PaperBLAST

PaperBLAST Hits for tr|Q9I4S2|Q9I4S2_PSEAE Glycerate kinase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA1052 PE=3 SV=1 (381 a.a., MKIVIAPDSF...)

Show query sequence

>tr|Q9I4S2|Q9I4S2_PSEAE Glycerate kinase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA1052 PE=3 SV=1
MKIVIAPDSFKESLSAPDVAEAIARGWRRVFPQAEVLLRPLADGGEGTVDAVLAATAGER
RECRVEGPLGEPTLAHWGWLDDATAVIEMASASGLHLVPRDRRDATRSSSRGTGELIRAA
LDAGARKIILGLGGSATNDAGAGLLGALGVRFLAADGEELAPGGAALAGLHSLDLGGLDP
RLVDVAVEVAADVDNPLCGPRGASAVFGPQKGASAEQVAQLDAALAHFAKVVAATLGEDF
SRVPGVGAAGGLGFAARAFLRARFRPGIELVAELAGLADALVGADLVLTGEGRLDAQSLH
GKTPVGVARIARQAGVPVVALAGSLGDGYQRLHDAGIDAAFSLAPGPISLEQACAGAAAE
LEARAEQIARLWRLAQASREG

Running BLASTp...

Found 58 similar proteins in the literature:

PA1052 hypothetical protein from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage

• Effect of anaerobiosis and nitrate on gene expression in Pseudomonas aeruginosa
  Filiatrault, Infection and immunity 2005
  • “...PA0918 PA0930 PA0997 PA0998 PA0999 PA1000 PA1002 PA1045 PA1052 PA1076 PA1140 PA1173 PA1174 PA1175 PA1176 PA1179 PA1180 PA1195 PA1282 PA1323 PA1324 PA1331 PA1418...”
• V-antigen genotype and phenotype analyses of clinical isolates of Pseudomonas aeruginosa
  Allmond, Journal of clinical microbiology 2004
  • “...PA2015 PA1007 PA1010 PA1001 PA1100 PA1019 PA1024 PA1034 PA1052 PA1060 PA1063 PA1064 PA1065 PA1067 PA1069 PA1070 PA1079 PA1080 PcrV phenotype for: Type of...”
  • “...marker - PA1060 PA1063 - PA1001 PA1019 PA1024 PA1034 PA1052 size marker - PA103 PA1027 PA1111 PA1085 PA2009 PA2015 PA1007 PA1010 - negative control - size...”

PS417_13970 / A0A1N7UI49 glycerate 2-kinase (EC 2.7.1.165) from Pseudomonas simiae (see paper)
PS417_13970 glycerate kinase from Pseudomonas simiae
63% identity, 99% coverage

• Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism
  Price, mSystems 2019
  • “...(PS417_07245) a -keto acid cleavage enzyme (PS417_07250) ( 12 ) a lactonase (PS417_07255) glycerate kinase (PS417_13970) and acetyl-CoA C-acetyltransferase (PS417_10515). The remaining genes that are specifically important for deoxyribose utilization are two putative transporters, two regulatory genes, and mobA (PS417_21490), which is involved in the biosynthesis...”
  • “...by assaying mutant strains with only one transposon insertion. The glycerate kinase of P. simiae (PS417_13970) is 51% identical to glycerate kinase 1 from Escherichia coli ( garK ), which forms 2-phosphoglycerate ( 14 , 15 ). 2-Phosphoglycerate is an intermediate in glycolysis and thus links...”

BAV0697 glycerate kinase from Bordetella avium 197N
64% identity, 97% coverage

• Detection of small RNAs in Bordetella pertussis and identification of a novel repeated genetic element
  Hot, BMC genomics 2011
  • “...- - - - - - - - - - - - 1 BAV0696 > BAV0697 > 11 - - - - - - - - - - - - - - - 2 BAV2006 > BAV2007 > 12 - - - - - - -...”

PP_3178 conserved hypothetical protein TIGR00045 from Pseudomonas putida KT2440
64% identity, 99% coverage

• The Cellular Response to Lanthanum Is Substrate Specific and Reveals a Novel Route for Glycerol Metabolism in Pseudomonas putida KT2440
  Wehrmann, mBio 2020
  • “...3.84 PP_3748 GlcG Conserved hypothetical protein 2.06 3.71 PP_3622 Isoquinoline 1-oxidoreductase, beta subunit 1.97 2.82 PP_3178 GarK Glycerate kinase 1.77 2.85 PP_3621 IorA-II Isoquinoline 1-oxidoreductase subunit alpha (2Fe-2S clusters) 1.60 2.34 PP_0554 AcoB Acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit beta 1.54 2.27 PP_3623 AdhB Alcohol dehydrogenase cytochrome c subunit...”
  • “...as follows. The 650-bp to 1,000-bp regions upstream and downstream of the calA (PP_2426), garK (PP_3178), glpFKRD (PP_1076 to PP_1973), and glcDEF (PP_3745 to PP_3747) genes were amplified from genomic DNA of P. putida KT2440 using primer pairs PcalA1/2 and PcalA3/4, PgarK1/2 and PgarK3/4, Pglp1/2 and...”

ACICU_02886 glycerate kinase from Acinetobacter baumannii ACICU
56% identity, 98% coverage

• New PCR-based open reading frame typing method for easy, rapid, and reliable identification of Acinetobacter baumannii international epidemic clones without performing multilocus sequence typing
  Suzuki, Journal of clinical microbiology 2014
  • “...ACICU_02468 ACICU_02520* ACICU_02597 AB57_2930 ACICU_02886 ACICU_02966*# AB57_3308*# ACICU_03137*# AB57_3624* ACICU_03379* ACICU_03418* A1S_3257 ACICU_03581*...”
  • “...(100) A1S_0767 (99) ACICU_02597 (100) ACICU_02697 (99) ACICU_02886 (100) ACICU_02966 (100) ABSDF1977 (98) Between A1S_1754 and A1S_1755 (96) A1S_1782 (95)...”

ETAE_3323 glycerate kinase from Edwardsiella tarda EIB202
57% identity, 99% coverage

• Metabolic proteins with crucial roles in Edwardsiella tarda antioxidative adaptation and intracellular proliferation
  Wang, mSystems 2023
  • “...DNA-binding protein Dps), ETAE_2289 (mannonate dehydratase), ETAE_2291 (fructuronate reductase), ETAE_2977 (putative dicarboxylate-binding periplasmic protein), and ETAE_3323 (glycerate 2 kinase) were significantly upregulated in the H 2 O 2 group, compared to the control group ( Table 1 ). These eight genes were the potential key proteins...”
  • “...4.686 0.144 b ACY85810.1 ETAE_2977 Putative dicarboxylate-binding periplasmic protein +2.30 b 3.131 0.178 b ACY86154.1 ETAE_3323 Glycerate 2 kinase + a 2.027 0.074 b a Proteomic DAPs detected only in the H 2 O 2 group. b P < 0.01. c P < 0.05. The roles...”

BSU40040 glycerate kinase from Bacillus subtilis subsp. subtilis str. 168
53% identity, 99% coverage

• Secondary structural entropy in RNA switch (Riboswitch) identification
  Manzourolajdad, BMC bioinformatics 2015
  • “...0.3885 15151 youB BSU21329 0.819 98 4118717 4118873 reverse BSU40110 bglA -2370 0.3758 5574 glxK BSU40040 0.818 99 4204755 4204911 reverse BSU40960 parB -722 0.3949 393 yyaD BSU40940 0.818 100 3648264 3648420 reverse BSU35530 tagO -311 0.363 1806 degS BSU35500 0.818 Top 50 hits of the...”
  • “...0.3885 15151 youB BSU21329 0.819 70 4118717 4118873 reverse BSU40110 bglA -2370 0.3758 5574 glxK BSU40040 0.818 71 4204755 4204911 reverse BSU40960 parB -722 0.3949 393 yyaD BSU40940 0.818 72 252357 252513 forward BSU02320 ybfP 36 0.3822 79 ybfQ BSU02330 0.818 73 3648264 3648420 reverse BSU35530...”

VP_RS15810 glycerate kinase from Vibrio parahaemolyticus RIMD 2210633
53% identity, 98% coverage

• Identification of Antibacterial Components in the Methanol-Phase Extract from Edible Herbaceous Plant Rumex madaio Makino and Their Antibacterial Action Modes
  Liu, Molecules (Basel, Switzerland) 2022
  • “...VP_RS01755 0.067 Dihydroxyacetone kinase subunit DhaK VP_RS21295 0.193 Diacylglycerol kinase VP_RS11580 0.239 Glycerol kinase GlpK VP_RS15810 0.431 Glycerate kinase VP_RS05740 2.015 Triacylglycerol lipase Apoptosis VP_RS23210 0.086 Alkyl hydroperoxide reductase subunit C VP_RS20650 0.282 C-type cytochrome VP_RS02795 0.415 Peroxiredoxin C Bacterial chemotaxis VP_RS22610 0.101 OmpA family protein...”

WU75_05330 glycerate kinase from Vibrio parahaemolyticus
53% identity, 98% coverage

• Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn
  Tang, Foods (Basel, Switzerland) 2023
  • “...0.397 Tryptophan synthase subunit beta WU75_05755 thrC 0.429 Threonine synthase WU75_05760 thrB 0.47 Serine kinase WU75_05330 glxK 0.495 Glycerate kinase Oxidative phosphorylation WU75_06010 petC 0.195 Cytochrome C WU75_06015 petB 0.209 Cytochrome B WU75_14570 ccoO 0.228 Peptidase S41 WU75_14575 ccoN 0.272 Cbb3-type cytochrome c oxidase subunit I...”

