Rv2628 Still unknown · low auto-curated
H37Rv Rv2628 · MTBC0 - ·
120 aa · 2955058–2955420 (+) ·
RefSeq NP_217144.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 7xzi-assembly1_F Cryo-EM structure of TOC-TIC supercomplex from Chlamy (prob 0.10, TM 0.32). |
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 |
P9WL65
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative uncharacterized protein Rv2628 |
UniProt still lists this protein as Putative uncharacterized protein Rv2628; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2B0W9 |
|---|---|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.507 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 60.5 (low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
7xzi-assembly1_F |
0.10 | 0.32 | 9.2e-01 | 7xzi-assembly1_F Cryo-EM structure of TOC-TIC supercomplex from Chlamydomonas reinhardtii |
8p23-assembly1_B |
0.10 | 0.53 | 2.1e+00 | 8p23-assembly1_B Cryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its dimeric, ATP/CTP-bound state |
1q1o-assembly1_A |
0.06 | 0.44 | 4.4e+00 | 1q1o-assembly1_A Solution Structure of the PB1 Domain of Cdc24p (Long Form) |
7bqn-assembly1_A |
0.02 | 0.36 | 7.9e+00 | 7bqn-assembly1_A Solution NMR structure of fold-C Rei; de novo designed protein with an asymmetric all-alpha topology |
4ic7-assembly2_E |
0.02 | 0.36 | 7.9e+00 | 4ic7-assembly2_E Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment |
2o2v-assembly1_A |
0.01 | 0.20 | 3.4e+00 | 2o2v-assembly1_A Crystal Structure of the Complex of Human Mitogen Activated Protein Kinase Kinase 5 Phox Domain (MAP2K5-phox) with Human Mitogen Activated Protein Kinase Kinase Kinase 3 (MAP3K3B-phox) |
4ic7-assembly1_B |
0.01 | 0.34 | 9.0e+00 | 4ic7-assembly1_B Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment |
9g6k-assembly1_LD |
0.01 | 0.18 | 8.4e+00 | 9g6k-assembly1_LD LSU structure derived from the LSU sample of the mitoribosome from T. gondii. |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2627c hyp |
hypothetical protein | 829 | 830 | coexpression:731 |
Rv2625c rip3 |
zinc metalloprotease Rip3 | 797 | 797 | coexpression:797 |
Rv2624c |
universal stress protein | 830 | 796 | coexpression:796 |
Rv1997 ctpF |
cation transporter ATPase F | 835 | 767 | coexpression:767 |
Rv2623 TB31.7 |
universal stress protein | 817 | 761 | coexpression:761 |
Rv2626c hrp1 |
hypoxic response protein | 904 | 735 | coexpression:735 textmining:654 |
Rv1736c narX |
nitrate reductase-like protein NarX | 747 | 731 | coexpression:731 |
Rv3132c devS |
two component sensor histidine kinase DevS | 703 | 703 | coexpression:703 |
Rv3128c |
Rv3128c, (MTCY164.38c), len: 337 aa. Conserved hypothetical protein, similar to other conserved hypothetical proteins. This ORF corresponds | 687 | 687 | coexpression:687 |
Rv2629 hyp |
hypothetical protein | 574 | 574 ctx | neighborhood:414 |
Rv2630 hyp |
hypothetical protein | 534 | 534 | |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 514 | 514 | coexpression:514 |
Rv2631 rtcB |
RNA-splicing ligase RtcB | 431 | 431 | |
Rv1733c |
transmembrane protein | 878 | 406 | coexpression:404 textmining:803 |
Rv3134c |
universal stress protein | 493 | 392 |
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
- Foldseek best: 7xzi-assembly1_F Cryo-EM structure of TOC-TIC supercomplex from Chlamydomonas re (prob 0.10, E=9e-01, TM=0.32)
- (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_217144.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2B0W9 - Curated reference: UniProt P9WL65 (SwissProt, reviewed; 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)
- Model confidence: ESMFold per-residue pLDDT (mean 60.5, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 26 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2628| MSTQRPRHSGIRAVGPYAWAGRCGRIGRWGVHQEAMMNLAIWHPRKVQSATIYQVTDRSHDGRTARVPGDEITSTVSGWLSELGTQSPLADELARAVRIGDWPAAYAIGEHLSVEIAVAV