2. PATHOGENS
Basic Information
Accession number
GCA_000344765.1
Release date
2013-03-06
Organism
Streptococcus suis SC070731
Species name
Streptococcus suis
Assembly level
Complete Genome
Assembly name
ASM34476v1
Assembly submitter
Nanjing Agricultural University
Assembly Type
haploid
Genome size
2.1 Mb
GC percent
41.0
Contig count
1
Collection date
-
Sample location
-
Host
-
Isolation source
-
Isolate type
-
Strain
SC070731
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
CP003922.1_559 # 621646 # 623565 300.0 1303.12 tet(O) 98.44 ARO:3000190 protein homolog model tetracycline antibiotic antibiotic target protection tetracycline-resistant ribosomal protection protein Tet(O) is a ribosomal protection protein. It is associated with conjugative plasmids.
CP003922.1_560 # 623616 # 624836 750.0 791.571 tet(40) 98.28 ARO:3000567 protein homolog model tetracycline antibiotic antibiotic efflux major facilitator superfamily (MFS) antibiotic efflux pump Tet40 is a tetracycline efflux pump found in the Gram-positive Clostridium. It is similar to tetA(P).
CP003922.1_656 # 712962 # 713756 500.0 536.184 APH(3')-IIIa 100.0 ARO:3002647 protein homolog model aminoglycoside antibiotic antibiotic inactivation APH(3') APH(3')-IIIa is a plasmid-encoded aminoglycoside phosphotransferase in S. aureus and Enterococcus spp.
CP003922.1_657 # 713849 # 714391 300.0 370.548 SAT-4 99.44 ARO:3002897 protein homolog model nucleoside antibiotic antibiotic inactivation streptothricin acetyltransferase (SAT) SAT-4 is a plasmid-mediated streptothricin acetyltransferase and streptothricin (a nucleoside antibiotic) resistant determinant. Originally described from a Campylobacter coli BE/G4 plasmid gene sequence by Jacob et al, 1994.
CP003922.1_658 # 714388 # 715296 500.0 573.933 aad(6) 100.0 ARO:3002628 protein homolog model aminoglycoside antibiotic antibiotic inactivation ANT(6) ANT(6)-Ia/aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis.
CP003922.1_660 # 715601 # 716338 400.0 491.115 ErmB 98.37 ARO:3000375 protein homolog model macrolide antibiotic; lincosamide antibiotic; streptogramin antibiotic; streptogramin A antibiotic; streptogramin B antibiotic antibiotic target alteration Erm 23S ribosomal RNA methyltransferase ErmB confers the MLSb phenotype. Similar to ErmC, expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present, it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.
CP003922.1_791 # 850742 # 851497 50.0 83.1889 vanY gene in vanB cluster 33.7 ARO:3002956 protein homolog model glycopeptide antibiotic antibiotic target alteration vanY; glycopeptide resistance gene cluster Also known as vanYB, is a vanY variant found in the vanB gene cluster.
CP003922.1_1895 # 1979319 # 1981103 750.0 835.484 patB 67.11 ARO:3000025 protein homolog model fluoroquinolone antibiotic antibiotic efflux ATP-binding cassette (ABC) antibiotic efflux pump PatB is an ABC transporter of Streptococcus pneumoniae that interacts with PatA to confer fluoroquinolone resistance..
CP003922.1_1896 # 1981104 # 1982810 750.0 801.586 patA 66.49 ARO:3000024 protein homolog model fluoroquinolone antibiotic antibiotic efflux ATP-binding cassette (ABC) antibiotic efflux pump PatA is an ABC transporter of Streptococcus pneumoniae that interacts with PatB to confer fluoroquinolone resistance.
