Rv3197 Family assigned · medium auto-curated
H37Rv Rv3197 · MTBC0 mtbc0_003399 ·
447 aa · 3589166–3590509 (+) ·
RefSeq NP_217713.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ABC transporter ATP-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | AarF/ABC1/UbiB kinase family protein |
| Revised (this work) | AarF/ABC1/UbiB kinase family protein. Pfam: ABC1 (PF03109.23), APH (PF01636.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53343
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved ATP-binding protein ABC transporter |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | ATP-binding protein |
| Orthologous group | COG0661 |
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 | 0.542 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
ABC1 | PF03109.23 | 4.9e-58 | 98–312 | ABC1 atypical kinase-like domain |
APH | PF01636.30 | 1.1e-06 | 260–307 | Phosphotransferase enzyme family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0474 (HTH-type transcriptional regulator), medium confidence from genomic context alone (score 678 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0821c phoY2 |
phosphate-transport system transcriptional regulator PhoY2 | 791 | 791 | coexpression:788 |
Rv2185c TB16.3 hyp |
hypothetical protein | 755 | 743 ctx | cooccurence:685 |
Rv0854 hyp |
hypothetical protein | 718 | 705 ctx | cooccurence:639 |
Rv0474 |
HTH-type transcriptional regulator | 677 | 678 ctx | cooccurence:673 |
Rv0857 hyp |
hypothetical protein | 674 | 675 ctx | cooccurence:670 |
Rv0502 hyp |
hypothetical protein | 574 | 574 ctx | cooccurence:567 |
Rv3195 hyp |
hypothetical protein | 546 | 547 ctx | neighborhood:544 |
Rv3196 hyp |
hypothetical protein | 546 | 547 ctx | neighborhood:544 |
Rv3196A hyp |
hypothetical protein | 546 | 546 ctx | neighborhood:543 |
Rv0487 hyp |
hypothetical protein | 538 | 539 ctx | cooccurence:530 |
Rv3679 |
anion transporter ATPase | 469 | 470 ctx | cooccurence:468 |
Rv3680 |
anion transporter ATPase | 431 | 432 ctx | cooccurence:425 |
Rv3113 |
phosphatase | 411 | 412 | coexpression:402 |
Rv2232 ptkA |
protein tyrosine kinase transcriptional regulator PtkA | 411 | 411 | coexpression:401 |
Rv1937 |
oxygenase | 442 | 223 |
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: ABC transporter ATP-binding protein
- MTBC0 PGAP product: AarF/ABC1/UbiB kinase family protein
- Pfam (hmmscan --cut_ga): ABC1 PF03109.23 (E=5e-58), APH PF01636.30 (E=1e-06)
- (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_217713.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC1 (PF03109.23), APH (PF01636.30)
- 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
COG0661 - Curated reference: UniProt O53343 (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 —
15 functional partner(s); context anchor
Rv0474 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003399|Rv3197| MDDGSVSDIKRGRAARNAKLASIPVGFAGRAALGLGKRLTGKSKDEVTAELMEKAANQLFTVLGELKGGAMKVGQALSVMEAAIPDEFGEPYREALTKLQKDAPPLPASKVHRVLDGQLGTKWRERFSSFNDTPVASASIGQVHKAIWSDGREVAVKIQYPGADEALRADLKTMQRMVGVLKQLSPGADVQGVVDELVERTEMELDYRLEAANQRAFAKAYHDHPRFQVPHVVASAPKVVIQEWIEGVPMAEIIRHGTTEQRDLIGTLLAELTFDAPRRLGLMHGDAHPGNFMLLPDGRMGIIDFGAVAPMPGGFPIELGMTIRLAREKNYDLLLPTMEKAGLIQRGRQVSVREIDEMLRQYVEPIQVEVFHYTRKWLQKMTVSQIDRSVAQIRTARQMDLPAKLAIPMRVIASVGAILCQLDAHVPIKALSEELIPGFAEPDAIVV