2. PATHOGENS
Basic Information
Accession number
GCA_000147095.1
Release date
2010-09-09
Organism
Streptococcus pneumoniae 670-6B
Species name
Streptococcus pneumoniae
Assembly level
Complete Genome
Assembly name
ASM14709v1
Assembly submitter
TIGR
Assembly Type
haploid
Genome size
2.2 Mb
GC percent
39.5
Contig count
1
Collection date
-
Sample location
-
Host
-
Isolation source
-
Isolate type
-
Strain
670-6B
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
CP002176.1_664 # 644160 # 644876 50.0 80.8777 vanY gene in vanM cluster 36.03 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.
CP002176.1_1091 # 1061018 # 1061668 350.0 426.017 Streptococcus suis chloramphenicol acetyltransferase 94.91 ARO:3004455 protein homolog model phenicol antibiotic antibiotic inactivation chloramphenicol acetyltransferase (CAT) A chloramphenicol resistance determinant described in Streptococcus suis.
CP002176.1_1108 # 1074324 # 1076243 300.0 1274.23 tet(M) 96.24 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.
CP002176.1_1118 # 1086161 # 1086898 400.0 494.197 ErmB 99.18 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.
CP002176.1_1291 # 1267620 # 1268819 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.
CP002176.1_2124 # 2058466 # 2060232 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..
CP002176.1_2126 # 2061023 # 2062717 750.0 1131.7 patA 98.94 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.
CP002176.1_2152 # 2089444 # 2090292 550.0 580.482 RlmA(II) 98.94 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
CP002176.1_96 94.654 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
CP002176.1_153 99.497 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
CP002176.1_372 98.875 0.0 hysA VF0146 Hyaluronidase Exoenzyme VFC0251 Surface protein: LPXTG-anchored proteins (hysA) hyaluronidase [Hyaluronidase (VF0146) - Exoenzyme (VFC0251)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP002176.1_406 93.347 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
CP002176.1_407 94.239 7.26E-175 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
CP002176.1_408 77.391 1.11E-130 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
CP002176.1_409 78.761 1.99E-134 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
CP002176.1_417 64.828 2.73E-139 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
CP002176.1_430 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
CP002176.1_446 98.387 3.52E-135 cbpG VF0145 CBPs Adherence VFC0001 Surface protein: choline-binding (cbpG) choline binding protein G [CBPs (VF0145) - Adherence (VFC0001)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP002176.1_447 92.784 5.77E-62 cbpG VF0145 CBPs Adherence VFC0001 Surface protein: choline-binding (cbpG) choline binding protein G [CBPs (VF0145) - Adherence (VFC0001)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP002176.1_518 83.108 0.0 rrgA 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 (rrgA) cell wall surface anchor family protein, pilus tip adhesin RrgA [RlrA islet (VF0529) - Adherence (VFC0001)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP002176.1_520 99.746 0.0 rrgC 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 (rrgC) cell wall surface anchor family protein, minor pili RrgC [RlrA islet (VF0529) - Adherence (VFC0001)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP002176.1_521 100.0 0.0 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
CP002176.1_522 95.27 0.0 srtC-2/srtC 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-2/srtC) sortase [RlrA islet (VF0529) - Adherence (VFC0001)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP002176.1_523 91.519 0.0 srtC-3/srtD 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-3/srtD) sortase [RlrA islet (VF0529) - Adherence (VFC0001)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP002176.1_774 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
CP002176.1_1152 85.892 0.0 iga VF0147 IgA1 protease Immune modulation VFC0258 Two more zinc metalloproteinase ZmpB and ZmpC may also contribute to virulence (iga) G5 domain-containing protein [IgA1 protease (VF0147) - Immune modulation (VFC0258)] [Streptococcus pneumoniae TIGR4] Streptococcus pneumoniae
CP002176.1_1264 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
CP002176.1_1297 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
CP002176.1_1331 97.608 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
CP002176.1_1506 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
CP002176.1_1655 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
CP002176.1_1691 98.899 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
CP002176.1_1694 98.394 2.06E-175 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
CP002176.1_1819 60.245 1.96E-145 galE VF0044 LOS Immune modulation VFC0258 Lic1A (phosphorylcholine (ChoP) kinase) 5'-CAAT-3' within the 5'-end of its coding sequence; lic2A, also referred to as lexA, variation in the number of 5'-CAAT-3' repeats has been shown to correlate directly with phase variation of the Gal-alpha(1-4)beta-Gal LPS structure; But lgtC (glycosyltransferase), another phase-variable gene, ultimately dictates whether this structure is synthesized. lic3A encode a sialyl transferase which directs the substitution of LPS with sialic acid. (galE) UDP-glucose 4-epimerase [LOS (VF0044) - Immune modulation (VFC0258)] [Haemophilus influenzae Rd KW20] Haemophilus influenzae
CP002176.1_1824 99.859 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
CP002176.1_1897 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
CP002176.1_1912 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
CP002176.1_1933 99.371 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
CP002176.1_2038 88.994 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
CP002176.1_2142 86.348 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
CP002176.1_2247 98.214 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