Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | signal recognition particle protein |
|---|
| MTBC0 PGAP re-annotation | signal recognition particle protein |
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| Revised (this work) | Signal recognition particle protein. Pfam: SRP54_N (PF02881.25), SRP54 (PF00448.29), SRP_SPB (PF02978.27). |
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Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGD7
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Signal recognition particle protein |
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| EC (curated) |
EC 3.6.5.4
|
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| Curated function | Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY (By similarity). Most of the substrate proteins are involved in stress regulation, lipid metabolism, intermediary metabolism, and cell wall processes. Shows GTPase activity. |
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Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
U Intracellular trafficking, secretion and vesicular transport
|
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| Preferred name | ffh |
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| eggNOG description | Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY |
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| Orthologous group | COG0541 |
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| EC number |
EC 3.6.5.4
|
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| KEGG orthology |
K03106
|
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| KEGG pathways |
map02024, map03060, map03070
|
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| KEGG modules |
M00335
|
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| Gene Ontology (10) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, GO:0044464, GO:0071944
|
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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 |
0.528 · relaxed/neutral
|
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| Polymorphic sites (≥ 0.1% of strains) |
2 synonymous, 3 missense, 0 nonsense, 0 frameshift
|
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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 |
|---|
SRP54_N | PF02881.25 |
1.8e-21 | 5–82 |
SRP54-type protein, helical bundle domain |
SRP54 | PF00448.29 |
1.8e-68 | 100–302 |
SRP54-type protein, GTPase domain |
SRP_SPB | PF02978.27 |
1.2e-42 | 316–439 |
Signal peptide binding domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2921c ftsY |
signal recognition particle receptor FtsY |
998 |
995 |
experimental:829 database:935 textmining:811 |
Rv0732 secY |
preprotein translocase SecY |
985 |
964 |
experimental:471 database:933 textmining:625 |
Rv0638 secE1 |
preprotein translocase SecE |
981 |
954 |
experimental:446 database:900 textmining:622 |
Rv1440 secG |
protein-export membrane protein SecG |
959 |
943 |
experimental:446 database:900 |
Rv0702 rplD |
50S ribosomal protein L4 |
943 |
920 |
experimental:827 |
Rv3921c yidC |
membrane protein insertase YidC |
956 |
917 |
database:900 textmining:496 |
Rv0703 rplW |
50S ribosomal protein L23 |
922 |
913 |
experimental:829 |
Rv0718 rpsH |
30S ribosomal protein S8 |
920 |
909 |
experimental:793 |
Rv2890c rpsB |
30S ribosomal protein S2 |
917 |
908 |
experimental:802 |
Rv2588c yajC |
membrane protein secretion factor YajC |
983 |
904 |
database:900 textmining:838 |
Rv3240c secA1 |
protein translocase subunit SecA |
986 |
903 |
database:900 textmining:862 |
Rv1821 secA2 |
accessory Sec system translocase SecA2 |
973 |
902 |
database:900 textmining:740 |
Rv0721 rpsE |
30S ribosomal protein S5 |
924 |
901 |
coexpression:403 experimental:801 |
Rv0715 rplX |
50S ribosomal protein L24 |
905 |
900 |
experimental:828 |
Rv0651 rplJ |
50S ribosomal protein L10 |
904 |
900 |
experimental:826 |
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: signal recognition particle protein
- MTBC0 PGAP product: signal recognition particle protein
- Pfam (hmmscan --cut_ga): SRP54_N PF02881.25 (E=2e-21), SRP54 PF00448.29 (E=2e-68), SRP_SPB PF02978.27 (E=1e-42)
- (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_217432.1)
- Domains: Pfam-A via hmmscan --cut_ga — SRP54_N (PF02881.25), SRP54 (PF00448.29), SRP_SPB (PF02978.27)
- 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
COG0541
- Curated reference: UniProt
P9WGD7
(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 —
155 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003098|Rv2916c|ffh
MFESLSDRLTAALQGLRGKGRLTDADIDATTREIRLALLEADVSLPVVRAFIHRIKERARGAEVSSALNPAQQVVKIVNEELISILGGETRELAFAKTPPTVVMLAGLQGSGKTTLAGKLAARLRGQGHTPLLVACDLQRPAAVNQLQVVGERAGVPVFAPHPGASPESGPGDPVAVAAAGLAEARAKHFDVVIVDTAGRLGIDEELMAQAAAIRDAINPDEVLFVLDAMIGQDAVTTAAAFGEGVGFTGVALTKLDGDARGGAALSVREVTGVPILFASTGEKLEDFDVFHPDRMASRILGMGDVLSLIEQAEQVFDAQQAEEAAAKIGAGELTLEDFLEQMLAVRKMGPIGNLLGMLPGAAQMKDALAEVDDKQLDRVQAIIRGMTPQERADPKIINASRRLRIANGSGVTVSEVNQLVERFFEARKMMSSMLGGMGIPGIGRKSATRKSKGAKGKSGKKSKKGTRGPTPPKVKSPFGVPGMPGLAGLPGGLPDLSQMPKGLDELPPGLADFDLSKLKFPGKK
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