2. PATHOGENS
Basic Information
Accession number
GCA_000193695.2
Release date
2010-12-29
Organism
Clostridioides difficile 6503
Species name
Clostridioides difficile
Assembly level
Contig
Assembly name
ASM19369v2
Assembly submitter
Cornell University
Assembly Type
haploid
Genome size
4.1 Mb
GC percent
28.0
Contig count
150
Collection date
-
Sample location
-
Host
-
Isolation source
-
Isolate type
-
Strain
6503
Isolate
-
ARG List
ORF_ID Pass_Bitscore Best_Hit_Bitscore Best_Hit_ARO Best_Identities ARO Model_type SNPs_in_Best_Hit_ARO Other_SNPs Drug class Resistance mechanism AMR gene family Description
ADEI01000128.1_50 # 43159 # 44322 175.0 201.83 vanT gene in vanG cluster 34.59 ARO:3002972 protein homolog model glycopeptide antibiotic antibiotic target alteration glycopeptide resistance gene cluster; vanT Also known as vanTG, is a vanT variant found in the vanG gene cluster.
ADEI01000086.1_61 # 64064 # 65533 50.0 134.806 vanW gene in vanI cluster 33.76 ARO:3003724 protein homolog model glycopeptide antibiotic antibiotic target alteration vanW; glycopeptide resistance gene cluster Also known as vanWI, is a vanW variant found in the vanI gene cluster.
ADEI01000073.1_23 # 19558 # 20274 50.0 116.701 vanY gene in vanG cluster 36.45 ARO:3002959 protein homolog model glycopeptide antibiotic antibiotic target alteration vanY; glycopeptide resistance gene cluster Also known as vanYG, is a vanY variant found in the vanG gene cluster.
ADEI01000070.1_36 # 37249 # 38508 50.0 97.0561 vanW gene in vanI cluster 27.39 ARO:3003724 protein homolog model glycopeptide antibiotic antibiotic target alteration vanW; glycopeptide resistance gene cluster Also known as vanWI, is a vanW variant found in the vanI gene cluster.
ADEI01000042.1_69 # 81111 # 82049 550.0 602.438 CDD-2 96.15 ARO:3006905 protein homolog model carbapenem antibiotic inactivation CDD beta-lactamase CDD-2 is a CDD beta-lactamase.
ADEI01000029.1_7 # 6190 # 7515 810.0 852.818 cdeA 98.87 ARO:3003835 protein homolog model fluoroquinolone antibiotic; disinfecting agents and antiseptics antibiotic efflux multidrug and toxic compound extrusion (MATE) transporter Clostridioides difficile and Escherichia coli multidrug efflux transporter with antiporter function. Confers resistance to fluoroquinolones in E. coli and acriflavin in Clostridioides difficile.
ADEI01000008.1_6 # 5682 # 6329 50.0 99.7525 vanY gene in vanB cluster 34.81 ARO:3002956 protein homolog model glycopeptide antibiotic antibiotic target alteration vanY; glycopeptide resistance gene cluster Also known as vanYB, is a vanY variant found in the vanB gene cluster.
VF List
Query_id %Identity E-value Related genes VF ID Virulence factor VFcategory VFcategoryID Characteristics Description Strain
ADEI01000132.1_41 98.052 0.0 CD0873 VF0593 CD0873 Adherence VFC0001 Numerous bacterial adhesins also characterized as lipoproteins, similar to CD0873, including the adhesin PsaA, a solute-binding lipoprotein of the Mn2+ ABC transporter of S. pneumoniae; CD0873 is annotated as a substrate-binding protein component SBP of an ABC transporter and is an immunoreactive protein in human infection (CD0873) ABC transporter substrate-binding protein [CD0873 (VF0593) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000118.1_1 74.559 0.0 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
ADEI01000103.1_1 98.276 1.79E-33 cbpA VF0592 CbpA Adherence VFC0001 MSCRAMMs have a common surface localization that in Gram-positive bacteria is usually mediated by a cell wall sorting signal through which they are covalently anchored to the cell wall peptidoglycan by sortase. (cbpA) collagen-binding adhesin CbpA [CbpA (VF0592) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000092.1_1 88.628 0.0 CD3246 VF0599 CD3246 Adherence VFC0001 Cell surface protein cleaved and covalently anchored to m-DAP in the peptidoglycan by SrtB (CD3246) Cys-Gln thioester bond-forming surface protein [CD3246 (VF0599) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000082.1_14 96.341 2.17E-47 CD3246 VF0599 CD3246 Adherence VFC0001 Cell surface protein cleaved and covalently anchored to m-DAP in the peptidoglycan by SrtB (CD3246) Cys-Gln thioester bond-forming surface protein [CD3246 (VF0599) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000075.1_43 98.477 0.0 fbpA/fbp68 VF0595 FbpA/Fbp68 Adherence VFC0001 Fibronectin is a dimeric glycoprotein (~440 kDa) which is present in a soluble form in plasma and in an immobilized form on cell surfaces and in extracellular matrix. It is an important target for bacterial attachment in many pathogens, such as S. pyogenes, S. pneumoniae and L. monocytogenes, where fibronectin-binding proteins are important virulence factors. (fbpA/fbp68) fibronectin-binding protein FbpA [FbpA/Fbp68 (VF0595) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000071.1_1 95.455 2.58E-38 CD3246 VF0599 CD3246 Adherence VFC0001 Cell surface protein cleaved and covalently anchored to m-DAP in the peptidoglycan by SrtB (CD3246) Cys-Gln thioester bond-forming surface protein [CD3246 (VF0599) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000069.1_1 99.091 2.98E-164 zmp1 VF0600 Zmp1 Exoenzyme VFC0251 (zmp1) zinc metalloprotease Zmp1 [Zmp1 (VF0600) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
ADEI01000069.1_44 78.689 0.0 cwp66 VF0591 Cwp66 Adherence VFC0001 (cwp66) cell wall-binding protein Cwp66 [Cwp66 (VF0591) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000069.1_46 98.731 0.0 cwp84 VF0590 Cwp84 Exoenzyme VFC0251 (cwp84) cell wall-binding cysteine protease Cwp84 [Cwp84 (VF0590) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
ADEI01000060.1_1 98.473 0.0 cwpV VF0596 CwpV Adherence VFC0001 CwpV is the largest member of the CWP family and consists of three distinct domains: (1) an N-terminal region with putative cell wall binding activity, (2) a region of unknown function terminating in a serine-glycine-rich flexible linker, (3) C-terminal domain; Five different types of CwpV have been described to date, each differing in its C-terminal domain. The characteristic feature of this domain is the presence of 4~9 tandem repeats of amino acids, each repeat comprising between 79 and 120 amino acids (cwpV) hemagglutinin/adhesin [CwpV (VF0596) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000055.1_61 96.154 3.38E-28 cbpA VF0592 CbpA Adherence VFC0001 MSCRAMMs have a common surface localization that in Gram-positive bacteria is usually mediated by a cell wall sorting signal through which they are covalently anchored to the cell wall peptidoglycan by sortase. (cbpA) collagen-binding adhesin CbpA [CbpA (VF0592) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000052.1_40 67.579 0.0 cwp84 VF0590 Cwp84 Exoenzyme VFC0251 (cwp84) cell wall-binding cysteine protease Cwp84 [Cwp84 (VF0590) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
ADEI01000048.1_11 94.753 0.0 CD2831 VF0598 CD2831 Adherence VFC0001 Cell surface protein cleaved and covalently anchored to m-DAP in the peptidoglycan by SrtB (CD2831) SrtB-anchored collagen-binding adhesin [CD2831 (VF0598) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000044.1_2 70.312 6.33E-168 CD0873 VF0593 CD0873 Adherence VFC0001 Numerous bacterial adhesins also characterized as lipoproteins, similar to CD0873, including the adhesin PsaA, a solute-binding lipoprotein of the Mn2+ ABC transporter of S. pneumoniae; CD0873 is annotated as a substrate-binding protein component SBP of an ABC transporter and is an immunoreactive protein in human infection (CD0873) ABC transporter substrate-binding protein [CD0873 (VF0593) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000032.1_54 60.556 9.86E-169 cps4I VF0144 Capsule Immune modulation VFC0258 Ninety different capsule types have been identified. Each has a structurally distinct capsule, composed of repeating oligosaccharide units joined by glycosidic linkages (cps4I) capsular polysaccharide biosynthesis protein Cps4I [Capsule (VF0144) - Immune modulation (VFC0258)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
ADEI01000030.1_3 61.565 2.24E-132 wbtL VF0542 LPS Immune modulation VFC0258 The structure of Francisella spp. lipid A is unique in that it is modified by various carbohydrates that greatly reduce TLR4 activation and allow for immune evasion (wbtL) glucose-1-phosphate thymidylyltransferase [LPS (VF0542) - Immune modulation (VFC0258)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
ADEI01000003.1_1 84.0 0.0 cbpA VF0592 CbpA Adherence VFC0001 MSCRAMMs have a common surface localization that in Gram-positive bacteria is usually mediated by a cell wall sorting signal through which they are covalently anchored to the cell wall peptidoglycan by sortase. (cbpA) collagen-binding adhesin CbpA [CbpA (VF0592) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000003.1_2 92.638 2.14E-98 cbpA VF0592 CbpA Adherence VFC0001 MSCRAMMs have a common surface localization that in Gram-positive bacteria is usually mediated by a cell wall sorting signal through which they are covalently anchored to the cell wall peptidoglycan by sortase. (cbpA) collagen-binding adhesin CbpA [CbpA (VF0592) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
ADEI01000001.1_46 65.789 2.02E-93 clpP VF0074 ClpP Stress survival VFC0282 21.6 kDa protein belongs to a family of proteases highly conserved in prokaryotes and eukaryotes (clpP) ATP-dependent Clp protease proteolytic subunit [ClpP (VF0074) - Stress survival (VFC0282)] [Listeria monocytogenes EGD-e] Listeria monocytogenes
ADEI01000001.1_72 69.43 7.02E-101 clpP VF0074 ClpP Stress survival VFC0282 21.6 kDa protein belongs to a family of proteases highly conserved in prokaryotes and eukaryotes (clpP) ATP-dependent Clp protease proteolytic subunit [ClpP (VF0074) - Stress survival (VFC0282)] [Listeria monocytogenes EGD-e] Listeria monocytogenes