Rv3919c (gid)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: ribosomal RNA small subunit methyltransferase G
- REFSEQ: 16S rRNA methyltransferase GidB
- PATRIC: rRNA small subunit 7-methylguanosine (m7G) methyltransferase GidB
- TUBERCULIST: Probable glucose-inhibited division protein B Gid
- NCBI: Probable glucose-inhibited division protein B Gid
- updated information (H37Rv4):
  - gene name: gid
  - function:
  - reference:
Type: Not Target
Start: 4407528
End: 4408202
Operon:

Trans-membrane region:
Role: III.C - Cell division
GO terms:
- GO:0070476 - rRNA (guanine-N7)-methylation (Uniprot)
- GO:0070043 - rRNA (guanine-N7-)-methyltransferase activity (Uniprot)
- GO:0032259 - methylation (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0008649 - rRNA methyltransferase activity (Uniprot)
- GO:0008168 - methyltransferase activity (Uniprot)
- GO:0006364 - rRNA processing (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0005737 - cytoplasm (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
Orthologs among selected mycobacteria
Protein structure:
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
3G8B	35%	Thermus thermophilus	T. thermophilus 16S rRNA G527 methyltransferase in complex with AdoMet in space group I222
3G8A	35%	Thermus thermophilus	T. thermophilus 16S rRNA G527 methyltransferase in complex with AdoHcy in space group P61
3G89	35%	Thermus thermophilus	T. thermophilus 16S rRNA G527 methyltransferase in complex with AdoMet and AMP in space group P61
3G88	35%	Thermus thermophilus	T. thermophilus 16S rRNA G527 methyltransferase in complex with AdoMet in space group P61

Links to additional information on gid:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -2.815 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MSPIEPAASAIFGPRLGLARRYAEALAGPGVERGLVGPREVGRLWDRHLLNCAVIGELLERGDRVVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRRTES
LREMVTDLGVAVEIVRGRAEESWVQDQLGGSDAAVSRAVAALDKLTKWSMPLIRPNGRMLAIKGERAHDEVREHRRVMIASGAVDVRVVTCGANYLRPPA
TVVFARRGKQIARGSARMASGGTA

(Nucleotide sequence available on KEGG)

Additional Information

Analysis of Positive Selection in Clinical Isolates new

Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
- Moldova: 2,057 clinical isolates
- global set: 5,195 clinical isolates from 15 other countries
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	YES	YES
omega peak height (95%CI lower bound)	3.54 (1.94)	4.54 (3.15)
codons under selection	16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 136, 137, 138, 139, 140	20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168
omega plots
genetic variants	link	link
statistics at each codon	link	link

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across >100 conditions *new*

Classification	Condition	Strain	Method	Reference	Notes
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.001400; 4 non-insertions in a row out of 13 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 13 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 13 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 13 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 13 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0023 (-)
- Rv2034 (-)

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0081 (-) (Direct binding)
- Rv0135c (-) (Direct binding)
- Rv0273c (-) (Direct binding)
- Rv0967 (csoR) (Direct binding)
- Rv1816 (-) (Direct binding)
- Rv3488 (-) (Direct binding)

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Not upregulated by other genes.
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0023 (-)
- Rv2034 (-)

TB Genome Annotation Portal