2. PATHOGENS
Basic Information
Accession number
GCA_000018985.1
Release date
2009-03-27
Organism
Streptococcus pneumoniae JJA
Species name
Streptococcus pneumoniae
Assembly level
Complete Genome
Assembly name
ASM1898v1
Assembly submitter
J. Craig Venter Institute
Assembly Type
haploid
Genome size
2.1 Mb
GC percent
39.5
Contig count
1
Collection date
-
Sample location
-
Host
-
Isolation source
-
Isolate type
-
Strain
JJA
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
CP000919.1_548 # 556926 # 557648 50.0 82.8037 vanY gene in vanB cluster 35.0 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.
CP000919.1_860 # 872688 # 873887 750.0 789.645 pmrA 100.0 ARO:3000822 protein homolog model fluoroquinolone antibiotic antibiotic efflux major facilitator superfamily (MFS) antibiotic efflux pump PmrA is a MFS-type efflux pump expressed in Streptococcus pneumoniae that confers low-level resistance to norfloxacin, ciprofloxacin, and acriflavine.
CP000919.1_1936 # 1942084 # 1943850 750.0 1195.26 patB 99.66 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..
CP000919.1_1938 # 1944641 # 1946335 750.0 1135.55 patA 99.65 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.
CP000919.1_1964 # 1973074 # 1973922 550.0 585.104 RlmA(II) 100.0 ARO:3001301 protein homolog model macrolide antibiotic; lincosamide antibiotic antibiotic target alteration non-erm 23S ribosomal RNA methyltransferase (G748) RlmA(II) is a methyltransferase found in Streptococcus pneumoniae and confers resistance to tylosin and mycinamicin. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering) of 23S ribosomal RNA.
VF List
Query_id %Identity E-value Related genes VF ID Virulence factor VFcategory VFcategoryID Characteristics Description Strain
CP000919.1_34 94.231 2.06E-68 lytA VF0143 Autolysin Exoenzyme VFC0251 Surface protein: choline-binding proteins anchored to the cell surface by a non-covalent interaction of a repeat region at the C-terminal with the phosphorylcholine of the cell wall; Attachment of the enzyme to the choline of the S. pneumoniae cell wall teichoic acid is essential for the lytic activity of the enzyme; two other cell wall hydrolases, LytB and LytC have recently been described, but their roles in virulence have not been assessed. LytB plays a role in pneumococcal daughter cell separation. LytC has a lysozyme-like activity (lytA) autolysin (N-acetylmuramoyl-L-alanine amidase) [Autolysin (VF0143) - Exoenzyme (VFC0251)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_94 99.332 0.0 pavB/pfbB VF0524 PavB Adherence VFC0001 (pavB/pfbB) cell wall surface anchor family protein, Plasminogen- and Fibronectin-binding protein B [PavB (VF0524) - Adherence (VFC0001)] [Streptococcus pneumoniae R6] Streptococcus pneumoniae
CP000919.1_133 84.727 0.0 pspA VF0152 PspA Immune modulation VFC0258 Surface protein: choline binding protein (pspA) surface protein A [PspA (VF0152) - Immune modulation (VFC0258)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_134 95.0 1.02E-77 pspA VF0152 PspA Immune modulation VFC0258 Surface protein: choline binding protein (pspA) surface protein A [PspA (VF0152) - Immune modulation (VFC0258)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_294 98.594 0.0 hysA VF0146 Hyaluronidase Exoenzyme VFC0251 Surface protein: LPXTG-anchored proteins (hysA) hyaluronidase [Hyaluronidase (VF0146) - Exoenzyme (VFC0251)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_320 95.634 0.0 cps4A 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 (cps4A) capsular polysaccharide biosynthesis protein Cps4A [Capsule (VF0144) - Immune modulation (VFC0258)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_321 86.42 9.78E-161 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
CP000919.1_322 88.696 6.1E-150 cpsC 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 (cpsC) capsular polysaccharide biosynthesis protein CpsC [Capsule (VF0144) - Immune modulation (VFC0258)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_323 94.714 5.54E-161 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
CP000919.1_325 83.221 5.62E-95 GBS_RS06585 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 (GBS_RS06585) UDP-N-acetylglucosamine--LPS N-acetylglucosamine transferase [Capsule (VF0274) - Immune modulation (VFC0258)] [Streptococcus agalactiae NEM316] Streptococcus agalactiae
CP000919.1_345 70.763 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
CP000919.1_359 99.267 0.0 cbpG VF0145 CBPs Adherence VFC0001 Surface protein: choline-binding (cbpG) choline binding protein G [CBPs (VF0145) - Adherence (VFC0001)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_647 63.918 1.79E-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
