TB Genome Annotation Portal

Rv3877 (eccD1)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: ESX-1 secretion system protein eccD1
  • REFSEQ: transmembrane protein
  • PATRIC: Putative ESX-1 secretion system component Rv3877
  • TUBERCULIST: ESX conserved component EccD1. ESX-1 type VII secretion system protein. Probable transmembrane protein.
  • NCBI: ESX conserved component EccD1 ESX-1 type VII secretion system protein Probable transmembrane protein
  • updated information (H37Rv4):
    • gene name: eccD1
    • function:
    • reference:
• Coordinates in H37Rv: 4355007 - 4356542
• Gene length: 1536 bp (with stop codon), 511 aa (without stop codon)
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0044117 - growth of symbiont in host (Uniprot)
  • GO:0042783 - active evasion of host immune response (Uniprot)
  • GO:0016021 - integral component of membrane (Uniprot)
  • GO:0016020 - membrane (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005618 - cell wall (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
  4KV2	100%	Mycobacterium tuberculosis	Ubiquitin-like domain of the mycobacterium tuberculosis type VII secretion system protein ECCD1
  4KV3	94%	Escherichia coli	Ubiquitin-like domain of the Mycobacterium tuberculosis type VII secretion system protein EccD1 as maltose-binding protein fusion

• Links to additional information on eccD1:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 1.29 (from Jeremy Rock's lab)
  • Mycobrowser
  • PATRIC
  • KEGG - nucleotide and amino acid sequences of gene
  • BioCyc
  • Systems Biology

Amino Acid Sequence

LSAPAVAAGPTAAGATAARPATTRVTILTGRRMTDLVLPAAVPMETYIDDTVAVLSEVLEDTPADVLGGFDFTAQGVWAFARPGSPPLKLDQSLDDAGVV
DGSLLTLVSVSRTERYRPLVEDVIDAIAVLDESPEFDRTALNRFVGAAIPLLTAPVIGMAMRAWWETGRSLWWPLAIGILGIAVLVGSFVANRFYQSGHL
AECLLVTTYLLIATAAALAVPLPRGVNSLGAPQVAGAATAVLFLTLMTRGGPRKRHELASFAVITAIAVIAAAAAFGYGYQDWVPAGGIAFGLFIVTNAA
KLTVAVARIALPPIPVPGETVDNEELLDPVATPEATSEETPTWQAIIASVPASAVRLTERSKLAKQLLIGYVTSGTLILAAGAIAVVVRGHFFVHSLVVA
GLITTVCGFRSRLYAERWCAWALLAATVAIPTGLTAKLIIWYPHYAWLLLSVYLTVALVALVVVGSMAHVRRVSPVVKRTLELIDGAMIAAIIPMLLWIT
GVYDTVRNIRF

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

• data from Culviner et al (2025) (55,259 Mtb clinical isolates)
  • overall pN/pS for Rv3877: 0.970833139
  • lineage-specific pN/pS in L1: 1.923743204
  • lineage-specific pN/pS in L2: 0.623373233
  • lineage-specific pN/pS in L3: 0.710440119
  • lineage-specific pN/pS in L4: 0.731065358

• 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?	NO	YES
omega peak height (95%CI lower bound)	1.38 (0.22)	2.12 (1.01)
codons under selection		346, 347, 348, 349, 350, 351
omega plots
genetic variants*	link	link
statistics at each codon	link	link

• collected by: Becky Audette (Rubin lab) (7/28/2015)
• SRA accession: PRJNA484233
• counts: TnSeq_EccD1_KO_H37Rv.wig
• reference: TnSeq_H37Rv_R96_H37Rv.wig
• resampling: resampling_EccD1_KO.xlsx