · MTBC0 mtbc0_001765 ·
307 aa · 1881964–1882887 (+) ·
RefSeq NP_216172.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ornithine carbamoyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | ornithine carbamoyltransferase |
| Revised (this work) | Ornithine carbamoyltransferase. Pfam: OTCace_N (PF02729.27), OTCace (PF00185.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIT9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ornithine carbamoyltransferase |
| EC (curated) |
EC 2.1.3.3
|
| Curated function | Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline, which is a substrate for argininosuccinate synthetase, the enzyme involved in the final step in arginine biosynthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | argF |
| eggNOG description | Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline |
| Orthologous group | COG0078 |
| EC number |
EC 2.1.3.3
|
| KEGG orthology |
K00611
|
| KEGG pathways |
map00220, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00029, M00844
|
| Gene Ontology (49) |
GO:0000050, GO:0003674, GO:0003824, GO:0004585, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0006082, GO:0006520, GO:0006525, GO:0006526 +37 more
|
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 | 0.471 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
OTCace_N | PF02729.27 | 7.4e-48 | 3–141 | Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain |
OTCace | PF00185.31 | 1.6e-55 | 148–303 | Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: argG (argininosuccinate synthase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1658 argG |
argininosuccinate synthase | 999 | 1000 ctx | neighborhood:879 coexpression:976 database:900 textmining:951 |
Rv1653 argJ |
bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase | 999 | 1000 ctx | neighborhood:881 cooccurence:489 coexpression:942 database:900 textmining:781 |
Rv1654 argB |
acetylglutamate kinase | 999 | 998 ctx | neighborhood:881 coexpression:976 textmining:929 |
Rv1655 argD |
acetylornithine aminotransferase | 999 | 997 ctx | neighborhood:882 coexpression:948 textmining:868 |
Rv1652 argC |
N-acetyl-gamma-glutamyl-phoshate reductase | 999 | 995 ctx | neighborhood:835 coexpression:961 textmining:895 |
Rv1659 argH |
argininosuccinate lyase | 997 | 994 ctx | neighborhood:783 coexpression:968 textmining:603 |
Rv1657 argR |
arginine repressor | 997 | 987 ctx | neighborhood:882 coexpression:892 textmining:804 |
Rv1001 arcA |
arginine deiminase | 987 | 983 | coexpression:767 database:900 |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 992 | 979 ctx | fusion:818 coexpression:431 database:800 textmining:657 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 957 | 951 ctx | fusion:550 coexpression:453 database:800 |
Rv1380 pyrB |
aspartate carbamoyltransferase | 861 | 840 | database:800 |
Rv2321c rocD2 |
Rv2321c, (MTCY3G12.13), len: 181 aa. Probable rocD2,ornithine aminotransferase, highly similar to C-terminal region of other ornithine amino | 802 | 736 | coexpression:645 |
Rv2322c rocD1 |
Rv2322c, (MTCY3G12.12), len: 221 aa. Probable rocD1,ornithine aminotransferase, highly similar to N-terminal region of other ornithine amino | 792 | 723 | coexpression:646 |
Rv1661 pks7 |
polyketide synthase | 669 | 641 ctx | neighborhood:588 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 772 | 550 ctx | neighborhood:544 textmining:515 |
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: ornithine carbamoyltransferase
- MTBC0 PGAP product: ornithine carbamoyltransferase
- Pfam (hmmscan --cut_ga): OTCace_N PF02729.27 (E=7e-48), OTCace PF00185.31 (E=2e-55)
- (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_216172.1)
- Domains: Pfam-A via hmmscan --cut_ga — OTCace_N (PF02729.27), OTCace (PF00185.31)
- 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
COG0078 - Curated reference: UniProt P9WIT9 (SwissProt, reviewed; 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 —
38 functional partner(s); context anchor
argG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001765|Rv1656|argF MIRHFLRDDDLSPAEQAEVLELAAELKKDPVSRRPLQGPRGVAVIFDKNSTRTRFSFELGIAQLGGHAVVVDSGSTQLGRDETLQDTAKVLSRYVDAIVWRTFGQERLDAMASVATVPVINALSDEFHPCQVLADLQTIAERKGALRGLRLSYFGDGANNMAHSLLLGGVTAGIHVTVAAPEGFLPDPSVRAAAERRAQDTGASVTVTADAHAAAAGADVLVTDTWTSMGQENDGLDRVKPFRPFQLNSRLLALADSDAIVLHCLPAHRGDEITDAVMDGPASAVWDEAENRLHAQKALLVWLLERS