Rv2708c Still unknown · low auto-curated
H37Rv Rv2708c · MTBC0 - ·
82 aa · 3021548–3021796 (-) ·
RefSeq NP_217224.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3039. Function unknown. Foldseek best (non-significant) hit: 1v6t-assembly1_A Crystal Structure of Lactam Utilization Protein from (prob 0.07, TM 0.34). |
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 |
I6X562
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DUF3039 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3039) |
| Orthologous group | 2CAFG |
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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF3039 | PF11238.14 | 2.1e-28 | 24–79 | Protein of unknown function (DUF3039) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 65.4 (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 |
|---|---|---|---|---|
1v6t-assembly1_A |
0.07 | 0.34 | 1.1e+00 | 1v6t-assembly1_A Crystal Structure of Lactam Utilization Protein from Pyrococcus horikoshii Ot3 |
1uys-assembly1_A |
0.04 | 0.19 | 7.2e-01 | 1uys-assembly1_A Acetyl-CoA carboxylase carboxyltransferase domain in complex with inhibitor haloxyfop |
5csk-assembly1_A |
0.02 | 0.15 | 6.8e-01 | 5csk-assembly1_A Crystal structure of yeast acetyl-CoA carboxylase, unbiotinylated |
2w8m-assembly1_B |
0.02 | 0.33 | 8.4e+00 | 2w8m-assembly1_B Structure of D212, a nuclease from a fusselovirus. |
1uyr-assembly1_B |
0.02 | 0.14 | 8.8e-01 | 1uyr-assembly1_B Acetyl-CoA Carboxylase Carboxyltransferase Domain in complex with inhibitor Diclofop |
6e5u-assembly2_X |
0.01 | 0.25 | 9.6e+00 | 6e5u-assembly2_X Crystal structure of the mRNA export receptor NXF1/NXT1 in complex with influenza virus NS1 protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2709 (transmembrane protein), high confidence from genomic context alone (score 820 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) |
|---|---|---|---|---|
Rv2709 |
transmembrane protein | 820 | 820 ctx | neighborhood:788 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 769 | 769 ctx | cooccurence:767 |
Rv2413c hyp |
hypothetical protein | 760 | 761 ctx | cooccurence:759 |
Rv2219 |
transmembrane protein | 755 | 755 ctx | cooccurence:753 |
Rv2699c hyp |
hypothetical protein | 724 | 725 ctx | cooccurence:722 |
Rv2731 hyp |
hypothetical protein | 687 | 688 ctx | cooccurence:686 |
Rv2696c hyp |
hypothetical protein | 686 | 686 ctx | cooccurence:685 |
Rv0807 hyp |
hypothetical protein | 684 | 685 ctx | cooccurence:682 |
Rv1830 |
HTH-type transcriptional regulator | 671 | 671 ctx | cooccurence:668 |
Rv2680 hyp |
hypothetical protein | 670 | 671 ctx | cooccurence:669 |
Rv2239c hyp |
hypothetical protein | 661 | 661 ctx | cooccurence:658 |
Rv3195 hyp |
hypothetical protein | 655 | 655 ctx | cooccurence:655 |
Rv2901c hyp |
hypothetical protein | 635 | 635 ctx | cooccurence:630 |
Rv2745c clgR |
transcriptional regulator ClgR | 634 | 635 ctx | cooccurence:627 |
Rv1002c pmt |
dolichyl-phosphate-mannose--protein mannosyltransferase | 634 | 635 ctx | cooccurence:633 |
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): DUF3039 PF11238.14 (E=2e-28)
- Foldseek best: 1v6t-assembly1_A Crystal Structure of Lactam Utilization Protein from Pyrococcus (prob 0.07, E=1e+00, TM=0.34)
- (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_217224.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3039 (PF11238.14)
- 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
2CAFG - Curated reference: UniProt I6X562 (TrEMBL, unreviewed; Evidence at protein level)
- Model confidence: ESMFold per-residue pLDDT (mean 65.4, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
48 functional partner(s); context anchor
Rv2709 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2708c| MSGMQTQTIERTDADERVDDGTGSDTPKYFHYVKKDKIAESAVMGSHVVALCGEVFPVTRAPKPGSPVCPDCKRIYDTLKKG