Rv1860 (apa)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: alanine and proline-rich secreted protein apa
- REFSEQ: hypothetical protein
- PATRIC: Alanine and proline-rich secreted protein Apa fibronectin attachment protein
- TUBERCULIST: Alanine and proline rich secreted protein Apa (fibronectin attachment protein) (immunogenic protein MPT32) (antigen MPT-32) (45-kDa glycoprotein) (45/47 kDa antigen)
- NCBI: Alanine and proline rich secreted protein Apa (fibronectin attachment protein) (immunogenic protein MPT32) (antigen MPT-32) (45-kDa glycoprotein) (45/47 kDa antigen)
- updated information (H37Rv4):
  - gene name: apa
  - function:
  - reference:
Type: Not Target
Start: 2107736
End: 2108713
Operon:

Trans-membrane region:
Role: III.A.4 - Anions
GO terms:
- GO:0052559 - induction by symbiont of host immune response (Uniprot)
- GO:0050840 - extracellular matrix binding (Uniprot)
- GO:0009986 - cell surface (Uniprot)
- GO:0009267 - cellular response to starvation (Uniprot)
- GO:0005576 - extracellular region (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
5ZX9	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of apo form fibronectin-binding protein Apa from Mycobacterium tuberculosis
5ZXA	99%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of fibronectin-binding protein Apa mutant from Mycobacterium tuberculosis

Links to additional information on apa:
- TBDB (updated)
- KEGG - nucleotide and amino acid sequences of gene
- BioCyc
- Systems Biology
- Mycobrowser
- PATRIC

Amino Acid Sequence

MHQVDPNLTRRKGRLAALAIAAMASASLVTVAVPATANADPEPAPPVPTTAASPPSTAAAPPAPATPVAPPPPAAANTPNAQPGDPNAAPPPADPNAPPP
PVIAPNAPQPVRIDNPVGGFSFALPAGWVESDAAHFDYGSALLSKTTGDPPFPGQPPPVANDTRIVLGRLDQKLYASAEATDSKAAARLGSDMGEFYMPY
PGTRINQETVSLDANGVSGSASYYEVKFSDPSKPNGQIWTGVIGSPAANAPDAGPPQRWFVVWLGTANNPVDKGAAKALAESIRPLVAPPPAPAPAPAEP
APAPAPAGEVAPTPTTPTPQRTLPA

(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
Uncertain	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.301400; 5 non-insertions in a row out of 16 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 16 sites
Uncertain	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.112900; 3 non-insertions in a row out of 16 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 16 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 16 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 3.01
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:
- Rv1423 (whiA) (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:

Property	Value	Creator	Evidence	PMID	Comment
Symbol	ModD	jlew			Tat substrate. Demonstrated by experimental verification that four secreted proteins from Mtb carrying putative Tat signals are bona fide Tat substrates M. Marrichi, L. Camacho et al. Genetic Toggling of Alkaline Phosphatase Folding Reveals Signal Peptides for All Major Modes of Transport across the Inner Membrane of Bacteria. J. Biol. Chem. 2008
Citation	Genetic Toggling of Alkaline Phosphatase Folding Reveals Signal Peptides for All Major Modes of Transport across the Inner Membrane of Bacteria. M. Marrichi, L. Camacho et al. J. Biol. Chem. 2008	jlew		18819916	Tat substrate. Demonstrated by experimental verification that four secreted proteins from Mtb carrying putative Tat signals are bona fide Tat substrates

TB Genome Annotation Portal