2. PATHOGENS
Basic Information
Accession number
GCA_000440095.1
Release date
2013-07-25
Organism
Streptococcus suis YS54
Species name
Streptococcus suis
Assembly level
Contig
Assembly name
version1
Assembly submitter
National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control
Assembly Type
haploid
Genome size
2.3 Mb
GC percent
41.0
Contig count
124
Collection date
-
Sample location
-
Host
-
Isolation source
-
Isolate type
-
Strain
YS54
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
ALMX01000003.1_48 # 54020 # 55939 900.0 1296.18 tet(O/W/32/O) 98.44 ARO:3007122 protein homolog model tetracycline antibiotic antibiotic target protection tetracycline-resistant ribosomal protection protein Tet(O/W/32/O) is a mosaic tetracycline resistance gene and ribosomal protection protein.
ALMX01000043.1_59 # 72593 # 73342 50.0 82.0333 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.
ALMX01000052.1_2 # 93 # 836 400.0 493.426 ErmB 98.78 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.
ALMX01000104.1_104 # 106007 # 107713 750.0 801.201 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.
ALMX01000104.1_105 # 107714 # 109498 750.0 836.639 patB 67.28 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..
VF List
Query_id %Identity E-value Related genes VF ID Virulence factor VFcategory VFcategoryID Characteristics Description Strain
ALMX01000012.1_1 68.571 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
ALMX01000018.1_14 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
ALMX01000027.1_2 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
ALMX01000032.1_1 64.42 8.62E-179 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
ALMX01000032.1_8 61.29 0.0 cps4K 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 (cps4K) capsular polysaccharide biosynthesis protein Cps4K [Capsule (VF0144) - Immune modulation (VFC0258)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
ALMX01000032.1_9 79.177 0.0 cps4L 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 (cps4L) capsular polysaccharide biosynthesis protein Cps4L [Capsule (VF0144) - Immune modulation (VFC0258)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
ALMX01000032.1_10 78.824 0.0 cps4J 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 (cps4J) capsular polysaccharide biosynthesis protein Cps4J [Capsule (VF0144) - Immune modulation (VFC0258)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
ALMX01000032.1_19 64.646 2.74E-91 wbtB 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 (wbtB) galactosyl transferase [LPS (VF0542) - Immune modulation (VFC0258)] [Francisella tularensis subsp. tularensis SCHU S4] Francisella tularensis
ALMX01000032.1_22 61.728 3.65E-115 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
ALMX01000032.1_23 60.352 7.45E-103 cps4D 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 (cps4D) capsular polysaccharide biosynthesis protein Cps4D [Capsule (VF0144) - Immune modulation (VFC0258)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
ALMX01000041.1_19 63.448 2.44E-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
ALMX01000101.1_36 73.321 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
ALMX01000104.1_101 88.176 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
ALMX01000108.1_10 70.975 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