PaperBLAST
PaperBLAST Hits for CharProtDB::CH_121570 alginate biosynthesis protein AlgA; EC 2.7.7.13; EC 5.3.1.8 (Pseudomonas fluorescens) (483 a.a., MIPVILSGGS...)
Show query sequence
>CharProtDB::CH_121570 alginate biosynthesis protein AlgA; EC 2.7.7.13; EC 5.3.1.8 (Pseudomonas fluorescens)
MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNKDHR
FIVNEQLANRKLECQRILMEPFGRNTAPAVALTAMMLVNEGRDELMLVLPADHVIDDQKA
LQRALALATVAAERGEMVLFGVPATRPETGYGYIKSTNDSLLPEGVSRVQQFVEKPDEKR
AVEFVKSGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCVLTLERSEQTADTVTLDDATF
ACCPDNSIDYAVMEKTQRACVVPLSAGWSDVGCWASLWAVNDKDIHGNVSKGDVVIQDSR
NCMIHGNGKLVSVIGLDNIVVVETKDAMMIAHKDKVQGVKQMVSTLNDQGRSETQNHCEV
YRPWGSYDSVDMGGRFQVKHISVKPGACLSLQMHHHRAEHWIVVSGTAEVTCDENVFLLT
ENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRSTPVERGVSVKT
IAQ
Running BLASTp...
Found 134 similar proteins in the literature:
algA / GI|31296823 alginate biosynthesis protein AlgA; EC 2.7.7.13; EC 5.3.1.8 from Pseudomonas fluorescens (see 2 papers)
100% identity, 100% coverage
- CharProtDB Including the following 2 domains: CC Mannose-6-phosphate isomerase EC=5.3.1.8 CC CC Mannose-1-phosphate guanylyltransferase EC=2.7.7.13
GIB64_10205 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudomonas lactis
97% identity, 100% coverage
GIB65_14920 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudomonas lactis
97% identity, 100% coverage
- Genomic Analysis of Three Cheese-Borne Pseudomonas lactis with Biofilm and Spoilage-Associated Behavior
Quintieri, Microorganisms 2020 - “...1 PROKKA_02829- PROKKA_02835 GIB64_21390- GIB64_21420 Alginatebiosynthesis muc R GIB65_00065 PROKKA_05333 GIB64_26185 alg D operon GIB65_14860- GIB65_14920 PROKKA_01700- PROKKA_01712 GIB64_10145- GIB64_10205 Detachment chemotaxis Biofilm dispersion protein BdlA GIB65_02045, GIB65_16355 PROKKA_03805, PROKKA_05334 GIB64_15510, GIB64_03410 Phytochrome-like protein cph 2 GIB65_12695 PROKKA_00099 GIB64_12320 1 NA: not annotated; *: pseudogene....”
ELZ14_25350 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudomonas brassicacearum
94% identity, 100% coverage
BLU14_RS00825, K659_RS0107135 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudomonas corrugata
94% identity, 100% coverage
- The LuxR Regulators PcoR and RfiA Co-regulate Antimicrobial Peptide and Alginate Production in Pseudomonas corrugata
Licciardello, Frontiers in microbiology 2018 - “...2.28 2.43 K659_RS0107140 BLU14_RS00830 algF Alginate biosynthesis protein Alginic acid biosynthetic process 3.38 3.28 K659_RS0107135 BLU14_RS00825 algA Alginate biosynthesis protein Alginic acid biosynthetic process 3.05 2.98 K659_RS0104930 Not found oprM_3 Outer membrane protein OprM Transporter activity -2.32 -2.13 K659_RS0104925 Not found bepE_1 Efflux pump membrane transporter...”
- “...process 2.28 2.43 K659_RS0107140 BLU14_RS00830 algF Alginate biosynthesis protein Alginic acid biosynthetic process 3.38 3.28 K659_RS0107135 BLU14_RS00825 algA Alginate biosynthesis protein Alginic acid biosynthetic process 3.05 2.98 K659_RS0104930 Not found oprM_3 Outer membrane protein OprM Transporter activity -2.32 -2.13 K659_RS0104925 Not found bepE_1 Efflux pump membrane...”
BV82_4701 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudomonas donghuensis
90% identity, 100% coverage
PP1277, PP_1277 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudomonas putida KT2440
89% identity, 100% coverage
- UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023 - Combinatorial metabolic engineering of Pseudomonas putida KT2440 for efficient mineralization of 1,2,3-trichloropropane
Gong, Scientific reports 2017 - “...(GenBank accession no.) Insertion site/targeted deletion dhaA90R 882 294 haloalkane dehalogenase Rhodococcus rhodochrous NCIMB13064 (AF060871) PP_1277 ( algA ) hheC 765 255 haloalcohol dehalogenase Agrobacterium radiobacter AD1 (AF397296) PP_1278/PP_1279 ( algF/algJ ) echA 885 295 epoxide hydrolase Agrobacterium radiobacter AD1 (Y12804) PP_1280 ( algI ) glpR...”
- Global Transcriptional Responses to Osmotic, Oxidative, and Imipenem Stress Conditions in Pseudomonas putida
Bojanovič, Applied and environmental microbiology 2017 - “...PP_4059 PP_4060 NAGGN and mannose biosynthesis PP_1748 PP_1750 PP_1277 PP_5288 Gene name proP gcvH gcvH glgA malQ glgB asnB algA Cardiolipin production PP_3263...”
- Self-Regulation and Interplay of Rsm Family Proteins Modulate the Lifestyle of Pseudomonas putida
Huertas-Rosales, Applied and environmental microbiology 2016 - “...AAAGCCTGATCCAGCCAT GAAATTCCACCACCCTCTACC qRT-PCR; alg cluster (PP_1277; algA)b a b RsmEP2-LacZ fusion (proximal promoter) RsmEP1P2-LacZ fusion (proximal...”
- “...using primers that correspond to the loci PP_1277 (Alg), PP_1795 (Peb), PP_2629 Applied and Environmental Microbiology aem.asm.org 5679 Downloaded from...”
- Engineering Pseudomonas putida KT2440 for simultaneous degradation of carbofuran and chlorpyrifos
Gong, Microbial biotechnology 2016 (no snippet) - Colony morphology and transcriptome profiling of Pseudomonas putida KT2440 and its mutants deficient in alginate or all EPS synthesis under controlled matric potentials
Gulez, MicrobiologyOpen 2014 - “...2.29 2.66 PP_1429 mucB Sigma factor algU regulatory protein MucB 1.76 2.63 2.72 AlgD operon PP_1277 algA Mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase 2.89 N/A N/A PP_1278 algF Alginate O-acetyltransferase 3.16 N/A N/A PP_1279 algJ Alginate O-acetylation protein AlgJ 0.87 N/A N/A PP_1280 algI Alginate O-acetylation protein AlgI 0.52...”
- Transcriptome dynamics of Pseudomonas putida KT2440 under water stress
Gülez, Applied and environmental microbiology 2012 - “...name Gene symbol Annotation 4h PP_0133 algB 2.10 PP_1277 algA PP_1278 PP_1279 PP_1280 PP_1287 PP_1288 PP_1427 PP_1428 algF algJ algI PP_1429 mucB Alginate...”
Psyr_1052 Mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudomonas syringae pv. syringae B728a
90% identity, 100% coverage
PSPTO_1232 alginate biosynthesis protein AlgA from Pseudomonas syringae pv. tomato str. DC3000
89% identity, 100% coverage
algA / P07874 phosphomannose isomerase (EC 5.3.1.8; EC 2.7.7.13) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 2 papers)
ALGA_PSEAE / P07874 Alginate biosynthesis protein AlgA; EC 5.3.1.8; EC 2.7.7.13 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
P07874 mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) from Pseudomonas aeruginosa (see 2 papers)
PA3551 phosphomannose isomerase / guanosine 5'-diphospho-D-mannose pyrophosphorylase from Pseudomonas aeruginosa PAO1
NP_252241 bifunctional mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudomonas aeruginosa PAO1
79% identity, 97% coverage
- function: Produces a precursor for alginate polymerization. The alginate layer provides a protective barrier against host immune defenses and antibiotics.
catalytic activity: D-mannose 6-phosphate = D-fructose 6-phosphate (RHEA:12356)
catalytic activity: alpha-D-mannose 1-phosphate + GTP + H(+) = GDP-alpha-D-mannose + diphosphate (RHEA:15229)
cofactor: Co(2+) (Co(2+) (for PMI).)
subunit: Monomer. - Functional Characterization of TetR-like Transcriptional Regulator PA3973 from Pseudomonas aeruginosa
Kotecka, International journal of molecular sciences 2022 - “...07345 PA3552 UDP-4-amino-4-deoxy-L-arabinose- oxoglutarate aminotransferase ArnB 1.31 1.00 AP; ARS; CWLC 1,536,054 6.29 T 07350 PA3551 alginate biosynthesis protein AlgA 1.06 1.05 AP; SF; CWLC 1,229,065 6.17 T+ 05895 PA3829 alpha/beta hydrolase 0.59 0.94 HUU 1,229,065 6.17 P+ 05900 PA3828 LPS export ABC transporter permease LptF...”
- Pf4 Phage Variant Infection Reduces Virulence-Associated Traits in Pseudomonas aeruginosa
Tortuel, Microbiology spectrum 2022 - “...RpoN RsmA 2.79 PA3550 algF Alginate O -acetyltransferase AlgF AlgU, AmrZ AlgR, RpoN RsmA 2.83 PA3551 algA Phosphomannose isomerase/guanosine 5-diphospho- d -mannose pyrophosphorylase AlgU, AmrZ AlgR, RpoN RsmA 2.48 PA3649 mucP MucP 2.77 PA4033 mucE MucE AlgU 2.10 PA5253 algP Alginate regulatory protein AlgP 9.90 PA5255...”
- Transcriptional Responses of Pseudomonas aeruginosa to Inhibition of Lipoprotein Transport by a Small Molecule Inhibitor
Lorenz, Journal of bacteriology 2020 - “...Poly(- d -mannuronate) lyase precursor AlgL alginate lyase (AlgL) PA2146 38.4 102.0 Conserved hypothetical protein PA3551 algA 38.1 33.0 Phosphomannose isomerase alginate biosynthesis protein AlgA PA3541 alg8 25.8 18.5 Alginate biosynthesis protein Alg8 PA3550 algF 24.8 22.2 Alginate O -acetyltransferase AlgF PA3544 algE 23.4 19.5 Alginate...”
- Overexpression of the Small RNA PA0805.1 in Pseudomonas aeruginosa Modulates the Expression of a Large Set of Genes and Proteins, Resulting in Altered Motility, Cytotoxicity, and Tobramycin Resistance
Coleman, mSystems 2020 - “...3.5E02 PA3548 algI Alginate o -acetyltransferase 1.80 3.9E02 PA3550 algF Alginate o -acetyltransferase 1.74 4.7E02 PA3551 algA Phosphomannose isomerase/GDP- d -mannose pyrophosphorylase 1.82 1.3E03 PA3724 lasB Elastase 1.64 1.7E07 PA4175 piv Protease IV 1.86 1.7E05 PA4212 phzC1 Phenazine biosynthesis protein 1.44 4.5E03 PA4213 phzD1 Phenazine biosynthesis...”
- Cystic Fibrosis and Pseudomonas aeruginosa: the Host-Microbe Interface
Malhotra, Clinical microbiology reviews 2019 (secret) - Inhibition of Pseudomonas aeruginosa Biofilm Formation by Traditional Chinese Medicinal Herb Herba patriniae
Fu, BioMed research international 2017 - “...Glycoside hydrolase; deacetylase pKD- pelA -S CGT CTCGAG CTTTCCACTTTGCCACAG pKD- pelA -A TAC GGATCC TACCAGAACGCCACGCT PA3551 algA Phosphomannose isomerase; guanosine 5-diphospho-D-mannose pyrophosphorylase pKD- algA -S TGA CTCGAG TGAAGGCGGACTGAGAC pKD- algA -A TAT GGATCC GCGACCAGTTTCATC PA2663 ppyR psl and pyoverdine operon regulator pKD- ppyR -S GCA CTCGAG...”
- Cleaning and Disinfection of Biofilms Composed of Listeria monocytogenes and Background Microbiota from Meat Processing Surfaces
Fagerlund, Applied and environmental microbiology 2017 - “...pelG (PA3064 to PA3058), the alg operon (PA3540 to PA3551), and cdrA (PA4625) from P. aeruginosa PAO1 (accession number AE004091); wssA to wssJ from P....”
- Effect of Shear Stress on Pseudomonas aeruginosa Isolated from the Cystic Fibrosis Lung
Dingemans, mBio 2016 - “...2.84 0.82 PA3550 ( algF ) Alginate o-acetyltransferase AlgF Alginate biosynthesis PA3540 ( algD ) PA3551 ( algA ) 1.83 1.94 0.29 PA4481 ( mreB ) Rod-shape-determining protein MreB Cell cycle control, cell division, chromosome partitioning PA4481 ( mreB ) PA4479 ( mreD ) 1.80 2.26...”
- “...) Mannose-1-phosphate guanylyltransferase (GDP) (EC 2.7.7.22)/mannose-6-phosphate isomerase (EC 5.3.1.8) Alginate biosynthesis PA3540 ( algD ) PA3551 ( algA ) 1.65 2.01 0.13 a FC, fold change; EC, enzyme class; HTH, helix-turn-helix; SSU, small subunit. TABLE3 Selection of genes that were downregulated under low fluid shear conditions...”
- More
- Unveiling the Microbiome Landscape: A Metagenomic Study of Bacterial Diversity, Antibiotic Resistance, and Virulence Factors in the Sediments of the River Ganga, India
Rout, Antibiotics (Basel, Switzerland) 2023 - “...NP_253699 waaF contigs_45; contigs_269352 Rasulabad Ghat; Sahidabad NP_251102 mbtH-like contigs_627 Bagwan AAF37887 ompA contigs_5362 Bagwan NP_252241 algA contigs_665 Rasulabad Ghat NP_252918 pchD Pyochelin (VF0095) ( Pseudomonas aeruginosa ) contigs_665 Rasulabad Ghat NP_252919 pchC contigs_665 Rasulabad Ghat NP_252914 pchG contigs_665 Rasulabad Ghat NP_252915 pchF contigs_665 Rasulabad Ghat...”
