Basic Information
Accession number
GCA_000210415.1
Release date
2010-03-24
Organism
Clostridioides difficile CF5
Species name
Clostridioides difficile

Assembly level
Complete Genome
Assembly name
ASM21041v1
Assembly submitter
Wellcome Trust Sanger Institute
Assembly Type
haploid
Genome size
4.2 Mb
GC percent
28.5
Contig count
1

Collection date
1995
Sample location
-
Host
-
Isolation source
Homo sapiens
Isolate type
-
Strain
CF5
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
FN665652.1_448 # 504615 # 505553 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.
FN665652.1_1381 # 1561110 # 1562579 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.
FN665652.1_1452 # 1636258 # 1637583 810.0 851.277 cdeA 98.41 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.
FN665652.1_1646 # 1834639 # 1835739 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.
FN665652.1_1647 # 1835736 # 1836542 125.0 307.76 vanXY gene in vanG cluster 59.22 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.
FN665652.1_1648 # 1836560 # 1838698 175.0 932.169 vanT gene in vanG cluster 61.38 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.
FN665652.1_2159 # 2383233 # 2384492 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.
FN665652.1_2517 # 2784731 # 2785378 50.0 100.908 vanY gene in vanF cluster 40.58 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.
FN665652.1_3493 # 3923542 # 3924699 175.0 207.608 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.
FN665652.1_3636 # 4074369 # 4075085 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.
VF List
Query_id %Identity E-value Related genes VF ID Virulence factor VFcategory VFcategoryID Characteristics Description Strain
FN665652.1_63 74.426 3.5E-157 tufA VF0460 EF-Tu Adherence VFC0001 (tufA) elongation factor Tu [EF-Tu (VF0460) - Adherence (VFC0001)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
FN665652.1_78 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
FN665652.1_203 99.815 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
FN665652.1_663 93.705 0.0 toxB VF0377 TcdB Exotoxin VFC0235 Many forms of variant toxin B have been identified, which are functional chimeras of toxin B (reference strain VPI 10463) and C. sordellii lethal toxin, e.g., C. difficile toxin B from strain 1470 and strain 8864. Their substrate specificities resemble that of lethal toxin. C. difficile strain C34 produces a toxin B variant modifying Rho, Rac, and Cdc42 as well as R-Ras, Ral, and Rap. (toxB) toxin B [TcdB (VF0377) - Exotoxin (VFC0235)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_666 100.0 8.04E-25 toxA VF0376 TcdA Exotoxin VFC0235 The toxin genes tcdA and tcdB are situated on the C. difficile chromosome in a 19.6-kilobase (kb) pathogenicity locus (PaLoc), along with the three accessory genes tcdC, tcdR and tcdE.; TcdA and TcdB are homologous to each other, to TcsH and TcsL of C. sordellii and to Tcnalpha of C. novyi. Because of their sequence homology, similar domain structure and glycosyltransferase properties these toxins are designated 'large clostridial cytotoxins'. (toxA) toxin A [TcdA (VF0376) - Exotoxin (VFC0235)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_667 97.619 5.29E-51 toxA VF0376 TcdA Exotoxin VFC0235 The toxin genes tcdA and tcdB are situated on the C. difficile chromosome in a 19.6-kilobase (kb) pathogenicity locus (PaLoc), along with the three accessory genes tcdC, tcdR and tcdE.; TcdA and TcdB are homologous to each other, to TcsH and TcsL of C. sordellii and to Tcnalpha of C. novyi. Because of their sequence homology, similar domain structure and glycosyltransferase properties these toxins are designated 'large clostridial cytotoxins'. (toxA) toxin A [TcdA (VF0376) - Exotoxin (VFC0235)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_668 98.02 5.45E-63 toxA VF0376 TcdA Exotoxin VFC0235 The toxin genes tcdA and tcdB are situated on the C. difficile chromosome in a 19.6-kilobase (kb) pathogenicity locus (PaLoc), along with the three accessory genes tcdC, tcdR and tcdE.; TcdA and TcdB are homologous to each other, to TcsH and TcsL of C. sordellii and to Tcnalpha of C. novyi. Because of their sequence homology, similar domain structure and glycosyltransferase properties these toxins are designated 'large clostridial cytotoxins'. (toxA) toxin A [TcdA (VF0376) - Exotoxin (VFC0235)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_669 98.806 0.0 toxA VF0376 TcdA Exotoxin VFC0235 The toxin genes tcdA and tcdB are situated on the C. difficile chromosome in a 19.6-kilobase (kb) pathogenicity locus (PaLoc), along with the three accessory genes tcdC, tcdR and tcdE.; TcdA and TcdB are homologous to each other, to TcsH and TcsL of C. sordellii and to Tcnalpha of C. novyi. Because of their sequence homology, similar domain structure and glycosyltransferase properties these toxins are designated 'large clostridial cytotoxins'. (toxA) toxin A [TcdA (VF0376) - Exotoxin (VFC0235)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_670 98.94 0.0 toxA VF0376 TcdA Exotoxin VFC0235 The toxin genes tcdA and tcdB are situated on the C. difficile chromosome in a 19.6-kilobase (kb) pathogenicity locus (PaLoc), along with the three accessory genes tcdC, tcdR and tcdE.; TcdA and TcdB are homologous to each other, to TcsH and TcsL of C. sordellii and to Tcnalpha of C. novyi. Because of their sequence homology, similar domain structure and glycosyltransferase properties these toxins are designated 'large clostridial cytotoxins'. (toxA) toxin A [TcdA (VF0376) - Exotoxin (VFC0235)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_671 85.93 0.0 toxA VF0376 TcdA Exotoxin VFC0235 The toxin genes tcdA and tcdB are situated on the C. difficile chromosome in a 19.6-kilobase (kb) pathogenicity locus (PaLoc), along with the three accessory genes tcdC, tcdR and tcdE.; TcdA and TcdB are homologous to each other, to TcsH and TcsL of C. sordellii and to Tcnalpha of C. novyi. Because of their sequence homology, similar domain structure and glycosyltransferase properties these toxins are designated 'large clostridial cytotoxins'. (toxA) toxin A [TcdA (VF0376) - Exotoxin (VFC0235)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_886 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
FN665652.1_889 69.322 2.0E-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
FN665652.1_974 60.833 5.77E-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
FN665652.1_1780 62.93 0.0 cwp84 VF0590 Cwp84 Exoenzyme VFC0251 (cwp84) cell wall-binding cysteine protease Cwp84 [Cwp84 (VF0590) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_2614 98.816 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
FN665652.1_2811 99.502 0.0 cwp84 VF0590 Cwp84 Exoenzyme VFC0251 (cwp84) cell wall-binding cysteine protease Cwp84 [Cwp84 (VF0590) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_2813 98.689 0.0 cwp66 VF0591 Cwp66 Adherence VFC0001 (cwp66) cell wall-binding protein Cwp66 [Cwp66 (VF0591) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_2817 81.163 0.0 slpA VF0589 SlpA Adherence VFC0001 S-layers have been observed in hundreds of prokaryotic species, including a diverse range of bacteria and virtually all archaea. A typical S-layer consists of a single protein arranged in a two dimensional paracrystalline array, forming the outermost surface of the cell;The majority of the C. difficile S-layer is formed by the low and high molecular weight S-layer proteins (LMW SLP and HMW SLP) which are coded by a single gene slpA;HMW SLP binds to the cell wall through a non-covalent interaction, while LMW SLP is presented as the outermost surface of the cell (slpA) cell surface protein (S-layer precursor protein) [SlpA (VF0589) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_2857 99.091 2.98E-164 zmp1 VF0600 Zmp1 Exoenzyme VFC0251 (zmp1) zinc metalloprotease Zmp1 [Zmp1 (VF0600) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
FN665652.1_2858 94.239 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
FN665652.1_3124 85.75 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
FN665652.1_3312 91.334 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
FN665652.1_3376 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
FN665652.1_3400 65.263 1.37E-92 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