smpB Family assigned · medium auto-curated
H37Rv Rv3100c · MTBC0 mtbc0_003296 ·
160 aa · 3490665–3491147 (-) ·
RefSeq NP_217616.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | SsrA-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | SsrA-binding protein SmpB |
| Revised (this work) | SsrA-binding protein SmpB. Pfam: SmpB (PF01668.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGD3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | SsrA-binding protein |
| Curated function | Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | smpB |
| eggNOG description | Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene |
| Orthologous group | COG0691 |
| KEGG orthology |
K03664
|
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, GO:0044464
|
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 | 0.165 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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 |
|---|---|---|---|---|
SmpB | PF01668.24 | 2.6e-59 | 12–152 | SmpB protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsO (30S ribosomal protein S15), high confidence from genomic context alone (score 956 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2785c rpsO |
30S ribosomal protein S15 | 961 | 956 ctx | cooccurence:506 experimental:911 |
Rv3458c rpsD |
30S ribosomal protein S4 | 958 | 956 | experimental:911 |
Rv2904c rplS |
50S ribosomal protein L19 | 981 | 954 ctx | cooccurence:436 experimental:911 textmining:607 |
Rv0723 rplO |
50S ribosomal protein L15 | 950 | 948 | experimental:911 |
Rv0718 rpsH |
30S ribosomal protein S8 | 953 | 944 | experimental:911 |
Rv0683 rpsG |
30S ribosomal protein S7 | 947 | 941 | experimental:911 |
Rv3456c rplQ |
50S ribosomal protein L17 | 944 | 937 | experimental:911 |
Rv1643 rplT |
50S ribosomal protein L20 | 972 | 935 | experimental:911 textmining:591 |
Rv2890c rpsB |
30S ribosomal protein S2 | 971 | 934 | experimental:911 textmining:590 |
Rv0701 rplC |
50S ribosomal protein L3 | 970 | 933 | experimental:911 textmining:577 |
Rv0707 rpsC |
30S ribosomal protein S3 | 970 | 931 | experimental:911 textmining:591 |
Rv2442c rplU |
50S ribosomal protein L21 | 933 | 930 | experimental:911 |
Rv0720 rplR |
50S ribosomal protein L18 | 933 | 930 | experimental:911 |
Rv3443c rplM |
50S ribosomal protein L13 | 969 | 929 | experimental:912 textmining:589 |
Rv0682 rpsL |
30S ribosomal protein S12 | 938 | 929 | experimental:911 |
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: SsrA-binding protein
- MTBC0 PGAP product: SsrA-binding protein SmpB
- Pfam (hmmscan --cut_ga): SmpB PF01668.24 (E=3e-59)
- (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_217616.1)
- Domains: Pfam-A via hmmscan --cut_ga — SmpB (PF01668.24)
- 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
COG0691 - Curated reference: UniProt P9WGD3 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
118 functional partner(s); context anchor
rpsO - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003296|Rv3100c|smpB MSKSSRGGRQIVASNRKARHNYSIIEVFEAGVALQGTEVKSLREGQASLADSFATIDDGEVWLRNAHIPEYRHGSWTNHEPRRNRKLLLHRRQIDTLVGKIREGNFALVPLSLYFAEGKVKVELALARGKQARDKRQDMARRDAQREVLRELGRRAKGMT