- Pseudomonas aeruginosa biofilm exopolysaccharides: assembly, function, and degradation
Gheorghita, FEMS microbiology reviews 2023 - “...Q51392 Q51393 4O8V AlgF Q06062 6D10, 6CZT AlgA P07874 AlgC P26276 a 1MFZ, 1MUU, 1MV8 7SP8 5C22 Mannuronan synthase, GT C-di-GMP-binding protein C-5 mannuronan...”
Avin_10860 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Azotobacter vinelandii AvOP
74% identity, 100% coverage
xanB / AAK53463.1 phosphomannose isomerase/GDP-D-mannose pyrophosphorylase from Xanthomonas campestris pv. campestris (see 4 papers)
58% identity, 97% coverage
XFF4834R_chr34740 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Xanthomonas citri pv. fuscans
57% identity, 97% coverage
XAUB_05850 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Xanthomonas citri pv. aurantifolii str. ICPB 11122
57% identity, 97% coverage
E2P69_RS22825 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Xanthomonas perforans
58% identity, 97% coverage
PXO_RS21065 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Xanthomonas oryzae pv. oryzae PXO99A
PXO_03173 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Xanthomonas oryzae pv. oryzae PXO99A
57% identity, 97% coverage
- Melatonin Treatment Inhibits the Growth of Xanthomonas oryzae pv. oryzae
Chen, Frontiers in microbiology 2018 - “...isomerase 39 PXO_RS01605 -4.72 Beta-1,4-xylanase 40 PXO_RS19450 +2.54 Glycosidases 41 PXO_RS19890 -2.48 Glycosyl transferase 42 PXO_RS21065 -1.75 Mannose-1-phosphate guanyltransferase 43 PXO_RS23055 +1.61 Fucose permease 44 PXO_RS19900 -2.48 UDP-2,3-diacylglucosamine hydrolase 45 PXO_RS18550 -1.50 Ubiquinol oxidase subunit II 46 PXO_RS22130 -2.61 Lipase 47 PXO_RS15625 -2.94 Peptidase S53 48...”
- Comparative transcriptome profiling reveals different expression patterns in Xanthomonas oryzae pv. oryzae strains with putative virulence-relevant genes
Zhang, PloS one 2013 - “...and PXO_04558 also had down-regulated expression in P2 compared with P6. Interestingly, xanA (PXO_03174), xanB (PXO_03173), wxoA (PXO_03160), wxoB (PXO_03161), wxoC (PXO_05411), and wxoE (PXO_03158) were also down-regulated in C5 compared with P6 and P2. However, xanA (PXO_03174) and xanB (PXO_03173) were up-regulated in P2 compared...”
XAC3580 phosphomannose isomerase from Xanthomonas axonopodis pv. citri str. 306
57% identity, 97% coverage
- GDP-mannose pyrophosphorylase is an efficient target in Xanthomonas citri for citrus canker control
Alexandrino, Microbiology spectrum 2024 - “...guanosine mannose diphosphate (GDP-mannose) ( 8 ). The putative PMI-GMP enzyme encoded by the ORF XAC3580 in Xcc [National Center for Biotechnology Information (NCBI)] is bifunctional, known as type II ( 9 ), consists of 467 amino acid residues, and belongs to the family of mannose-1-phosphate...”
- “...its essentiality for Xcc pathogenicity. Our research group previously identified XanB, encoded by the ORF XAC3580, as a potential contributor to pathogenicity through differential surface proteomics analysis of Xcc cells under in vivo and in vitro conditions ( 5 ). XanB was also identified in a...”
- Periplasm-enriched fractions from Xanthomonas citri subsp. citri type A and X. fuscans subsp. aurantifolii type B present distinct proteomic profiles under in vitro pathogenicity induction
Zandonadi, PloS one 2020 - “...20 28 II (XAC0476) C XAUB_05850 GDP-mannose pyrophosphorylase (6) 51.0 5.6 260 16 32 VII (XAC3580) C XAUB_39520 S-adenosyl-L-homocysteine hydrolase (4) 53.2 5.5 100 8 14 I (XAC0804) C 10 XauB 4,21E-01 Unique 0,00248762 XAUB_41080 Isocitrate dehydrogenase 35.7 5.4 38.4 4.6 401 15 25 I (XAC1046)...”
- “...12 15 III (XAC0542) C XAUB_05850 GDP-mannose pyrophosphorylase (6) 51.0 5.6 46 2 3 VII (XAC3580) C XAUB_10980 Outer membrane receptor for transport of vitamin B (3) 67.7 5.4 24 2 1 IV (XAC3194) OM 25* XauB 0,762 1,77 104 XAUB_41470 Acyl-carrier-protein S-malonyltransferase (2) 33.0 5.7...”
XHV734_4229 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Xanthomonas hortorum pv. vitians
58% identity, 97% coverage
NBC2815_00824 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Xanthomonas fragariae
57% identity, 97% coverage
- Transcriptome analysis of Xanthomonas fragariae in strawberry leaves
Puławska, Scientific reports 2020 - “...changes in the expression of the nucleotide precursor of xanthan synthesis genes xanA and xanB (NBC2815_00824) were observed. Among the rpf genes known to be involved in the regulation of pathogenicity factors in other Xanthomonas species 14 , only rpfA was highly upregulated in planta ,...”
PD0212 phosphomannose isomerase-GDP-mannose pyrophosphorylase from Xylella fastidiosa Temecula1
55% identity, 97% coverage
ZP_01218698 mannose-1-phosphate guanylyltransferase from Photobacterium profundum 3TCK
54% identity, 97% coverage
- Implication of lateral genetic transfer in the emergence of Aeromonas hydrophila isolates of epidemic outbreaks in channel catfish
Hossain, PloS one 2013 - “...wcaE Shigella dysenteriae 1012 67 ZP_03065870.1 ORF10 11717.13018 mannose-1-phosphate guanylyltransferase manC Photobacterium profundum 3TCK 71 ZP_01218698.1 ORF11 13128.13610 GDP-mannose mannosyl hydrolase gmm Tolumonas auensis DSM 9187 63 YP_002893236.1 ORF12 13594.14574 GDP-fucose synthetase fcl Yersinia pestis KIM 10 84 NP_668408.1 ORF13 14578.15684 GDP-mannose 4,6-dehydratase gmd Vibrio angustum...”
- “...wcaE Shigella dysenteriae 1012 67 ZP_03065870 ORF10 11717.13018 mannose-1-phosphate guanylyltransferase manC Photobacterium profundum 3TCK 71 ZP_01218698 ORF11 13128.13610 GDP-mannose mannosyl hydrolase gmm Tolumonas auensis DSM 9187 63 YP_002893236 ORF12 13594.14574 GDP-fucose synthetase fcl Yersinia pestis KIM 10 84 NP_668408 ORF13 14578.15684 GDP-mannose 4,6-dehydratase gmd Vibrio angustum...”
CDW43_06820 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Methylophaga nitratireducenticrescens
54% identity, 97% coverage
YP_002413091 Mannose-1-phosphate guanylyltransferase [GDP] (GDP-mannose pyrophosphorylase) (GMP) from Escherichia coli UMN026
54% identity, 97% coverage
XALc_2693 probable mannose-6-phosphate isomerase protein from Xanthomonas albilineans
56% identity, 97% coverage
- Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels
Pieretti, BMC genomics 2012 - “...two key genes xanA , encoding a phosphoglucomutase (XALc_2692), and xanB encoding a phosphomannose isomerase (XALc_2693), are involved in biosynthesis of xanthan. Other EPS genes, such as pgi , galU and ugd , which encode a glucose-6-phosphate isomerase, an UTP-glucose-1-phosphate uridylyltransferase and an UDP-glucose 6-dehydrogenase, respectively,...”
YPK_3181 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Yersinia pseudotuberculosis YPIII
53% identity, 96% coverage
YPTB1011 mannose-1-phosphate guanylyltransferase from Yersinia pseudotuberculosis IP 32953
51% identity, 96% coverage
YPO3099 mannose-1-phosphate guanylyltransferase from Yersinia pestis CO92
51% identity, 96% coverage
YE3073 mannose-1-phosphate guanylyltransferase from Yersinia enterocolitica subsp. enterocolitica 8081
52% identity, 96% coverage
ACIAD0086 bifunctional protein [Includes: Mannose-6-phosphate isomerase (Phosphomannose isomerase) (Pmi) (Phosphohexomutase); Mannose-1-phosphate guanylyl transferase (Gdp) (GDP-mannose pyrophosphorylase) (Gmp)] from Acinetobacter sp. ADP1
51% identity, 97% coverage
- Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining
Suárez, Nucleic acids research 2020 - “...tag Description ( gene ) MGD1 Rich ACIAD0083 Polysaccharide polymerase Rich ACIAD0084 Mannosyl transferase Rich ACIAD0086 Mannose-6-phosphate isomerase/mannose-1-phosphate guanylyl transferase ( epsM ) Rich ACIAD0090 Glycosyl transferase Rich ACIAD0091 Glycosyl transferase MGD3 Rich ACIAD0335 Multifunctional fatty acid oxidation complex subunit alpha ( fadB ) MGD5 Rich...”
- “...in minimal medium (Table 1 ). These genes included several sugar transferases ( ACIAD0084 , ACIAD0086 , ACIAD0090 , ACIAD0091 ), an OmpA-like outer membrane protein ( ACIAD0697 ), a translation elongation factor ( typA ), a putative hemolysin ( ACIAD0944 ), isocitrate dehydrogenase ( idh...”
- Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data
Durot, BMC systems biology 2008 - “...ACIAD0856 (bioA) E step 2 ACIAD0080 (rmlC) D step 2 ACIAD0857 (bioF) E step 2 ACIAD0086 (epsM) D step 2 ACIAD0859 (bioD) E step 2 ACIAD0099 (galU) D step 2 ACIAD2045 (bioB) E step 2 ACIAD0101 (pgi) D step 2 unmodeled auxotrophy 1 ACIAD0104 (manB) D...”
- “...ACIAD1105 (adk) E step 2 ACIAD3510 (lpxC) D step 2 ACIAD1920 (glnS) E step 2 ACIAD0086 (epsM) E step 3 ACIAD2560 (proB) E step 2 ACIAD0335 (fadB) E step 3 ACIAD3032 (proC) E step 2 ACIAD0382 (ubiB) D step 3 ACIAD0901 (dut) E step 2 ACIAD0922...”
Q43941 mannose-1-phosphate guanylyltransferase from Acinetobacter calcoaceticus
51% identity, 97% coverage
epsQ / BAC55145.1 GDP-mannose pyrophosphorylase EpsQ from Methylobacillus sp. 12S (see paper)
54% identity, 97% coverage
I5G01_08515 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Klebsiella pneumoniae
50% identity, 97% coverage
VK055_5027 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Klebsiella pneumoniae subsp. pneumoniae
Q48462 Mannose-1-phosphate guanylyltransferase from Klebsiella pneumoniae
50% identity, 97% coverage
rfbM / BAA07745.1 GDP-mannose pyrophosphorylase from Escherichia coli (see 2 papers)
Q59427 mannose-1-phosphate guanylyltransferase from Escherichia coli
50% identity, 97% coverage
KP1_RS17280 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
KP1_3703 mannose-1-phosphate guanylyltransferase from Klebsiella pneumoniae NTUH-K2044
50% identity, 97% coverage
- Characterization and comparative analysis of the Escherichia marmotae M-12 isolate from bank vole (Myodes glareolus)
Zhurilov, Scientific reports 2023 - “...28 . 12 homolog proteins from the capsule category of the Klebsiella pneumoniae were found: KP1_RS17280, KP1_RS17295, KP1_RS17305, KP1_RS17340, RfbK1, GndA, RcsA, RcsB, Ugd, WcaJ, Gmd, GalF. Capsule assists in evading the host immune system by protecting bacteria from opsonophagocytosis and serum killing 29 . 12...”
- The KbvR Regulator Contributes to Capsule Production, Outer Membrane Protein Biosynthesis, Antiphagocytosis, and Virulence in Klebsiella pneumoniae
Xu, Infection and immunity 2021 (secret) - The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort
Dorman, mBio 2018 - “...1.00 KP1_3542 VK055_0032 rmpA Regulator of mucoid phenotype 0.05 KP1_3619 VK055_5097 manC Mannose-1-phosphate guanylyltransferase 0.24 KP1_3703 VK055_5027 galF UDP-glucose pyrophosphorylase 0.88 KP1_3726 VK055_5012 rcsB DNA-binding capsular synthesis response regulator RcsB 0.77 KP1_3872 VK055_4883 glnB Nitrogen regulatory protein P-II 1.00 KP1_4132 VK055_4623 rluD 23S rRNA pseudouridine synthase...”
Q07024 Putative mannose-1-phosphate guanylyltransferase from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
VC0241 mannose-1-phosphate guanylyltransferase from Vibrio cholerae O1 biovar eltor str. N16961
52% identity, 96% coverage
- Novel Vibrio cholerae O139 genes involved in lipopolysaccharide biosynthesis
Stroeher, Journal of bacteriology 1997 - “...(374) 31.9 (373) 52.1 (461) 56.3 (469) 55.4 (464) L36823 L34167 Q07024 P24174 Q01410 a RfbD and ORF1 to -4 are from Bik et al. (4) and Comstock et al. (8),...”
- Vibrio cholerae phage ICP3 requires O1 antigen for infection
Beckman, Infection and immunity 2023 (secret) - A simple mechanism for integration of quorum sensing and cAMP signalling in Vibrio cholerae
Walker, eLife 2023 - “...Identified as activated (A) or repressed (R) by Nielsen et al., 2006 , VC0206, VC0240, VC0241, VC0583, VC0668, VC0916, VC1021, VC1142, VC1143, VCA0219 correspond to murQ , rfaD , rfbA , hapR , mutH , vpsU , luxO , cspD , clpS , hlyA respectively. Nearest...”
- “...4 correspond to previously identified direct targets [ hapR ( Lin et al., 2005 ), VC0241 ( Tsou et al., 2009 ), VC1851 ( Waters et al., 2008 ) and VCA0148 ( Tsou et al., 2009 )]. However, some known targets had weak or poorly reproducible...”
- A simple mechanism for integration of quorum sensing and cAMP signalling inV. cholerae
Walker, 2023 - Impact of Gene Repression on Biofilm Formation of Vibrio cholerae
Pombo, Frontiers in microbiology 2022 - “...VC0233-237 VC0233 3-Deoxy-D-manno-octulosonic acid transferase 1 VC0234 Hypothetical protein 1 VC0240 ADP-L-glycero-D-manno-heptose 6-epimerase 1 VC0241-251 VC0241 Mannose-1-phosphate guanylyltransferase 1 VC0242 Phosphomannomutase 1 VC0243 GDP-mannose 4,6-dehydratase 1 VC0245 RfbG protein 2 VC0246 Lipopolysaccharide/O-antigen transport protein 1 VC0249 RfbL protein 6 VC0250 Iron-containing alcohol dehydrogenase 15 VC0251 Acyl...”
- Functional Specialization in Vibrio cholerae Diguanylate Cyclases: Distinct Modes of Motility Suppression and c-di-GMP Production
Zamorano-Sánchez, mBio 2019 - “...33 ). Previous studies revealed that mutations in genes predicted to participate in perosamine biosynthesis (VC0241 to VC0244) result in loss of O-antigen and associated phenotypes such as sensitivity to bacteriophages K139 and VP4 ( 34 36 ). To analyze the role of O-antigen biosynthesis in...”
- OmpU as a biomarker for rapid discrimination between toxigenic and epidemic Vibrio cholerae O1/O139 and non-epidemic Vibrio cholerae in a modified MALDI-TOF MS assay
Paauw, BMC microbiology 2014 - “...identified translation start. c Presumed serotype O1 based on sequence similarity with O-antigen biosynthesis genes VC0241 to VC0244A from N16961. d Presumed serotype non-O1/O139, based on lack of sequence similarity with O-antigen biosynthesis genes VC0241 to VC0244A from N16961 and O139. Accession: AB012956 bp 2208424660 wbfH...”
- Phase variable O antigen biosynthetic genes control expression of the major protective antigen and bacteriophage receptor in Vibrio cholerae O1
Seed, PLoS pathogens 2012 - “...clearly distinguishable on the basis of size or even sequence similarity [49] . Indeed ManC (VC0241) in V. cholerae O1 has the bioinformatic designation of a type II PMI, however our results below suggest this enzyme lacks PMI activity. The presence of two putative type I...”
- Regulatory targets of quorum sensing in Vibrio cholerae: evidence for two distinct HapR-binding motifs
Tsou, Nucleic acids research 2009 - “...S1. As discussed further in the experimental results, all the predicted targets except one ( vc0241 ) were validated by gel retardation assays. The binding sites for the experimentally validated targets were used to generate a revised PSWM for HapR based solely on targets in V....”
- “...11 of the tested promoters containing a Motif 1-binding site and all but one ( vc0241 ) of the eight promoters containing a Motif 2-binding site ( Figure 2 ) Thus, the Motif 1-binding sequence reliably predicts promoter regions capable of being bound by HapR. The...”
- More
ESA_01169 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
53% identity, 97% coverage
c2575 Mannose-1-phosphate guanylyltransferase from Escherichia coli CFT073
52% identity, 97% coverage
BTH_I1324 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Burkholderia thailandensis E264
53% identity, 97% coverage
MANC1_ECO57 / Q8X7P1 Mannose-1-phosphate guanylyltransferase 1; GDP-mannose pyrophosphorylase 1; GMP 1; GMPP 1; EC 2.7.7.13 from Escherichia coli O157:H7
Z3213 mannose-1-phosphate guanyltransferase from Escherichia coli O157:H7 EDL933
52% identity, 97% coverage
- function: Involved in GDP-mannose biosynthesis which serves as the activated sugar nucleotide precursor for mannose residues in cell surface polysaccharides. In vitro, shows very broad substrate specificities for four nucleotides and various hexose-1-phosphates, yielding ADP-mannose, CDP-mannose, UDP-mannose, GDP-mannose, GDP- glucose and GDP-2-deoxy-glucose.
catalytic activity: alpha-D-mannose 1-phosphate + GTP + H(+) = GDP-alpha-D-mannose + diphosphate (RHEA:15229) - Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
Sharma, BMC microbiology 2017 - “...protein 6.36 0.01 wcaK Z3209 Pyruvyl transferase 12.75 0.03 cpsG Z3212 Phosphomannomutase 14.59 3.4E-03 cspB Z3213 Mannose-1-phosphate guanylly-trasferase 13.91 7.0E-04 wcaI Z3214 Glycosyl transferase 14.28 4.0E-03 wcaH Z3215 GDP-D-mannose dehydratase 13.95 3.1E-03 wcaG Z3216 Nucleotide di-P-sugar epimerase 16.20 0.03 gmd Z3217 GDP-D-mannose dehydratase 15.73 0.04 wcaF...”
Q5A_007950 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Serratia inhibens PRI-2C
51% identity, 97% coverage
RfbM / b2049 mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) from Escherichia coli K-12 substr. MG1655 (see 11 papers)
cpsB / P24174 mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) from Escherichia coli (strain K12) (see 11 papers)
P24174 Mannose-1-phosphate guanylyltransferase from Escherichia coli (strain K12)
b2049 mannose-1-phosphate guanyltransferase from Escherichia coli str. K-12 substr. MG1655
52% identity, 97% coverage
- The Role of Propionate-Induced Rearrangement of Membrane Proteins in the Formation of the Virulent Phenotype of Crohn's Disease-Associated Adherent-Invasive Escherichia coli
Pobeguts, International journal of molecular sciences 2024 - “...protein FtsA 101 2.62 0.34 P0A9X4 Rod shape-determining protein MreB 133 3.13 0.40 Lipopolysaccharides biosynthesis P24174 Mannose-1-phosphate guanylyltransferase ManC 14 10.34 1.24 P0A715 2-dehydro-3-deoxyphosphooctonate aldolase KdsA 79 7.18 0.93 P45395 arabinose 5-phosphate isomerase KdsD 49 3.30 0.43 P0AEP3 UTP-glucose-1-phosphate uridylyltransferase GalU 68 2.99 0.39 ATP- synthase...”
- Novel Vibrio cholerae O139 genes involved in lipopolysaccharide biosynthesis
Stroeher, Journal of bacteriology 1997 - “...31.9 (373) 52.1 (461) 56.3 (469) 55.4 (464) L36823 L34167 Q07024 P24174 Q01410 a RfbD and ORF1 to -4 are from Bik et al. (4) and Comstock et al. (8),...”
- The three genes lipB, lipC, and lipD involved in the extracellular secretion of the Serratia marcescens lipase which lacks an N-terminal signal peptide
Akatsuka, Journal of bacteriology 1995 - “...rfbM (16), E. coli cpsB (accession no. P24174), and S. choleraesuis cpsB (20) gene products, respectively, which were GDP-mannose pyrophosphorylase (EC...”
- Multidomain organization of eukaryotic guanine nucleotide exchange translation initiation factor eIF-2B subunits revealed by analysis of conserved sequence motifs
Koonin, Protein science : a publication of the Protein Society 1995 - “...P39124 52 LMLVLAADHVIADEDAFRA 50 LLLVLPSDHVIRDEAAFQA P24174 P29956 41 IYINLQGDEPMIRPRDVET C48492 5: VIVIPARYGSSRLPG--""-KPLLDIVGKPMIQHVYERALQVAGVAE~A 4 :...”
- Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
Sabina, Journal of bacteriology 2003 - “...yfiD ylcB b3686 b3687 b2577 b4013 b0702 b2592 b4242 b2049 b2451 b1776 b2656 b2681 b3238 b3875 b2597 b2886 b2680 b0691 b0429 b0557 b2818 b1627 b1814 b0473 b3563...”
A4U42_06115 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Dickeya solani
51% identity, 95% coverage
Dda3937_00442 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Dickeya dadantii 3937
51% identity, 95% coverage
Dd586_1250 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Dickeya dadantii Ech586
50% identity, 97% coverage
STM2105.S mannose-1-phosphate guanylyltransferase from Salmonella typhimurium LT2
51% identity, 97% coverage
BCAL3246 putative GDP-mannose pyrophosphorylase from Burkholderia cenocepacia J2315
52% identity, 97% coverage
- Subfunctionalization influences the expansion of bacterial multidrug antibiotic resistance
Perrin, BMC genomics 2017 - “...Partial BCAL1308, BCAL131517 1 197 From 3,554,574 to 3,554,770 No coding region between BCAL3245 and BCAL3246 3 26,613 From 8888 to 35,500 Partial BCAS0007, BCAS0080031 3 79,445 From 493,762 to 573,206 BCAS04210503 Insertions 3 886 867,051 Partial BCAS2756 and partial BCAL2755, inserted up to BCAS0768 Fig....”
- The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients
Holden, Journal of bacteriology 2009 - “...environmental conditions. One of these clusters (BCAL3217 to BCAL3246) (105) is similar to the capsular polysaccharide cluster of B. pseudomallei K96243 (51),...”
- “...of similarity (BCAL3217 to BCAL3223 and BCAL3240 to BCAL3246) separated by a block of divergent sequence (BCAL3227 to BCAL3239). This cluster is probably not...”
t0789 mannose-1-phosphate guanylyltransferase from Salmonella enterica subsp. enterica serovar Typhi Ty2
49% identity, 97% coverage
- Genome-wide Analysis of Salmonella enterica serovar Typhi in Humanized Mice Reveals Key Virulence Features
Karlinsey, Cell host & microbe 2019 - “...O-antigen transporter 2.9 rfbV/wbaV t0786 putative glycosyl transferase 2.79 rfbN/wbaN t0788 putative rhamnosyltransferase 4.55 rfbM/manC t0789 mannose-1-phosphate guanylyltransferase 3.27 rfbK/manK t0790 phosphomannomutase 3.82 rfbP/wbaP t0791 undecaprenyl-phosphate galactosephosphotransferase 3.77 wzxE t3371 putative lipopolysaccharide biosynthesis protein 4.47 waaL t3806 O-antigen ligase 4.67 LPS biosynthesis; Outer core waaB t3800...”
RFBM_SALTY / P26404 Mannose-1-phosphate guanylyltransferase RfbM; GDP-mannose pyrophosphorylase; GMP; GMPP; GTP--mannose-1-phosphate guanylyltransferase; EC 2.7.7.13 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
manC / CAA40128.1 mannose-1-phosphate guanylyltransferase (GDP) from Salmonella enterica (see 6 papers)
STM2084 LPS side chain defect: mannose-1-phosphate guanylyltransferase from Salmonella typhimurium LT2
49% identity, 97% coverage
- function: Involved in GDP-mannose biosynthesis which serves as the activated sugar nucleotide precursor for mannose residues in cell surface polysaccharides. This enzyme participates in synthesis of the LPS group B O antigen
catalytic activity: alpha-D-mannose 1-phosphate + GTP + H(+) = GDP-alpha-D-mannose + diphosphate (RHEA:15229)
subunit: Homodimer. - Effect of iacP mutation on flagellar phase variation in Salmonella enterica serovar typhimurium strain UK-1
Eom, Journal of bacteriology 2012 - “...ccmG psd yjgA STM1911 STM4258 recR malE STM2084 STM1312 STM3241 STM4269 STM2879 STM2248 STM4348 STM4437 STM1911 STM4258 STM0486 STM4229 Mannose-1-phosphate...”
- Intraspecies variation in the emergence of hyperinfectious bacterial strains in nature
Heithoff, PLoS pathogens 2012 - “...Involved in quorum sensing; encodes periplasmic receptor for AI-2 [151] ; also called lsrB . STM2084 rfbM 2.03 0.13 0.33 Involved in O-antigen synthesis [152] ; also known as manC . a The log 2 LPM/LB gene expression ratios values for conventionally virulent S. Typhimurium (ST),...”
- Salmonella serovar identification using PCR-based detection of gene presence and absence
Arrach, Journal of clinical microbiology 2008 - “...STM2007, STM2008, STM2026, STM2050, STM2051, STM2052, STM2084, STM2085, STM2092, STM2099, STM2133, STM2135, STM2151, STM2152, STM2232, STM2240, STM2243,...”
- Identification of Salmonella enterica serovar Typhimurium genes important for survival in the swine gastric environment
Bearson, Applied and environmental microbiology 2006 - “...STM1091 PSLT078 STM2585 PSLT018 pSLT017 STM3713 STM2120 STM2084 709/1,686 218/312 468/546 108/519 175/2,409 211/1,215 718/1,866 291/1,440 Cell envelope Cell...”
- Microbial responses to microgravity and other low-shear environments
Nickerson, Microbiology and molecular biology reviews : MMBR 2004 - “...STM2896 STM2902 STM1398 STM1412 STM1414 STM1631 STM0543 STM2082 STM2084 STM2093 STM1371 STM1373 orgA prgH sipD invI invA pigB sseB ssaL ssaV sseJ fimA rfbP...”
BPSL2810 putative GDP-mannose pyrophosphorylase from Burkholderia pseudomallei K96243
51% identity, 97% coverage
- Identification of Burkholderia cepacia strains that express a Burkholderia pseudomallei-like capsular polysaccharide
Burtnick, Microbiology spectrum 2024 - “...Figure showing a 34.5-kb region of B. pseudomallei (Bp) K96243 containing 24 genes (BPSL2787 to BPSL2810, wcbT-manC ) responsible for CPS biosynthesis. Similar regions in B. cepacia (Bc) strains 10223, 39628, LNT40, and B. thailandensis (Bt) strains SBXCC001 and SBXPR001 are aligned below the reference genome....”
