Rv3447c (eccC4)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: ESX-4 secretion system protein eccC4
- REFSEQ: hypothetical protein
- PATRIC: FtsK/SpoIIIE family protein
- TUBERCULIST: ESX conserved component EccC4. ESX-4 type VII secretion system protein. Probable membrane protein.
- NCBI: ESX conserved component EccC4 ESX-4 type VII secretion system protein Probable membrane protein
- updated information (H37Rv4):
  - gene name: eccC4
  - function:
  - reference:
Type: Not Target
Start: 3864528
End: 3868238
Operon:

Trans-membrane region:
Role: II.C.5 - Other membrane proteins
GO terms:
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005524 - ATP binding (Uniprot)
- GO:0003677 - DNA binding (Uniprot)
- GO:0000166 - nucleotide binding (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
4N1A	45%	Thermomonospora curvata	Thermomonospora curvata EccC (ATPases 2 and 3) in complex with a signal sequence peptide
4NH0	45%	Thermomonospora curvata	Cytoplasmic domain of the Thermomonospora curvata Type VII Secretion ATPase EccC
6SGZ	38%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of protomer 2 of the ESX-3 core complex
6UMM	35%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	A complete structure of the ESX-3 translocon complex
6SGX	35%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of protomer 1 of the ESX-3 core complex
6SGW	35%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of the ESX-3 core complex

Links to additional information on eccC4:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.738 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MNSGPACATADILVAPPPELRRSEPSSLLIRLLPVVMSVATVGVMVTVFLPGSPATRHPTFLAFPMMMLVSLVVTAVTGRGRRHVSGIHNDRVDYLGYLS
VLRTSVTQTAAAQHVSLNWTHPDPATLWTLIGGPRMWERRPGAADFCRIRVGVGSAPLATRLVVGQLPPAQRADPVTRAALRCFLAAHATIADAPIAIPL
RVGGPIAIDGDPTKVRGLLRAMICQLAVWHSPEELLIAGVVSDRNRAHWDWLKWLPHNQHPNACDALGPAPMVYSTLAEMQNALAATVLAHVVAIVDTAE
RGNGAITGVITIEVGARRDGAPPVVRCAGEVTALACPDQLEPQDALVCARRLAAHRVGHSGRTFIRGSGWAELVGIGDVAAFDPSTLWRNVNQHDRLRVP
IGVTPDGTAVQLDIKEAAEQGMGPHGLCVGATGSGKSELLRTIALGMMARNSPEVLNLLLVDFKGGATFLDLAGAPHVAAVITNLAEEAPLVARMQDALA
GEMSRRQQLLRMAGHLVSVTAYQRARQTGAQLPCLPILFIVVDEFSELLSQHPEFVDVFLAIGRVGRSLGMHLLLASQRLDEGRLRGLETHLSYRMCLKT
WSASESRNVLGTQDAYQLPNTPGAGLLQTGTGELIRFQTAFVSGPLRRASPSAVHPVAPPSVRPFTTHAAAPVTAGPVGGTAEVPTPTVLHAVLDRLVGH
GPAAHQVWLPPLDEPPMLGALLRDAEPAQAELAVPIGIVDRPFEQSRVPLTIDLSGAAGNVAVVGAPQTGKSTALRTLIMALAATHDAGRVQFYCLDFGG
GALAQVDELPHVGAVAGRAQPQLASRMLAELESAVRFREAFFRDHGIDSVARYRQLRAKSAAESFADIFLVIDGWASLRQEFAALEESIVALAAQGLSFG
VHVALSAARWAEIRPSLRDQIGSRIELRLADPADSELDRRQAQRVPVDRPGRGLSRDGMHMVIALPDLDGVALRRRSGDPVAPPIPLLPARVDYDSVVAR
AGDELGAHILLGLEERRGQPVAVDFGRHPHLLVLGDNECGKTAALRTLCREIVRTHTAARAQLLIVDFRHTLLDVIESEHMSGYVSSPAALGAKLSSLVD
LLQARMPAPDVSQAQLRARSWWSGPDIYVVVDDYDLVAVSSGNPLMVLLEYLPHARDLGLHLVVARRSGGAARALFEPVLASLRDLGCRALLMSGRPDEG
ALFGSSRPMPLPPGRGILVTGAGDEQLVQVAWSPPP

(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: 0.764800; 10 non-insertions in a row out of 46 sites
Uncertain	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.760050; 8 non-insertions in a row out of 46 sites
Uncertain	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.941000; 9 non-insertions in a row out of 46 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.053250; 5 non-insertions in a row out of 46 sites
Uncertain	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.052500; 5 non-insertions in a row out of 46 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:
- Rv0022c (whiB5)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings to other targets were found.

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0022c (whiB5)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Citation	Characterization of the Mycobacterium tuberculosis sigma factor SigM by assessment of virulence and identification of SigM-dependent genes. N. Agarwal, SC. Woolwine et al. Infect. Immun. 2007	yashabhasin	IEP	17088352	Co-expression (Functional linkage)
Interaction	Regulatory Rv3911	yashabhasin	IEP		Co-expression (Functional linkage) N. Agarwal, SC. Woolwine et al. Characterization of the Mycobacterium tuberculosis sigma factor SigM by assessment of virulence and identification of SigM-dependent genes. Infect. Immun. 2007

TB Genome Annotation Portal