CP000919.1_820 96.651 0.0 pce/cbpE VF0145 CBPs Adherence VFC0001 Surface protein: choline-binding (pce/cbpE) choline binding protein E [CBPs (VF0145) - Adherence (VFC0001)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_854 99.093 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
CP000919.1_887 63.279 4.5E-139 lmb VF0275 Lmb Adherence VFC0001 Lmb is an extracellular protein that was first identified in S. agalactiae. Homologs of this protein were reported in S. pyogenes and S. pneumonia and termed Lbp and AdcAII, respectively (lmb) laminin-binding surface protein [Lmb (VF0275) - Adherence (VFC0001)] [Streptococcus agalactiae NEM316] Streptococcus agalactiae
CP000919.1_1306 69.697 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
CP000919.1_1452 96.764 0.0 psaA VF0151 PsaA Nutritional/Metabolic factor VFC0272 Surface protein: lipid-attached; AdcABC is another ABC transporter for Zn2+ uptake (psaA) manganese ABC transporter, manganese-binding adhesion liprotein [PsaA (VF0151) - Nutritional/Metabolic factor (VFC0272)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_1486 99.139 0.0 nanB VF0148 Neuraminidase Exoenzyme VFC0251 Surface protein: LPXTG-anchored; two forms of the pneumococcal neuraminidase enzymes, NanA and NanB. The activity of NanB is approximately 100 times lower than that of NanA. NanA but not NanB contains a LPXTG motif in C-terminal, the sequence similarity between the two enzymes is only 20%; maximum activity: NanA at ~pH5, NanB at ~pH7 (nanB) neuraminidase B [Neuraminidase (VF0148) - Exoenzyme (VFC0251)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_1638 100.0 0.0 pfbA VF0525 PfbA Adherence VFC0001 (pfbA) cell wall surface anchor family protein, Plasminogen- and Fibronectin-binding protein A [PfbA (VF0525) - Adherence (VFC0001)] [Streptococcus pneumoniae R6] Streptococcus pneumoniae
CP000919.1_1710 69.143 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
CP000919.1_1714 93.082 0.0 lytA VF0143 Autolysin Exoenzyme VFC0251 Surface protein: choline-binding proteins anchored to the cell surface by a non-covalent interaction of a repeat region at the C-terminal with the phosphorylcholine of the cell wall; Attachment of the enzyme to the choline of the S. pneumoniae cell wall teichoic acid is essential for the lytic activity of the enzyme; two other cell wall hydrolases, LytB and LytC have recently been described, but their roles in virulence have not been assessed. LytB plays a role in pneumococcal daughter cell separation. LytC has a lysozyme-like activity (lytA) autolysin (N-acetylmuramoyl-L-alanine amidase) [Autolysin (VF0143) - Exoenzyme (VFC0251)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_1794 100.0 0.0 ply VF0149 Pneumolysin Exotoxin VFC0235 Shares amino acid homology with similar hemolysins such as SLO, LLO, but pneumolysin is a cytoplasmic protein rather than a secreted protein (ply) pneumolysin [Pneumolysin (VF0149) - Exotoxin (VFC0235)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_1807 100.0 0.0 lytA VF0143 Autolysin Exoenzyme VFC0251 Surface protein: choline-binding proteins anchored to the cell surface by a non-covalent interaction of a repeat region at the C-terminal with the phosphorylcholine of the cell wall; Attachment of the enzyme to the choline of the S. pneumoniae cell wall teichoic acid is essential for the lytic activity of the enzyme; two other cell wall hydrolases, LytB and LytC have recently been described, but their roles in virulence have not been assessed. LytB plays a role in pneumococcal daughter cell separation. LytC has a lysozyme-like activity (lytA) autolysin (N-acetylmuramoyl-L-alanine amidase) [Autolysin (VF0143) - Exoenzyme (VFC0251)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_1954 86.007 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
CP000919.1_2049 69.811 0.0 cbpA/pspC VF0150 CbpA/PspC Adherence VFC0001 Also known as PspC, SpsA, Hic (factor H-binding inhibitor of complement); surface protein: choline-binding protein (cbpA/pspC) choline binding protein A [CbpA/PspC (VF0150) - Adherence (VFC0001)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000919.1_2059 68.653 0.0 cbpD VF0143 Autolysin Exoenzyme VFC0251 Surface protein: choline-binding proteins anchored to the cell surface by a non-covalent interaction of a repeat region at the C-terminal with the phosphorylcholine of the cell wall; Attachment of the enzyme to the choline of the S. pneumoniae cell wall teichoic acid is essential for the lytic activity of the enzyme; two other cell wall hydrolases, LytB and LytC have recently been described, but their roles in virulence have not been assessed. LytB plays a role in pneumococcal daughter cell separation. LytC has a lysozyme-like activity (cbpD) choline binding protein D [Autolysin (VF0143) - Exoenzyme (VFC0251)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae