arfA Family assigned · medium auto-curated
H37Rv Rv0899 · MTBC0 mtbc0_000953 ·
326 aa · 1006026–1007006 (+) ·
RefSeq NP_215414.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | peptidoglycan-binding protein ArfA |
|---|---|
| MTBC0 PGAP re-annotation | peptidoglycan-binding protein ArfA |
| Revised (this work) | Peptidoglycan-binding protein ArfA. Pfam: BON_like (PF21923.2), BON (PF04972.23), OmpA (PF00691.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIU5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Peptidoglycan-binding protein ArfA |
| Curated function | Probably plays a role in ammonia secretion that neutralizes the medium at pH 5.5, although it does not play a direct role in ammonia transport. The OmpA-like domain (196-326) binds M.tuberculosis peptidoglycan. Overexpression in M.bovis or M.smegmatis gives channels with average conductance value of 1,600 +/- 100 pS, but this may not be physiologically relevant. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | ompA |
| eggNOG description | Belongs to the ompA family |
| Orthologous group | COG2885 |
| KEGG orthology |
K16191
|
| Gene Ontology (60) |
GO:0003674, GO:0005215, GO:0005488, GO:0005539, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0005887 +48 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 | 1.435 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (194) · 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 |
|---|---|---|---|---|
BON_like | PF21923.2 | 2.7e-25 | 82–128 | BON-like domain |
BON | PF04972.23 | 4.1e-06 | 150–195 | BON domain |
OmpA | PF00691.26 | 1.2e-22 | 225–319 | OmpA family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arfC (membrane protein), high confidence from genomic context alone (score 905 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0901 arfC |
membrane protein | 986 | 905 ctx | neighborhood:869 textmining:861 |
Rv0898c hyp |
hypothetical protein | 780 | 780 ctx | neighborhood:779 |
Rv0900 arfB |
membrane protein | 969 | 777 ctx | neighborhood:777 textmining:870 |
Rv0897c |
oxidoreductase | 759 | 759 ctx | neighborhood:758 |
Rv0053 rpsF |
30S ribosomal protein S6 | 631 | 632 | experimental:405 |
Rv1157c hyp |
hypothetical protein | 654 | 611 | |
Rv0056 rplI |
50S ribosomal protein L9 | 581 | 565 | experimental:405 |
Rv0341 iniB |
isoniazid inducible protein IniB | 576 | 557 | |
Rv2098c PE_PGRS36 |
PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub | 532 | 533 | |
Rv3443c rplM |
50S ribosomal protein L13 | 531 | 532 | experimental:405 |
Rv1288 hyp |
hypothetical protein | 559 | 531 | |
Rv0979A rpmF |
50S ribosomal protein L32 | 528 | 528 | experimental:405 |
Rv0682 rpsL |
30S ribosomal protein S12 | 565 | 527 | experimental:405 |
Rv2890c rpsB |
30S ribosomal protein S2 | 547 | 525 | experimental:405 |
Rv0720 rplR |
50S ribosomal protein L18 | 523 | 524 | experimental:405 |
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: peptidoglycan-binding protein ArfA
- MTBC0 PGAP product: peptidoglycan-binding protein ArfA
- Pfam (hmmscan --cut_ga): BON_like PF21923.2 (E=3e-25), BON PF04972.23 (E=4e-06), OmpA PF00691.26 (E=1e-22)
- (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_215414.1)
- Domains: Pfam-A via hmmscan --cut_ga — BON_like (PF21923.2), BON (PF04972.23), OmpA (PF00691.26)
- 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
COG2885 - Curated reference: UniProt P9WIU5 (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 —
82 functional partner(s); context anchor
arfC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000953|Rv0899|arfA MASKAGLGQTPATTDARRTQKFYRGSPGRPWLIGAVVIPLLIAAIGYGAFERPQSVTGPTGVLPTLTPTSTRGASALSLSLLSISRSGNTVTLIGDFPDEAAKAALMTALNGLLAPGVNVIDQIHVDPVVRSLDFSSAEPVFTASVPIPDFGLKVERDTVTLTGTAPSSEHKDAVKRAATSTWPDMKIVNNIEVTGQAPPGPPASGPCADLQSAINAVTGGPIAFGNDGASLIPADYEILNRVADKLKACPDARVTINGYTDNTGSEGINIPLSAQRAKIVADYLVARGVAGDHIATVGLGSVNPIASNATPEGRAKNRRVEIVVN