- Peptidyl-Prolyl Isomerase ppiB Is Essential for Proteome Homeostasis and Virulence in Burkholderia pseudomallei
Bzdyl, Infection and immunity 2019 (secret) - Transcriptomic analysis of longitudinal Burkholderia pseudomallei infecting the cystic fibrosis lung
Price, Microbial genomics 2018 - “...species, including B. pseudomallei [ 14, 28 ]. Encoded by the 34.5kb wcb operon BPSL2786 BPSL2810 [ 44, 45 ], the B. pseudomallei CPS-I is a potent virulence determinant that imparts high-level serum resistance and facilitates phagocytic evasion [ 45 ]. This capsule is also intact...”
- Genome-wide saturation mutagenesis of Burkholderia pseudomallei K96243 predicts essential genes and novel targets for antimicrobial development
Moule, mBio 2014 - “...synthesis I (CPS I) locus of B.pseudomallei K96243 located in the region of bpsl2787 to bpsl2810 , which has an overall lower GC content than the rest of the genome, was highly represented by transposon insertion mutants, with many of the genes in this locus containing...”
- Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates
Challacombe, PloS one 2014 - “...capsular polysaccharide biosynthesis protein various BPSL2803 glycosyltransferase various BPSL2808 capsular polysaccharide glycosyltransferase biosynthesis protein various BPSL2810 GDP-mannose pyrophosphorylase; mannose-1-phosphate guanylyltransferase (EC 2.7.7.13/EC 2.7.7.22) Fructose and mannose metabolism, Amino sugar and nucleotide sugar metabolism, Biosynthesis of secondary metabolites BPSL2818 phosphoribosylaminoimidazole synthetase (EC 6.3.3.1)# Purine metabolism, Biosynthesis of...”
- Characterization of the Burkholderia pseudomallei K96243 capsular polysaccharide I coding region
Cuccui, Infection and immunity 2012 - “...deletion mutants were generated for the manC (BPSL2810), wcbG (BPSL2801), wcbL (BPSL2796), gmhA (BPSL2795), wcbM (BPSL2794), and wcbP (BPSL2791) genes....”
- Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates
Sim, Genome biology 2010 - “...BtCDC3015869 and BtE555. Bottom: signal peaks in the Bp CPS region (red genes, BPSL2787 to BPSL2810 , wcbT-manC ) indicate gain of this region in both BtCDC3015869 and BtE555. All aCGH signals represent comparisons against BtE264. Breakpoints in both BtCDC3015869 and BtE555 are demarcated by solid...”
- Development of signature-tagged mutagenesis in Burkholderia pseudomallei to identify genes important in survival and pathogenesis
Cuccui, Infection and immunity 2007 - “...the capsule polysaccharide gene cluster located between BPSL2787 and BPSL2810 have an average GC content of 58%, 10% lower than the rest of the genome,...”
B4EMQ6 mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) from Burkholderia cenocepacia (see paper)
BCAM0854 bifunctional exopolysaccharide biosynthesis protein (phosphomannose isomerase and GDP-D-mannose pyrophosphorylase) from Burkholderia cenocepacia J2315
49% identity, 91% coverage
- Oridonin Attenuates Burkholderia cenocepacia Virulence by Suppressing Quorum-Sensing Signaling
Li, Microbiology spectrum 2022 - “...-F GATGGACAAGGCGTTCCTGA BCAM2307 -R GTGCAGCTCTTGTTGTACGC BCAS0292 -F GTCTGGTGTTCGTTGCGATG BCAS0292 -R CAAAGAGCCGGTTGTCGTTG BCAL0524-F CAGATGGTGCTCAAGGAAGT BCAL0524-R GACATGTTCGCGAGGAACT BCAM0854 -F GGGACGATGGCGATTTCTT BCAM0854 -R GGTTCCATCACCGCATAGTC gapdh -F AACGGATTTGGTCGTATTG gapdh -R GCTCCTGGAAGATGGTGAT NLRP3 -F AAAGCCAAGAATCCACAGTGTAAC NLRP3 -R TTGCCTCGCAGGTAAAGGT caspase1 -F AGGCATGACAATGCTGCTACAA caspase1 -R TGTGCAAATGCCTCCAGCTC ASC -F GGATGCTCTGTACGGGAAGG ASC -R CGCATCTTGCTTGGGTTG IL-1...”
- The BDSF quorum sensing receptor RpfR regulates Bep exopolysaccharide synthesis in Burkholderia cenocepacia via interaction with the transcriptional regulator BerB
Eberl, 2022 - σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111
Lardi, Applied and environmental microbiology 2015 - “...BCAL3115 BCAL1790 BCAL3508 BCAM0184 BCAM0185 BCAM0186 BCAM0717 BCAM0854 wbxA tonB cidB bclB bclC bclA BCAM0855 BCAM0858 BCAM0859 BCAM0860 BCAM0861 BCAM0863...”
- “...I35_4767 I35_4923 I35_0767 I35_2935 BCAM2143 BCAM0185 BCAS0293 BCAM0854 BCAM1004 BCAL3106 BCAL0730 Large protein BapA Lectin BclC Nematocidal protein AidA...”
- The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111
Schmid, PloS one 2012 - “...0.8 CCE46709 BCAM0196 5.9 0.9 14.0 0.9 CCE50899 BCAM0853 Transposase 3.1 0.8 10.0 0.7 CCE50898 BCAM0854 Mannose-6-phosphate isomerase 8.3 0.4 na 0.4 CCE50892 BCAM0859 Protein involved in capsule organization 31.8 0.4 na 0.7 CCE48736 BCAM1004 Gdp-Mannose 4,6-dehydratase 4.3 0.3 na 0.5 CCE47169 BCAM1572 Methyl-Apting chemotaxis protein...”
- “...protein cepR 1.7 1.8 0.6 0.3 CCE50476 BCAL2353 Sulfate permease 6 1.8 4.2 1.1 CCE50898 BCAM0854 Mannose-6-phosphate isomerase 11.3 1 6.3 0.6 CCE52109 BCAS0293 AidA aidA 6 1.8 685.0 0.5 a Nomenclature according to GenBank file CAFQ01000001.1. b Orthologs were identified as described in the Material...”
- Transcriptional responses of Burkholderia cenocepacia to polymyxin B in isogenic strains with diverse polymyxin B resistance phenotypes
Loutet, BMC genomics 2011 - “...predicted to encode proteins with a variety of functions, a cluster of genes spanning from BCAM0854 to BCAM0864 and known to be involved in biosynthesis of the exopolysaccharide cepacian [ 24 , 25 ], and BCAM2453 which is a monocistronic gene that is predicted to encode...”
- The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients
Holden, Journal of bacteriology 2009 - “...to BCAL2408; BCAL3110 to BCAL3125; BCAL1929 to BCAL1935 BCAM0854 to BCAM0865 BCAL3217* to BCAL3246*; BCAM0203 to BCAM0214; BCAM1003 to BCAM1011; BCAM1224 to...”
ECA1438 mannose-1-phosphate guanylyltransferase from Erwinia carotovora subsp. atroseptica SCRI1043
ECA1438 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pectobacterium atrosepticum SCRI1043
49% identity, 97% coverage
AWY96_RS17195 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Serratia plymuthica
50% identity, 97% coverage
ZMO1233 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Zymomonas mobilis subsp. mobilis ZM4
49% identity, 96% coverage
BPSS1835 putative LPS biosynthesis mannose-1-phosphate guanylyltransferase from Burkholderia pseudomallei K96243
47% identity, 96% coverage
- Biofilm Signaling, Composition and Regulation in Burkholderia pseudomallei
Nyanasegran, Journal of microbiology and biotechnology 2023 - “...manC ) [ 45 , 54 , 97 ] Bcam1340 (mannose-1-gyanylyltransferase) Burkholderia cenocepacia J2315 74.61 BPSS1835 LPS biosynthesis mannose-1-phosphate guanylyltransferase ( BceA ) [ 54 , 97 ] Bcam1341 (hypothetical protein) Burkholderia cenocepacia J2315 77.67 BPSL0606 Hypothetical protein [ 54 , 97 ] - Burkholderia pseudomallei...”
- Identification of Burkholderia pseudomallei Genes Induced During Infection of Macrophages by Differential Fluorescence Induction
Jitprasutwit, Frontiers in microbiology 2020 - “...981 6.1% 115 8 bpss1442 * + 2/3 1,362 257 109 1,158 9.4% 150 9 bpss1835 * + 1/1 4 224 171 1,461 11.7% 53 Group B 10 bpsl3338 * 1/1 52 191 191 1,818 10.5% 20 11 bpss0547 * + 1/2 121 94 94 1,290...”
- “...0.33 4.62 bpss0769 Esterase/lipase 9.86 12.16 6.92 10.80 bpss1442 Hypothetical protein 7.54 7.13 4.60 5.77 bpss1835 LPS biosynthesis mannose-1-phosphate guanylyltransferase 5.74 7.18 2.80 5.82 Group B b bpsl3338 Methyl-accepting chemotaxis protein 9.38 8.52 6.44 7.16 bpss0547 Serine hydroxymethyl transferase 7.04 9.80 4.10 8.44 bpss1039 irls ,...”
- Bacteriophage-associated genes responsible for the widely divergent phenotypes of variants of Burkholderia pseudomallei strain MSHR5848
DeShazer, Journal of medical microbiology 2019 (secret) - Burkholderia pseudomallei transcriptional adaptation in macrophages
Chieng, BMC genomics 2012 - “...GCCGAGACCCGAGTTAT atpB atpB _F atpB _R GTGGCTTTAACGATATGGC TGATGCGAGGTGGAGAA fliC fliC _F fliC _R CAGACGAACTACAACGGC ATGCTTTGCGTGAGGTC BPSS1835 BPSS1835_F BPSS1835_R CGTGAAGAAAATCGTCG GAGTCGTAATGTCCCCAC Competing interests The authors declare that they have no competing interests Authors contributions SC contributed to the design of the study, performed all the experiments and...”
V8V93_16175 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudodesulfovibrio sp. 5S69
51% identity, 96% coverage
Bphy_1056 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Paraburkholderia phymatum STM815
Bphy_1056 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Burkholderia phymatum STM815
48% identity, 92% coverage
- The Exopolysaccharide Cepacian Plays a Role in the Establishment of the Paraburkholderia phymatum - Phaseolus vulgaris Symbiosis
Liu, Frontiers in microbiology 2020 - “...followed by the bce -II cluster ( bceNVOPQRST , Bphy_1069Bphy_1077). While the gene products BceA (Bphy_1056), BceC (Bphy_1058), BceN (Bphy_1069), and BceT (Bphy_1077) are predicted to be involved in sugar-nucleotide biosynthesis, BceB (Bphy_1057), BceG (Bphy_1062), BceH (Bphy_1063), BceJ (Bphy_1065), BceK (Bphy_1066), BceO (Bphy_1071), BceR (Bphy_1074), and...”
Bphy_2475 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Paraburkholderia phymatum STM815
Bphy_2475 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Burkholderia phymatum STM815
48% identity, 93% coverage
ABD05_RS29500 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Burkholderia pyrrocinia
47% identity, 89% coverage
manC / AAC27538.1 ManC from Escherichia coli (see 6 papers)
48% identity, 96% coverage
BCAM1340 mannose-1-phosphate guanylyltransferase from Burkholderia cenocepacia J2315
48% identity, 93% coverage
- Biofilm Signaling, Composition and Regulation in Burkholderia pseudomallei
Nyanasegran, Journal of microbiology and biotechnology 2023 - “...] Bcam1339 (hypothetical protein) Burkholderia cenocepacia J2315 73.68 BPSL1233 Lipoprotein [ 54 , 97 ] Bcam1340 (mannose-1-gyanylyltransferase) Burkholderia cenocepacia J2315 83.60 BPSL0605 Mannose-1-phosphate guanylyltransferase ( manC ) [ 45 , 54 , 97 ] Bcam1340 (mannose-1-gyanylyltransferase) Burkholderia cenocepacia J2315 74.61 BPSS1835 LPS biosynthesis mannose-1-phosphate guanylyltransferase (...”
- The Bep gene cluster in Burkholderia cenocepacia H111 codes for a water-insoluble exopolysaccharide essential for biofilm formation
Bellich, Carbohydrate polymers 2023 - “...BCAM1339 bepJ Thioredoxin reductase 1446 (481) FIG018396 - Thioredoxin reductase IPR039448 - GH87 Unknown I35_RS22410 BCAM1340 bepK Mannose-1-phosphate guanylyltransferase 1521 (506) UR000000909 - Belongs to the mannose-6-phosphate isomerase type 2 family COG0836 - Mannose-1-phosphate guanylyltransferase COG0662 - Mannose-6-phosphate isomerase FIG118535 - Mannose-1-phosphate guanylyltransferase (GDP) IPR029044 -Nucleotide-diphosphosugar...”
- Pellicle Biofilm Formation in Burkholderia cenocepacia J2315 is Epigenetically Regulated through WspH, a Hybrid Two-Component System Kinase-Response Regulator
Sass, Journal of bacteriology 2022 (secret) - Genome-scale analysis of the genes that contribute to Burkholderia pseudomallei biofilm formation identifies a crucial exopolysaccharide biosynthesis gene cluster
Borlee, PLoS neglected tropical diseases 2017 - “...that is required to catalyze the formation of nucleotide sugar GDP-mannose, shares 82.3% identity with BCAM1340. Additionally, Bp1026b_I2910 ( becD ), shares 74.9% identity with BCAM1349, the proposed transcriptional regulator of the exopolysaccharide gene cluster in B . cenocepacia J2315 [ 55 ]. These results indicate...”
- The exopolysaccharide gene cluster Bcam1330-Bcam1341 is involved in Burkholderia cenocepacia biofilm formation, and its expression is regulated by c-di-GMP and Bcam1349
Fazli, MicrobiologyOpen 2013 - “...TIGR03805, parallel beta-helix repeat-containing protein (TIGRFAM prediction) 1 transmembrane; eight PbH1, parallel beta-helix repeats Unknown Bcam1340 Mannose-1-phosphate guanylyltransferase COG0836, ManC, mannose-1-phosphate guanylyltransferase; pfam00483, nucleotidyltransferase NTP_transferase; MannoseP_isomer; Cupin_2 Cytoplasmic Bcam1341 Hypothetical protein COG2153, predicted acyltransferase Cytoplasmic Phenotypic characterization of mutants suggests that the bcam1330bcam1341 gene cluster encodes...”
