Clostridioides difficile Online 结果示例

PBGdango

Species result

Clostridioides difficile

├──── Kingdom：Bacteria
├────────Phylum： Firmicutes
├────────────Class: Clostridia
├───────────────Order: Clostridiales
├──────────────────Family： Peptostreptococcaceae
├─────────────────────Genus：Clostridioides

Download: Taxonomy.txt

2 Average Nucleotide Identity

ANI and AF vs Type material Genome
GENOME1	GENOME2	ANI(1->2)	ANI(2->1)	AF(1->2)	AF(2->1)
cd.genome.ffn	Clostridioides_difficile.630.GCA_000009205.2.gene.fa	99.40	99.40	0.90	0.90
cd.genome.ffn	Clostridioides_difficile.ATCC-9689.AQWV01.gene.fa	100.00	100.00	0.97	1.00
cd.genome.ffn	Clostridioides_difficile.DSM-1296.AUOX01.gene.fa	99.99	99.99	0.97	1.00

Download: ANIcalculator.all.txt

Gene annotation
Gene_num	3983
Gene_total_length(bp)	3,606,169
Gene_average_length(bp)	905.39
GC_content_in_gene_region(%)	30.04
Gene/Genome(%)	84.13
Intergenetic_region_length(bp)	680,036
GC_content_in_intergenetic_region(%)	21.58
Intergenetic/Genome(%)	15.87

3 Multilocus sequence typing

MLST result：ST3，Housekeeping gene allele number：

ST	adk	atpA	dxr	glyA	recA	sodA	tpi
3	1	1	2	1	1	1	1

Download: MLST.STtype.txt

Query	Target	identity(%)	Alignment length	mismatches	gap opens	Start position in query	End position in query	Start position in target	End position in target	E-value	score
CP011968.1	adk_1	100.000	501	0	0	118598	119098	1	501	0.0	926
CP011968.1	atpA_1	100.000	555	0	0	3883615	3884169	555	1	0.0	1026
CP011968.1	dxr_2	100.000	411	0	0	2321872	2322282	411	1	0.0	760
CP011968.1	glyA_1	100.000	516	0	0	3023741	3024256	516	1	0.0	953
CP011968.1	recA_1	100.000	564	0	0	1437818	1438381	1	564	0.0	1042
CP011968.1	sodA_1	100.000	450	0	0	1777204	1777653	450	1	0.0	832
CP011968.1	tpi_1	100.000	504	0	0	3540331	3540834	504	1	0.0	931

4 Resistance gene

result table：

ARoutput.result.txt

resistance gene table
Query_ID	ARO_Accession	Protein	Identities	ARO Name	Model_type	SNPs_in_Best_Hit_ARO	Other_SNPs	Drug Class	Resistance Mechanism	AMR Gene Family
CP011968.1\|1772361:1773167	ARO:3003069	ABA71732.1	58.82	vanXYG	protein homolog model	n/a	n/a	glycopeptide antibiotic	antibiotic target alteration	glycopeptide resistance gene cluster; vanXY
CP011968.1\|1632091:1633416	ARO:3003835	CAE00499.1	99.32	cdeA	protein homolog model	n/a	n/a	acridine dye; fluoroquinolone antibiotic	antibiotic efflux	multidrug and toxic compound extrusion (MATE) transporter