VF List
Query_id %Identity E-value Related genes VF ID Virulence factor VFcategory VFcategoryID Characteristics Description Strain
CP003922.1_140 68.19 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
CP003922.1_468 68.939 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
CP003922.1_502 62.397 1.56E-113 cps4B 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 (cps4B) capsular polysaccharide biosynthesis protein Cps4B [Capsule (VF0144) - Immune modulation (VFC0258)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP003922.1_514 80.769 0.0 neuB VF0274 Capsule Immune modulation VFC0258 GBS can be subclassified into serotypes according to the immunologic type of the polysaccharide capsule. Of the nine serotypes described so far, the type Ia, Ib, II, III and V are responsible for the majority of invasive human GBS disease; serotype III is particularly important because it causes the majority of infection to neonates (neuB) N-acetylneuraminate synthase [Capsule (VF0274) - Immune modulation (VFC0258)] [Streptococcus agalactiae NEM316] Streptococcus agalactiae
CP003922.1_663 66.667 1.66E-17 cpsI VF0361 Capsule Immune modulation VFC0258 The biosynthesis of capsular polysaccharides by E. faecalis is encoded by the csp operon, which includes 11 open reading frames (cpsA to cpsK). However, only 7 open reading frames in the cps operon are essential for capsule production (cpsC, cpsD, cpsE, cpsG, cpsI, cpsJ, and cpsK); Previous genetic evidence demonstrated that E. faecalis isolates can be classified in 1 of 3 capsule operon polymorphisms. CPS 1 presents only cpsA and cpsB. CPS 2 presents all 11 genes in the cps operon. CPS 5 presents all genes except for cpsF. Furthermore, CPS 2 and 5 express the capsular polysaccharide, whereas CPS 1 does not. (cpsI) UDP-galactopyranose mutase [Capsule (VF0361) - Immune modulation (VFC0258)] [Enterococcus faecalis V583] Enterococcus faecalis
CP003922.1_664 63.576 8.61E-141 cpsI VF0361 Capsule Immune modulation VFC0258 The biosynthesis of capsular polysaccharides by E. faecalis is encoded by the csp operon, which includes 11 open reading frames (cpsA to cpsK). However, only 7 open reading frames in the cps operon are essential for capsule production (cpsC, cpsD, cpsE, cpsG, cpsI, cpsJ, and cpsK); Previous genetic evidence demonstrated that E. faecalis isolates can be classified in 1 of 3 capsule operon polymorphisms. CPS 1 presents only cpsA and cpsB. CPS 2 presents all 11 genes in the cps operon. CPS 5 presents all genes except for cpsF. Furthermore, CPS 2 and 5 express the capsular polysaccharide, whereas CPS 1 does not. (cpsI) UDP-galactopyranose mutase [Capsule (VF0361) - Immune modulation (VFC0258)] [Enterococcus faecalis V583] Enterococcus faecalis
CP003922.1_1203 63.448 2.09E-138 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
CP003922.1_1389 73.503 0.0 pavA VF0283 PavA Adherence VFC0001 PavA was the first Fibronectin-binding protein identified in S. pneumoniae and shares about 70% sequence identity with the Fibronectin-binding proteins FBP54 of S. pyogenes and FbpA of S. gordonii (pavA) Fibronectin-binding protein-like protein A [PavA (VF0283) - Adherence (VFC0001)] [Streptococcus pneumoniae R6] Streptococcus pneumoniae
CP003922.1_1445 62.5 1.72E-88 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
CP003922.1_1615 70.339 0.0 gndA VF0560 Capsule Immune modulation VFC0258 The Klebsiella polysaccharide capsule is produced through a Wzy-dependent process, for which the synthesis and export machinery are encoded in a single 10-30 kb region of the genome known as the K locus.; 78 distinct capsule phenotypes have been recognized by serological typing, but many isolates are serologically non-typable.; capsular serotypes vary substantially in the degree of serum resistance; K1, K2 and K5 are highly serum resistant and are associated with hypervirulent strains that differ from classical K. pneumoniae in that they commonly cause community-acquired disease. (gndA) NADP-dependent phosphogluconate dehydrogenase [Capsule (VF0560) - Immune modulation (VFC0258)] [Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044] Klebsiella pneumoniae
CP003922.1_1899 87.584 0.0 hasC VF0244 Hyaluronic acid capsule Immune modulation VFC0258 (hasC) UTP--glucose-1-phosphate uridylyltransferase HasC [Hyaluronic acid capsule (VF0244) - Immune modulation (VFC0258)] [Streptococcus pyogenes M1 GAS] Streptococcus pyogenes
CP003922.1_1952 60.215 4.07E-123 srtC-1/srtB VF0529 RlrA islet Adherence VFC0001 Pili are encoded by the rlrA pathogenicity islet, which carries genes for three pilin proteins (the major pilin RrgB and two minor pilins, RrgA and RrgC, RrgA is the tip adhesin) as well as three sortases (srtC-1/srtB) sortase [RlrA islet (VF0529) - Adherence (VFC0001)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae