MTBC Gene Atlas

Rv0308 Family assigned · medium auto-curated

H37Rv Rv0308 · MTBC0 mtbc0_000328 · 238 aa · 380436–381152 (+) · RefSeq NP_214822.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)integral membrane protein
MTBC0 PGAP re-annotationphosphatase PAP2 family protein
Revised (this work)Phosphatase PAP2 family protein. Pfam: PAP2 (PF01569.28).

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

Curated reference (UniProt)

UniProt O07235 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable conserved integral membrane protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category I Lipid transport and metabolism
eggNOG descriptionMembrane-associated phospholipid phosphatase
Orthologous groupCOG0671
EC number EC 3.6.1.27
KEGG orthology K19302
KEGG pathways map00550

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 0.363 · purifying
Polymorphic sites (≥ 0.1% of strains) 2 synonymous, 2 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
PAP2PF01569.28 1.7e-1592–205 PAP2 superfamily

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv0309 hyp hypothetical protein 817 817 ctx neighborhood:771
Rv0307c hyp hypothetical protein 788 789 ctx neighborhood:787
Rv0719 rplF 50S ribosomal protein L6 784 776 experimental:405 database:630
Rv1252c lprE lipoprotein LprE 762 754 experimental:405 database:599
Rv1880c cyp140 cytochrome P450 Cyp140 646 646 database:524
Rv3059 cyp136 cytochrome P450 Cyp136 674 634 database:524
Rv1785c cyp143 cytochrome P450 Cyp143 633 633 database:524
Rv2276 cyp121 cytochrome P450 Cyp121 632 632 database:524
Rv3121 cyp141 cytochrome P450 Cyp141 632 632 database:524
Rv2268c cyp128 cytochrome P450 Cyp128 632 632 database:524
Rv3518c cyp142 cytochrome P450 monooxygenase Cyp142 641 631 database:524
Rv0568 cyp135B1 cytochrome P450 Cyp135B1 630 631 database:524
Rv0778 cyp126 cytochrome P450 Cyp126 630 631 database:524
Rv0766c cyp123 cytochrome P450 Cyp123 630 631 database:524
Rv0327c cyp135A1 cytochrome P450 Cyp135A1 630 631 database:524

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: integral membrane protein
  • MTBC0 PGAP product: phosphatase PAP2 family protein
  • Pfam (hmmscan --cut_ga): PAP2 PF01569.28 (E=2e-15)
  • (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_214822.1)
  • Domains: Pfam-A via hmmscan --cut_ga — PAP2 (PF01569.28)
  • 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 COG0671
  • Curated reference: UniProt O07235 (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 — 73 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000328|Rv0308|
MTRPQALLAVSLAFVATAVYAVMWVGHSQDWGWLHSFDWSLLNAAHDIGIKNPAWVRFWDGVSLILGPVVLRPLGLLAAMVALAKRKIRIALLLLACLPLNAIMTIAAKSVAHRPRPATALVSAHSTSFPSGHALEATASVLALLTVLLPMLHSRFTRHIAITVGALCVLTVGVARVALNVHHPTDVVAGWALGYLYFLVCLCVFRPPSIFGAQRASHALSPPVEVSRQPEPEVDTAR