infB Resolved · high auto-curated
H37Rv Rv2839c · MTBC0 mtbc0_003018 ·
900 aa · 3165837–3168539 (-) ·
RefSeq NP_217355.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | translation initiation factor IF-2 |
|---|---|
| MTBC0 PGAP re-annotation | translation initiation factor IF-2 |
| Revised (this work) | Translation initiation factor IF-2. Pfam: IF2_N (PF04760.22), GTP_EFTU (PF00009.34), MMR_HSR1 (PF01926.30), Ras (PF00071.29), EF-G_D2 (PF22042.3), IF-2 (PF11987.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKK1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Translation initiation factor IF-2 |
| Curated function | One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | infB |
| eggNOG description | One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex |
| Orthologous group | COG0481 |
| KEGG orthology |
K02519
|
| Gene Ontology (11) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, 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 | 0.194 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 13 synonymous, 7 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 |
|---|---|---|---|---|
IF2_N | PF04760.22 | 1.4e-13 | 5–54 | Translation initiation factor IF-2, N-terminal region |
GTP_EFTU | PF00009.34 | 1.6e-33 | 401–560 | Elongation factor Tu GTP binding domain |
MMR_HSR1 | PF01926.30 | 2.6e-08 | 401–510 | 50S ribosome-binding GTPase |
Ras | PF00071.29 | 3.9e-07 | 402–555 | Ras family |
EF-G_D2 | PF22042.3 | 2.0e-26 | 576–655 | Elongation factor G domain 2 |
IF-2 | PF11987.14 | 3.9e-36 | 679–791 | Translation-initiation factor 2 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rbfA (ribosome-binding factor RbfA), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2838c rbfA |
ribosome-binding factor RbfA | 998 | 997 ctx | neighborhood:882 coexpression:969 textmining:611 |
Rv2890c rpsB |
30S ribosomal protein S2 | 994 | 993 | coexpression:743 experimental:928 database:444 |
Rv0704 rplB |
50S ribosomal protein L2 | 995 | 992 | coexpression:790 experimental:928 database:412 textmining:456 |
Rv0723 rplO |
50S ribosomal protein L15 | 992 | 991 | coexpression:764 experimental:928 database:428 |
Rv0683 rpsG |
30S ribosomal protein S7 | 992 | 990 | coexpression:681 experimental:928 database:444 |
Rv0721 rpsE |
30S ribosomal protein S5 | 992 | 990 | coexpression:695 experimental:928 database:444 |
Rv0702 rplD |
50S ribosomal protein L4 | 991 | 990 | coexpression:732 experimental:928 database:412 |
Rv0701 rplC |
50S ribosomal protein L3 | 991 | 989 | coexpression:712 experimental:923 database:412 |
Rv3459c rpsK |
30S ribosomal protein S11 | 992 | 988 | coexpression:724 experimental:928 database:429 textmining:438 |
Rv0708 rplP |
50S ribosomal protein L16 | 990 | 988 | coexpression:764 experimental:922 database:412 |
Rv3458c rpsD |
30S ribosomal protein S4 | 989 | 986 | coexpression:780 experimental:928 |
Rv0707 rpsC |
30S ribosomal protein S3 | 989 | 985 | coexpression:797 experimental:928 |
Rv0706 rplV |
50S ribosomal protein L22 | 987 | 984 | coexpression:649 experimental:928 database:418 |
Rv0640 rplK |
50S ribosomal protein L11 | 986 | 982 | coexpression:695 experimental:904 database:407 |
Rv3443c rplM |
50S ribosomal protein L13 | 986 | 982 | coexpression:521 experimental:923 database:412 |
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: translation initiation factor IF-2
- MTBC0 PGAP product: translation initiation factor IF-2
- Pfam (hmmscan --cut_ga): IF2_N PF04760.22 (E=1e-13), GTP_EFTU PF00009.34 (E=2e-33), MMR_HSR1 PF01926.30 (E=3e-08), Ras PF00071.29 (E=4e-07), EF-G_D2 PF22042.3 (E=2e-26), IF-2 PF11987.14 (E=4e-36)
- (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_217355.1)
- Domains: Pfam-A via hmmscan --cut_ga — IF2_N (PF04760.22), GTP_EFTU (PF00009.34), MMR_HSR1 (PF01926.30), Ras (PF00071.29), EF-G_D2 (PF22042.3), IF-2 (PF11987.14)
- 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
COG0481 - Curated reference: UniProt P9WKK1 (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 —
245 functional partner(s); context anchor
rbfA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003018|Rv2839c|infB MAAGKARVHELAKELGVTSKEVLARLSEQGEFVKSASSTVEAPVARRLRESFGGSKPAPAKGTAKSPGKGPDKSLDKALDAAIDMAAGNGKATAAPAKAADSGGAAIVSPTTPAAPEPPTAVPPSPQAPHPGMAPGARPGPVPKPGIRTPRVGNNPFSSAQPADRPIPRPPAPRPGTARPGVPRPGASPGSMPPRPGGAVGGARPPRPGAPRPGGRPGAPGAGRSDAGGGNYRGGGVGAAPGTGFRGRPGGGGGGRPGQRGGAAGAFGRPGGAPRRGRKSKRQKRQEYDSMQAPVVGGVRLPHGNGETIRLARGASLSDFADKIDANPAALVQALFNLGEMVTATQSVGDETLELLGSEMNYNVQVVSPEDEDRELLESFDLSYGEDEGGEEDLQVRPPVVTVMGHVDHGKTRLLDTIRKANVREAEAGGITQHIGAYQVAVDLDGSQRLITFIDTPGHEAFTAMRARGAKATDIAILVVAADDGVMPQTVEAINHAQAADVPIVVAVNKIDKEGADPAKIRGQLTEYGLVPEEFGGDTMFVDISAKQGTNIEALEEAVLLTADAALDLRANPDMEAQGVAIEAHLDRGRGPVATVLVQRGTLRVGDSVVAGDAYGRVRRMVDEHGEDVEVALPSRPVQVIGFTSVPGAGDNFLVVDEDRIARQIADRRSARKRNALAARSRKRISLEDLDSALKETSQLNLILKGDNAGTVEALEEALMGIQVDDEVVLRVIDRGVGGITETNVNLASASDAVIIGFNVRAEGKATELASREGVEIRYYSVIYQAIDEIEQALRGLLKPIYEENQLGRAEIRALFRSSKVGLIAGCLVTSGVMRRNAKARLLRDNIVVAENLSIASLRREKDDVTEVRDGFECGLTLGYADIKEGDVIESYELVQKERA