- “...functions required for most of the above steps. The cluster appears to contain one gene, bcam1340 , for sugar precursor production. It is predicted to encode a mannose-1-phosphate guanylyltransferase catalyzing the formation of GDP-mannose precursor. Currently, we do not know the sugar composition of the putative...”
I35_RS22410 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Burkholderia cenocepacia H111
48% identity, 93% coverage
- The Bep gene cluster in Burkholderia cenocepacia H111 codes for a water-insoluble exopolysaccharide essential for biofilm formation
Bellich, Carbohydrate polymers 2023 - “...polymerization, and transport. Regarding precursors synthesis, there is only one gene in the cluster, bepK (I35_RS22410), which encodes mannose 1-P-guanylyltransferase. The other genes necessary for mannose activation, namely glucose 6-phosphate isomerase (I35_RS09535), mannose 6-phosphate isomerase (I35_RS25055) and phosphoglucomutase (I35_RS03815), are located outside the cluster ( Fig....”
- “...I35_RS22405 BCAM1339 bepJ Thioredoxin reductase 1446 (481) FIG018396 - Thioredoxin reductase IPR039448 - GH87 Unknown I35_RS22410 BCAM1340 bepK Mannose-1-phosphate guanylyltransferase 1521 (506) UR000000909 - Belongs to the mannose-6-phosphate isomerase type 2 family COG0836 - Mannose-1-phosphate guanylyltransferase COG0662 - Mannose-6-phosphate isomerase FIG118535 - Mannose-1-phosphate guanylyltransferase (GDP) IPR029044...”
AL01_07360 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Bombella intestini
46% identity, 97% coverage
- Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius
Li, PloS one 2016 - “...(AL01_06130); 38, ribulose-phosphate 3-epimerase (AL01_09060); 39, polyol:NADP oxidoreductase (AL01_07080); 40, phosphomannomutase (AL_0102400); 41, mannose-1-phosphate guanyltransferase (AL01_07360); 42, carbohydrate kinase (AL01_03675); 43, mannose06-phosphate isomerase (AL01_00140); 44, 2-dehydro-3-deoxyphosphogluconate aldolase (AL01_04330). All genes encoding the enzymes of the EMP pathway were identified, except for the phosphofructokinase-coding gene, suggesting incomplete...”
Rmet_5843 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Ralstonia metallidurans CH34
Rmet_5843 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Cupriavidus metallidurans CH34
48% identity, 94% coverage
BTH_I0522 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Burkholderia thailandensis E264
48% identity, 89% coverage
lpg2887 phosphomannose isomerase GDP mannose pyrophosphorylase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
48% identity, 94% coverage
MANC2_ECO57 / O85342 Mannose-1-phosphate guanylyltransferase 2; GDP-mannose pyrophosphorylase 2; GMP 2; GMPP 2; EC 2.7.7.13 from Escherichia coli O157:H7 (see paper)
ECs2836 mannose-1-P guanosyltransferase from Escherichia coli O157:H7 str. Sakai
Z3195 mannose-1-P guanosyltransferase from Escherichia coli O157:H7 EDL933
48% identity, 96% coverage
- function: Involved in GDP-mannose biosynthesis which serves as the activated sugar nucleotide precursor for mannose residues in cell surface polysaccharides. This enzyme participates in synthesis of the LPS O antigen.
catalytic activity: alpha-D-mannose 1-phosphate + GTP + H(+) = GDP-alpha-D-mannose + diphosphate (RHEA:15229) - Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies
Jackson, BMC genomics 2011 - “...O157:H7 Sakai 2780369-2780601 ECs5479 - hypothetical protein 2693774 1759443_s_at NC_002695.1 Escherichia coli O157:H7 Sakai 2776834-2778282 ECs2836 - mannose-1-P guanosyltransferase 912820 1759443_s_at NC_002655.2 Escherichia coli O157:H7 EDL933 2847048-2848496 Z3195 manC mannose-1-P guanosyltransferase 962090 1762953_s_at NC_002695.1 Escherichia coli O157:H7 Sakai 2783218-2784603 ECs2842 - O antigen flippase 912601 1762953_s_at...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...decrease in expression (Table 3 , Fig. 3 ; QTC 1) as well as ECs2835, ECs2836, ECs2838, ECs2841, ECs2844, and ECs2845 (1.6 to 3 fold decrease) from that genomic region. ECs2113, part of the F9 fimbrial operon [ 47 ], decreased in expression from exponential to...”
- RcsB contributes to the distinct stress fitness among Escherichia coli O157:H7 curli variants of the 1993 hamburger-associated outbreak strains
Carter, Applied and environmental microbiology 2012 - “...fcl gmd wbdP per wzx wzy Z3192 Z3194 Z3195 Z3196 Z3197 Z3198 Z3199 Z3200 Z3201 Z3203 Acetyltransferase, related to O-antigen biosynthesis Phosphomannomutase...”
- Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies
Jackson, BMC genomics 2011 - “...O157:H7 Sakai 2776834-2778282 ECs2836 - mannose-1-P guanosyltransferase 912820 1759443_s_at NC_002655.2 Escherichia coli O157:H7 EDL933 2847048-2848496 Z3195 manC mannose-1-P guanosyltransferase 962090 1762953_s_at NC_002695.1 Escherichia coli O157:H7 Sakai 2783218-2784603 ECs2842 - O antigen flippase 912601 1762953_s_at NC_002655.2 Escherichia coli O157:H7 EDL933 2853432-2854823 Z3201 wzx O antigen flippase Wzx...”
- Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies
Pieper, PloS one 2011 - “...53 261 n.d. C1 phosphomannomutase Z3194 manB 50338 CY 91 4107 5.23E-08 C2 mannose-1-P guanosyltransferase Z3195 manC 54268 CY 44 6027 1.06E-09 C3 GDP-mannose mannosylhydrolase (gmm) Z3196 wbdQ 19567 CY 23 4400 1.06E-09 C3 fucose synthetase Z3197 fcI 36267 CY 170 4328 4.75E-08 C3 GDP-mannose dehydratase...”
KW89_2960 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Piscirickettsia salmonis
46% identity, 96% coverage
Bcen2424_4206 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Burkholderia cenocepacia HI2424
48% identity, 89% coverage
- One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity
Mhatre, Proceedings of the National Academy of Sciences of the United States of America 2020 - “...expression of genes within the Bep cluster varied among mutants, with the most up-regulated being Bcen2424_4206 (a manC homolog), which encodes mannose-1-phosphate guanylyltransferase. This enzyme plays dual roles, acting as a transferase to convert mannose-1-phosphate to GDP-mannose, a precursor for other sugar nucleotides such as GDP-fucose...”
Bphy_2283 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Burkholderia phymatum STM815
Bphy_2283 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Paraburkholderia phymatum STM815
49% identity, 91% coverage
BMA0029 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Burkholderia mallei ATCC 23344
47% identity, 89% coverage
BPSL0605 putative mannose-1-phosphate guanylyltransferase from Burkholderia pseudomallei K96243
47% identity, 89% coverage
- Biofilm Signaling, Composition and Regulation in Burkholderia pseudomallei
Nyanasegran, Journal of microbiology and biotechnology 2023 - “...high BP biofilm producers revealed several genes within the becA-R gene cluster ( bpsl0603 , bpsl0605 , bpsl0618 , bpsl0619 , and bpsl0620 ) were highly expressed in the high biofilm-producing strain [ 45 ]. Apart from the becA-R gene cluster, the wbiA gene cluster that...”
- “...J2315 73.68 BPSL1233 Lipoprotein [ 54 , 97 ] Bcam1340 (mannose-1-gyanylyltransferase) Burkholderia cenocepacia J2315 83.60 BPSL0605 Mannose-1-phosphate guanylyltransferase ( manC ) [ 45 , 54 , 97 ] Bcam1340 (mannose-1-gyanylyltransferase) Burkholderia cenocepacia J2315 74.61 BPSS1835 LPS biosynthesis mannose-1-phosphate guanylyltransferase ( BceA ) [ 54 , 97...”
- Global transcriptional analysis of Burkholderia pseudomallei high and low biofilm producers reveals insights into biofilm production and virulence
Chin, BMC genomics 2015 - “...matrix components for development of B. pseudomallei biofilm architecture Genes encoding for polysaccharides ( BPSL0603, BPSL0605, BPSL0618, BPSL0619, BPSL0620, BPSS1649 ) and EPS ( BPSS1978 ) were over-expressed in UM6 (Fig. 2a and Additional file 4 ). Observations based on SEM micrographs support the expression profile...”
Q2YMQ9 mannose-1-phosphate guanylyltransferase from Brucella abortus (strain 2308)
BAB1_0561 Mannose-6-phosphate isomerase, type II:Nucleotidyl transferase:Mannose-1-phosphate guanylyltransferase/mannose-6-phosphate is... from Brucella melitensis biovar Abortus 2308
BR0538 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Brucella suis 1330
44% identity, 97% coverage
- Lysine Acylation Modification Landscape of Brucella abortus Proteome and its Virulent Proteins
Zhang, Frontiers in cell and developmental biology 2022 - “...4 5 pgm BAB1_0055 Q2YPS4 19 18 15 14 9 wbpZ manAoAg BAB1_0563 manCoAg BAB1_0561 Q2YMQ9 4 7 5 4 2 pmm BAB1_0560 wbkA BAB1_0553 Q2YMN5 2 1 0 0 0 gmd BAB1_0545 Q2YMP3 8 9 8 7 7 per BAB1_0544 Q2YMP4 5 5 8 3...”
- Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid
Barton, mBio 2023 - “...BAB1_0544 O-chain synthesis 47 gmd BAB1_0545 O-chain synthesis 118 wbkA BAB1_0553 O-chain synthesis 32 manC BAB1_0561 O-chain synthesis 74,170,229 manA BAB1_0562 O-chain synthesis 74,170,229 wbkE BAB1_0563 O-chain synthesis 116 wadA BAB1_0639 Core biosynthesis 341,322 wadD BAB1_0953 Core biosynthesis 60 wboA BAB1_0999 O-chain synthesis 1,217 wboB BAB1_1000...”
- Lysine Acylation Modification Landscape of Brucella abortus Proteome and its Virulent Proteins
Zhang, Frontiers in cell and developmental biology 2022 - “...4 4 5 pgm BAB1_0055 Q2YPS4 19 18 15 14 9 wbpZ manAoAg BAB1_0563 manCoAg BAB1_0561 Q2YMQ9 4 7 5 4 2 pmm BAB1_0560 wbkA BAB1_0553 Q2YMN5 2 1 0 0 0 gmd BAB1_0545 Q2YMP3 8 9 8 7 7 per BAB1_0544 Q2YMP4 5 5 8...”
- Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
Lamontagne, BMC genomics 2010 - “...N-terminal BAB1_1174 FabZ BAB1_1872 PrfA BAB2_0459 Pgl BAB1_0544 DegT/DnrJ/EryC1/StrS BAB1_1187 Endoribonuclease BAB1_1874 LysC BAB2_0460 Zwf BAB1_0561 Man-6-P isomerase L-PSP BAB1_1879 GrxC BAB2_0483 ShuT type II BAB1_1188 GDPD BAB1_1887 HemC BAB2_0513 GcvT BAB1_0570 XylA BAB1_1205 ElaB-domain BAB1_1895 FtsK-gamma BAB2_0518 PutA BAB1_0587 Unknown BAB1_1212 BhbA BAB1_1918 LpdA-2 BAB2_0566...”
- The Complete Genome of Brucella Suis 019 Provides Insights on Cross-Species Infection
Wang, Genes 2016 - “...526375 NA 498887 498927 mannosyltransferase, putative BR0537 1 529702 531039 chr1_345 361179 362516 phosphomannomutase, putative BR0538 * 1 531064 532488 chr1_344 359730 361154 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase BR0539 * 1 532521 533693 chr1_343 358525 359697 mannose-6-phosphate isomerase BR0540 1 533776 534885 chr1_342 357333 358442 glycosyl transferase, group...”
- “...in a rough phenotype in B. melitensis and six genes, WbkC (BR0517), Wzt (BR0519), ManC (BR0538), ManA (BR0539), LpcC (BR1503) and ManCcore (BRA0347), were identified as playing roles that had not been fully determined ( Table 3 ). Based on the alignment results, we found that...”
BMEI1395 MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE from Brucella melitensis 16M
44% identity, 97% coverage
Gdia_1182 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Gluconacetobacter diazotrophicus PAl 5
47% identity, 96% coverage
- A deoxyviolacein-based transposon insertion vector for pigmented tracer studies
Dietz, MicrobiologyOpen 2024 - “...a genomic insertion located at a specific TA site (insertions found in Gdia_0263, Gdia_0657, Gdia_1202, Gdia_1182, Gdia_2010, Gdia_2094 and Gdia_2169) (Giongo et al., 2010 ), indicating that the Mariner transposon functioned as designed with the vioABCE operon inserted into a random TA site within the genome....”
FTN_1418 mannose-1-phosphate guanylyltransferase from Francisella tularensis subsp. novicida U112
45% identity, 96% coverage
- Functional Characterization of the DNA Gyrases in Fluoroquinolone-Resistant Mutants of Francisella novicida
Caspar, Antimicrobial agents and chemotherapy 2017 - “...FTN_0480 fevR Francisella effector of virulence regulation FTN_1418 FTN_1510 FTN_1652 Fno2 D87G D487E, K488 FTN_0402 FTN_0480 FTN_1083 FTN_1421 FTN_1550...”
- Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
Asare, Environmental microbiology 2010 - “...dimethyladenosine transferase 3 tnfn1_pw060419p04q168 FTN_1091 aroA 3-phosphoshikimate 1-carboxyvinyltransferase 2 tnfn1_pw060418p03q185 FTN_1400 S-adenosylmethionine-dependent methyltransferase 5 tnfn1_pw060418p04q172 FTN_1418 manC mannose-1-phosphate guanylyltransferase 4 DNA Modification tnfn1_pw060510p04q169 FTN_0122 recA recombinase A protein 2 tnfn1_pw060328p06q179 FTN_0492 parC DNA topoisomerase IV subunit A 2 # tnfn1_pw060510p04q168 FTN_0666 uvrA excinuclease ABC, subunit A...”
- “...tnfn1_pw060323p06q168 FTN_0545 68 Phagosomal tnfn1_pw060510p01q158 FTN_0988 prmA 78 Phagosomal tnfn1_pw060510p02q144 FTN_1234 queA 67 Phagosomal tnfn1_pw060418p04q172 FTN_1418 manC 68 Phagosomal tnfn1_pw060510p01q119 FTN_1428 wbtO 82 Phagosomal Transcription/Translation tnfn1_pw060510p03q168 FTN_0598 42 Cytoplasmic tnfn1_pw060419p04q129 FTN_1290 mglA 71 Phagosomal Type IV Pilin tnfn1_pw060418p02q167 FTN_1137 pilQ 66 Phagosomal tnfn1_pw060323p06q157 FTN_1139 pilO 67...”
- Exploitation of host cell biology and evasion of immunity by francisella tularensis
Asare, Frontiers in microbiology 2010 - “...FTN_1231 gloA Lactoylglutathione lyase FTN_1234 queA S-adenosylmethionine: tRNA ribosyltransferase- isomerase FTN_1333 tktA Transketolase I FTN_1376 FTN_1418 manC FTN_1428 wbtO Transferase FTN_1494 aceE Pyruvate dehydrogenase complex, E1 component, pyruvate dehydrogenase FTN_1553 nudH dGTP pyrophosphohydrolase FTN_1597 prfC Peptide chain release factor 3 FTN_1621 Predicted NAD/FAD-dependent oxidoreductase FTN_1655 rluC...”
- Molecular bases of proliferation of Francisella tularensis in arthropod vectors
Asare, Environmental microbiology 2010 - “...dimethyladenosine transferase 3 tnfn1_pw060419p04q168 FTN_1091 aroA 3-phosphoshikimate 1-carboxyvinyltransferase 2 tnfn1_pw060418p03q185 FTN_1400 S-adenosylmethionine-dependent methyltransferase 5 tnfn1_pw060418p04q172 FTN_1418 manC mannose-1-phosphate guanylyltransferase 4 DNA Modification tnfn1_pw060510p04q169 FTN_0122 recA recombinase A protein 2 tnfn1_pw060328p06q179 FTN_0492 parC DNA topoisomerase IV subunit A 2 tnfn1_pw060510p04q168 FTN_0666 uvrA excinuclease ABC, subunit A 2...”
- “...tnfn1_pw060510p01q103 FTN_0063 ilvE branched-chain amino acid aminotransferase protein (class IV) 5 3 13% 3.1E-01 tnfn1_pw060418p04q172 FTN_1418 manC mannose-1-phosphate guanylyltransferase 4 10% 8.3E-01 Transporter proteins tnfn1_pw060420p01q180 FTN_0097 hydroxy/aromatic amino acid permease (HAAAP) family protein 4 4 89% 3.0E-05 tnfn1_pw060420p01q189 FTN_1611 - major facilitator superfamily (MFS) transport protein...”
BAB2_0856 Mannose-6-phosphate isomerase, type II:ATP/GTP-binding site motif A (P-loop):Nucleotidyl transferase:Mannose-1-phosphate guan... from Brucella melitensis biovar Abortus 2308
Q2YK24 mannose-1-phosphate guanylyltransferase from Brucella abortus (strain 2308)
46% identity, 97% coverage
BMEII0900 MANNOSE-6-PHOSPHATE ISOMERASE / MANNOSE-1-PHOSPHATE GUANYLYL TRANSFERASE (GDP) from Brucella melitensis 16M
46% identity, 97% coverage
- Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics
He, Frontiers in cellular and infection microbiology 2012 - “...Macrophages 14979322 108 wbkA BMEI1404 Mice 14979322 109 wbpL BMEI1426 Mice, macrophages 14979322 110 wbpW BMEII0900 Macrophages 14979322 111 wbpZ BMEI1393 Mice, macrophages 14979322 N: CELL MOTILITY** 112 flgE BMEII0159 Mice 14979322 113 flgI BMEII1084 Mice 14979322 114 fliC BMEII0150 Mice 14979322 115 motB BMEII0154 Mice...”
- Lipopolysaccharide-Deficient Brucella Variants Arise Spontaneously during Infection
Turse, Frontiers in microbiology 2011 - “...LPS locus, genetic mutation at either B. melitensis or B. abortus manBA (phosphomannomutase/phosphomannoisomerase; BMEII0899 and BMEII0900 or BAB2_0855 and BAB2_0856 respectively) is cause for loss of LPS expression and putative core defect (Allen et al., 1998 ; Gonzalez et al., 2008 ). Previous work in our...”
- DNA polymorphism analysis of Brucella lipopolysaccharide genes reveals marked differences in O-polysaccharide biosynthetic genes between smooth and rough Brucella species and novel species-specific markers
Zygmunt, BMC microbiology 2009 - “...synthesis but also pointed out that the existence of manB core - manC core (ORFs BMEII0900 and BMEII0899) preclude to rule out any role for the wbk putative mannose synthesis genes since there could be internal complementation [ 12 ]. All these results are fully consistent...”
RHECIAT_CH0003488 mannose-1-phosphate guanylyltransferase (GDP) protein from Rhizobium etli CIAT 652
44% identity, 97% coverage
BRA0347 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Brucella suis 1330
45% identity, 97% coverage
- The Complete Genome of Brucella Suis 019 Provides Insights on Cross-Species Infection
Wang, Genes 2016 - “...family protein BR1503 * 1 1457802 1458866 chr1_1441 1531664 1532728 lipopolysaccharide core biosynthesis mannosyltransferase LpcC BRA0347 * 2 326808 328223 chr2_723 778336 779751 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase BRA0348 2 328220 329653 chr2_722 776906 778339 phosphoglucomutase, putative * Three groups of featured genes are separated by a blank...”
- “...and six genes, WbkC (BR0517), Wzt (BR0519), ManC (BR0538), ManA (BR0539), LpcC (BR1503) and ManCcore (BRA0347), were identified as playing roles that had not been fully determined ( Table 3 ). Based on the alignment results, we found that the WbkA gene was disrupted in the...”
- Characterization of Brucella abortus O-polysaccharide and core lipopolysaccharide mutants and demonstration that a complete core is required for rough vaccines to be efficient against Brucella abortus and Brucella ovis in the mouse model
Monreal, Infection and immunity 2003 - “...mannose6-P-isomerase and mannose-1-P-guanylyltransferase activities (BMEII 0900, BRA0347) (Fig. 2). Since phenotypic analysis (see below) revealed a severe core...”
Psyr_3302 Mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudomonas syringae pv. syringae B728a
45% identity, 96% coverage
Atu3353 mannose-1-phosphate guanylyltransferase (GDP) from Agrobacterium tumefaciens str. C58 (Cereon)
ATU_RS15505 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Agrobacterium fabrum str. C58
45% identity, 97% coverage
CBU_0671 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Coxiella burnetii RSA 493
44% identity, 97% coverage
- In silico biosynthesis of virenose, a methylated deoxy-sugar unique to Coxiella burnetii lipopolysaccharide
Flores-Ramirez, Proteome science 2012 - “...to C. burnetii genome, the PMI-GMP activity might be catalyzed by the product of the CBU_0671 gene, which includes both of these signatures. It shares 45% (E value e-113), 46% (E value 3e-122), and 39% amino acid identity (E value 4e-88) with the PMI-GMP from Salmonella...”
- “...GDP--D-mannose (7) by mannose-1-phosphate guanylyltransferase. Results from BLAST analyses indicate similarity with the product of CBU_0671 and the guanylyltransferase. NDP-4-keto-6-deoxy-hexose is the key intermediate After activation, any of the proposed intermediates will need to be transformed into the key precursor for all NDTP-sugars, an NDP-4-keto-6-deoxy-hexose. This...”
HZ99_RS00120 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudomonas fluorescens
44% identity, 97% coverage
PA14_71970 GDP-mannose pyrophosphorylase from Pseudomonas aeruginosa UCBPP-PA14
46% identity, 97% coverage
PA5452 phosphomannose isomerase/GDP-mannose WbpW from Pseudomonas aeruginosa PAO1
46% identity, 97% coverage
- Pseudomonas aeruginosa partitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of a parS-related motif
Kawalek, Nucleic acids research 2018 - “...6 140 926 6 143 944 6 142 506 3019 23.5 22.6 42.4 46.8 46.6 PA5452 c 412 6 203 326 6 217 050 6 215 975 13725 11.6 16.1 23.8 29.0 27.6 PA5523 88 552 324 554 217 552 921 1894 5.8 11.1 nd 15.5...”
- Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa
Hong, BMC microbiology 2017 - “...in the rmd mutant. We also observed that the transfer efficiency of the wbpW mutant (PA5452) was comparable to the positive control. This is not surprising since it has been recently found that PslB gene is able to substitute wbpW to promote CPA production in a...”
- Biosynthesis of the Pseudomonas aeruginosa Extracellular Polysaccharides, Alginate, Pel, and Psl
Franklin, Frontiers in microbiology 2011 - “...N-terminal GMP domain and C-terminal PMI domain. P. aeruginosa PAO1 encodes three PMI/GMPs; PslB, WbpW (PA5452 on an LPS biosynthetic operon), and AlgA. A double mutant of PslB and wbpW resulted in loss of Psl production suggesting that the different PMI/GMPs are functionally interchangeable for the...”
- Genetic and Functional Diversity of Pseudomonas aeruginosa Lipopolysaccharide
Lam, Frontiers in microbiology 2011 - “...). Three of the genes rmd , gmd , wbpW ( pa5454 , pa5453 , pa5452 ) plus another gene located in the alginate biosynthesis cluster, algC ( pa5322 ), encode enzymes responsible for the biosynthesis of GDP- D -Rha, the nucleotide sugar precursor for CPA....”
- Evaluation of a microarray-hybridization based method applicable for discovery of single nucleotide polymorphisms (SNPs) in the Pseudomonas aeruginosa genome
Dötsch, BMC genomics 2009 - “...45 1.00 3 0.60 PA5451 PA14_71960 wzm 24 5 0 0 29 0.99 3 0.60 PA5452 PA14_71970 wbpW 42 6 1 0 49 0.99 4 0.57 * genes belonging to the PAO1 specific region. a see Figure 2 for a definition of the similarity classes. b...”
O24884 mannose-1-phosphate guanylyltransferase from Helicobacter pylori (strain ATCC 700392 / 26695)
HP0043 mannose-6-phosphate isomerase (pmi) or (algA) from Helicobacter pylori 26695
42% identity, 96% coverage
- Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
Wei, ACS omega 2022 - “...O25931 TyrA 319 P66185 rpmE 320 P56162 pyrE 321 O25853 nuoD 322 P56067 cysM 323 O24884 HP_0043 324 O25510 OmpP1 325 O25421 HP_0719 326 P56075 ndk 327 P55976 nusG 328 O24991 lpxD 329 P56396 trpS 330 O25019 HP_0233 331 O25529 hldE 332 O25614 gpsA 333 P43312...”
- Helicobacter pylori employs a general protein glycosylation system for the modification of outer membrane adhesins
Teng, Gut microbes 2022 - “...is controlled by phase variation and inactivated (out-of-frame allele) in the tested strain 26695. 20 HP0043 gene codes for the bifunctional isomerase RfbM, which is involved in the fucose biosynthesis pathway. Fucose is a key component in the terminal and central trio region of LPS O-antigen...”
- “...(Supplementary Table S1). The molecular sizes of these adhesins in the LPS biosynthesis-related knockout mutants HP0043, HP0360 , and HP0826 were smaller than those in the wild-type strain 26695 ( Figure 1c ). The molecular sizes of adhesins recovered fully after the HP0858 gene was complemented...”
- The Effects of HP0044 and HP1275 Knockout Mutations on the Structure and Function of Lipopolysaccharide in Helicobacter pylori Strain 26695
Liu, Biomedicines 2022 - “...(2) the formation of -D-mannose-6-phosphate, catalyzed by the isomerase activity from the mannose-6-phosphate isomerase (AlgA, HP0043); (3) the conversion of -D-mannose-6-phosphate into -D-mannose-1-phosphate by the phosphomannomutase (PMM, HP1275); (4) the formation of GDP--D-mannose by the transferase activity from the mannose-1-phosphate guanylyltransferase (AlgA, HP0043); (5) the conversion...”
- “...bps to 43,250 bps of the H. pylori genomic DNA, and is flanked by the HP0043 and HP0045 genes ( Figure 2 a). Similarly, the HP1275 coding sequence is located in the plus strand from 1,350,206 bps to 1,351,585 bps of the H. pylori genomic DNA,...”
- Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
Voss, Proteomics. Clinical applications 2015 - “...Rep helicase, single-stranded DNA-dependent ATPase (Rep) HP0911 HPB8_1582 D7FG32 polysaccharide metabolic process 2.17 Mannose-1-phosphate guanylyltransferase HP0043 HPB8_622 D7FDC2 proteolysis 2.16 Protease HtpX homolog HP0927 HPB8_1057 * D7FEK7 DNA modification 2.15 Type I restriction enzyme, S subunit HP0790 HPB8_1600 * & D7FG51 NA 2.12 Outer membrane protein...”
- Helicobacter hepaticus Hh0072 gene encodes a novel alpha1-3-fucosyltransferase belonging to CAZy GT11 family
Zhang, Glycobiology 2010 - “...HP0326 (neuA) as well as GDP-fucose biosynthetic genes rfbM (HP0043), rfbD (HP0044) and wbcJ (HP0045), which are involved in the synthesis of Lewis antigen in...”
- Helicobacter pylori lipopolysaccharide modification, Lewis antigen expression, and gastric colonization are cholesterol-dependent
Hildebrandt, BMC microbiology 2009 - “...G27 are as follows: [ cgt: hp0421, G27_952 ], [ pmi ( rfbM ) : hp0043, G27_38 ], [ lpxE: hp0021, G27_20 ], [ eptA: hp0022, G27_21 ]. b Righthand column lists the brief primer designations used in Figure 1. Figure 1 PCR verification of allelic...”
- Role of virulence factors, cell components and adhesion in Helicobacter pylori-mediated iNOS induction in murine macrophages
Assmann, FEMS immunology and medical microbiology 2001 (PubMed)- “...pathogenicity island, vacA, katA, alpAB genes and the hp0043 gene taking part in lipopolysaccharide biosynthesis when direct cell contact was allowed but not...”
- “...katA and the lipopolysaccharide synthesis genes encoded by hp0043 (according to 26695 nomenclature) to examine whether genetic variants of H. pylori might show...”
V8V93_09910 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudodesulfovibrio sp. 5S69
45% identity, 96% coverage
D7FG32 mannose-1-phosphate guanylyltransferase from Helicobacter pylori (strain B8)
42% identity, 96% coverage
HPB8_1582 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Helicobacter pylori B8
42% identity, 96% coverage
YP_626781 mannose-6-phosphate isomerase from Helicobacter pylori HPAG1
42% identity, 96% coverage
DVU0697 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Desulfovibrio vulgaris Hildenborough
45% identity, 96% coverage
MPAO1_14370 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Pseudomonas aeruginosa
NP_250922 biofilm formation protein PslB from Pseudomonas aeruginosa PAO1
Q9I1N7 mannose-1-phosphate guanylyltransferase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA2232 probable phosphomannose isomerase/GDP-mannose pyrophosphorylase from Pseudomonas aeruginosa PAO1
43% identity, 96% coverage
- An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1
Varadarajan, NPJ biofilms and microbiomes 2020 - “...to positive and negative controls for biofilm formation (Fig. 5a ). The pslB mutant (PA2232; MPAO1_14370), a gene whose product is involved in the synthesis and export of polysaccharides, was used as a reference point for low biofilm formation 39 , while a retS mutant (PA4856;...”
- Genetic and biochemical analyses of the Pseudomonas aeruginosa Psl exopolysaccharide reveal overlapping roles for polysaccharide synthesis enzymes in Psl and LPS production.
Byrd, Molecular microbiology 2009 - GeneRIF: PslB is the PMI/GMP that promotes A-band LPS production in a wbpW mutant.
- Identification of amino acid residues important for the phosphomannose isomerase activity of PslB in Pseudomonas aeruginosa PAO1.
Lee, FEBS letters 2008 (PubMed)- GeneRIF: These results provide a basis for understanding the catalytic mechanism of phosphomannose isomerase PslB.
- Proteomic approach to identify host cell attachment proteins provides protective Pseudomonas aeruginosa vaccine antigen FtsZ
Jurado-Martín, NPJ vaccines 2024 - “...42.9 5.4 P09591 Elongation factor Tu (EF-Tu) LES 431, 57P31PA, A5803 4 53.424.2 43.4 5.22 Q9I1N7 Mannose-1-phosphate guanylyltransferase (PslB) LES 431, 57P31PA, A5803 4 30.720.3 53.5 5.74 Q9HX05 NAD+ dependent acetaldehyde dehydrogenase (ExaC) LES 431, 57P31PA, A5803 4 45.815.0 54.9 5.43 Q9I6J9 Agmatine deiminase (AguA) LES...”
- Pseudomonas aeruginosa biofilm exopolysaccharides: assembly, function, and degradation
Gheorghita, FEMS microbiology reviews 2023 - “...structure Function or predicted function PslA Q9I1N8 3NKL, 5W7L PslB Q9I1N7 2 x 65, 2PFW PslC PslD Q9I1N6 Q9I1N5 7SP8 2J58 GT OPX PslE Q9I1N4 7NII PCP PslF PslG...”
- Pseudomonas aeruginosa Activates Quorum Sensing, Antioxidant Enzymes and Type VI Secretion in Response to Oxidative Stress to Initiate Biofilm Formation and Wound Chronicity
Kim, Antioxidants (Basel, Switzerland) 2024 - “...pelA AGTACTACGCGCCGATCATCAA AAGTGGTAGTACAGGTGCAGGC PA3064 pelD TGCCTGTATGCCTTCGAGTTGA GAAGTCAGCGGCAACAACACC PA3061 pslA GCTACAACAACCGGCTGATCTG GATGCTGGTCTTGCGGATGAAG PA2231 pslB CCTCAACACCAACGAATCCACC CGTAGATGTCGTTGAAGCGGAC PA2232 recA TCACCGGCAATATCAAGAACGC GACCGAGGCGTAGAACTTCAGT PA3617 lexA GCGAGGAGGTCACGGTGAAA GCCTTCGATGATCAGTTCCTGC PA3007 proC CAGGCCGGGCAGTTGCTGTC GGTCAGGCGCGAGGCTGTCT PA0393 oxyR CCGCTGTACATCGAGGAGAACT ACATAGAAGGGCTCGTCGAACA PA5344 phzA1&2 GACCGAGGATCCGAACCACTTC CGTTTTATCCGGCCGTTCTCG PA4210, PA1899 phzM GTGGCCTTCGAGATCTTCCAGG GGAACTCCTCGCCGTAGAACAG PA4209...”
- <i>cmpX</i> overexpression in <i>Pseudomonas aeruginosa</i> affects biofilm formation and cell morphology in response to shear stress
David, Biofilm 2024 - “...PA1774 cfrX CfrX 1.3 PA0762 algU ECF sigma factor 1.7 PA3540 algD GDP-mannose 6-dehydrogenase 0.7 PA2232 pslB PslB 1.2 PA3063 pelB PelB 2.5 ** PA4625 cdrA Cyclic diguanylate-regulated TPS partner A 2.8 ** PA1181 PA1181 Diguanylate cyclase 2.3** PA4407 ftsZ Cell division protein 2.7 ** Fig....”
- Multidrug resistance in Pseudomonas aeruginosa: genetic control mechanisms and therapeutic advances
Zhao, Molecular biomedicine 2024 - “...extracellular polysaccharide Psl, which affects the stability of biological periplasmic membranes [ 180 ] pslB PA2232 53.5 2,455,103..2456569 (+) 1467 / pslC PA2233 33.6 2,456,569..2457480 (+) 912 / algD PA3540 47.6 3,962,825..3964135 (+) 1311 Enzymes in the extracellular polysaccharide alginate synthesis pathway [ 181 ] algT...”
- Identification of novel targets of azithromycin activity against Pseudomonas aeruginosa grown in physiologically relevant media
Belanger, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret) - An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1
Varadarajan, NPJ biofilms and microbiomes 2020 - “...compared to positive and negative controls for biofilm formation (Fig. 5a ). The pslB mutant (PA2232; MPAO1_14370), a gene whose product is involved in the synthesis and export of polysaccharides, was used as a reference point for low biofilm formation 39 , while a retS mutant...”
- Overexpression of the Small RNA PA0805.1 in Pseudomonas aeruginosa Modulates the Expression of a Large Set of Genes and Proteins, Resulting in Altered Motility, Cytotoxicity, and Tobramycin Resistance
Coleman, mSystems 2020 - “...5-phosphate oxidase 1.53 2.7E05 1.16 9.7E03 PA2231 pslA Undecaprenyl-phosphate glucose phosphotransferase 1.85 1.3E09 1.29 2.2E03 PA2232 pslB Mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase 1.80 8.7E12 1.34 6.5E03 PA2233 pslC Putative glycosyl transferase 1.58 5.4E09 1.14 4.5E02 PA2234 pslD Polysaccharide export protein 1.71 4.9E18 1.29 5.6E03 PA2235 pslE Psl exopolysaccharide...”
- Mechanism of pyocyanin abolishment caused by mvaT mvaU double knockout in Pseudomonas aeruginosa PAO1
Dong, Virulence 2019 - “...subunit B PA1130 rhlC 2.0056 0.0300 rhamnosyltransferase PA3724 lasB 5.7022 0.0764 elastase LasB Biofilm formation PA2232 pslB 1.5192 0.0215 biofilm formation protein PslB PA2233 pslC 1.2947 0.0231 biofilm formation protein PslC PA2234 pslD 1.3012 0.0229 biofilm formation protein PslD PA2235 pslE 1.4038 0.0215 biofilm formation protein...”
- Pseudomonas aeruginosa ceftolozane-tazobactam resistance development requires multiple mutations leading to overexpression and structural modification of AmpC
Cabot, Antimicrobial agents and chemotherapy 2014 - “...PA1730 PA1797 PA1802 PA2023 PA2040 PA2138 Intergenic PA2232 PA2250 Intergenic PA2387 PA2399 PA2402 PA2443 PA2540 PA2597 PA2615 PA2643 Intergenic PA2938 PA3047...”
- More
SPV1_07961 phosphomannose isomerase / GDPmannose dehydrogenase from Mariprofundus ferrooxydans PV-1
43% identity, 96% coverage
PH0925 / O58649 GDP-D-mannose pyrophosphorylase (EC 2.7.7.13; EC 5.3.1.8) from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (see paper)
PH0925 mannose-1-phosphate guanylyl transferase from Pyrococcus horikoshii OT3
40% identity, 97% coverage
PF0589 mannose-6-phosphate isomerase/mannose-1-phosphate guanylyl transferase from Pyrococcus furiosus DSM 3638
41% identity, 97% coverage
HH0675 conserved hypothetical protein from Helicobacter hepaticus ATCC 51449
41% identity, 97% coverage
Dd703_3281 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Dickeya dadantii Ech703
42% identity, 94% coverage
Teth514_2275 mannose-1-phosphate guanylyltransferase (GDP) from Thermoanaerobacter ethanolicus X514
39% identity, 72% coverage
NX02_23250 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase from Sphingomonas sanxanigenens DSM 19645 = NX02
40% identity, 72% coverage
- The evolutionary life cycle of the polysaccharide biosynthetic gene cluster based on the Sphingomonadaceae
Wu, Scientific reports 2017 - “...5.3.1.8, NX02_27530), phosphomannomutase (ManB, EC 5.4.2.8, bifunctional gene NX02_28160), and Mannose-1-phosphate guanylyltransferase (ManC, EC 2.7.7.22, NX02_23250). These related genes were scattered among the genome. Identity or similarity analysis between proteins related to precursor synthesis from S. sanxanigenens and S. elodea ATCC 31461, Sphingomonas sp. ATCC 31555,...”
C7W88_RS03395 mannose-1-phosphate guanylyltransferase from Novosphingobium sp. THN1
42% identity, 72% coverage
CD630_27790, CDIF630erm_03042 mannose-1-phosphate guanylyltransferase from Clostridioides difficile 630
CD2779 putative mannose-1-phosphate guanylyltransferase from Clostridium difficile 630
36% identity, 72% coverage
- Iron Regulation in Clostridioides difficile
Berges, Frontiers in microbiology 2018 - “...ligase 2.59 -0.26 2.74 0.21 CD630_27780 CDIF630erm_03041 Glycosyl transferase family protein 0.98 -0.10 1.26 0.10 CD630_27790 CDIF630erm_03042 manC Mannose-1-phosphate guanylyltransferase 1.33 0.81 2.47 0.33 CD630_27800 CDIF630erm_03043 pgm Phosphoglucomutase 2.75 0.22 3.20 0.06 CD630_27810 CDIF630erm_03044 mviN Transmembrane virulence factor 3.67 -0.93 4.13 0.78 CD630_02840 CDIF630erm_00408 PTS system...”
- “...2.59 -0.26 2.74 0.21 CD630_27780 CDIF630erm_03041 Glycosyl transferase family protein 0.98 -0.10 1.26 0.10 CD630_27790 CDIF630erm_03042 manC Mannose-1-phosphate guanylyltransferase 1.33 0.81 2.47 0.33 CD630_27800 CDIF630erm_03043 pgm Phosphoglucomutase 2.75 0.22 3.20 0.06 CD630_27810 CDIF630erm_03044 mviN Transmembrane virulence factor 3.67 -0.93 4.13 0.78 CD630_02840 CDIF630erm_00408 PTS system mannose/fructose/sorbose...”
- A Clostridium difficile Cell Wall Glycopolymer Locus Influences Bacterial Shape, Polysaccharide Production and Virulence
Chu, PLoS pathogens 2016 - “...genome sequence, were targeted for disruption: CD2783, CD2781 ( mviN ), CD2780 ( pgm2 ), CD2779 ( manC ), CD2769, CD2765 ( lcpA ), and CD2766 ( lcpB ). The gene-specific ClosTron insertion site was chosen based on the Perutka algorithm [ 27 ]. Targeting regions...”
- “...were unable to disrupt five genes in the CWG biosynthetic locus (CD2783, mviN , CD2780, CD2779, and CD2769) via ClosTron mutagenesis. However, mviN expression was successfully diminished using an antisense RNA approach, and resulted in multiple phenotypes. First, mviN -specific antisense RNA-expressing bacteria exhibited a growth...”
- Clostridium difficile surface proteins are anchored to the cell wall using CWB2 motifs that recognise the anionic polymer PSII
Willing, Molecular microbiology 2015 - “...2014 ). The AP locus contains two genes involved in conversion of mannose6phospate to GDPmannose (CD2779 and 2780) and disruption of CD2780 gene (pgm2) expression by RNA knockdown leads to loss of CWPs on the cell wall. Given PSII contains mannose, it is likely that the...”
- Transcriptional analysis of temporal gene expression in germinating Clostridium difficile 630 endospores
Dembek, PloS one 2013 - “...0.0408 +2.4 CD2777 putative polysaccharide polymerase 0.0182 +2.5 CD2778 putative polysaccharide biosynthesis protein 0.0311 +2.5 CD2779 putative mannose-1-phosphate guanylyltransferase 0.0116 +2.2 CD2780 putative phosphomannomutase/phosphoglycerate mutase 0.00636 +2.7 Toxins Of central importance in C. difficile is the pathogenicity locus (PaLoc) containing five genes encoding two large clostridial...”
