MTBC Gene Atlas

Rv1473 Family assigned · medium auto-curated

H37Rv Rv1473 · MTBC0 mtbc0_001575 · 542 aa · 1670461–1672089 (+) · RefSeq NP_215989.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)macrolide ABC transporter ATP-binding protein
MTBC0 PGAP re-annotationmacrolide ABC transporter ATP-binding protein
Revised (this work)Macrolide ABC transporter ATP-binding protein. Pfam: ABC_tran_Xtn (PF12848.14), ABC_tran (PF00005.34), AAA_21 (PF13304.13).

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

Curated reference (UniProt)

UniProt O53164 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable macrolide-transport ATP-binding protein ABC transporter

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category S Function unknown
Preferred nameybiT
eggNOG descriptionABC transporter
Orthologous groupCOG0488
KEGG orthology K06158

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 0.22 · purifying
Polymorphic sites (≥ 0.1% of strains) 5 synonymous, 3 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
ABC_tran_XtnPF12848.14 6.3e-08241–314 ABC transporter
ABC_tranPF00005.34 4.3e-24352–481 ABC transporter
AAA_21PF13304.13 1.7e-07447–510 AAA domain, putative AbiEii toxin, Type IV TA system

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

Closest characterised functional partner: Rv1473A (transcriptional regulator), high confidence from genomic context alone (score 940 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv1473A transcriptional regulator 940 940 ctx neighborhood:774 coexpression:746
Rv1472 echA12 enoyl-CoA hydratase EchA12 845 845 ctx neighborhood:829
Rv3442c rpsI 30S ribosomal protein S9 826 827 experimental:773
Rv0723 rplO 50S ribosomal protein L15 825 825 experimental:773
Rv2909c rpsP 30S ribosomal protein S16 823 824 experimental:772
Rv2442c rplU 50S ribosomal protein L21 822 822 experimental:773
Rv2785c rpsO 30S ribosomal protein S15 822 816 experimental:773
Rv0721 rpsE 30S ribosomal protein S5 821 816 experimental:773
Rv3443c rplM 50S ribosomal protein L13 816 816 experimental:773
Rv0707 rpsC 30S ribosomal protein S3 814 815 experimental:773
Rv0702 rplD 50S ribosomal protein L4 820 809 experimental:773
Rv0714 rplN 50S ribosomal protein L14 813 806 experimental:773
Rv0720 rplR 50S ribosomal protein L18 802 802 experimental:773
Rv0701 rplC 50S ribosomal protein L3 813 801 experimental:773
Rv0979A rpmF 50S ribosomal protein L32 795 796 experimental:773

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: macrolide ABC transporter ATP-binding protein
  • MTBC0 PGAP product: macrolide ABC transporter ATP-binding protein
  • Pfam (hmmscan --cut_ga): ABC_tran_Xtn PF12848.14 (E=6e-08), ABC_tran PF00005.34 (E=4e-24), AAA_21 PF13304.13 (E=2e-07)
  • (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_215989.1)
  • Domains: Pfam-A via hmmscan --cut_ga — ABC_tran_Xtn (PF12848.14), ABC_tran (PF00005.34), AAA_21 (PF13304.13)
  • 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 COG0488
  • Curated reference: UniProt O53164 (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 — 114 functional partner(s); context anchor Rv1473A
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001575|Rv1473|
MITATDLEVRAGARILLAPDGPDLRVQPGDRIGLVGRNGAGKTTTLRILAGEVEPYAGSVTRAGEIGYLPQDPKVGDLDVLARDRVLSARGLDVLLTDLEKQQALMAEVADEDERDRAIRRYGQLEERFVALGGYGAESEAGRICASLGLPERVLTQRLRTLSGGQRRRVELARILFAASESGAGNSTTLLLDEPTNHLDADSLGWLRDFLRLHTGGLVVISHNVDLVADVVNKVWFLDAVRGQVDVYNMGWQRYVDARATDEQRRIRERANAERKAAALRAQAAKLGAKATKAVAAQNMLRRADRMMAALDEERVADKVARIKFPTPAACGRTPLVANGLGKTYGSLEVFTGVDLAIDRGSRVVILGLNGAGKTTLLRLLAGVEQPDTGVLEPGYGLRIGYFAQEHDTLDNDATVWENVRHAAPDAGEQDLRGLLGAFMFTGPQLEQPAGTLSGGEKTRLALAGLVASTANVLLLDEPTNNLDPASREQVLDALRSYRGAVVLVTHDPGAAAALGPQRVVLLPDGTEDYWSDEYRDLIELA