speE Resolved · high auto-curated
H37Rv Rv2601 · MTBC0 - ·
523 aa · 2928388–2929959 (+) ·
RefSeq YP_177892.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | spermidine synthase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Spermidine synthase. Pfam: Spermine_synth (PF01564.24). |
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 |
P9WGE5
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Polyamine aminopropyltransferase |
| EC (curated) |
EC 2.5.1.16
|
| Curated function | Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy-AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | speE |
| eggNOG description | Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy- AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine |
| Orthologous group | COG4262 |
| EC number |
EC 2.5.1.16
|
| KEGG orthology |
K00797
|
| KEGG pathways |
map00270, map00330, map00410, map00480, map01100
|
| KEGG modules |
M00034, M00133
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.701 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 9 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (192) · clonal |
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 |
|---|---|---|---|---|
Spermine_synth | PF01564.24 | 2.5e-33 | 298–460 | Spermine/spermidine synthase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2600 (integral membrane protein), high confidence from genomic context alone (score 953 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2600 |
integral membrane protein | 952 | 953 ctx | neighborhood:881 cooccurence:596 |
Rv2598 hyp |
hypothetical protein | 912 | 912 ctx | neighborhood:638 cooccurence:757 |
Rv2597 |
membrane protein | 905 | 906 ctx | neighborhood:629 cooccurence:753 |
Rv0535 pnp |
5'-methylthioadenosine phosphorylase | 986 | 901 | database:900 textmining:870 |
Rv0091 mtn |
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | 979 | 900 | database:900 textmining:804 |
Rv2599 |
membrane protein | 650 | 650 ctx | neighborhood:638 |
Rv2602 vapC41 |
ribonuclease VapC41 | 531 | 531 ctx | neighborhood:528 |
Rv2601A vapB41 |
antitoxin VapB41 | 530 | 529 ctx | neighborhood:528 |
Rv2596 vapC40 |
ribonuclease VapC40 | 416 | 416 ctx | neighborhood:410 |
Rv3033 hyp |
hypothetical protein | 412 | 413 ctx | cooccurence:407 |
Rv2595 vapB40 |
antitoxin VapB40 | 410 | 410 ctx | neighborhood:410 |
Rv0671 lpqP |
lipoprotein LpqP | 608 | 190 | textmining:537 |
Rv1905c aao |
D-amino acid oxidase | 412 | 171 | |
Rv0075 |
aminotransferase | 685 | 102 | textmining:664 |
Rv2294 |
cystathionine beta-lyase | 670 | 96 | textmining:651 |
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): spermidine synthase
- Pfam (hmmscan --cut_ga): Spermine_synth PF01564.24 (E=3e-33)
- (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 YP_177892.1)
- Domains: Pfam-A via hmmscan --cut_ga — Spermine_synth (PF01564.24)
- 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
COG4262 - Curated reference: UniProt P9WGE5 (SwissProt, reviewed; Inferred from homology)
- 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 —
24 functional partner(s); context anchor
Rv2600 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2601|speE MTSTRQAGEATEASVRWRAVLLAAVAACAACGLVYELALLTLAASLNGGGIVATSLIVAGYIAALGAGALLIKPLLAHAAIAFIAVEAVLGIIGGLSAAALYAAFAFLDELDGSTLVLAVGTALIGGLVGAEVPLLMTLLQRGRVAGAADAGRTLANLNAADYLGALVGGLAWPFLLLPQLGMIRGAAVTGIVNLAAAGVVSIFLLRHVVSGRQLVTALCALAAALGLIATLLVHSHDIETTGRQQLYADPIIAYRHSAYQEIVVTRRGDDLRLYLDGGLQFCTRDEYRYTESLVYPAVSDGARSVLVLGGGDGLAARELLRQPGIEQIVQVELDPAVIELARTTLRDVNAGSLDNPRVHVVIDDAMSWLRGAAVPPAGFDAVIVDLRDPDTPVLGRLYSTEFYALAARALAPGGLMVVQAGSPYSTPTAFWRIISTIRSAGYAVTPYHVHVPTFGDWGFALARLTDIAPTPAVPSTAPALRFLDQQVLEAATVFSGDIRPRTLDPSTLDNPHIVEDMRHGWD