MTBC Gene Atlas

arcA Resolved · high auto-curated

H37Rv Rv1001 · MTBC0 mtbc0_001076 · 402 aa · 1124521–1125729 (+) · RefSeq NP_215517.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)arginine deiminase
MTBC0 PGAP re-annotationarginine deiminase
Revised (this work)Arginine deiminase. Pfam: ADI (PF02274.23).

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

Curated reference (UniProt)

UniProt P9WQ05 SwissProt · reviewed · Evidence at protein level
UniProt nameArginine deiminase
EC (curated) EC 3.5.3.6

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category E Amino acid transport and metabolism
Preferred namearcA
eggNOG descriptionArginine
Orthologous groupCOG2235
EC number EC 3.5.3.6
KEGG orthology K01478
KEGG pathways map00220, map01100, map01110, map01130
Gene Ontology (6) GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944

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 0.36 · purifying
Polymorphic sites (≥ 0.1% of strains) 5 synonymous, 5 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)

PfamAccessioni-EvalueResiduesDescription
ADIPF02274.23 7.0e-13335–399 Arginine deiminase

Functional interaction network (STRING v12, guilt-by-association)

PartnerProductScoreNo text-miningChannels (≥400)
Rv1656 argF ornithine carbamoyltransferase 987 983 coexpression:767 database:900
Rv1659 argH argininosuccinate lyase 919 901 database:900
Rv1658 argG argininosuccinate synthase 914 901 database:900
Rv2531c amino acid decarboxylase 901 806 database:800 textmining:513
Rv1000c hyp hypothetical protein 679 679 ctx neighborhood:677
Rv2216 epimerase family protein 659 660 coexpression:660
Rv0408 pta phosphate acetyltransferase 751 540 coexpression:540 textmining:482
Rv1155 pyridoxine/pyridoxamine 5'-phosphate oxidase 446 446 coexpression:446
Rv2074 pyridoxamine 5'-phosphate oxidase 443 443 coexpression:443
Rv3369 hyp hypothetical protein 443 443 coexpression:443
Rv2991 hyp hypothetical protein 441 442 coexpression:442
Rv1903 membrane protein 409 409 coexpression:409
Rv2043c pncA pyrazinamidase/nicotinamidase PncA 404 404 coexpression:404
Rv2763c dfrA dihydrofolate reductase 402 401 coexpression:401
Rv0310c hyp hypothetical protein 400 401 coexpression:401

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: arginine deiminase
  • MTBC0 PGAP product: arginine deiminase
  • Pfam (hmmscan --cut_ga): ADI PF02274.23 (E=7e-133)
  • (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_215517.1)
  • Domains: Pfam-A via hmmscan --cut_ga — ADI (PF02274.23)
  • 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 COG2235
  • Curated reference: UniProt P9WQ05 (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 — 22 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001076|Rv1001|arcA
MGVELGSNSEVGALRVVILHRPGAELRRLTPRNTDQLLFDGLPWVSRAQDEHDEFAELLASRGAEVLLLSDLLTEALHHSGAARMQGIAAAVDAPRLGLPLAQELSAYLRSLDPGRLAHVLTAGMTFNELPSDTRTDVSLVLRMHHGGDFVIEPLPNLVFTRDSSIWIGPRVVIPSLALRARVREASLTDLIYAHHPRFTGVRRAYESRTAPVEGGDVLLLAPGVVAVGVGERTTPAGAEALARSLFDDDLAHTVLAVPIAQQRAQMHLDTVCTMVDTDTMVMYANVVDTLEAFTIQRTPDGVTIGDAAPFAEAAAKAMGIDKLRVIHTGMDPVVAEREQWDDGNNTLALAPGVVVAYERNVQTNARLQDAGIEVLTIAGSELGTGRGGPRCMSCPAARDPL