Rv1000c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: Alkylated DNA repair protein AlkB
- TUBERCULIST: Conserved hypothetical protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Type: Not Target
Start: 1116531
End: 1117148
Operon:

Trans-membrane region:
Role: -
GO terms:
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0051213 - dioxygenase activity (Uniprot)
- GO:0035552 - oxidative single-stranded DNA demethylation (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0009432 - SOS response (Uniprot)
- GO:0006307 - DNA dealkylation involved in DNA repair (Uniprot)
- GO:0006281 - DNA repair (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
4MGT	35%	Homo sapiens	ALKBH2 R110A cross-linked to undamaged dsDNA
4MG2	35%	Homo sapiens	ALKBH2 F102A cross-linked to undamaged dsDNA
3S5A	35%	Homo sapiens	ABH2 cross-linked to undamaged dsDNA-2 with cofactors
3S57	35%	Homo sapiens	ABH2 cross-linked with undamaged dsDNA-1 containing cofactors
3RZM	35%	Homo sapiens	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage
3RZL	35%	Homo sapiens	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage
3RZK	35%	Homo sapiens	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage
3RZJ	35%	Homo sapiens	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage
3RZH	35%	Homo sapiens	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage
3RZG	35%	Homo sapiens	Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage

Links to additional information on Rv1000c:
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.326 (from Jeremy Rock's lab)

Amino Acid Sequence

MCDKLGGVAIAVQGALFEHNERRQLGDGAFIDIRSGWLTGGEELLDALLSTVPWRAERRQMYDRVVDVPRLVSFHDLTIEDPPHPQLARMRRRLNDIYGG
ELGEPFTTAGLCYYRDGSDSVAWHGDTIGRGSTEDTMVAIVSLGATRVFALRPRGRGPSLRLPLAHGDLLVMGGSCQRTFEHAVPKTSAPTGPRVSIQFR
PRDVR

(Nucleotide sequence available on KEGG)

Additional Information

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: 0.000000; 2 non-insertions in a row out of 8 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 8 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 8 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 9 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 9 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:

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0691c (-) (Direct binding)
- Rv2034 (-) (Direct binding)
- Rv2324 (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0023 (-)
- Rv1990c (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv2720 (lexA)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Regulatory Rv2720	harsharohiratruefriend	TAS		Structural Analysis EO. Davis, EM. Dullaghan et al. Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis. J. Bacteriol. 2002
Citation	The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of RecA. L. Rand, J. Hinds et al. Mol. Microbiol. 2003	harsharohiratruefriend	TAS	14617159	Structural Analysis
Interaction	Regulatory Rv2720	harsharohiratruefriend	TAS		Structural Analysis L. Rand, J. Hinds et al. The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of RecA. Mol. Microbiol. 2003
Citation	The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. authors,L. Aravind,EV. Koonin Genome Biol. 2001	harsharohiratruefriend	TAS	11276424	Structural Analysis
Interaction	Regulatory Rv2720	harsharohiratruefriend	TAS		Structural Analysis authors,L. Aravind,EV. Koonin The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Genome Biol. 2001
Citation	Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis. EO. Davis, EM. Dullaghan et al. J. Bacteriol. 2002	harsharohiratruefriend	TAS	12029045	Spectrophotometric Assay
Interaction	Regulatory Rv2720	harsharohiratruefriend	TAS		Spectrophotometric Assay EO. Davis, EM. Dullaghan et al. Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis. J. Bacteriol. 2002
Citation	The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of RecA. L. Rand, J. Hinds et al. Mol. Microbiol. 2003	harsharohiratruefriend	TAS	14617159	Spectrophotometric Assay
Interaction	Regulatory Rv2720	harsharohiratruefriend	TAS		Spectrophotometric Assay L. Rand, J. Hinds et al. The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of RecA. Mol. Microbiol. 2003
Citation	The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. authors,L. Aravind,EV. Koonin Genome Biol. 2001	harsharohiratruefriend	TAS	11276424	Spectrophotometric Assay
Interaction	Regulatory Rv2720	harsharohiratruefriend	TAS		Spectrophotometric Assay authors,L. Aravind,EV. Koonin The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Genome Biol. 2001
Citation	Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis. EO. Davis, EM. Dullaghan et al. J. Bacteriol. 2002	harsharohiratruefriend	TAS	12029045	Structural Analysis
Interaction	RegulatedBy Rv2720	yamir.moreno	TAS		Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008

TB Genome Annotation Portal