X276_RS25120 mannose-1-phosphate guanylyltransferase from Clostridium beijerinckii NRRL B-598
36% identity, 73% coverage
A4XL18 Mannose-1-phosphate guanylyltransferase (GDP) from Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)
34% identity, 72% coverage
EHI_052810 mannose-1-phosphate guanylyltransferase, putative from Entamoeba histolytica HM-1:IMSS
36% identity, 71% coverage
- Horizontal Gene Transfers from Bacteria to Entamoeba Complex: A Strategy for Dating Events along Species Divergence
Romero, Journal of parasitology research 2016 - “...dates were found, some of them from the same donor group: alpha-1,2-mannosidase (EHI_009520), mannose-1-phosphate guanylyltransferase (EHI_052810), and fructokinase (EHI_054510) from Bacteroidetes ranging from 55.53Mya to 77.8715Mya, nicotinate-phosphoribosyltransferase (EHI_023260) and hypothetical protein (EHI_072640) from Bacteroidales ranging from 94.98Mya to 164.16Mya, and Fe-S cluster assembly protein NifU (EHI_049620)...”
- “...functionally related. Two genes shared most of these attributes: the genes for the mannose-1-phosphate guanylyltransferase (EHI_052810) and the fructokinase (EHI_054510) were donated by Bacteroidales, probably between 60 and 70 million years in the past. Both genes are involved in fructose, mannose, amino sugar, and nucleotide sugar...”
CCNA_03733 mannose-1-phosphate guanylyltransferase (GDP) from Caulobacter crescentus NA1000
CC_3618 mannose-1-phosphate guanylyltransferase from Caulobacter crescentus CB15
40% identity, 73% coverage
- Caulobacter lipid A is conditionally dispensable in the absence of fur and in the presence of anionic sphingolipids
Zik, Cell reports 2022 - “...encodes a glycosyltransferase that initiates O-antigen synthesis on undecaprenyl-phosphate ( Toh and Brun, 2008 ). CCNA_03733 encodes a homolog of manC involved in synthesizing the activated sugar guanosine diphosphate (GDP)-D-mannose ( Samuel and Reeves, 2003 ), which is incorporated into the core oligosaccharide and O-antigen of...”
- “...was markedly improved when CtpA was depleted from the strains lacking CCNA_00497, CCNA_01553 , or CCNA_03733 . Despite the persistence of morphological defects, deletion of fur, CCNA_01553, or CCNA_03733 significantly improved cell viability during CtpA depletion ( Figure 1B ). Deletion of CCNA_00497 improved survival on...”
- The LovK-LovR two-component system is a regulator of the general stress pathway in Caulobacter crescentus
Foreman, Journal of bacteriology 2012 - “...CC_3225 CC_3466 CC_3473 CC_3474 CC_3475 CC_3476 CC_3477 CC_3618 EPS associated protein OmpA-family outer membrane lipoprotein Conserved cell surface protein...”
CPE0495 probable mannose-1-phosphate guanylyltransferase from Clostridium perfringens str. 13
35% identity, 71% coverage
BC343_03170 mannose-1-phosphate guanylyltransferase from Mucilaginibacter pedocola
36% identity, 72% coverage
- High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30T
Fan, Standards in genomic sciences 2018 - “...BC343_14065 6-phosphofructokinase BC343_20710, BC343_25175 Mannose-6-phosphate isomerase ManA BC343_15810, BC343_21400 Phosphoglucosamine mutase phosphomannomutase BC343_21600 Mannose-1-phosphate guanylyltransferase BC343_03170 EPS biosynthesis 3-Deoxy-D-manno-octulosonic-acid transferase KdtA BC343_09425 Priming glycosyltransferase CpsE BC343_04560 Glycosyltransferase BC343_04600, BC343_09445 ABC transporter KpsMT BC343_09400, BC343_09585 Polysaccharide co-polymerase protein PCP BC343_04670 Outer membrane polysaccharide protein OPX BC343_04675 Flippase...”
Q9X0C3 mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) from Thermotoga maritima (see paper)
TM1033 mannose-1-phosphate guanylyltransferase from Thermotoga maritima MSB8
38% identity, 72% coverage
2x65A / Q9X0C3 Crystal structure of t. Maritima gdp-mannose pyrophosphorylase in complex with mannose-1-phosphate. (see paper)
38% identity, 72% coverage
- Ligand: 1-o-phosphono-alpha-d-mannopyranose (2x65A)
ZPR_0538 mannose-1-phosphate guanylyltransferase (GDP) from Zunongwangia profunda SM-A87
37% identity, 72% coverage
sll1370 GDP-mannose pyrophosphorylase from Synechocystis sp. PCC 6803
37% identity, 73% coverage
Cbei_0318 mannose-1-phosphate guanylyltransferase (GDP) from Clostridium beijerincki NCIMB 8052
33% identity, 72% coverage
YP_149157 mannose-6-phosphate isomerase (phosphomannose isomerase) ; mannose-1-phosphate guanylyl transferase (GDP-mannose pyrophosphorylase) from Geobacillus kaustophilus HTA426
32% identity, 96% coverage
- S-layer nanoglycobiology of bacteria
Messner, Carbohydrate research 2008 - “...(NP_243386) transposase ORFA120 172 19.7 47.5 Transposase (BAD18254) manC manC 464 52.8 30.1 Mannose-1-phosphate guanylyltransferase (YP_149157) wscJ ORFA122 389 44.9 30.4 Mannosyltransferase (CAJ74004) wscK ORFA123 377 43.1 27.1 Glycosyltransferase (ZP_01425292) wscL ORFA124 (fragment) 111 12.6 48.3 Mannosyltransferase (NP_285363) (d) Description of the slg gene cluster of...”
alr0188 GDP-mannose pyrophosphorylase from Nostoc sp. PCC 7120
35% identity, 73% coverage
PG2215 mannose-1-phosphate guanylyltransferase from Porphyromonas gingivalis W83
35% identity, 71% coverage
TTC1388 No description from Thermus thermophilus HB27
36% identity, 72% coverage
- Transposon mutagenesis of the extremely thermophilic bacterium Thermus thermophilus HB27
Carr, Extremophiles : life under extreme conditions 2015 - “...; phosphate regulon sensor protein 1 JC1090 TTC3024 rrsB ; 16S rRNA 8 e.g. JC914 TTC1388 mannose-6-phosphate isomerase 1 JC1064 TTC1396 acetyl-lysine deacetylase 1 JC1040 TTC1401 high-affinity iron permease 1 JC852 TTC1482 ABC transporter permease 1 JC942 TTC1547 3-isopropylmalate dehydratase large subunit 1 JC1044 TTC1604 parB...”
CPE2308 mannose-1-phosphate guanylyltransferase from Clostridium perfringens str. 13
30% identity, 74% coverage
Tery_1856 Mannose-1-phosphate guanylyltransferase (GDP) from Trichodesmium erythraeum IMS101
36% identity, 72% coverage
BT2781 putative mannose-1-phosphate guanylyltransferase from Bacteroides thetaiotaomicron VPI-5482
33% identity, 71% coverage
BT_0558 mannose-1-phosphate guanylyltransferase from Bacteroides thetaiotaomicron VPI-5482
34% identity, 70% coverage
- Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
Heinken, Gut microbes 2013 - “...exGF MM _ B . The rescued gene knockouts were: BT_0554 (glutamine-fructose-6-phosphate transaminase, EC 2.6.1.16), BT_0558 (mannose-1-phosphate guanylyltransferase, EC 2.7.7.22), BT_1224 (GDP-D-mannose dehydratase, EC 4.2.1.47), and BT_1225 (GDP-L-fucose synthase, EC 1.1.1.271). The deletion of mouse genes did not cause any lethality in B. thetaiotaomicron , but...”
- “...thetaiotaomicron can be rescued by the presence of the murine host. Three of these genes (BT_0558, BT_1224, and BT_1225) were involved in the GDP-fucose biosynthesis pathway. Bacteroides species are well known for their L-fucose containing cell surface and mutants with deficient L-fucose synthesis cannot colonize the...”
BTB_RS26870, BTB_c54660 sugar phosphate nucleotidyltransferase from Bacillus thuringiensis Bt407
32% identity, 95% coverage
- Species and condition shape the mutational spectrum in experimentally evolved biofilms
Hu, mSystems 2023 - “...disrupted by the inserted IS 231 A elements. We found that the cupin domain-containing protein (BTB_RS26870, rfbM gene) was disrupted by IS 231 A in three out of the six lineages in Bth_bead with max frequencies from 13.37% to 48.66%, which show high parallelism of adaptation...”
- Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes
Lin, NPJ biofilms and microbiomes 2022 - “...hyspank -mKATE2 31 Oligos oYL51 Forward oligo to check if a mutation is present in BTB_RS26870 CCGGAATTCTCTAGCTACTCTCACTACT This study oYL52 Reverse oligo to check if a mutation is present in BTB_RS26870 CGCGGATCCCTAGGGTGAGGAGATAATA This study oYL55 Forward oligo to amplify left arm of the homologous fragment with...”
- “...ancestor and the N variants, all six FS isolates contained an insertion element in the BTB_c54660 gene, annotated as cupin domain-containing protein. Subsequent detailed analysis revealed that this gene encodes a mannose-1-phosphate guanylyltransferase (GDP) enzyme, which belongs to the glycosyltransferase family A. In numerous organisms, GDP...”
SYNPCC7002_A1554 mannose-1-phosphate guanylyltransferase from Synechococcus sp. PCC 7002
34% identity, 72% coverage
D8IEW7 Mannose-1-phosphate guanylyltransferase from Brachyspira pilosicoli (strain ATCC BAA-1826 / 95/1000)
30% identity, 72% coverage
- Brachyspira hyodysenteriae and B. pilosicoli Proteins Recognized by Sera of Challenged Pigs
Casas, Frontiers in microbiology 2017 - “...46 * ATCCBP X 38 38 D8ICU0 VspD 42.7 J9TU32 Ribonucleotide-diphosphate reductase subunit beta 41.1 D8IEW7 Mannose-1-phosphate guanylyltransferase 40.5 J9URY6 2-oxoacid:ferredoxin oxidoreductase subunit alpha-like protein 82.8 J9UBH8 ATP-dependent 6-phosphofructokinase 34.8 D8ICA2 Toxic anion resistance family protein 40.9 D8I9T4 Uncharacterized protein 39.9 D8ICR1 Pyruvate oxireductase 35.5 47...”
WP_015708896 mannose-1-phosphate guanylyltransferase from Treponema primitia ZAS-2
31% identity, 72% coverage
- On the Ancestral UDP-Glucose Pyrophosphorylase Activity of GalF from Escherichia coli
Ebrecht, Frontiers in microbiology 2015 - “...(GDP-mannose 1-phosphate guanylyltransferase, EC: 2.7.7.22) are: Eco, E. coli K-12, AAC75110; Tpr, Treponema primitia , WP_015708896. Sequences and their accession numbers of thymidylyltransferases (dTTP:- D -glucose-1-phosphate thymidylyltransferase, EC: 2.7.7.24) are: Eco, E. coli , WP_000783975; Pae, Pseudomonas aeruginosa , WP_003105518. Sequences and their accession numbers of...”
all4342 mannose-6-phosphate isomerase from Nostoc sp. PCC 7120
54% identity, 27% coverage
all4538 mannose-6-phosphate isomerase from Nostoc sp. PCC 7120
49% identity, 22% coverage
- The composition of the global and feature specific cyanobacterial core-genomes
Simm, Frontiers in microbiology 2015 - “...protease 2,1 1,0 0/0 None all4051 Prc barrel domain containing protein 2,3 2,7 0/30 None all4538 Mannose-6-phosphate isomerase 1,5 1,2 0/107 None all4729 Putative metalloprotein 1,0 100,8 0/1 c None asl4754 PetM Cytochrome b6f complex subunit 2,5 1,8 0/0 None all4768 ErfK/YbiS/YcfS/YnhG family protein 2,7 7,5...”
FTN_0408 mannose-6-phosphate isomerase from Francisella tularensis subsp. novicida U112
43% identity, 31% coverage
- Genotype-phenotype associations in a nonmodel prokaryote
Enstrom, mBio 2012 - “...and mannose-negative mutants. Mutations in the gene predicted to encode mannose-6-phosphate isomerase ( manA , FTN_0408) prevented growth on mannose, as expected (see Data SetS2 ). Two additional genes required for growth on the sugars correspond to a predicted sugar kinase (FTN_0646), which appears to act...”
WD1227 mannose-1-phosphate guanylyltransferase, interruption-C from Wolbachia endosymbiont of Drosophila melanogaster
28% identity, 56% coverage
WD1224 mannose-1-phosphate guanylyltransferase, interruption-N from Wolbachia endosymbiont of Drosophila melanogaster
40% identity, 42% coverage
AS87_RS07030 phosphomannose isomerase type II C-terminal cupin domain from Riemerella anatipestifer Yb2
40% identity, 22% coverage
- Riemerella anatipestifer AS87_RS09170 gene is responsible for biotin synthesis, bacterial morphology and virulence
Ren, Scientific reports 2018 - “...AS87_RS01395 transcription activator effector-binding protein 0.97 AS87_RS10270 hypothetical protein 0.96 AS87_RS02825 HIT family protein 0.96 AS87_RS07030 mannose-6-phosphate isomerase 0.95 AS87_RS10115 hypothetical protein 0.91 AS87_RS01890 hypothetical protein 0.86 AS87_RS10350 IS982 family transposase 0.86 AS87_RS06890 hypothetical protein 0.85 AS87_RS02260 polyphosphate kinase 2 0.84 AS87_RS01190 DUF465 domain-containing protein 0.79...”
SYNW0919 similar to mannose-6-phosphate isomerase WbpW from Synechococcus sp. WH 8102
41% identity, 23% coverage
RC1040 similarity to mannose-1-phosphate guanylyltransferase from Rickettsia conorii str. Malish 7
27% identity, 36% coverage
RC1039 similarity to mannose-1-phosphate guanylyltransferase from Rickettsia conorii str. Malish 7
39% identity, 24% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory