2. PATHOGENS
Basic Information
Accession number
GCA_000027105.1
Release date
2009-10-01
Organism
Clostridioides difficile R20291
Species name
Clostridioides difficile
Assembly level
Chromosome
Assembly name
ASM2710v1
Assembly submitter
Wellcome Trust Sanger Institute
Assembly Type
haploid
Genome size
4.2 Mb
GC percent
29.0
Contig count
1
Collection date
-
Sample location
-
Host
-
Isolation source
-
Isolate type
-
Strain
R20291
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
FN545816.1_423 # 480875 # 481813 550.0 616.69 CDD-2 98.72 ARO:3006905 protein homolog model carbapenem antibiotic inactivation CDD beta-lactamase CDD-2 is a CDD beta-lactamase.
FN545816.1_1333 # 1525782 # 1527251 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.
FN545816.1_1402 # 1599564 # 1600889 810.0 852.047 cdeA 99.09 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.
FN545816.1_1598 # 1796485 # 1797585 250.0 513.842 vanG 67.3 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.
FN545816.1_1599 # 1797582 # 1798388 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.
FN545816.1_1600 # 1798406 # 1800544 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.
FN545816.1_2157 # 2406915 # 2408174 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.
FN545816.1_2508 # 2807048 # 2807695 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.
FN545816.1_3450 # 3936313 # 3937470 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.
FN545816.1_3593 # 4086864 # 4087580 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.
FN545816.1_6 # 6066 # 8492 1500.0 1623.6 Clostridioides difficile gyrA conferring resistance to fluoroquinolones 99.63 ARO:3003995 protein variant model T82I fluoroquinolone antibiotic antibiotic target alteration fluoroquinolone resistant gyrA Amino acid substitutions in Clostridioides difficile gyrase subunit A which when present confer functional resistance to fluoroquinolone antibiotics.
VF List
Query_id %Identity E-value Related genes VF ID Virulence factor VFcategory VFcategoryID Characteristics Description Strain
FN545816.1_67 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
FN545816.1_81 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
FN545816.1_210 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
FN545816.1_239 61.224 7.33E-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
FN545816.1_619 92.181 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
FN545816.1_622 98.192 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
FN545816.1_840 99.412 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
FN545816.1_843 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
FN545816.1_929 60.833 4.29E-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
FN545816.1_1723 62.675 0.0 cwp84 VF0590 Cwp84 Exoenzyme VFC0251 (cwp84) cell wall-binding cysteine protease Cwp84 [Cwp84 (VF0590) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
FN545816.1_2592 99.154 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
FN545816.1_2604 81.319 0.0 iap VF0381 Iota-toxin Exotoxin VFC0235 ADP-ribosylating toxin (ADPRT) family can be classified into four groups, at least with respect to their protein acceptors, as follows:; (I) heterotrimeric GTP-binding protein ADPRT (e.g. cholera toxin, B. pertussis pertussis toxin, E. coli heat-labile enterotoxin); (II) elongation factor 2 ADPRT (e.g. diphtheria toxin, P. aeruginosa exotoxin A); (III) small GTP-binding protein ADPRT (e.g. C. botulinum C3 exoenzyme, P. aeruginosa exoenzyme S); (IV) actin ADPRT. (e.g. B. cereus VIP, C. perfringens iota-toxin, C. botulinum C2 toxin, C. spiroforme toxin, and C. difficile toxin.); The binary iota toxin is produced exclusively by C. perfringens type E strains; The two proteins that comprise iota toxin were designated iota a or Ia (slower moving) and iota b or Ib (faster moving), based on electrophoretic mobility in crossed immunoelectrophoresis; Iota toxin requires proteolytic activation. The proteolytic activation of Ib precursor into Ib occurs at A211, which then facilitates Ia docking, formation of voltage-dependent ion-permeable channels in membranes, and formation of heptamers on cell membrane. Ia is also proteolytically activated by proteases, with a resultant loss of 9 to 13 amino acids from the N terminus. Proteolytic activation of Ia is unique among the 'A' components from binary toxins (iap) iota toxin component Ia [Iota-toxin (VF0381) - Exotoxin (VFC0235)] [Clostridium perfringens E str. NCIB 10748] Clostridium perfringens
FN545816.1_2605 80.16 0.0 ibp VF0381 Iota-toxin Exotoxin VFC0235 ADP-ribosylating toxin (ADPRT) family can be classified into four groups, at least with respect to their protein acceptors, as follows:; (I) heterotrimeric GTP-binding protein ADPRT (e.g. cholera toxin, B. pertussis pertussis toxin, E. coli heat-labile enterotoxin); (II) elongation factor 2 ADPRT (e.g. diphtheria toxin, P. aeruginosa exotoxin A); (III) small GTP-binding protein ADPRT (e.g. C. botulinum C3 exoenzyme, P. aeruginosa exoenzyme S); (IV) actin ADPRT. (e.g. B. cereus VIP, C. perfringens iota-toxin, C. botulinum C2 toxin, C. spiroforme toxin, and C. difficile toxin.); The binary iota toxin is produced exclusively by C. perfringens type E strains; The two proteins that comprise iota toxin were designated iota a or Ia (slower moving) and iota b or Ib (faster moving), based on electrophoretic mobility in crossed immunoelectrophoresis; Iota toxin requires proteolytic activation. The proteolytic activation of Ib precursor into Ib occurs at A211, which then facilitates Ia docking, formation of voltage-dependent ion-permeable channels in membranes, and formation of heptamers on cell membrane. Ia is also proteolytically activated by proteases, with a resultant loss of 9 to 13 amino acids from the N terminus. Proteolytic activation of Ia is unique among the 'A' components from binary toxins (ibp) iota toxin component Ib [Iota-toxin (VF0381) - Exotoxin (VFC0235)] [Clostridium perfringens E str. NCIB 10748] Clostridium perfringens
FN545816.1_2788 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
FN545816.1_2790 79.542 0.0 cwp66 VF0591 Cwp66 Adherence VFC0001 (cwp66) cell wall-binding protein Cwp66 [Cwp66 (VF0591) - Adherence (VFC0001)] [Clostridium difficile 630] Clostridium difficile
FN545816.1_2838 97.727 2.06E-161 zmp1 VF0600 Zmp1 Exoenzyme VFC0251 (zmp1) zinc metalloprotease Zmp1 [Zmp1 (VF0600) - Exoenzyme (VFC0251)] [Clostridium difficile 630] Clostridium difficile
FN545816.1_2839 94.732 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
FN545816.1_3307 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
FN545816.1_3338 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