Rv1005c Resolved · high auto-curated
H37Rv Rv1005c · MTBC0 - ·
458 aa · 1122222–1123598 (-) ·
RefSeq NP_215521.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | para-aminobenzoate synthase component I |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Para-aminobenzoate synthase component I. Pfam: Chorismate_bind (PF00425.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O05591
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable para-aminobenzoate synthase component I PABD |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | pabB |
| eggNOG description | synthase component I |
| Orthologous group | COG1169 |
| EC number |
EC 2.6.1.85
|
| KEGG orthology |
K01665
|
| KEGG pathways |
map00790
|
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 | 0.761 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (221) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Chorismate_bind | PF00425.25 | 2.2e-66 | 188–435 | chorismate binding enzyme |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trpG (anthranilate synthase component II), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0013 trpG |
anthranilate synthase component II | 999 | 1000 ctx | fusion:900 cooccurence:769 coexpression:696 experimental:788 database:900 |
Rv2192c trpD |
anthranilate phosphoribosyltransferase | 982 | 980 ctx | cooccurence:725 coexpression:695 experimental:778 |
Rv1611 trpC |
indole-3-glycerol phosphate synthase | 952 | 949 ctx | cooccurence:744 coexpression:647 experimental:461 |
Rv0812 |
4-amino-4-deoxychorismate lyase | 973 | 923 | database:900 textmining:664 |
Rv2540c aroF |
chorismate synthase | 918 | 910 ctx | cooccurence:433 database:800 |
Rv1613 trpA |
tryptophan synthase subunit alpha | 906 | 896 ctx | cooccurence:707 coexpression:648 |
Rv1612 trpB |
tryptophan synthase subunit beta | 898 | 888 ctx | cooccurence:637 coexpression:692 |
Rv1609 trpE |
anthranilate synthase component I | 856 | 856 | database:800 |
Rv0948c |
chorismate mutase | 822 | 811 | database:800 |
Rv1885c |
chorismate mutase | 821 | 810 | database:800 |
Rv1435c hyp |
hypothetical protein | 820 | 809 | coexpression:648 experimental:461 |
Rv1006 hyp |
hypothetical protein | 786 | 726 ctx | neighborhood:725 |
Rv1004c |
membrane protein | 650 | 636 ctx | neighborhood:582 |
Rv3859c gltB |
glutamate synthase large subunit | 549 | 533 ctx | neighborhood:504 |
Rv3608c folP1 |
dihydropteroate synthase | 580 | 517 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): para-aminobenzoate synthase component I
- Pfam (hmmscan --cut_ga): Chorismate_bind PF00425.25 (E=2e-66)
- (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_215521.1)
- Domains: Pfam-A via hmmscan --cut_ga — Chorismate_bind (PF00425.25)
- 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
COG1169 - Curated reference: UniProt O05591 (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 —
31 functional partner(s); context anchor
trpG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1005c| MNLAWELSTRTKSPRSHLRCENPQFCQARTVRIDRLGDLGGAPAVLRAVGRATSRLDLPPPAALTGEWFGALAVIAPSVSIQPVSGDDVFSGPPGTGGPDATGAVGGGWVGYLSYPDAGADGRPHRIPEAAGGWTDCVLRRDRDGQWWYESLSGAPIADWLASALATTRASVARPAPACRIDWEPADRAAHRDGVLACLEAIGAGEVYQACVCTQFAGTVTGSPLDFFIDGFGRTAPSRSAFVAGPWGAVASLSPELFLRRRGSVVTSSPIKGTLPLDAPPSALRASAKEVAENIMIVDLVRNDLGRVAVTGTVTVPELLVVRPAPGVWHLVSTVSARVPLEEPMSALLDAAFPPASVTGTPKLRARQLISQWERYRRGIYCGTVGLASPVAGCELNVAIRTVEFDTAGNAVLGVGGGITADSDPDAEWAECLHKAAPIVGLPAATRTTPARLASKVR