Rv2059 Family assigned · medium auto-curated
H37Rv Rv2059 · MTBC0 - ·
511 aa · 2315174–2316709 (+) ·
RefSeq NP_216575.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains ZnuA (PF01297.23) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O07257
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Adhesion protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | psaA |
| eggNOG description | periplasmic solute binding protein |
| Orthologous group | COG0803 |
| KEGG orthology |
K02077
|
| KEGG modules |
M00244
|
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 | 1.135 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 9 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 |
|---|---|---|---|---|
ZnuA | PF01297.23 | 2.6e-47 | 110–346 | Zinc-uptake complex component A periplasmic |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2060 (integral membrane protein), high confidence from genomic context alone (score 977 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2060 |
integral membrane protein | 998 | 977 ctx | neighborhood:544 cooccurence:762 coexpression:809 textmining:921 |
Rv2058c rpmB2 |
50S ribosomal protein L28 | 986 | 909 ctx | neighborhood:565 coexpression:799 textmining:862 |
Rv2056c rpsN2 |
30S ribosomal protein S14 | 923 | 891 ctx | neighborhood:576 coexpression:753 |
Rv0106 hyp |
hypothetical protein | 978 | 820 | coexpression:805 textmining:887 |
Rv0280 PPE3 |
PPE family protein PPE3 | 778 | 732 | coexpression:732 |
Rv2057c rpmG1 |
50S ribosomal protein L33 | 707 | 692 ctx | neighborhood:592 |
Rv2055c rpsR2 |
30S ribosomal protein S18 | 952 | 655 ctx | neighborhood:552 textmining:867 |
Rv2990c hyp |
hypothetical protein | 615 | 615 | coexpression:615 |
Rv3575c |
LacI family transcriptional regulator | 553 | 549 ctx | neighborhood:544 |
Rv3576 lppH |
lipoprotein LppH | 550 | 532 ctx | neighborhood:531 |
Rv2788 sirR |
transcriptional repressor SirR | 495 | 411 | |
Rv0924c mntH |
divalent metal cation transporter MntH | 779 | 404 | textmining:646 |
Rv2711 ideR |
iron-dependent repressor and activator IdeR | 599 | 349 | textmining:409 |
Rv2359 zur |
zinc uptake regulation protein | 610 | 334 | textmining:439 |
Rv2856 nicT |
nickel-transport integral membrane protein NicT | 642 | 295 | textmining:514 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): ZnuA PF01297.23 (E=3e-47)
- (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_216575.1)
- Domains: Pfam-A via hmmscan --cut_ga — ZnuA (PF01297.23)
- 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
COG0803 - Curated reference: UniProt O07257 (TrEMBL, unreviewed; Predicted)
- 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 —
25 functional partner(s); context anchor
Rv2060 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2059| MATPVILVTGHEGTAAVTADLLGLLTDHGTATLRSVAPGSVRRADPRPRCHRREQRRRHRASMKSAIHPDHHPRRLPRCPVLRRDQVVLEMIVITMVGRPSGPGERKWDVWGSVARAVTGGHVPVKSILTGAHADPHSYQASPADAAAIVDAELVIYNGGGYDPWVDQVLAGHPGVQAVDAYSLLGAVGDDDAPNEHVFYDPNVAKAVAATIADRLADLDPSNSGNYRANAAEFSRGADAIAISEHAIATTYPDAAVIATEPVVHYLLAAAGLKNRTPATFIAANENGNDPTPADMAAVLDMIAGREVAALLVNPQTPTAATDELQVAARRAGVPITELTETLPSGTDRDQFCAADRPDRRGRSLRADHADRGLSARGHRVGDLLPTALVCHRRSGGRGRPRRASARPGNCVRRTDGRGSRPGCPDRRGTPRDVFADHPRRGGRPGRGCPGRRDRDLGGLRRGFRRRRHPAVAGAWSPGVGVRGHHLVCDLPDLLVAPAAPLTSRSRFRPL