Rv1100 Still unknown · low auto-curated
H37Rv Rv1100 · MTBC0 - ·
233 aa · 1228683–1229384 (+) ·
RefSeq NP_215616.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF4245. Function unknown. Foldseek best (non-significant) hit: 2p4b-assembly1_B Crystal structure of E.coli RseB (prob 0.41, TM 0.41). |
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 |
O53448
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 | Protein of unknown function (DUF4245) |
| Orthologous group | 2E5JR |
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 | 0.716 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
DUF4245 | PF14030.12 | 9.2e-52 | 34–223 | Protein of unknown function (DUF4245) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 93.1 (very high). A confident model makes the fold comparison meaningful.
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 |
|---|---|---|---|---|
2p4b-assembly1_B |
0.41 | 0.41 | 4.3e-01 | 2p4b-assembly1_B Crystal structure of E.coli RseB |
4fpw-assembly3_B |
0.23 | 0.25 | 5.4e-02 | 4fpw-assembly3_B Crystal Structure of CalU16 from Micromonospora echinospora. Northeast Structural Genomics Consortium Target MiR12. |
8f2u-assembly1_J |
0.18 | 0.54 | 2.5e+00 | 8f2u-assembly1_J Human CCC complex |
8iex-assembly1_A |
0.16 | 0.52 | 2.3e+00 | 8iex-assembly1_A Solution structure of AtWRKY11-DBD |
3pu2-assembly3_C |
0.16 | 0.22 | 6.0e-02 | 3pu2-assembly3_C Crystal Structure of the Q3J4M4_RHOS4 protein from Rhodobacter sphaeroides. Northeast Structural Genomics Consortium Target RhR263. |
4fpw-assembly3_A |
0.16 | 0.26 | 1.2e-01 | 4fpw-assembly3_A Crystal Structure of CalU16 from Micromonospora echinospora. Northeast Structural Genomics Consortium Target MiR12. |
6pny-assembly1_A |
0.15 | 0.38 | 1.0e+00 | 6pny-assembly1_A X-ray Structure of Flpp3 |
3rd6-assembly2_B-2 |
0.14 | 0.30 | 4.6e-01 | 3rd6-assembly2_B-2 Crystal structure of Mll3558 protein from Rhizobium loti. Northeast Structural Genomics Consortium target id MlR403 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2732c (transmembrane protein), high confidence from genomic context alone (score 754 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) |
|---|---|---|---|---|
Rv0038 hyp |
hypothetical protein | 763 | 764 | coexpression:730 |
Rv1019 |
transcriptional regulator | 759 | 759 | coexpression:759 |
Rv1488 hyp |
hypothetical protein | 757 | 757 | coexpression:757 |
Rv2732c |
transmembrane protein | 753 | 754 ctx | cooccurence:750 |
Rv1098c fum |
fumarate hydratase | 751 | 751 ctx | neighborhood:747 |
Rv1610 |
membrane protein | 747 | 748 ctx | cooccurence:746 |
Rv3802c |
membrane protein | 742 | 743 ctx | cooccurence:739 |
Rv0358 hyp |
hypothetical protein | 742 | 742 ctx | cooccurence:742 |
Rv0010c |
membrane protein | 734 | 734 ctx | cooccurence:733 |
Rv0903c prrA |
two component transcriptional regulator PrrA | 734 | 734 | coexpression:734 |
Rv2788 sirR |
transcriptional repressor SirR | 733 | 733 | coexpression:733 |
Rv3792 aftA |
arabinofuranosyltransferase | 733 | 733 ctx | cooccurence:733 |
Rv3668c |
protease | 731 | 731 ctx | cooccurence:731 |
Rv0377 |
HTH-type transcriptional regulator | 729 | 729 | coexpression:729 |
Rv2171 lppM |
lipoprotein LppM | 720 | 720 ctx | cooccurence:720 |
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): DUF4245 PF14030.12 (E=9e-52)
- Foldseek best: 2p4b-assembly1_B Crystal structure of E.coli RseB (prob 0.41, E=4e-01, TM=0.41)
- (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_215616.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF4245 (PF14030.12)
- 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
2E5JR - Curated reference: UniProt O53448 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 93.1, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
101 functional partner(s); context anchor
Rv2732c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1100| MVGDCPRSRTVRWSWDTGHVTAEPQPTPRPAKPRLLQDGRDMFWSLAPLVVGCILLAGLVGMCSFQLGGTKRGPIPSYDAAQALRADAKTLGFPIRLPQLPGGWTPNSGGRGGIENGRADPATGQRRNAATSIVGFISPTGRYLSLTQSNADEDKLVGSIHPSMYPTGTVDVGGTRWVVYEGSDENGAVEPVWTTRLTGPGGATQLAITGAGSIDQFRTLASATQSQPPLPAR