DSVG11_1884 glycerate kinase from Desulfovibrio sp. G11
56% identity, 95% coverage

• The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans
  Sánchez-Andrea, Nature communications 2020
  • “...dehydrogenases DSVG11_0256 or DSVG11_0961) and finally the generation of phospho-glycerate by glycerate kinase (DSVG11_0656 or DSVG11_1884). During autotrophic growth, assimilation probably proceeds primarily via the glycine reduction route rather than the serine route, as GR was highly upregulated, while SHMT, SDA and alternative serine assimilation enzymes...”

STM0525 glycerate kinase II from Salmonella typhimurium LT2
54% identity, 98% coverage

• Genetic types, gene repertoire, and evolution of isolates of the Salmonella enterica serovar 4,5,12:i:- Spanish clone assigned to different phage types
  García, Journal of clinical microbiology 2013
  • “...isolates of the European clone carry the glxK (STM0525) gene of the allantoin-glyoxylate operon (cluster I) (P. Garcia, unpublished data; E. Hauser, unpublished...”

t2336 glycerate kinase from Salmonella enterica subsp. enterica serovar Typhi Ty2
54% identity, 98% coverage

• Mycobacterium tuberculosis (Mtb) lipid mediated lysosomal rewiring in infected macrophages modulates intracellular Mtb trafficking and survival
  Sachdeva, The Journal of biological chemistry 2020 (secret)

APL_0142 glycerate kinase from Actinobacillus pleuropneumoniae L20
51% identity, 98% coverage

• Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
  Labrie, Veterinary research 2010
  • “...Putative acyl CoA thioester hydrolase 1.796 APL_0652 manB Phosphomannomutase 1.677 APL_0483 APL_0483 Predicted nitroreductase 1.668 APL_0142 glxK Glycerate kinase 1.564 APL_0452 sucC Succinyl-CoA synthetase beta chain 1.515 APL_0461 APL_0461 Predicted hydrolases of the HAD superfamily 1.456 APL_0687 Dld D-lactate dehydrogenase 1.439 APL_1510 gpsA Glycerol-3-phosphate dehydrogenase (NAD(P)+)...”
• Regulation of pga operon expression and biofilm formation in Actinobacillus pleuropneumoniae by sigmaE and H-NS
  Bossé, Journal of bacteriology 2010
  • “...APL_1739 APL_1920 APL_1883 APL_0119 APL_1948 APL_1724 APL_1405 APL_0142 APL_1639 APL_1493 APL_0141 rpoE APL_1417 APL_0308 oapB mutY APL_1920 ptrA proQ APL_1948...”

BBMN68_585 glycerate kinase from Bifidobacterium longum subsp. longum BBMN68
55% identity, 98% coverage

• Transcriptomic analysis of Bifidobacterium longum subsp. longum BBMN68 in response to oxidative shock
  Zuo, Scientific reports 2018
  • “...sequence (53) Size of product (bp) Forward Reverse sufB1 (BBMN68_611) ACGACGGTGACGCACGACT AGATGCCGAGCATGTTGAGGT 243 glycerate kinase (BBMN68_585) GCCCTCGGCGTTCGTCTTCT CAATGTGGCGACATCATCTTTGGA 225 grxC2 (BBMN68_1397) GCAGTGCGATGCCACCAAG CAGGAGTTGTCCGGCGTGAT 147 tatC (BBMN68_1285) GGAGCCGGACTGGCATGGTATCT CGTTGCGAGACGCCACTGCTT 228 hcaD (BBMN68_1524) ACGCCAGAACCCTCACCTACC CCGATCACCACTGCCGACTT 217 16S rRNA (BBMN68_rRNA7) CGTAGGGTGCAAGCGTTATC GCCTTCGCCATTGGTGTT 197 nrdI (BBMN68_1398) GGATGCCGTTTGCAGGAC TCGTTGAGGAAGCGTTTGAC 164 nrdE...”

YhaD / b3124 glycerate 2-kinase 1 (EC 2.7.1.165) from Escherichia coli K-12 substr. MG1655 (see 6 papers)
garK / P23524 glycerate 2-kinase 1 (EC 2.7.1.165) from Escherichia coli (strain K12) (see 5 papers)
GLXK1_ECOLI / P23524 Glycerate 2-kinase; Glycerate kinase 1; GK1; EC 2.7.1.165 from Escherichia coli (strain K12) (see 2 papers)
P23524 glycerate 2-kinase (EC 2.7.1.165) from Escherichia coli K-12 (see paper)
b3124 glycerate kinase I from Escherichia coli str. K-12 substr. MG1655
52% identity, 97% coverage

• function: Catalyzes the transfer of the phosphate group from adenosine triphosphate (ATP) to (R)-glycerate to form (2R)-2-phosphoglycerate, an enzymatic step in (L)-glucarate/galactarate catabolic pathway.
  catalytic activity: (R)-glycerate + ATP = (2R)-2-phosphoglycerate + ADP + H(+) (RHEA:27377)
• Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
  Ren, Applied and environmental microbiology 2005
  • “...1.6 0.0020 1.4 0.0446 1.5 0.0210 ybiK yhaD yhaF b0828 b3124 b3126 2.4 0.0007 2.2 0.0051 1.6 0.0254 2.6 0.0091 1.5 0.0089 2.4 0.0023 yhaG b3128 2.0 0.0039 2.2...”
• The catabolism of ethylene glycol by <i>Rhodococcus jostii</i> RHA1 and its dependence on mycofactocin
  Roccor, Applied and environmental microbiology 2024 (secret)

KPN_03129 glycerate kinase I from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
53% identity, 98% coverage

• Comparative Proteomics Demonstrates Altered Metabolism Pathways in Cotrimoxazole- Resistant and Amikacin-Resistant Klebsiella pneumoniae Isolates
  Shen, Frontiers in microbiology 2021
  • “...protein sets. Gene_ID Symbol a Pearson r b Function FC c p d CTX group KPN_03129 garK 0.9 Monocarboxylic acid catabolic process 0.30 4.72e-2 KPN_03520 uxaC 0.98 Monocarboxylic acid catabolic process 0.35 1.11e-4 KPN_03521 exuT 0.91 Monocarboxylic acid catabolic process 0.24 6.67e-4 KPN_04780 hpaB 0.95 Monocarboxylic...”

YP_002394749 Glycerate kinase from Vibrio splendidus LGP32
49% identity, 97% coverage

• Molecular cloning and heterologous expression of the dehydrophos biosynthetic gene cluster
  Circello, Chemistry & biology 2010
  • “...299 uncultured microorganism putative -butyrobetaine hydroxylase (ABZ07908) 72/254 (28%) dhpB 383 Vibrio splendidus glycerate kinase (YP_002394749) 115/332 (35%) dhpC 371 Aciduliprofundum boonei malate/ l -lactate dehydrogenase (YP_002578914) 130/367(35%) dhpD 397 Candidatus Pelagibacter ubique aspartate transaminase (ZP_01264754) 112/403 (28%) dhpE 296 Frankia alni putative PEP phosphomutase (YP_716511)...”

EcolC_3109 glycerate kinase from Escherichia coli C str. ATCC 8739
51% identity, 100% coverage

• Loop-mediated isothermal amplification assay for detection of generic and verocytotoxin-producing Escherichia coli among indigenous individuals in Malaysia
  Teh, TheScientificWorldJournal 2014
  • “...against the database by using NCBI BLAST ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ). A CDS encoding glycerate kinase (EcolC_3109, Accession number: CP000946) was selected and used for primers design. Two pairs of primers, including F3 (5-GGTAGATCGAACGGTCATCG-3), B3 (5-GGCCAGCAACGGATTACG-3), forward inner primer (FIP) (5-CGCAGACTTCAAGCGTCACGATCGAAGGAACGGTGGATGC-3), and backward inner primer (BIP) (5-CCTTACCGGCGACGGGAAAA-CTTTTCAGGCGCGACCAG-3)...”

YbbZ / b0514 glycerate 2-kinase 2 (EC 2.7.1.165) from Escherichia coli K-12 substr. MG1655 (see 6 papers)
glxK / P77364 glycerate 2-kinase 2 (EC 2.7.1.165) from Escherichia coli (strain K12) (see 6 papers)
GLXK2_ECOLI / P77364 Glycerate 3-kinase; D-Glycerate-3-kinase; Glycerate kinase 2; GK2; EC 2.7.1.31 from Escherichia coli (strain K12) (see 3 papers)
P77364 glycerate 2-kinase (EC 2.7.1.165) from Escherichia coli K-12 (see paper)
glxK / GB|AP_001162.1 glycerate kinase; EC 2.7.1.31 from Escherichia coli K12 (see paper)
51% identity, 100% coverage

• catalytic activity: (R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+) (RHEA:23516)
  cofactor: Mg(2+) Co(2+) Mn(2+) Fe(2+) Ca(2+) (Divalent metal cations; Mg(2+) and Co(2+) are better than Mn(2+), Fe(2+) or Ca(2+).)
  disruption phenotype: Loss of glycerate kinase activity.
• The catabolism of ethylene glycol by <i>Rhodococcus jostii</i> RHA1 and its dependence on mycofactocin
  Roccor, Applied and environmental microbiology 2024 (secret)
• New Insights into the Mechanism of Antibacterial Action of Synthetic Peptide Mo-CBP₃-PepI against Klebsiella pneumoniae
  Branco, Antibiotics (Basel, Switzerland) 2022
  • “...K12) Plasma membrane 3.486 UDP-glucose 6-dehydrogenase P76373 Escherichia coli (strain K12) Cytoplasm 0.902 Glycerate 3-kinase P77364 Escherichia coli (strain K12) Cytoplasm 0.745 Phenylacetate-coenzyme A ligase P76085 Escherichia coli (strain K12) Cytoplasm 1.666 Pantothenate kinase P0A6I3 Escherichia coli (strain K12) Cytoplasm 0.548 Pyruvate kinase P78031 Mycoplasma pneumoniae...”

HI0091 conserved hypothetical protein from Haemophilus influenzae Rd KW20
P44507 Glycerate kinase from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
49% identity, 98% coverage

• There is a specific response to pH by isolates of Haemophilus influenzae and this has a direct influence on biofilm formation
  Ishak, BMC microbiology 2014
  • “...(or sugar acid) metabolic genes (HI1010-1015, see Figure 3 ) and a potential glycerate kinase (HI0091) that links into glycolysis. It is worth noting that these genes/pathways are genetically unlinked, adding to validity of the response. In addition to the HI1015/ gntP symporter, the HI1010-1015 genes...”
  • “...1.5410 -3 Sugar epimerase HI1015 1.12 1.1810 -3 4.7010 -2 GntP family, gluconate:H + symporter HI0091 1.74 5.9810 -7 5.3310 -5 Hypothetical protein; homologous to GlxK, glycerate kinase HI0092 2.14 1.4910 -9 2.4110 -7 GntP family, gluconate:H + symporter Iron uptake genes Gene Log 2 fold...”
• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...HP HI0082 950979 P43937 Acyl-CoA dehydrogenase 13. HP HI0090 950992 P44506 Alanine racemase 14. HP HI0091 950989 P44507 Glycerate kinase 15. HP HI0092 950987 Q57493 Gluconate transporter 16. HP HI0093 950994 P44509 Putative sugar diacid recognition 17. HP HI0094 950995 P43939 GntP family permease 18. HP...”
• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...950979 P43937 Acyl-CoA dehydrogenase 13. HP HI0090 950992 P44506 Alanine racemase 14. HP HI0091 950989 P44507 Glycerate kinase 15. HP HI0092 950987 Q57493 Gluconate transporter 16. HP HI0093 950994 P44509 Putative sugar diacid recognition 17. HP HI0094 950995 P43939 GntP family permease 18. HP HI0095 950997...”
• Genetic complementation of an outer membrane cytochrome omcB mutant of Shewanella putrefaciens MR-1 requires omcB plus downstream DNA
  Myers, Applied and environmental microbiology 2002
  • “...225 278 A82343 (PIR) B64740 (PIR) F82402 (PIR) P44507 (SP) H82234 (PIR) NP_046537.1 AAF39790.1 (GB) AAF60966.1 (GB) AAF63432.1 (GB) F82388 (PIR) Vibrio cholerae...”

SO1770 glycerate kinase, putative from Shewanella oneidensis MR-1
51% identity, 98% coverage

• Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation
  Castillo, PloS one 2018
  • “...argH Argininosuccinate lyase 1.10 SO0818 metE Homocysteine methyltransferase 1.13 1.32 SO1361 aroF Phospho-2-dehydro-3-deoxyheptonate aldolase 1.01 SO1770 garK Glycerate kinase 1.01 SO2074 hisG ATP phosphoribosyltransferase 1.11 1.20 SO2767 asnB Asparagine synthetase [glutamine-hydrolyzing] 1.02 SO3986 lysC Aspartokinase 1.11 SO4245 argA N-acetylglutamate synthase 1.01 1.11 SO2305 lrp Leucine-responsive regulatory...”
• SO2426 is a positive regulator of siderophore expression in Shewanella oneidensis MR-1
  Henne, BMC microbiology 2011
  • “...conserved hypothetical protein AAAACTCAGCAGAA - -113 2.08E-06 SO1190 conserved hypothetical protein CTAAGGCAACAAAA - +12 2.38E-05 SO1770 glycerate kinase, putative ACAACCCAGAAGAA - -177 2.61E-05 SO3025 conserved hypothetical protein GCAAAACATCAAAA + -234 1.13E-04 SO3062 hypothetical protein ATAAATCAGGAGAA + -5 7.64E-06 SO4499 hypothetical protein CTGCAACAGGAGAA + -5 1.19E-05 SO4504...”
• Transcriptome analysis reveals response regulator SO2426-mediated gene expression in Shewanella oneidensis MR-1 under chromate challenge
  Chourey, BMC genomics 2008
  • “...0.022 0.006 0.004 0.005 1.68* SO1190 Conserved hypothetical protein 0.01 0.014 0.02 0.009 0.02 1.03* SO1770 Glycerate kinase, putative 0.56 0.48 0.35 0.18 0.22 0.72* SO1967 Hypothetical protein 0.97* 0.78* 0.34 0.55* 0.72 0.42 SO2128 Hypothetical protein 0.38 0.43 0.32 1.21 0.54 0.89* SO2425 Hypothetical protein...”

SL1344_2940 glycerate kinase from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
STM2959 putative glycerate kinase 2 from Salmonella typhimurium LT2
51% identity, 99% coverage

• Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme
  Kristofich, PLoS genetics 2018
  • “...as the parental strain, contained identical mutations in menC , manX , ybdN , and SL1344_2940 compared to the reference genome. menC encodes an enzyme involved in menaquinone biosynthesis, which is primarily required for anaerobic growth [ 18 ]. manX encodes a mannose-specific phosphotransferase IIAB component....”
  • “...reverted; carries unexpected mutations in menC and manX JK328 JK411 argC ; proA* (E382A ProA); SL1344_2940 V333A (GTT->GCC); YbdN T381I (ACA->ATA) "parental strain"; mutations in SL1344_2940 and ybdN JC559 JK328 + M1 (C365750T); GlnD D837V (GAT->GTT) contains a mutation in glnD JC592 JC559 + M4 (C366925T)...”
• speG Is Required for Intracellular Replication of Salmonella in Various Human Cells and Affects Its Polyamine Metabolism and Global Transcriptomes
  Fang, Frontiers in microbiology 2017
  • “...SL1344_3662 Putative racemase 1.552 SL1344_0211 SL1344_0211 Hypothetical protein 1.495 dctA SL1344_3579 C4-dicarboxylate transport protein 1.454 SL1344_2940 SL1344_2940 Hypothetical protein 1.319 hutU SL1344_0767 Urocanate hydratase 1.237 SL1344_3732 SL1344_3732 Hypothetical protein 1.227 SL1344_0790 SL1344_0790 Hypothetical protein 1.163 SL1344_1227 SL1344_1227 Hypothetical protein 1.010 hutH SL1344_0768 Histidine ammonia-lyase 1.002 (B)...”
• Salmonella versus the Microbiome
  Rogers, Microbiology and molecular biology reviews : MMBR 2021 (secret)
• Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion
  Faber, Nature 2016
  • “...promote growth in mucus, we constructed a S. Typhimurium strain lacking the gudT ygcY gudD STM2959 operon ( gudT-STM2959 mutant, Extended Data Fig. 1c ), which encodes proteins involved in galactarate uptake and catabolism 7 . Expression of the gudT ygcY gudD STM2959 operon in S....”
  • “...contained biologically relevant quantities of a substrate for enzymes encoded by the gudT ygcY gudD STM2959 operon. We next investigated the contribution of the gudT ygcY gudD STM2959 operon to post-antibiotic pathogen expansion. Treatment of mice with a single dose of streptomycin one day prior to...”

STM3247 glycerate kinase from Salmonella typhimurium LT2
50% identity, 97% coverage

• Hydrogen-stimulated carbon acquisition and conservation in Salmonella enterica serovar Typhimurium
  Lamichhane-Khadka, Journal of bacteriology 2011
  • “...conservation and assimilation STM4183 STM3248 STM3249 STM4184 STM3247 STM4187 STM0772 STM0210 STM1173-79 STM2082-90 STM3326 STM0310 STM3326 STM1752 a 15.2/2.0...”

LCA_RS03600 glycerate kinase from Latilactobacillus sakei subsp. sakei 23K
48% identity, 98% coverage

• Transcriptome Analysis Reveals the Role of Sucrose in the Production of Latilactobacillus sakei L3 Exopolysaccharide
  Wang, International journal of molecular sciences 2024
  • “...by four down-regulated ncRNAs ( Figure 9 c and Table 3 and Table S1 ). LCA_RS03600 encoding a glycerate kinase was also coregulated by four down-regulated ncRNAs ( Figure 9 c and Table 3 and Table S1 ). Intriguingly, all of the three target genes were...”
  • “...LCA_RS00775 1.6 Oxidoreductase LCA_RS04120 1.65 Beta-ketoacyl-ACP reductase LCA_RS02325 1.58 NAD(P)-dependent dehydrogenase LCA_RS04135 1.54 Beta-hydroxyacyl-ACP dehydratase LCA_RS03600 1.69 Glycerate kinase LCA_RS05480 1.32 Folylpolyglutamate synthase LCA_RS09375 1.04 TVP38/TMEM64 family protein LCA_RS05495 1.38 Dihydroneopterin aldolase LCA_RS05475 1.48 Dihydropteroate synthase LCA_RS05000 1.31 Dihydrofolate reductase...”

YP_218181 glycerate kinase from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
50% identity, 97% coverage

• HLA-DR3 restricted T cell epitope mimicry in induction of autoimmune response to lupus-associated antigen SmD
  Deshmukh, Journal of autoimmunity 2011
  • “...144158 ( Pseudomonas syringae ) YP_234921 16 DILELDPRLKLCAIR Glycerate kinase 175189 ( Salmonella enterica ) YP_218181 17 EIVDLDPKLKQINLI TcmP methyltransferase 215229 ( Streptococcus agalactiae ) NP_688496 18 QQLEVDPKIKAETAF Monooxygenase 93107 ( Trypanosoma cruzi ) XP_805876 19 PALELDPKLTTPLLR Monoglyceride lipase 164178 ( Trypanosoma cruzi ) XP_805120 20...”

A1S_2641 Glycerate kinase from Acinetobacter baumannii ATCC 17978
54% identity, 89% coverage

• New PCR-based open reading frame typing method for easy, rapid, and reliable identification of Acinetobacter baumannii international epidemic clones without performing multilocus sequence typing
  Suzuki, Journal of clinical microbiology 2014
  • “...(99) Between A1S_2318 and A1S_2319 (99) A1S_2485 (98) A1S_2641 (97) Between A1S_2707 and A1S_2708 (98) ABSDF1960 (96) ABSDF1260 (97) ABSDF0764 (98) AB57_3308...”

NWMN_2331 glycerate kinase from Staphylococcus aureus subsp. aureus str. Newman
SA2220 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAOUHSC_02723 glycerate kinase, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_2377 glycerate kinase from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL2435 glycerate kinase from Staphylococcus aureus subsp. aureus COL
SAEMRSA15_RS12840 glycerate kinase from Staphylococcus aureus M1179
45% identity, 98% coverage

• Integrative omics analysis reveals insights into small colony variants of Staphylococcus aureus induced by sulfamethoxazole-trimethoprim
  Zhou, BMC microbiology 2024
  • “...from RNA sequencing. Contradictory data (RNA sequencing: up-regulated; qRT-PCR: down-regulated) were observed for the gene NWMN_2331 (Fig. 4 E). Although there were isolated discrepancies between the two technologies, overall, the transcriptome data were reliable. Fig. 4 qRT-PCR analysis for confirmation of transcription levels of selected 48...”
  • “...in the SCV showed matching results between the two detection technologies. E The expression of NWMN_2331, as assayed by qRT-PCR, was confirmed to be opposite to that observed in RNA sequencing. The black bar represents qRT-PCR, while the gray bar represents RNA sequencing. qRT-PCR stands for...”
• NWMN2330 May Be Associated with the Virulence of Staphylococcus aureus by Increasing the Expression of hla and saeRS
  Liu, Infection and drug resistance 2022
  • “...catabolic TdcB NWMN_1239 1.7232 6.55E-11 2.79E-10 Aspartokinase 3 NWMN_2510 1.3361 1.07E-49 1.51E-48 Betaine aldehyde dehydrogenase NWMN_2331 1.4893 7.89E-22 5.58E-21 Glycerate kinase NWMN_1441 1.4886 2.01E-43 2.57E-42 Aminomethyltransferase NWMN_1242 1.3081 1.86E-17 1.11E-16 Homoserine kinase NWMN_1241 1.1079 1.13E-24 9.04E-24 Threonine synthase NWMN_1240 1.3098 1.39E-36 1.61E-35 Homoserine dehydrogenase Note :...”
• Comparative mechanistic studies of brilacidin, daptomycin, and the antimicrobial peptide LL16
  Mensa, Antimicrobial agents and chemotherapy 2014
  • “...vraR NWMN_2405 NWMN_1824 proP NWMN_2211 NWMN_1835 NWMN_1621 NWMN_2331 NWMN_1732 NWMN_1825 NWMN_2404 tcaA ctpA murZ NWMN_0931 plsC NWMN_0977 NWMN_2518 NWMN_0946...”
• Respiration and Small Colony Variants of Staphylococcus aureus
  Proctor, Microbiology spectrum 2019 (secret)
• Insertion of epicatechin gallate into the cytoplasmic membrane of methicillin-resistant Staphylococcus aureus disrupts penicillin-binding protein (PBP) 2a-mediated beta-lactam resistance by delocalizing PBP2
  Bernal, The Journal of biological chemistry 2010
  • “...(encoding PBP2), yvqF , tcaA (implicated in teicoplainin resistance), prsA (protease maturation), and N315 ORFs SA2220, SA1703, SA1712, SA2103, SA2221, and SA2343 were up-regulated following exposure to ECg ( Table 1 ). These genes belong to the core cell wall stress stimulon, defined as genes common...”
  • “...acid biosynthesis SAR1024 SA0903 Conserved hypothetical protein 2.33 3.6 Up Carbohydrate transport and metabolism SAR2522 SA2220 Glycerate kinase 2.88 Up 14.8 Carbohydrate transport and metabolism SAR1374 SA1195 msrR Reductase regulator 2.84 4.8 2.5 Transcription SAR2394 SA2103 Transcriptional regulator 3.2 2.7 3.4 14 Regulation/transcription SAR2585 SA2296 Transcriptional...”
• Revealing fosfomycin primary effect on Staphylococcus aureus transcriptome: modulation of cell envelope biosynthesis and phosphoenolpyruvate induced starvation
  Petek, BMC microbiology 2010
  • “...divergon expression Regulatory functions SA2146 tcaA 0.27 2.07 1.27 2.69 + TcaA protein Energy metabolism SA2220 0.95 0.47 1.48 + hypothetical protein Energy metabolism SA2221 1.92 0.96 2.59 + hypothetical protein Unclassified SA2297 0.37 + hypothetical protein, similar to GTP-pyrophosphokinase Unclassified SA2343 -0.73 2.11 7.08 5.50...”
• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...2.8 15 stable rplN SA2229 50S ribosomal protein L14 sa_c4824s4130_a_at * 2.7 15 stable rplO SA2220 50S ribosomal protein L15 sa_c4864s4170_at * 2.7 15 stable rplP SA2232 50S ribosomal protein L16 sa_c4792s4098_at * 2.3 15 stable rplQ SA2212 50S ribosomal protein L17 sa_c4836s4142_at * 2.4 15...”
  • “...5.0 15 15 rplN SA2229 50S ribosomal protein L14 sa_c4824s4130_a_at * 3.9 15 15 rplO SA2220 50S ribosomal protein L15 sa_c4864s4170_at * 4.4 15 15 rplP SA2232 50S ribosomal protein L16 sa_c4792s4098_at * 5.5 15 15 rplQ SA2212 50S ribosomal protein L17 sa_c4836s4142_at * 4.2 15...”
• Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
  Donat, Journal of bacteriology 2009
  • “...SA2125 Hypothetical protein, similar to formiminoglutamase SA2220 Glycerate kinase SA2318 Putative L-serine dehydratase SA2319 Putative beta subunit of...”
  • “...9 of 13 genes of the VraSR regulon (proP, SA2220, sgtB, murZ, prsA, SA1476, SA1702, SA1703, and SA2221) that were described by Kuroda et al. under...”
• The lantibiotic mersacidin is a strong inducer of the cell wall stress response of Staphylococcus aureus
  Sass, BMC microbiology 2008
  • “...SA2113 hypothetical protein 14.9 11.8 4.9 11.4 SA2146 tcaA TcaA protein 3.3 1.6 2.2 4.0 SA2220 conserved hypothetical protein 7.0 12.2 3.7 21.4 SA2221 hypothetical protein 25.6 18.3 5.2 42.7 SA2222 hypothetical protein, similar to TcaB Protein transport and binding 1.2 0.6 1.0 SA2296 hypothetical protein,...”
• Overexpression of genes of the cell wall stimulon in clinical isolates of Staphylococcus aureus exhibiting vancomycin-intermediate- S. aureus-type resistance to vancomycin
  McAleese, Journal of bacteriology 2006
  • “...vancomycin at 8 g/ml N315 ORF a SA0418 SA0903 SA0905 SA2220 SA0182 Gene 1 g/ml cysM atl SA1691 sgtB SA1926 murZ SA0909 SA0312 fmt SA0820 SA0937 glpQ SA0969...”
  • “...to cell wall active antibiotics N315 ORF a Upregulated SA2220 SA1691 SA1926 SA0909 SA1702 SA2146 SA1549 SA1659 SA1701 SA1703 SA1712 SA2103 Gene sgtB murZ fmt...”
• Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small-colony-variant phenotype
  Seggewiss, Journal of bacteriology 2006
  • “...Similar to unknown proteins SA0175 SA1702 SA0412 SA0213 SA2220 SA0413 SA0212 SA0588 SA2329 SA1712 SA0908 SA2146 SA0919 SA0725 SA1021 SA1031 SA1032 SA0824 SA1433...”
  • “...hemB mutant (Fig. 3): glycerate kinase (SA2220, 3.25-fold), glycerol diffusional facilitator (glpF, SA1140, 5.58-fold), and aerobic glycerol-3-phosphate...”
• Bactericidal Action of Shrimp Shell Chitooligosaccharide Conjugated with Epigallocatechin Gallate (COS-EGCG) against Listeria monocytogenes
  Buatong, Foods (Basel, Switzerland) 2023
  • “...growth of S. aureus by upregulating the expression of gntP , gntK , rumA , SAOUHSC_02723 , SAOUHSC_01311 , and vraS genes related to the membrane transport [ 41 ]. COS and chitosan with a low molecular weight and degree of polymerization (DP) can enter the...”
• Effect of epigallocatechin gallate on gene expression of Staphylococcus aureus
  Kitichalermkiat, Journal of global antimicrobial resistance 2020 (PubMed)
  • “...to membrane transport included gntP, gntK, rumA, SAOUHSC_02723, SAOUHSC_01311, and vraS. Decreased transcription was observed in genes involved in toxin...”
• Reversible antibiotic tolerance induced in Staphylococcus aureus by concurrent drug exposure
  Haaber, mBio 2015
  • “...citC ) Isocitrate dehydrogenase 2.97 SAUSA300_1641 gltA Citrate synthetase 3.75 SAUSA300_2319 Pyridine nucelotide-disulfide oxidoreductase 6.26 SAUSA300_2377 Glycerate kinase 3.64 Transport SAUSA300_1790 prsA Foldase protein PrsA 2.52 SAUSA300_2630 nixA High-affinity nickel transporter 1.81 SAUSA300_2409 nikC Oligopeptide ABC transporter permease 1.66 SAUSA300_2411 nikA Oligopeptide permease, peptide-binding protein 1.80...”
• Reduced vancomycin susceptibility in Staphylococcus aureus, including vancomycin-intermediate and heterogeneous vancomycin-intermediate strains: resistance mechanisms, laboratory detection, and clinical implications
  Howden, Clinical microbiology reviews 2010
  • “...sgtB vraS SACOL2302 SACOL2352 lytR tcaA murZ SACOL2435 SACOL2436 SACOL2518 SACOL2571 Additional genes SACOL0033 SACOL0636 SACOL0693 mecA mvaK1 tagA SACOL0743...”
• A functional menadione biosynthesis pathway is required for capsule production by Staphylococcus aureus
  Altwiley, Microbiology (Reading, England) 2021
  • “...SAEMRSA15_RS10690 GHKL domain-containing protein 0.00077225 SAEMRSA15_RS02555 RNA polymerase sigma factor 0.00120048 ileS isoleucine--tRNA ligase 0.00139006 SAEMRSA15_RS12840 glycerate kinase 0.00280998 SAEMRSA15_RS11120 ATP synthase subunit I 0.0030996 SAEMRSA15_RS02630 amidohydrolase 0.00366703 SAEMRSA15_RS12955 APC family permease 0.00386528 SAEMRSA15_RS13455 LrgB family protein 0.00400753 menD 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase 0.00507518 SAEMRSA15_RS09800 metal-dependent hydrolase 0.00516556...”

SARLGA251_22130 glycerate kinase from Staphylococcus aureus subsp. aureus LGA251
45% identity, 98% coverage

• Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC
  Harrison, EMBO molecular medicine 2013
  • “...SARLGA251_22000 sbi IgG-binding protein 1104 1310 C T No No No Yes Yes Yes Yes SARLGA251_22130 Putative glycerate kinase 1137 1142 C T Yes Yes Yes Yes Yes Yes Yes a The location from the start codon in base pairs. b Base in the reference genome...”

SAR2522 putative glycerate kinase from Staphylococcus aureus subsp. aureus MRSA252
45% identity, 98% coverage

• A functional menadione biosynthesis pathway is required for capsule production by Staphylococcus aureus
  Altwiley, Microbiology (Reading, England) 2021
  • “...0.010100134 thiE putative thiamine-phosphate pyrophosphorylase 0.010702445 fabD ACP S-malonyltransferase 0.011824195 SAR1343 amino acid permease 0.01386841 SAR2522 putative glycerate kinase 0.01579356 SAR1674 putative GTPase 0.018539766 SAR0122 putative transport protein 0.018645214 SAR1668 conserved hypothetical protein 0.019293181 ilvA threonine dehydratase biosynthetic 0.020495129 dfrB dihydrofolate reductase type I 0.021075917 Intergenic...”
• Insertion of epicatechin gallate into the cytoplasmic membrane of methicillin-resistant Staphylococcus aureus disrupts penicillin-binding protein (PBP) 2a-mediated beta-lactam resistance by delocalizing PBP2
  Bernal, The Journal of biological chemistry 2010
  • “...Amino acid biosynthesis SAR1024 SA0903 Conserved hypothetical protein 2.33 3.6 Up Carbohydrate transport and metabolism SAR2522 SA2220 Glycerate kinase 2.88 Up 14.8 Carbohydrate transport and metabolism SAR1374 SA1195 msrR Reductase regulator 2.84 4.8 2.5 Transcription SAR2394 SA2103 Transcriptional regulator 3.2 2.7 3.4 14 Regulation/transcription SAR2585 SA2296...”

EF2646 glycerate kinase, putative from Enterococcus faecalis V583
47% identity, 98% coverage

• The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood
  Vebø, PloS one 2009
  • “...consistent with depletion of intracellular glucose catabolic intermediates. Simultaneously, glycolysis genes gap-1 (EF1526), glycerate kinase (EF2646) and pgm (EF2982) were up-regulated, indicating increased carbon flux from sources other than hexose sugars. Interestingly, the glycerol catabolic pathway (EF1929-27), was highly up-regulated in response to growth in blood,...”
• Transcriptional response of Enterococcus faecalis V583 to erythromycin
  Aakra, Antimicrobial agents and chemotherapy 2005
  • “...EF2736 EF3113 EF0956 EF0957 EF1071 EF1347 EF1348 EF1349 EF1411 EF1543 EF1606 EF2646 EF0283 EF0848 EF1608 EF2691 EF2883 EF3112 EF2320 0 0 0 0 0 0 0 0 0 0 0 0 0...”
  • “...EF1347 EF1348 EF1349 EF1526 EF1612 EF1613 EF1826 EF2589 EF2646 EF2863 EF2961 EF3157 EF0169 EF0514 EF0913 EF0302 EF0685 EF0897 EF1111 EF1817 EF3027 EF3178 EF0045...”

LF82_729 glycerate kinase from Escherichia coli LF82
48% identity, 98% coverage

• Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis
  Zhang, PloS one 2015
  • “...4 LF82_727 dihydrolipoamide dehydrogenase CdlD 3.5 5.4 4 LF82_728 carnitine transporter CniT 3.0 7.9 4 LF82_729 glycerate kinase GclK 2.4 6.6 4 LF82_730 3hydroxyisobutyrate dehydrogenase GhbD(EC 11131) 1.9 2.9 4 LF82_731 regulatory protein GclR 1.8 3.1 4 LF82_732 glycoxylate carboligase GclA 0.6 1.7 4 LF82_733 regulatory...”

MSMEG_2528 glycerate kinase from Mycobacterium smegmatis str. MC2 155
54% identity, 93% coverage

• Domains within RbpA Serve Specific Functional Roles That Regulate the Expression of Distinct Mycobacterial Gene Subsets
  Prusa, Journal of bacteriology 2018
  • “...MSMEG_3855, MSMEG_1680, MSMEG_2259, MSMEG_4222, MSMEG_2758, MSMEG_2528, MSMEG_4497, MSMEG_6466, MSMEG_6947, and MSMEG_2387 transcript levels were measured and...”
• Quantitative mass spectrometry reveals plasticity of metabolic networks in Mycobacterium smegmatis
  Chopra, Molecular & cellular proteomics : MCP 2014
  • “...These proteins, together with glycerate kinase (MSMEG_2528), could potentially convert glyoxylate to 3-phosphoglycerate (green highlighting in Fig. 4...”

PG1859 glycerate kinase family protein from Porphyromonas gingivalis W83
48% identity, 97% coverage

• Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
  Moon, BMC microbiology 2014
  • “...malic enzyme 1.82 PG1017 Pyruvate phosphate dikinase 1.75 PG1513 Phosphoribosyltransferase, putative/phosphoglycerate mutase family protein 3.05 PG1859 Glycerate kinase family protein 1.76 Biosynthesis of pyridine nucleotides PG0058 Nicotinic acid mononucleotide adenyltransferase 1.93 PG1578 Quinolinate synthetase 1.62 PG0057 Nicotinate phosphoribosyltransferase 1.61 PG0678 Pyrazinamidase/nicotinamidase, putative 2.00 Biosynthesis of menaquinone...”
• VimA-dependent modulation of acetyl coenzyme A levels and lipid A biosynthesis can alter virulence in Porphyromonas gingivalis
  Aruni, Infection and immunity 2012
  • “...regulator, PG1237 Glycerate kinase family protein, PG1859 Iron compound ABC transporter, permease protein, PG0671 Short-chain dehydrogenase/ reductase family...”

gbs0813 Unknown from Streptococcus agalactiae NEM316
41% identity, 98% coverage

• Analysis of growth-phase regulated genes in Streptococcus agalactiae by global transcript profiling
  Sitkiewicz, BMC microbiology 2009
  • “...gbs0669 SUGAR SODIUM SYMPORTER AGATAACGGTTACA 690270 690283 92 gbs0673 4-Hydroxy-2-oxoglutarate aldolase TAAAAACGCTAACA 837159 837172 92 gbs0813 Glycerate kinase TTAGAGCGTTTTCA 870536 870549 92 gbs0844 udk Uridine kinase TGTAAGCCTTGTCA 879217 879230 92 gbs0852 Hypothetical protein TGTAAACCATCTCA 903332 903345 92 gbs0875 atpE ATP synthase C chain TGAAAACGTAATCA 903356 903369...”

CIMG_00534 glycerate kinase from Coccidioides immitis RS
45% identity, 85% coverage

• Transcriptional Analysis of Coccidioides immitis Mycelia and Spherules by RNA Sequencing
  Carlin, Journal of fungi (Basel, Switzerland) 2021
  • “...458 279 7 N 5.752 N CIMG_11264 Hypothetical protein 59 76 1 Y 5.693 N CIMG_00534 Glycerate kinase 37 437 1 N 5.635 N CIMG_10013 Hypothetical proteingenus-specific 0 114 0 N 5.586 Y CIMG_01211 Putative major facilitator superfamily (MFS) transporter 11 553 13 N 5.294 N...”

lmo2832 similar to unknown proteins from Listeria monocytogenes EGD-e
41% identity, 98% coverage

• Exploring Listeria monocytogenes Transcriptomes in Correlation with Divergence of Lineages and Virulence as Measured in Galleria mellonella
  Lee, Applied and environmental microbiology 2019 (secret)
• Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
  Oliver, Applied and environmental microbiology 2010
  • “...lmo2638 lmo2670 lmo2695 lmo2696 lmo2720 lmo2739 lmo2741 lmo2742 lmo2832 lmof2365_1394 Fold changec Productb VOL. 76, 2010 B IN L. MONOCYTOGENES STRAINS OF...”
• Phenotypic and transcriptomic analyses demonstrate interactions between the transcriptional regulators CtsR and Sigma B in Listeria monocytogenes
  Hu, Applied and environmental microbiology 2007
  • “...lmo2105 lmo2158 lmo2230 lmo2340 lmo2362 lmo2363 lmo2637 lmo2638 lmo2832 ctsR tRNAArg::pLIV2 ctsR-mcsA vs ctsR L. monocytogenes parent strain vs ctsR 7976 HU ET...”

FTN_0674 glycerate kinase from Francisella tularensis subsp. novicida U112
40% identity, 98% coverage

• Molecular bases of proliferation of Francisella tularensis in arthropod vectors
  Asare, Environmental microbiology 2010
  • “...FTN_0651 cdd cytidine deaminase 2 # tnfn1_pw060328p04q151 FTN_0661 guaB IMP dehydrogenase/GMP reductase 6 # tnfn1_pw060328p06q131 FTN_0674 glxK glycerate kinase 3 tnfn1_pw060420p01q148 FTN_0694 nadB L-aspartate oxidase 4 tnfn1_pw060323p06q103 FTN_0711 predicted metal-dependent hydrolase 2 tnfn1_pw060328p04q116 FTN_0765 choloylglycine hydrolase family protein 2 tnfn1_pw060510p03q119 FTN_0806 glycosyl hydrolase family 3 3...”
  • “...tnfn1_pw060328p02q139 FTN_0621 eno enolase (2-phosphoglycerate dehydratase) tnfn1_pw060510p03q188 FTN_0627 chiA chitinase, glycosyl hydrolase family 18 tnfn1_pw060328p06q131 FTN_0674 glxK glycerate kinase tnfn1_pw060510p03q119 FTN_0806 glycosyl hydrolase family 3 tnfn1_pw060510p02q187 FTN_1018 aldolase/adducin class II family protein tnfn1_pw060328p03q107 FTN_1222 kpsF phosphosugar isomerase tnfn1_pw060328p05q128 FTN_1329 fbaA fructose bisphosphate aldolase Class II tnfn1_pw060510p04q137...”
• Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
  Asare, Environmental microbiology 2010
  • “...FTN_0651 cdd cytidine deaminase 2 # tnfn1_pw060328p04q151 FTN_0661 guaB IMP dehydrogenase/GMP reductase 6 # tnfn1_pw060328p06q131 FTN_0674 glxK glycerate kinase 3 tnfn1_pw060420p01q148 FTN_0694 nadB L-aspartate oxidase 4 tnfn1_pw060323p06q103 FTN_0711 predicted metal-dependent hydrolase 2 tnfn1_pw060328p04q116 FTN_0765 choloylglycine hydrolase family protein 2 tnfn1_pw060510p03q119 FTN_0806 glycosyl hydrolase family 3 3...”

SCO6466 transferase from Streptomyces coelicolor A3(2)
52% identity, 97% coverage

• Expression of genes of the Pho regulon is altered in Streptomyces coelicolor
  Millan-Oropeza, Scientific reports 2020
  • “...S4 ) as well as the 3 to 7 fold higher abundance of the 1,4-beta-N-acetylmuramidase (SCO6466) and alpha-mannosidase (SCO0948) involved in cell wall degradation in SC compared to SL at early time points (File S2). The degradation of these cellular constituents and the resulting supply of...”

LMOf2365_2723 glycerate kinase 2 from Listeria monocytogenes str. 4b F2365
41% identity, 97% coverage

• In vivo transcriptional profiling of Listeria monocytogenes and mutagenesis identify new virulence factors involved in infection
  Camejo, PLoS pathogens 2009
  • “...to PTS system, fructose-specific IIABC component LMOf6854_2852 LMOf2365_2720 LMOh7858_2997 2,35 lmo2736 lmo2736 unknown protein LMOf6854_2855 LMOf2365_2723 LMOh7858_3000 2,48 lmo1081 lmo1081 similar to glucose-1-phosphate thymidyl transferase LMOf6854_1134 8,25 5,99 5,17 lmo1082 lmo1082 similar to dTDP-sugar epimerase LMOf6854_1135 47,21 24,06 21,01 lmo1083 lmo1083 similar to dTDP-D-glucose 4,6-dehydratase LMOf6854_1136...”

LMOh7858_3000 glycerate kinase 2 from Listeria monocytogenes str. 4b H7858
41% identity, 97% coverage

• In vivo transcriptional profiling of Listeria monocytogenes and mutagenesis identify new virulence factors involved in infection
  Camejo, PLoS pathogens 2009
  • “...PTS system, fructose-specific IIABC component LMOf6854_2852 LMOf2365_2720 LMOh7858_2997 2,35 lmo2736 lmo2736 unknown protein LMOf6854_2855 LMOf2365_2723 LMOh7858_3000 2,48 lmo1081 lmo1081 similar to glucose-1-phosphate thymidyl transferase LMOf6854_1134 8,25 5,99 5,17 lmo1082 lmo1082 similar to dTDP-sugar epimerase LMOf6854_1135 47,21 24,06 21,01 lmo1083 lmo1083 similar to dTDP-D-glucose 4,6-dehydratase LMOf6854_1136 3,49...”

LMOf6854_2855 glycerate kinase 2 from Listeria monocytogenes str. 1/2a F6854
41% identity, 97% coverage

• In vivo transcriptional profiling of Listeria monocytogenes and mutagenesis identify new virulence factors involved in infection
  Camejo, PLoS pathogens 2009
  • “...similar to PTS system, fructose-specific IIABC component LMOf6854_2852 LMOf2365_2720 LMOh7858_2997 2,35 lmo2736 lmo2736 unknown protein LMOf6854_2855 LMOf2365_2723 LMOh7858_3000 2,48 lmo1081 lmo1081 similar to glucose-1-phosphate thymidyl transferase LMOf6854_1134 8,25 5,99 5,17 lmo1082 lmo1082 similar to dTDP-sugar epimerase LMOf6854_1135 47,21 24,06 21,01 lmo1083 lmo1083 similar to dTDP-D-glucose 4,6-dehydratase...”

LMRG_01960 glycerate kinase 2 from Listeria monocytogenes 10403S
41% identity, 97% coverage

• Home Alone: Elimination of All but One Alternative Sigma Factor in Listeria monocytogenes Allows Prediction of New Roles for σ^B
  Liu, Frontiers in microbiology 2017
  • “...LMRG_00596-00599, 00601,00603-00606, 00608-00611 lmo1153-1156,1160-1163, 1165-1168 LMRG_00594-LMRG_00611 Enzymes that degrade carbon compound 1,2-propanediol METABOLISM OF CARBON LMRG_01960 LMRG_01962 lmo2736 lmo2734 LMRG_01960-LMRG_01963 A glycerate kinase and a glycosyl hydrolase TRANSCRIPTIONAL REGULATION LMRG_01913 lmo2784 LMRG_01913 Transcriptional antiterminator of lichenan operon, BglG family LMRG_00050 LMRG_00051 lmo0359 lmo0360 LMRG_00050-LMRG_00051 A fructose-biphosphate...”
  • “...data also newly identified a B -dependent promoter upstream of the three-gene operon LMRG_01960-LMRG_01962 with LMRG_01960 and LMRG_01962 newly identified as B -dependent. We also newly identified a B -dependent promoter upstream of LMRG_01432-LMRG_01431, suggesting direct B regulation of this operon. Figure 2 Pathway of uridine-5-phosphate...”

lmo2736 conserved hypothetical protein from Listeria monocytogenes EGD-e
41% identity, 97% coverage

• Home Alone: Elimination of All but One Alternative Sigma Factor in Listeria monocytogenes Allows Prediction of New Roles for σ^B
  Liu, Frontiers in microbiology 2017
  • “...00608-00611 lmo1153-1156,1160-1163, 1165-1168 LMRG_00594-LMRG_00611 Enzymes that degrade carbon compound 1,2-propanediol METABOLISM OF CARBON LMRG_01960 LMRG_01962 lmo2736 lmo2734 LMRG_01960-LMRG_01963 A glycerate kinase and a glycosyl hydrolase TRANSCRIPTIONAL REGULATION LMRG_01913 lmo2784 LMRG_01913 Transcriptional antiterminator of lichenan operon, BglG family LMRG_00050 LMRG_00051 lmo0359 lmo0360 LMRG_00050-LMRG_00051 A fructose-biphosphate hydrolase and...”
• Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
  Deng, BMC genomics 2010
  • “...Similar to sugar hydrolase IIIA + 494 lmo2735 Similar to Sucrose phosphorylase IIIA + 494 lmo2736 Hypothetical protein IIIA + 494 lmo2771 Similar to beta-glucosidase IIIA + - lmo2772 Similar to PTS system, beta-glucoside-specific enzyme IIABC IIIA + - lmo2847 Similar to rhamnulose-1-phosphate aldolase IIIA +...”
• In vivo transcriptional profiling of Listeria monocytogenes and mutagenesis identify new virulence factors involved in infection
  Camejo, PLoS pathogens 2009
  • “...LMOh7858_2935 2,31 lmo2733 lmo2733 similar to PTS system, fructose-specific IIABC component LMOf6854_2852 LMOf2365_2720 LMOh7858_2997 2,35 lmo2736 lmo2736 unknown protein LMOf6854_2855 LMOf2365_2723 LMOh7858_3000 2,48 lmo1081 lmo1081 similar to glucose-1-phosphate thymidyl transferase LMOf6854_1134 8,25 5,99 5,17 lmo1082 lmo1082 similar to dTDP-sugar epimerase LMOf6854_1135 47,21 24,06 21,01 lmo1083 lmo1083...”
• New aspects regarding evolution and virulence of Listeria monocytogenes revealed by comparative genomics and DNA arrays
  Doumith, Infection and immunity 2004
  • “...3 3 3 3 3 3 3 3 3 3 3 3 3 3 Lmo2734 Lmo2736 Lmo0017 Lmo0094 inlH inlE Lmo0333 Lmo0549 Lmo0832 Lmo0834 Lmo0835 Lmo1441 Lmo1451 Lmo2821 2 2 2 0 2 2 2 2 0 2 0 0 0...”

OA34_11740 glycerate kinase from Sulfurospirillum sp. MES
42% identity, 99% coverage

• Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from the Metagenome of an Electrosynthetic Microbiome
  Ross, PloS one 2016
  • “...to convert glycerate to pyruvate. The pathway includes glycerate kinase ( S . cavolei MES: OA34_11740), which converts D-glycerate into 3-phospho-D-glycerate, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase ( S . cavolei MES: OA34_12420), enolase ( S . cavolei MES: OA34_11835), and pyruvate kinase ( S . cavolei MES: OA34_02705)....”

BPHYT_RS09440 glycerate kinase from Paraburkholderia phytofirmans PsJN
50% identity, 97% coverage

• Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism
  Price, mSystems 2019
  • “...). In particular, deoxyribonate dehydrogenase (BPHYT_RS04775), the -keto acid cleavage enzyme (BPHYT_RS04760), and glycerate kinase (BPHYT_RS09440) are all important during growth on deoxyribonate, although -keto acid cleavage enzyme mutants have a milder phenotype. One unexplained result is that the acetyl-CoA C-acetyltransferase (BPHYT_RS09150) is detrimental to fitness...”

lp_3266 glycerate kinase from Lactobacillus plantarum WCFS1
42% identity, 97% coverage

• Selection and characterization of conditionally active promoters in Lactobacillus plantarum, using alanine racemase as a promoter probe
  Bron, Applied and environmental microbiology 2004
  • “...2 1 2 1 1 1 2 lp_1459 lp_1435 lp_3266 (glyK) ORF162b lp_2509 ORF165b lp_3045 lp_3330 Unknown Integral membrane protein Glycerate kinase Unknown Permease, DMT...”

BWI76_RS23730 glycerate kinase from Klebsiella sp. M5al
44% identity, 95% coverage

• Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism
  Price, mSystems 2019
  • “...CoA-synthetase (BWI76_RS23695), a -hydroxyacyl-CoA dehydrogenase (BWI76_RS23705), a thiolase (BWI76_RS23710), a CoA-transferase (BWI76_23700), and glycerate kinase (BWI76_RS23730). We propose that the CoA-synthetase converts deoxyribonate to deoxyribonyl-CoA, the dehydrogenase oxidizes this to 3-ketodeoxyribonyl-CoA, and the thiolase cleaves this to glyceryl-CoA and acetyl-CoA (see Fig.S1 in the supplemental material)....”

BCAL1181 putative glycerate kinase from Burkholderia cenocepacia J2315
43% identity, 96% coverage

• The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients
  Holden, Journal of bacteriology 2009
  • “...(BCAL1176 to BCAL1178), and glycerate kinase (BCAL1181) Miscellaneous island Prophage, Mu-like Miscellaneous island, contains miscellaneous metabolism including...”

P57099 Glycerate kinase from Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)
40% identity, 99% coverage

• Towards New Drug Targets? Function Prediction of Putative Proteins of Neisseria meningitidis MC58 and Their Virulence Characterization
  Shahbaaz, Omics : a journal of integrative biology 2015
  • “...Q9JXD5 Q9JXR9 Q9JXW5 Q9JYR5 Q7DDH9 Q9K188 Q9K0K2 Q9K0A0 Q9K071 Q9JRZ9 P57099 Q9JY37 40. 41. 42. 43. 44. 45. 46. 47. 48. 49. 50. 51. 52. 53. Q9K1P6 Q9K1A1 Q9K163...”
  • “...toxic substances (Lissina et al., 2013). The HP P57099 was identified as glycerate kinase, which may be involved in the phosphorylation of glycerate,...”

Pcar_1226 glycerate kinase from Pelobacter carbinolicus str. DSM 2380
43% identity, 93% coverage

• The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features
  Aklujkar, BMC genomics 2012
  • “...searched for an alternative pathway to dispose of excess glycine. The discovery of glycerate 3-kinase (Pcar_1226) led to the hypothesis that two glycine molecules are deaminated, fused, and funnelled into glycolysis through glycerate (Figure 11 ). Three uncharacterized thiamin diphosphate-dependent enzymes (Pcar_0189, Pcar_1121 and Pcar_2858) are...”

glyK / P73408 glycerate 2-kinase (EC 2.7.1.165) from Synechocystis sp. (strain PCC 6803 / Kazusa) (see paper)
P73408 glycerate 2-kinase (EC 2.7.1.165) from Synechocystis sp. (see paper)
slr1840 hypothetical protein from Synechocystis sp. PCC 6803
40% identity, 97% coverage

• The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants
  Eisenhut, Proceedings of the National Academy of Sciences of the United States of America 2008
  • “...At3g17240 At4g37930 At1g23310 At1g68010 At4g33010 (At3g16950*) slr1840 sll1981 slr0229 sll1556 sll0891 sll1358 sll1359 alr2873 all3555 alr3358 alr0058 alr4322...”
• Glycerate kinase of the hyperthermophilic archaeon Thermoproteus tenax: new insights into the phylogenetic distribution and physiological role of members of the three different glycerate kinase classes
  Kehrer, BMC genomics 2007
  • “...in cyanobacteria two Synechococcus strains (JA-2-3B'a (ABD02569), JA-3-3Ab (ABC99586)) as well as Synechocystis sp. Pcc6803 (P73408) possess only a class I glycerate kinase homolog. The enzymes of Arabidopsis thaliana ( At1g80380 ) and Saccharomyces cerevisiae (NP_011721) were shown to possess glycerate kinase activity and were characterized...”

SP_1126 hypothetical protein from Streptococcus pneumoniae TIGR4
38% identity, 99% coverage

• Site-specific contributions of glutamine-dependent regulator GlnR and GlnR-regulated genes to virulence of Streptococcus pneumoniae
  Hendriksen, Infection and immunity 2008
  • “...SP_0884 spr0788 SP_0885 SP_0955 SP_1013 SP_1014 SP_1119 SP_1126 spr1179 SP_1306 SP_1356 SP_1357 SP_1358 spr1302 SP_1651 SP_1659 SP_1688 spr1598 SP_1754 spr1620...”

SPD_1011 glycerate kinase from Streptococcus pneumoniae D39
38% identity, 99% coverage

• Deletion of the Zinc Transporter Lipoprotein AdcAII Causes Hyperencapsulation of Streptococcus pneumoniae Associated with Distinct Alleles of the Type I Restriction-Modification System
  Durmort, mBio 2020
  • “...5.95 SPD_0889 phtD Hypothetical protein 1.78 2.50 4.2 SPD_1009 serB Phosphoserine phosphatase 1.51 1.24 1.60 SPD_1011 glxK Glycerate kinase 1.63 1.26 1.58 SPD_1035 PTS system, IIA component 4.70 4.83 1.91 SPD_1036 PTS system, IIA component 7.26 5.84 2.93 SPD_1050 lacD Tagatose 1,6-diphosphate aldolase 1.61 1.60 1.44...”
• Site-specific contributions of glutamine-dependent regulator GlnR and GlnR-regulated genes to virulence of Streptococcus pneumoniae
  Hendriksen, Infection and immunity 2008
  • “...SPD_0780 SPD_0781 SPD_0844 SPD_0900 SPD_0901 SPD_1004 SPD_1011 SPD_1156 SPD_1158 SPD_1190 SPD_1191 SPD_1192 SPD_1276 SPD_1464 SPD_1472 SPD_1500 SPD_1563...”

Rv2205c hypothetical protein from Mycobacterium tuberculosis H37Rv
41% identity, 97% coverage

• Understanding the Genetic Diversity of Mycobacterium africanum Using Phylogenetics and Population Genomics Approaches
  Balamurugan, Frontiers in genetics 2022
  • “...Additional six SNPs, identified in the current study, viz., Ala126Ala (Rv1558), Trp687* (Rv 2082), Ala120Val (Rv2205c), upstream SNP 4,469 (Rv3424c), Gly236Asp (Rv3710), and Gly81Gly (Rv3792) are also found to be present across all L5.2 samples (as per nomenclature given by Coscolla et al. (2021 ) and...”
• Draft Genome Sequences of Two Pyrazinamide-Resistant Clinical Isolates, Mycobacterium tuberculosis 13-4152 and 13-2459
  Maslov, Genome announcements 2015
  • “...), rv1032c ( trcS ), rv1349 ( irtB ), rv1775 , rv2006 ( otsB ), rv2205c , rv2215 ( dlaT ), rv2241 ( aceE ), rv2752c , rv3383c ( idsB ), rv3384c ( vapC46 ), and rv3634c ( galE1 ). Further functional analysis of these mutations...”
• Mycobacterium tuberculosis H37Rv: In Silico Drug Targets Identification by Metabolic Pathways Analysis
  Amir, International journal of evolutionary biology 2014
  • “...24. Rv1240 Malate dehydrogenase (EC: 1.1.1.37) Yes 25. Rv0070c Serine hydroxymethyltransferase (EC: 2.1.2.1) Yes 26. Rv2205c Hypothetical protein Yes 27. Rv0761c Zinc-containing alcohol dehydrogenase NAD dependent AdhB (EC: 1.1.1.1) Yes 28. Rv0489 Phosphoglyceromutase (EC: 5.4.2.1) Yes 29. Rv0363c Fructose-bisphosphate aldolase (EC: 4.1.2.13) Yes 30. Rv2029c Phosphofructokinase...”
  • “...acid cycle L-malate dehydrogenase activity, binding 23. Rv0070c Not known Not known Not known 24. Rv2205c Not known Organic acid phosphorylation Glycerate kinase activity 25. Rv0761c Oxidation-reduction process Cytoplasm, plasma membrane alcohol dehydrogenase (NAD) activity, zinc ion binding 26. Rv0489 Plasma membrane Glycolysis Phosphoglycerate mutase activity...”
• Potassium availability triggers Mycobacterium tuberculosis transition to, and resuscitation from, non-culturable (dormant) states
  Salina, Open biology 2014
  • “...2.68 10 10 ), II.A synthesis and modification of macromolecules (hp 8.63 10 5 ). Rv2205c was induced in the NC state (although it did not pass the statistical testing threshold) and was also repressed on resuscitation from the NC state. Rv2205 has been recently annotated...”
  • “...of NC bacteria compared to log-phase bacilli. For log cells, enzymatic activity of glycerate kinase (Rv2205c) was 1.67(0.06) 10 20 mol ATP cell 1 min 1 , whereas for NC cells activity was 1.15(0.01) 10 19 mol ATP cell 1 min 1 . The conversion of...”
• Proteomic definition of the cell wall of Mycobacterium tuberculosis
  Wolfe, Journal of proteome research 2010
  • “...LIPOPROTEIN LPPM 3 II.C.1 D Rv2198c mmpS3 PROBABLE CONSERVED MEMBRANE PROTEIN MMPS3 3 II.C.4 D Rv2205c Rv2205c CONSERVED HYPOTHETICAL PROTEIN 10 V B Rv2211c gcvT PROBABLE AMINOMETHYLTRANSFERASE GCVT (GLYCINE CLEAVAGE SYSTEM T PROTEIN) 7 I.C.1 D Rv2223c Rv2223c PROBABLE EXPORTED PROTEASE 3 II.C.2 B Rv2247 accD6...”
• Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories
  Ioerger, Journal of bacteriology 2010
  • “...Rv1815 NC Rv1925 NC Rv1979c NC Rv2037c Rv2048c Rv2101 Rv2205c NC NC Rv2251 NC Rv2450c Rv2495c Rv2614A Rv2627c Rv2680 Rv2695 Rv2896c Rv2932 Rv3011c Rv3144c NC NC...”
• The gene expression data of Mycobacterium tuberculosis based on Affymetrix gene chips provide insight into regulatory and hypothetical genes
  Fu, BMC microbiology 2007
  • “...Rv2024C FADE26 SCOA Rv0657C AMT Rv2348C Rv3750C Rv3491 Rv0137C Rv3887C Rv1037C Rv3874 Rv2137C LLDD2 Rv2311 Rv2205C NARJ NARH Rv2369C Rv0621 Rv1398C FURA Rv1154C Rv2472 Rv3449 FADD16 LPQO Rv0168 Rv0767C Rv0736 INFC FRDB Rv0245 NARI Rv0167 RIBC Rv0258C Rv2765 Rv1425 Rv1968) (PDHA Rv3802C LPPD GUAB1 Rv1783 Rv1782...”
  • “...Rv3616c Rv3399 Rv2638 Rv3615c Rv3614c Rv3733c Rv2632c Rv1868 Rv2598 Rv1871c Rv0387c Rv2024c Rv0657c Rv2137c Rv2311 Rv2205c Rv1398c Rv2472 Rv0767c Rv0258c Rv1425 Rv1978 Rv1885c Rv0760c PRA Rv0192) (Rv2628 Rv2517c Rv2662 Rv1772 Rv2016 Rv0572c Rv2630 Rv1179c Rv0108c Rv3123 Rv2297 Rv2255c Rv1535 Rv2288 Rv3288c Rv2633c Rv2557 Rv2558 Rv2336 Rv3491...”

SERP0409 glycerate kinase family protein from Staphylococcus epidermidis RP62A
24% identity, 90% coverage

• Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis
  Gonçalves, Frontiers in microbiology 2022
  • “...N55 and N77 conditions. Increased at pH 5.5 Protein ID Gene Glycerolipids pathway Glycerate kinase SERP0409 garK Aldehyde dehydrogenase SERP1729/2084 aldA Glycerol dehydrogenase SERP2346 gldA Dihydroxyacetone kinase SERP2344/5 Triacylglycerol lipase SERP2388 geh-1 Processive diacylglycerol beta-glucosyltransferase SERP0606 ypfP Oxidative phosphorylation/Oxidative stress Lactaldehyde dehydrogenase SERP2080 Alcohol dehydrogenase, zinc-containing...”
• Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach
  Sivaranjani, Frontiers in microbiology 2019
  • “...Cell division protein FtsQ, putative INF 0.003 SERP2293 icaA Intercellular adhesion protein A INF 0.003 SERP0409 Glycerate kinase family protein INF 0 . 003 INF 0 . 003 SERP1872 ureE Urease accessory protein UreE INF 0.003 SERP1900 PTS system, IIBC components INF 0.003 SERP1407 Conserved hypothetical...”

SAOUHSC_00756 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
24% identity, 90% coverage

• Phenotypic Plasticity of Staphylococcus aureus in Liquid Medium Containing Vancomycin
  Rong, Frontiers in microbiology 2019
  • “...antiporter subunit A 738836 non-coding region T/C / 39.02% Non-coding region between SAOUHSC_00755 and glxK (SAOUHSC_00756) 906471 SAOUHSC_00933 trpS G/A L < - > L 58.54% Tryptophanyl-tRNA synthetase 965494 SAOUHSC_00994 atl C/T K < - > K 43.90% Bifunctional autolysin 1307807 SAOUHSC_01364 tyrA G/T L <...”
  • “...-value (33.60515) at 4 h, is located in a non-coding region between SAOUHSC_00755 and glxK (SAOUHSC_00756). Based on the comparison of the two genotypes, the growth plasticity was significantly different between genotypes T and C ( Figure 5 ). Position 1394043 was the most significant locus...”
• Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells
  Tsuchiya, The Biochemical journal 2018
  • “...135.02 SAKOR_02109 Uncharacterized protein 12.497 TAETNYFWLNC*GYNR 141.34 HMPREF0776_2410 ABC transporter, ATP-binding protein 13.659 FTEGNC*YGLIGANGAGK 128.85 SAOUHSC_00756 Uncharacterized protein 41.797 IAELC*HK 96.034 yloU General stress protein, Gls24 family 13.345 AVEC*YGIVGMASR 161.48 rap 50S ribosomal protein L2 30.026 MILSTC*R 128.6 cmk Cytidylate kinase 24.595 GQC*VILDNEDVTDFLR 91.622 sarS HTH-type...”

SA0697 hypothetical protein from Staphylococcus aureus subsp. aureus N315
24% identity, 90% coverage

• Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells
  Scherr, Infection and immunity 2013
  • “...SA1141 SA1994 SA1138 SA1779 SA0969 SA1142 SA1932 SA0486 SA0697 SA0700 SA1169 SA2539 SA0783 SA2660 SA0203 SA0611 SA0242 SA0935 SA1806 SA1043 SA1951 SA2431 SA2685...”

dhpB / D7PC14 1,2-dihydroxyethylphosphonate kinase from Streptomyces luridus (see paper)
39% identity, 83% coverage

New Search

Statistics

How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.