mihF Resolved · high auto-curated
H37Rv Rv1388 · MTBC0 - ·
190 aa · 1563694–1564266 (+) ·
RefSeq NP_215904.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integration host factor MihF |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Integration host factor MihF. Pfam: H2TH_5 (PF22525.2). |
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 |
P71658
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Integration host factor |
| Curated function | A nucleoid-associated protein (NAP) required for septum formation and normal cell division as well as for DNA segregation. Binds about 135 sites across the chromosome, most of which are genes involved in virulence; most DNA-binding sites are immediately upstream of transcription start sites. When mIHF is depleted most of the genes are down-regulated. Binds supercoiled and linear dsDNA in a concentration-dependent manner, probably non-sequence specifically. Binding compacts DNA, protecting it from degradation. Initial binding to supercoiled DNA opens it fully, followed by bending and compaction. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | mihF |
| eggNOG description | integration host factor |
| Orthologous group | COG0099 |
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 | 0.343 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
H2TH_5 | PF22525.2 | 1.5e-33 | 117–187 | S13-like H2TH domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0721 rpsE |
30S ribosomal protein S5 | 986 | 985 | coexpression:744 experimental:829 database:662 |
Rv3458c rpsD |
30S ribosomal protein S4 | 988 | 984 | coexpression:736 experimental:829 database:662 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 986 | 984 | coexpression:733 experimental:829 database:662 |
Rv0705 rpsS |
30S ribosomal protein S19 | 986 | 984 | coexpression:734 experimental:829 database:662 |
Rv0718 rpsH |
30S ribosomal protein S8 | 986 | 984 | coexpression:738 experimental:829 database:662 |
Rv0683 rpsG |
30S ribosomal protein S7 | 986 | 984 | coexpression:736 experimental:829 database:662 |
Rv2890c rpsB |
30S ribosomal protein S2 | 986 | 984 | coexpression:734 experimental:829 database:662 |
Rv0707 rpsC |
30S ribosomal protein S3 | 986 | 984 | coexpression:735 experimental:829 database:662 |
Rv0702 rplD |
50S ribosomal protein L4 | 986 | 984 | coexpression:737 experimental:829 database:662 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 986 | 984 | coexpression:733 experimental:829 database:662 |
Rv2785c rpsO |
30S ribosomal protein S15 | 985 | 984 | coexpression:734 experimental:829 database:662 |
Rv3459c rpsK |
30S ribosomal protein S11 | 985 | 984 | coexpression:733 experimental:829 database:662 |
Rv0682 rpsL |
30S ribosomal protein S12 | 985 | 984 | coexpression:732 experimental:829 database:662 |
Rv3462c infA |
translation initiation factor IF-1 | 984 | 983 | coexpression:732 experimental:829 database:629 |
Rv3443c rplM |
50S ribosomal protein L13 | 977 | 975 | coexpression:784 experimental:829 |
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): integration host factor MihF
- Pfam (hmmscan --cut_ga): H2TH_5 PF22525.2 (E=2e-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 NP_215904.1)
- Domains: Pfam-A via hmmscan --cut_ga — H2TH_5 (PF22525.2)
- 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
COG0099 - Curated reference: UniProt P71658 (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 — 251 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1388|mihF MLGNTIHVPCQPCRHGHGAPSRGLRGRPADRWPVARATPTLHVCPQNQGVGLDFVRKPEYGRLRWPAYPAGTNNDRLISMRDGGIVALPQLTDEQRAAALEKAAAARRARAELKDRLKRGGTNLTQVLKDAESDEVLGKMKVSALLEALPKVGKVKAQEIMTELEIAPTRRLRGLGDRQRKALLEKFGSA