5 Virulence factor

result table：

1. VFDB.filter.txt

2. VFDB.allinfo.txt

Virulence factor table
Query_id	%Identity	E-value	Related genes	Virulence factors	Class	Description	Strain
CP011968.1\|260220:261848	100.000	0.0	groEL	GroEL	Adherence	(groEL) 60 kDa chaperonin [GroEL(Hsp60) (AI317)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|353644:353958	94.231	9.65e-65	fliN	HexNAc	--	(fliN) flagellar motor switch protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|354390:354806	92.029	2.56e-87	CD0230	HexNAc	--	(CD0230) putative flagellar biosynthesis protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|354824:356134	95.413	0.0	flgK	HexNAc	--	(flgK) putative flagellar hook-associated protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|357721:358116	93.130	3.44e-91	fliS1	HexNAc	--	(fliS1) flagellar protein FliS [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|373368:373685	99.048	1.89e-73	flgB	HexNAc	--	(flgB) flagellar basal-body rod protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|373693:374097	99.254	3.20e-95	flgC	HexNAc	--	(flgC) flagellar basal-body rod protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|374107:374421	97.143	8.64e-69	fliE	HexNAc	--	(fliE) flagellar hook-basal body protein FliE [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|374446:375996	98.450	0.0	fliF	HexNAc	--	(fliF) flagellar MS-ring protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|376009:377079	97.191	0.0	fliG	HexNAc	--	(fliG) flagellar motor switch protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|377069:377803	96.296	9.93e-167	fliH	HexNAc	--	(fliH) flagellar assembly protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|377807:379126	98.633	0.0	fliI	HexNAc	--	(fliI) flagellum-specific ATP synthase [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|379158:379604	95.946	2.17e-88	fliJ	HexNAc	--	(fliJ) flagellar protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|379632:380837	97.007	0.0	fliK	HexNAc	--	(fliK) putative flagellar hook-length control protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|380855:381463	99.505	1.35e-145	flgD	HexNAc	--	(flgD) putative basal-body rod modification protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|381490:382473	99.388	0.0	flgE	HexNAc	--	(flgE) flagellar hook protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|382486:382689	100.000	4.11e-41	CD0255A	HexNAc	--	(CD0255A) putative flagellar protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|382689:383507	100.000	0.0	motA	HexNAc	--	(motA) chemotaxis protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|383497:384192	100.000	1.57e-170	motB	HexNAc	--	(motB) chemotaxis protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|384204:384647	100.000	3.55e-102	fliL	HexNAc	--	(fliL) flagellar basal body-associated protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|384662:385036	98.387	3.47e-80	CD0259	HexNAc	--	(CD0259) putative flagellar protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|385037:385702	100.000	7.50e-156	fliP	HexNAc	--	(fliP) flagellar biosynthesis protein FliP [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|385715:385984	100.000	3.26e-57	fliQ	HexNAc	--	(fliQ) flagellar export protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|385996:387810	99.669	0.0	flhB	HexNAc	--	(flhB) bifunctional flagellar biosynthesis protein FliR/FlhB [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|387819:389894	99.421	0.0	flhA	HexNAc	--	(flhA) flagellar biosynthesis protein FlhA [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|389869:390885	96.154	0.0	flhF	HexNAc	--	(flhF) flagellar biosynthesis regulator FlhF [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|390882:391760	97.260	0.0	fleN	HexNAc	--	(fleN) flagellar number regulator [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|391774:392475	100.000	7.34e-165	fliA	HexNAc	--	(fliA) RNA polymerase sigma factor for flagellar operon [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|393124:393897	99.611	0.0	flgG	HexNAc	--	(flgG) flagellar basal body rod protein FlgG [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|393918:394679	99.605	0.0	flgG	HexNAc	--	(flgG) flagellar basal body rod protein FlgG [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|394702:395583	98.976	0.0	fliM	HexNAc	--	(fliM) putative flagellar motor switch protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|395586:395960	100.000	6.54e-81	fliN	HexNAc	--	(fliN) putative flagellar motor switch protein [HexNAc (AI148)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|786827:793927	99.958	0.0	toxB	Toxin B	Toxin	(toxB) toxin B [TcdB (VF0377)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|795277:803409	99.926	0.0	toxA	Toxin A	Toxin	(toxA) toxin A [TcdA (VF0376)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|1319034:1319846	100.000	0.0	CD1208	Hemolysin	Toxin	(CD1208) putative RNA methyltransferase [Hemolysin (CVF417)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|1683496:1684149	100.000	2.22e-157	CD1546	Hemolysin	Toxin	(CD1546) putative hemolysin-like membrane protein [Hemolysin (CVF417)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|2854128:2855903	99.323	0.0	fbpA	Fibronectin-binding protein	--	(fbpA) fibronectin-binding protein [Fibronectin-binding protein (AI155)] [Clostridium difficile 630]	Clostridium difficile 630
CP011968.1\|2869254:2869436	90.000	6.24e-32	cdtA	Clostridium difficile toxin (CDT)	Toxin	(cdtA) ADP-ribosyltransferase enzymatic component [CDT: CDTa, CDTb (TX009)] [Clostridium difficile CD196]	Clostridium difficile CD196

CGMLST

The Closest Genome: Key Name : ATCC_9689_=_DSM_1296 ,Genome information: ATCC 9689 = DSM 1296

CGMLST picture：