2. PATHOGENS
Basic Information
Accession number
GCA_000019005.1
Release date
2009-03-27
Organism
Streptococcus pneumoniae P1031
Species name
Streptococcus pneumoniae
Assembly level
Complete Genome
Assembly name
ASM1900v1
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
P1031
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
CP000920.1_599 # 584865 # 585581 50.0 78.9518 vanY gene in vanM cluster 35.29 ARO:3002961 protein homolog model glycopeptide antibiotic antibiotic target alteration vanY; glycopeptide resistance gene cluster Also known as vanYM, is a vanY variant found in the vanM gene cluster.
CP000920.1_908 # 895857 # 897056 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.
CP000920.1_1078 # 1072571 # 1074490 300.0 1268.83 tet(M) 95.62 ARO:3000186 protein homolog model tetracycline antibiotic antibiotic target protection tetracycline-resistant ribosomal protection protein Tet(M) is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented.
CP000920.1_1946 # 1937387 # 1939153 750.0 1194.87 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..
CP000920.1_1948 # 1939944 # 1941638 750.0 1134.78 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.
CP000920.1_1975 # 1969759 # 1970607 550.0 583.178 RlmA(II) 99.65 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
CP000920.1_75 90.252 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
CP000920.1_132 98.355 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
CP000920.1_330 98.688 0.0 hysA VF0146 Hyaluronidase Exoenzyme VFC0251 Surface protein: LPXTG-anchored proteins (hysA) hyaluronidase [Hyaluronidase (VF0146) - Exoenzyme (VFC0251)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000920.1_363 93.555 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
CP000920.1_364 86.831 9.88E-162 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
CP000920.1_365 89.565 1.08E-152 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
CP000920.1_366 94.521 5.57E-155 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
CP000920.1_378 64.138 4.01E-135 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
CP000920.1_392 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
CP000920.1_406 98.985 3.51E-143 cbpG VF0145 CBPs Adherence VFC0001 Surface protein: choline-binding (cbpG) choline binding protein G [CBPs (VF0145) - Adherence (VFC0001)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP000920.1_698 63.402 8.75E-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
CP000920.1_868 96.81 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
CP000920.1_902 98.911 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
CP000920.1_935 63.607 3.17E-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
CP000920.1_1413 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
CP000920.1_1562 99.676 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
CP000920.1_1595 99.713 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
CP000920.1_1719 99.576 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
CP000920.1_1793 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
CP000920.1_1809 99.788 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
CP000920.1_1822 99.686 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
CP000920.1_1964 86.689 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
CP000920.1_2063 97.991 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