2. PATHOGENS
Basic Information
Accession number
GCA_001757615.1
Release date
2016-10-11
Organism
Clostridioides difficile
Species name
Clostridioides difficile
Assembly level
Contig
Assembly name
ASM175761v1
Assembly submitter
University of Technology Sydney
Assembly Type
haploid
Genome size
4.1 Mb
GC percent
28.5
Contig count
76
Collection date
2008
Sample location
Australia: NSW
Host
equine
Isolation source
feces
Isolate type
-
Strain
H3
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
JFOI01000015.1_49 # 46464 # 47621 175.0 208.764 vanT gene in vanG cluster 34.78 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.
JFOI01000021.1_100 # 111165 # 111812 50.0 100.908 vanY gene in vanF cluster 39.31 ARO:3002958 protein homolog model glycopeptide antibiotic antibiotic target alteration vanY; glycopeptide resistance gene cluster Also known as vanYF, is a vanY variant found in the vanF gene cluster.
JFOI01000036.1_104 # 122069 # 123007 550.0 605.134 CDD-1 96.79 ARO:3006904 protein homolog model carbapenem antibiotic inactivation CDD beta-lactamase CDD-1 is a CDD beta-lactamase.
JFOI01000047.1_33 # 42444 # 44582 175.0 932.939 vanT gene in vanG cluster 61.52 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.
JFOI01000047.1_34 # 44600 # 45406 125.0 306.22 vanXY gene in vanG cluster 58.82 ARO:3003069 protein homolog model glycopeptide antibiotic antibiotic target alteration glycopeptide resistance gene cluster; vanXY Also known as vanXYG, is a vanXY variant found in the vanG gene cluster.
JFOI01000047.1_35 # 45403 # 46503 250.0 512.301 vanG 67.03 ARO:3002909 protein homolog model glycopeptide antibiotic antibiotic target alteration glycopeptide resistance gene cluster; Van ligase VanG is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Ser, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity in Enterococcus faecalis.
JFOI01000047.1_159 # 184427 # 185752 810.0 857.44 cdeA 99.55 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.
JFOI01000065.1_165 # 185120 # 186379 50.0 96.6709 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.
JFOI01000007.1_53 # 56744 # 57460 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.
JFOI01000009.1_133 # 146785 # 148254 50.0 133.65 vanW gene in vanI cluster 33.33 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.
VF List
Query_id %Identity E-value Related genes VF ID Virulence factor VFcategory VFcategoryID Characteristics Description Strain
JFOI01000014.1_121 99.662 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
JFOI01000017.1_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
JFOI01000019.1_1 70.13 4.56E-32 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
JFOI01000019.1_15 79.012 3.0E-42 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
JFOI01000020.1_1 79.012 3.0E-42 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
JFOI01000022.1_56 100.0 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
JFOI01000023.1_100 99.626 0.0 cwp84 VF0590 Cwp84 Exoenzyme VFC0251 (cwp84) cell wall-binding cysteine protease Cwp84 [Cwp84 (VF0590) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
JFOI01000023.1_102 77.377 0.0 cwp66 VF0591 Cwp66 Adherence VFC0001 (cwp66) cell wall-binding protein Cwp66 [Cwp66 (VF0591) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
JFOI01000023.1_143 100.0 1.92E-165 zmp1 VF0600 Zmp1 Exoenzyme VFC0251 (zmp1) zinc metalloprotease Zmp1 [Zmp1 (VF0600) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
JFOI01000023.1_144 98.765 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
JFOI01000028.1_1 81.865 1.02E-87 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
JFOI01000044.1_11 65.263 2.57E-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
JFOI01000044.1_43 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
JFOI01000044.1_103 93.535 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
JFOI01000044.1_215 76.8 4.48E-110 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
JFOI01000044.1_216 97.775 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
JFOI01000056.1_73 63.057 0.0 cwp84 VF0590 Cwp84 Exoenzyme VFC0251 (cwp84) cell wall-binding cysteine protease Cwp84 [Cwp84 (VF0590) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
JFOI01000064.1_1 70.13 4.56E-32 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
JFOI01000066.1_88 100.0 0.0 groEL VF0594 GroEL Adherence VFC0001 GroEL of numerous bacteria, such as L. pneumophila, H. pylori, H. ducreyi, M. avium, S. typhimurium, A. actinomycetemcomitans and B. burgdorferi, has been shown to be involved in adhesion or invasion of various target cells or tissues. (groEL) chaperonin GroEL [GroEL (VF0594) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
JFOI01000066.1_118 61.224 8.27E-131 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
JFOI01000073.1_3 69.208 3.02E-174 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
JFOI01000008.1_80 60.833 4.79E-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