Rv1628c Family assigned · medium auto-curated
H37Rv Rv1628c · MTBC0 mtbc0_001736 ·
163 aa · 1842034–1842525 (-) ·
RefSeq NP_216144.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | Zn-ribbon domain-containing OB-fold protein |
| Revised (this work) | Zn-ribbon domain-containing OB-fold protein. Pfam: zf-ChsH2 (PF12172.15), OB_ChsH2_C (PF01796.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06145
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | nucleic-acid-binding protein containing a Zn-ribbon |
| Orthologous group | COG1545 |
| KEGG orthology |
K07068
|
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 | 0.224 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
zf-ChsH2 | PF12172.15 | 1.6e-09 | 20–56 | ChsH2, rubredoxin-like zinc ribbon domain |
OB_ChsH2_C | PF01796.24 | 6.0e-12 | 59–125 | ChsH2, C-terminal OB-fold domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1627c (nonspecific lipid-transfer protein), high confidence from genomic context alone (score 990 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) |
|---|---|---|---|---|
Rv1627c |
nonspecific lipid-transfer protein | 994 | 990 ctx | neighborhood:881 cooccurence:765 coexpression:444 experimental:415 textmining:479 |
Rv3523 ltp3 |
lipid carrier protein | 807 | 800 ctx | cooccurence:435 coexpression:427 experimental:415 |
Rv3540c ltp2 |
lipid transfer protein | 857 | 782 | coexpression:420 experimental:415 |
Rv1629 polA |
DNA polymerase I | 780 | 781 ctx | neighborhood:780 |
Rv3522 ltp4 |
lipid transfer protein | 868 | 756 | coexpression:423 experimental:415 textmining:485 |
Rv2790c ltp1 |
lipid-transfer protein | 781 | 750 | coexpression:422 experimental:415 |
Rv1867 hyp |
hypothetical protein | 753 | 743 | coexpression:420 experimental:415 |
Rv0914c |
lipid carrier protein or keto acyl-CoA thiolase | 750 | 714 | coexpression:422 experimental:415 |
Rv3556c fadA6 |
acetyl-CoA acetyltransferase FadA | 709 | 698 | coexpression:424 experimental:415 |
Rv1074c fadA3 |
beta-ketoacyl CoA thiolase FadA | 672 | 659 | coexpression:425 experimental:415 |
Rv3546 fadA5 |
acetyl-CoA acetyltransferase FadA | 672 | 659 | coexpression:425 experimental:415 |
Rv0859 fadA |
acyltransferase | 671 | 658 | coexpression:424 experimental:415 |
Rv0243 fadA2 |
acetyl-CoA acetyltransferase FadA | 671 | 658 | coexpression:423 experimental:415 |
Rv1323 fadA4 |
acetyl-CoA acetyltransferase | 671 | 658 | coexpression:423 experimental:415 |
Rv1135A |
Rv1135A, len: 80 aa. Possible acetyl-CoA acetyltransferase (possible gene fragment), highly similar to other acetyl-CoA acetyltransferases e | 669 | 656 | coexpression:420 experimental:415 |
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: hypothetical protein
- MTBC0 PGAP product: Zn-ribbon domain-containing OB-fold protein
- Pfam (hmmscan --cut_ga): zf-ChsH2 PF12172.15 (E=2e-09), OB_ChsH2_C PF01796.24 (E=6e-12)
- (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_216144.1)
- Domains: Pfam-A via hmmscan --cut_ga — zf-ChsH2 (PF12172.15), OB_ChsH2_C (PF01796.24)
- 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
COG1545 - Curated reference: UniProt O06145 (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 —
29 functional partner(s); context anchor
Rv1627c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001736|Rv1628c| MPEVTREEPAIDGWFTTDKAGNPHLLGGKCPQCGTYVFPPRADNCPNPACGSDTLESVGLSTRGKLWSYTENRYAPPPPYPAPDPFEPFAVAAVELADEGLIVLGKVVDGTLAADLKVGMEMELTTMPLFADDDGVQRIVYAWRIPSRAGDDAERSDAEERRR