2. PATHOGENS
Basic Information
Accession number
GCA_001263695.1
Release date
2015-07-10
Organism
Clostridioides difficile
Species name
Clostridioides difficile
Assembly level
Contig
Assembly name
ASM126369v1
Assembly submitter
Rakuno Gakuen University
Assembly Type
haploid
Genome size
4.0 Mb
GC percent
28.5
Contig count
270
Collection date
2013
Sample location
Japan:Hokkaido
Host
Canis lupus familiaris
Isolation source
-
Isolate type
-
Strain
RU-17
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
BBYE01000041.1_34 # 44848 # 46986 175.0 925.235 vanT gene in vanG cluster 61.24 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.
BBYE01000041.1_35 # 47004 # 47810 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.
BBYE01000041.1_36 # 47807 # 48907 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.
BBYE01000073.1_113 # 103199 # 103915 50.0 118.242 vanY gene in vanG cluster 34.04 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.
BBYE01000090.1_91 # 99606 # 100865 50.0 96.6709 vanW gene in vanI cluster 24.86 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.
BBYE01000122.1_12 # 10885 # 11532 50.0 99.3673 vanY gene in vanF cluster 38.62 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.
BBYE01000190.1_56 # 69945 # 70871 550.0 622.083 CDD-2 100.0 ARO:3006905 protein homolog model carbapenem antibiotic inactivation CDD beta-lactamase CDD-2 is a CDD beta-lactamase.
BBYE01000203.1_6 # 7513 # 8982 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.
BBYE01000203.1_74 # 81587 # 82912 810.0 858.981 cdeA 100.0 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.
BBYE01000251.1_91 # 87976 # 89133 175.0 207.223 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.
VF List
Query_id %Identity E-value Related genes VF ID Virulence factor VFcategory VFcategoryID Characteristics Description Strain
BBYE01000001.1_1 99.194 1.24E-74 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
BBYE01000005.1_1 100.0 5.29E-42 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
BBYE01000031.1_1 100.0 1.09E-46 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
BBYE01000051.1_2 99.706 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
BBYE01000052.1_2 69.208 3.54E-175 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
BBYE01000053.1_54 99.492 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
BBYE01000066.1_1 63.514 1.93E-28 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000067.1_1 63.514 1.93E-28 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000100.1_3 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
BBYE01000105.1_97 99.073 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
BBYE01000105.1_98 100.0 1.92E-165 zmp1 VF0600 Zmp1 Exoenzyme VFC0251 (zmp1) zinc metalloprotease Zmp1 [Zmp1 (VF0600) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
BBYE01000105.1_140 60.984 0.0 cwp66 VF0591 Cwp66 Adherence VFC0001 (cwp66) cell wall-binding protein Cwp66 [Cwp66 (VF0591) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
BBYE01000105.1_142 98.381 0.0 cwp84 VF0590 Cwp84 Exoenzyme VFC0251 (cwp84) cell wall-binding cysteine protease Cwp84 [Cwp84 (VF0590) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
BBYE01000130.1_1 100.0 1.32E-61 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
BBYE01000131.1_1 100.0 1.32E-61 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
BBYE01000138.1_1 86.869 7.98E-60 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000140.1_1 86.869 7.98E-60 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000142.1_13 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
BBYE01000146.1_18 96.579 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
BBYE01000155.1_30 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
BBYE01000155.1_90 93.137 4.58E-57 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
BBYE01000156.1_1 86.076 8.76E-33 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000159.1_19 83.549 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
BBYE01000190.1_101 99.588 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
BBYE01000192.1_1 72.619 1.47E-38 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000209.1_1 65.934 5.08E-39 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000210.1_1 65.934 5.08E-39 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000213.1_1 100.0 1.3E-24 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
BBYE01000218.1_79 100.0 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
BBYE01000218.1_110 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
BBYE01000233.1_1 74.126 2.91E-76 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000237.1_1 76.923 5.2E-17 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000238.1_1 76.923 5.2E-17 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000238.1_15 72.727 2.23E-16 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000244.1_1 67.797 8.08E-25 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
BBYE01000258.1_2 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
BBYE01000259.1_40 72.727 2.23E-16 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis