PaperBLAST

PaperBLAST Hits for SwissProt::O05256 Na(+)-malate symporter; Sodium-dependent malate transporter (Bacillus subtilis (strain 168)) (448 a.a., MGAIPKTGTI...)

Show query sequence

>SwissProt::O05256 Na(+)-malate symporter; Sodium-dependent malate transporter (Bacillus subtilis (strain 168))
MGAIPKTGTISPEQKDSQEKNLFQKIWSWEIGVIPLPLYTVLAVIIILAAYYNELPANML
GGFAIIMILGVFLGDIGQRIPILKDIGGPAILSLFVPSFLVFYNVLNSTSLDAVTNLMKT
SNFLYFYIACLVVGSILGMNRIVLIQGFIRMFVPLVAGTIAAVAAGILVGFIFGYSAYDS
FFFVVVPIIAGGIGEGILPLSIAYSQILGSSADVFVSQLVPAAIIGNVFAIICAALMKKL
GDKRPDLNGNGRLVKSKKANEIFNQKEAEAKIDFKLMGAGVLLACTFFIFGGLLEKFIFI
PGAILMIISAAAVKYANILPKKMEEGAYQLYKFISSSFTWPLMVGLGILFIPLDDVASVI
SIPFVIICISVVIAMIGSGYFVGKLMNMYPVESAIVTCCHSGLGGTGDVAILSASGRMGL
MPFAQISTRLGGAGTVICATVLLRFFTS

Running BLASTp...

Found 37 similar proteins in the literature:

MAEN_BACSU / O05256 Na(+)-malate symporter; Sodium-dependent malate transporter from Bacillus subtilis (strain 168) (see 2 papers)
TC 2.A.24.2.3 / O05256 Malate:Na+ symporter from Bacillus subtilis (see 4 papers)
100% identity, 100% coverage

• function: Acts as a Na(+)-malate symporter, as it catalyzes malate- dependent uptake of Na(+) and Na(+)-dependent uptake of malate.
• substrates: Na+, malate

BC0579 Malate-sodium symport from Bacillus cereus ATCC 14579
BAS0547 citrate cation symporter family from Bacillus anthracis str. Sterne
66% identity, 97% coverage

• BC4707 is a major facilitator superfamily multidrug resistance transport protein from Bacillus cereus implicated in fluoroquinolone tolerance
  Simm, PloS one 2012
  • “...growth (OD 600 0.5) in rich medium. Gene Predicted protein function bc4707 /WT (fold change) bc0579 malate sodium symporter 2.06 bc0580 malate dehydrogenase 1.61 bc0659 ribose operon repressor 1.54 bc0660 ribokinase 1.52 bc0662 ribose ABC transporter, ATP-binding protein 1.52 bc0872 cystine-binding protein 0.41 bc0873 cystine permease...”
• A genetic approach for the identification of exosporium assembly determinants of Bacillus anthracis
  Spreng, Journal of microbiological methods 2013
  • “...Insertion Sterne gene number Gene annotation BAS0047 SpoVG BAS0389 Conserved hypothetical protein BAS0483 Hypothetical protein BAS0547 Citrate cation symporter family protein BAS0605 Sodium/alanine symporter family protein BAS1291 Hypothetical protein BAS1726 Acetyl CoA hydrolase/transferase family protein BAS1747 Hypothetical protein BAS1820 Aminoglycoside 6-adenylytransferase, putative BAS3594 Sensory box/GGDEF family...”

Bcer98_0498 Citrate carrier protein from Bacillus cereus subsp. cytotoxis NVH 391-98
67% identity, 97% coverage

• Divergence of the SigB regulon and pathogenesis of the Bacillus cereus sensu lato group
  Scott, BMC genomics 2012
  • “...bID_Cluster_10550 7 Bcer98_0367 methyl-accepting chemotaxis sensory transducer bID_Cluster_4143 7 Bcer98_0430 NAD-dependent epimerase/ dehydratase bID_Cluster_1966 8 Bcer98_0498 citrate carrier protein bID_Cluster_2625 8 Bcer98_0499 malate dehydrogenase, putative bID_Cluster_3344 9 Bcer98_0651 hypothetical protein bID_Cluster_2017 10 Bcer98_1017 hypothetical protein bID_Cluster_6230 11 Bcer98_1200 two component transcriptional regulator, ResD bID_Cluster_857 11 Bcer98_1201...”

KPK_1918 sodium:citrate symporter family protein from Klebsiella pneumoniae 342
58% identity, 97% coverage

• Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice
  Fouts, PLoS genetics 2008
  • “...anoxic conditions where acetate is the main end-product of citrate fermentation [41] . CitS and KPK_1918 are sodium ion-dependent citrate permeases [42] . CitX facilitates transfer of the prosthetic group (2-(5-triphosphoribosyl)-3-dephospho-CoA) to the citrate lyase gamma chain. In contrast, E. coli K12 encodes a single protein,...”

DDA3937_RS00455 2-hydroxycarboxylate transporter family protein from Dickeya dadantii 3937
59% identity, 95% coverage

• Cell-length heterogeneity: a population-level solution to growth/virulence trade-offs in the plant pathogen Dickeya dadantii
  Cui, PLoS pathogens 2019
  • “...4.93 1E-03 Regulation rseA (anti-sigma factor) DDA3937_RS18965 5.06 5E-04 Respiration Fumarate reductase (quinol) flavoprotein subunit DDA3937_RS00455 5.07 5E-04 Transportation Malate permease To determine if the higher rate of metabolism in filamentous cells would result in faster growth on potato tuber, we compared the number of progenies...”

YE2507 putative citrate/sodium-family symporter from Yersinia enterocolitica subsp. enterocolitica 8081
57% identity, 94% coverage

• Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity
  Heermann, BMC genomics 2008
  • “...Na + dependent citrate symporter CitS of S. enterica , which the Y. enterocolitica protein YE2507 is homologous to, is induced by the CitA/CitB system for fermentation of citrate under anoxic conditions [ 110 ], indicating a general difference of citrate utilization in P. luminescens and...”

gbs1907 Unknown from Streptococcus agalactiae NEM316
53% identity, 97% coverage

• Analysis of growth-phase regulated genes in Streptococcus agalactiae by global transcript profiling
  Sitkiewicz, BMC microbiology 2009
  • “...Organization of this chromosomal region in GBS is very similar to GAS, and gbs1906 and gbs1907 encode putative homologues to the GAS NAD-dependent malic enzyme and malate-sodium symport proteins, respectively. Genes gbs1906/7 are 63/81 times up-regulated in S phase; therefore this operon appears to be regulated...”

EF1207 citrate carrier protein, CCS family from Enterococcus faecalis V583
55% identity, 96% coverage

• Influence of the Alternative Sigma Factor RpoN on Global Gene Expression and Carbon Catabolism in Enterococcus faecalis V583
  Keffeler, mBio 2021
  • “...system, IIB component 4.49 173 158 TT G GAAA CG CACA C AA NA 8 EF1207 Citrate carrier protein, CCS family 8.54 53 39 AT G TAAA CG TTTTCT NA 12 EF1232-34 EF1232 ABC transporter, permease protein 8.63 81 67 AT G TAAGG G TTTACA NA...”
• Genomewide Profiling of the Enterococcus faecalis Transcriptional Response to Teixobactin Reveals CroRS as an Essential Regulator of Antimicrobial Tolerance
  Darnell, mSphere 2019
  • “...8.6 PTS mannose/fructose/sorbose/ N -acetylglucosamine subunit IIA EF1031 742 8.4 PTS sugar transporter subunit IIC EF1207 991 maeP 8.4 l -Malate permease a F/C, log 2 fold change. Cell wall precursors as a target of teixobactin. Lipid II and lipid III are precursors of peptidoglycan and...”
• Fine-tuned transcriptional regulation of malate operons in Enterococcus faecalis
  Mortera, Applied and environmental microbiology 2012
  • “...divergent operons, maePE and maeKR (Fig. 1A). The maeP (EF1207) (35) gene encodes a putative H/malate symporter, and the maeE (EF1206) (35) gene encodes a malic...”
• Transcriptional responses of Enterococcus faecalis V583 to bovine bile and sodium dodecyl sulfate
  Solheim, Applied and environmental microbiology 2007
  • “...(EF1027, which codes for a putative membrane protein; EF1207, which codes for a citrate carrier protein; and EF2983, which codes for a putative glutamyl-tRNA...”

OG1RF_10979 2-hydroxycarboxylate transporter family protein from Enterococcus faecalis OG1RF
55% identity, 96% coverage

• (p)ppGpp and CodY Promote Enterococcus faecalis Virulence in a Murine Model of Catheter-Associated Urinary Tract Infection
  Colomer-Winter, mSphere 2019
  • “...Locus or gene name Function Fold change a (p)ppGpp 0 (p)ppGpp 0 codY Citrate metabolism OG1RF_10979 Citrate carrier +31.2 citC Citrate metabolism +17.0 5.0 citD Citrate metabolism +18.7 3.3 citE Citrate metabolism +15.6 5.0 citF Citrate metabolism +15.0 5.0 citX Citrate metabolism +13.4 5.0 citXG Citrate...”

TC 2.A.24.2.1 / Q53787 L-Malate permease from Streptococcus bovis (see paper)
55% identity, 96% coverage

• substrates: L-malate

SPy1109 putative L-malate permease from Streptococcus pyogenes M1 GAS
M5005_Spy_0832 malate-sodium symport from Streptococcus pyogenes MGAS5005
55% identity, 97% coverage

• The <i>Streptococcus pyogenes</i> stand-alone regulator RofA exhibits characteristics of a PRD-containing virulence regulator
  Hart, Infection and immunity 2024 (secret)
• New Pathogenesis Mechanisms and Translational Leads Identified by Multidimensional Analysis of Necrotizing Myositis in Primates
  Kachroo, mBio 2020
  • “...Putative extracellular matrix binding protein Spy0597 2.4 2.6 Spy0740 fbp Fibronectin-binding protein Spy0771 NS 2.1 Spy1109 slr Internalin protein Spy1122 54.1 48.6 Spy1719 emm1 M protein Spy1700 NS 2.1 Transcriptional regulators Spy0947 ciaH TCS g histidine kinase Spy0962 10.2 8.4 Spy0948 ciaR TCS response regulator Spy0963...”
  • “...We studied a third gene in the context of experimental NHP necrotizing myositis. slr ( Spy1109 ) encodes an extracellular protein with leucine-rich repeats that is homologous to InlA in the Listeria monocytogenes internalin family of proteins ( 76 ). L. monocytogenes InlA anchors the pathogen...”
• Regulation of SpeB in Streptococcus pyogenes by pH and NaCl: a model for in vivo gene expression
  Loughman, Journal of bacteriology 2006
  • “...SPy2039 SPy1915 SPy0739 SPy1065 SPy1738 SPy1378 Spy1228 SPy1109 SPy1815 SPy0149 Gene (putative function) VOL. 188, 2006 MODELING IN VIVO STREPTOCOCCAL GENE...”
• Expression microarray and mouse virulence analysis of four conserved two-component gene regulatory systems in group a streptococcus
  Sitkiewicz, Infection and immunity 2006
  • “...genes encode homologs of a malate-sodium symporter (M5005_Spy_0832) and an NAD-dependent malic enzyme (M5005_Spy_0833). Second, consistent with these findings,...”

Spy49_0863 Putative L-malate permease from Streptococcus pyogenes NZ131
54% identity, 97% coverage

• Effects of the ERES pathogenicity region regulator Ralp3 on Streptococcus pyogenes serotype M49 virulence factor expression
  Siemens, Journal of bacteriology 2012
  • “...sclA Upregulated genes spy49_0564c spy49_0565c spy49_0863 spy49_0864 spy49_1114c spy49_1115c spy49_1239 spy49_1332c spy49_1334c spy49_1374c spy49_1375c...”

CV2167 Na+/malate symporter from Chromobacterium violaceum ATCC 12472
53% identity, 88% coverage

• Cloning and sequencing of a genomic island found in the Brazilian purpuric fever clone of Haemophilus influenzae biogroup aegyptius
  McGillivary, Infection and immunity 2005
  • “...island sequences (Fig. 3), is next to an ORF (CV2167) with an encoded product similar to a sodium/malate symporter (4). The production of a bacteriocin in...”

GYA98_RS17095 2-hydroxycarboxylate transporter family protein from Bacillus velezensis
39% identity, 99% coverage

• Comparative transcriptome analysis reveals the biocontrol mechanism of Bacillus velezensis E68 against Fusarium graminearum DAOMC 180378, the causal agent of Fusarium head blight
  Liang, PloS one 2023
  • “...11905), succinyl-CoA ligase (GYA98_RS07090, 07095) and fumarate dehydrogenase (GYA98_RS14210), as well as a citrate/malate transporter (GYA98_RS17095) ( S2 Table ). Malate dehydrogenase (GYA98_RS12230), which was not annotated with the TCA cycle GO terms, was also significantly down-regulated. The GO term for polysaccharide biosynthetic process was also...”

CIMH_BACSU / P94363 Citrate/malate-proton symporter; CimHbs; Citrate/malate transporter from Bacillus subtilis (strain 168) (see 2 papers)
TC 2.A.24.2.4 / P94363 L-malate/citrate:H+ symporter (electroneutral) from Bacillus subtilis (see 3 papers)
38% identity, 98% coverage

• function: Proton motive force-driven secondary transporter that catalyzes the uptake of both citrate and malate (PubMed:11566984). Is an electroneutral proton-solute symporter: the number of protons transported is equal to the valence of the transported anions (PubMed:11566984). Translocates the free citrate and malate anions (PubMed:11566984). Citramalate binds to the transporter, but it is not translocated (PubMed:11566984). Is strictly stereoselective, recognizing only the (S)-enantiomers of malate and citramalate (PubMed:11566984).
  catalytic activity: citrate(in) + 3 H(+)(in) = citrate(out) + 3 H(+)(out) (RHEA:79307)
  catalytic activity: (S)-malate(in) + 2 H(+)(in) = (S)-malate(out) + 2 H(+)(out) (RHEA:29339)
• substrates: Citrate, H+, L-malate

BCAM2532 putative citrate/malate transporter (citrate/malate-proton symporter) from Burkholderia cenocepacia J2315
38% identity, 93% coverage

• σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111
  Lardi, Applied and environmental microbiology 2015
  • “...BCAM1683 BCAM1685 BCAM1833 BCAM2132 BCAM2323 BCAM2532 Putative dihydrolipoamide dehydrogenase Pyruvate dehydrogenase E1 component Assimilatory nitrate reductase...”

KPK_4687 citrate:acetate antiporter from Klebsiella pneumoniae 342
37% identity, 93% coverage

• Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice
  Fouts, PLoS genetics 2008
  • “...of transporters present in K. pneumoniae but absent in E. coli , including the citW (KPK_4687), citS (KPK_4716) and citX (KPK_4686) homologs of the 2-hydroxycarboxylate transporter (2-HCT) family. Many species of enterobacteria, including K. pneumoniae and E. coli can grow with citrate as the sole carbon...”

TC 2.A.24.2.5 / Q8VS41 Citrate:acetate antiporter, CitW from Klebsiella pneumoniae (see paper)
T643_RS19470 2-hydroxycarboxylate transporter family protein from Klebsiella pneumoniae MRSN 1319
36% identity, 93% coverage

• substrates: Acetate, Citrate
• Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells
  Chan, Scientific reports 2018
  • “...downregulated ( acnB , T643_RS19850; gabT _2, T643_RS11485) and 3 upregulated (aminotransferase, T643_RS18930; cimH , T643_RS19470; PTS system fructose IIA component, T643_RS18905) genes were tested. For A . baumannii , 3 downregulated ( papD , T634_RS02055; mmsA _1, T634_RS14320; EamA-like transporter, T634_RS10710) and 4 upregulated (...”

Rmet_4998 2-hydroxycarboxylate transporter family protein from Cupriavidus metallidurans CH34
Rmet_4998 citrate symporter citrate carrier protein from Ralstonia metallidurans CH34
39% identity, 95% coverage

• The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments
  Janssen, PloS one 2010
  • “...the Iron/Lead Transporter (ILT) Family (TC9.A.10). The former is represented in C. metallidurans by gene Rmet_4998 (situated on CHR2 and listed in MaGe as encoding a citrate carrier) while the latter is represented by two members Rmet_5945 and Rmet_6106 (both located on plasmid pMOL30 as part...”

OA04_25230 2-hydroxycarboxylate transporter family protein from Pectobacterium versatile
37% identity, 95% coverage

• The PhoPQ Two-Component System Is the Major Regulator of Cell Surface Properties, Stress Responses and Plant-Derived Substrate Utilisation During Development of Pectobacterium versatile-Host Plant Pathosystems
  Kravchenko, Frontiers in microbiology 2020
  • “...10.7 OA04_13340 2.55 FecI-like RNA polymerase sigma factor Di- and tricarboxylate sensing and import citW OA04_25230 3.79 Citrate/acetate antiporter GAGTTTTAAAGGCGTTTAT 8.1 citM_OA04_29000 OA04_28990-OA04_29000 0.07 CitMHS family citrate/H + symporter and transcriptional regulator TGGTTTAGACACCGTTTAA 10.2 OA04_29010 0.48 Sodium:dicarboxylate symporter TAATTTTTTAATTATTTAA 10.6 tcp OA04_13410 0.39 Methyl-accepting chemotaxis protein...”

BH0400 sodium-dependent citrate transporter (symport system) from Bacillus halodurans C-125
41% identity, 89% coverage

• Phenotypic and genotypic characterization of some lactic Acid bacteria isolated from bee pollen: a preliminary study
  Belhadj, Bioscience of microbiota, food and health 2014
  • “...carbohydrate fermentation Cluster A 18 isolates Cluster B (BH1511) Cluster C 6 isolates Cluster D (BH0400 BH0500) Cluster E 12 isolates Cluster F 4 isolates Cluster G (BH0600) Cluster H (BH2722 BH2422) Cluster I 8 isolates D-Arabinose 5.5 0 0 0 0 0 0 50 100...”
  • “...cluster I) fermented cellobiose but not maltose. Also, cellobiose was not fermented by Lactobacillus fermentum BH0400, Lactobacillus sp. BH0500 (cluster D), members of cluster H ( Lactobacillus fermentum BH2722, and BH2422) and members of clusters B and G. Arabinose, glucose, fructose, mannose, mannitol, B-gentiobiose, melezitose, melibiose,...”
• The 2-hydroxycarboxylate transporter family: physiology, structure, and mechanism
  Sobczak, Microbiology and molecular biology reviews : MMBR 2005
  • “...A 2HCT member which is a close relative of BH0400 of B. halodurans (Fig. 1, cluster II) is distantly located. Finally, the fusobacterium Fusobacterium nucleatum...”
  • “...78 positions between the N- and C-terminal halves of BH0400 of B. halodurans. All local alignments involved more or less corresponding parts of both halves. A...”

KPK_4716 citrate:sodium symporter from Klebsiella pneumoniae 342
33% identity, 96% coverage

• Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice
  Fouts, PLoS genetics 2008
  • “...present in K. pneumoniae but absent in E. coli , including the citW (KPK_4687), citS (KPK_4716) and citX (KPK_4686) homologs of the 2-hydroxycarboxylate transporter (2-HCT) family. Many species of enterobacteria, including K. pneumoniae and E. coli can grow with citrate as the sole carbon and energy...”

YP_005225043 putative citrate-sodium symport from Klebsiella pneumoniae subsp. pneumoniae HS11286
33% identity, 96% coverage

• Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS.
  Kim, Scientific reports 2017
  • GeneRIF: Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS have been presented.

CITN_KLEPN / P31602 Citrate/sodium symporter; Citrate transporter CitS; Na(+)-dependent citrate carrier; Sodium-dependent citrate transport system from Klebsiella pneumoniae (see 15 papers)
TC 2.A.24.1.1 / P31602 Citrate:Na+ symporter, CitS from Klebsiella pneumoniae (see 2 papers)
citS / AAA25060.1 citrate carrier protein from Klebsiella pneumoniae (see paper)
33% identity, 96% coverage

• function: Secondary active transporter that catalyzes the uptake of citrate across the membrane with the concomitant uptake of sodium (PubMed:10985744, PubMed:12911322, PubMed:1577734, PubMed:1629151, PubMed:8125105, PubMed:8547237). There are conflicting data regarding exact substrate stoichiometry: the sodium/citrate stoichiometry was predicted to be 1, but the latest studies suggest that CitS transports citrate in symport with 2 sodium ions (PubMed:12911322, PubMed:1629151, PubMed:8125105, PubMed:8547237). Transports citrate as a divalent citrate anion, H-citrate(2-) (PubMed:10985744, PubMed:1629151, PubMed:8547237). Shows narrow substrate specificity and is very specific, transporting only citrate and to a low extent citromalate (PubMed:9218448). Symport of Na(+) is absolutely required in the range pH 5-7 because no uptake can be detected in the absence of Na(+) (PubMed:12911322, PubMed:8125105). Lithium can replace Na(+) in the symport reaction but it takes about a 200-fold higher concentration of Li(+) over Na(+) to achieve the same rate of uptake (PubMed:8125105).
  catalytic activity: citrate(out) + 2 Na(+)(out) = citrate(in) + 2 Na(+)(in) (RHEA:79471)
  subunit: Homodimer.
• substrates: Citrate
  tcdb comment: Kebbel et al. 2013 presented the three-dimensional map of dimeric CitS obtained with electron crystallography. Each monomer has 13 alpha-helical transmembrane segments; six are organized in a distal helix cluster and seven in the central dimer interface domain. Based on structural analyses and comparison to VcINDY, a molecular model with assigned helices, a model with internal structural symmetry was proposed. Projections of CitS in several conformational states induced by the presence and absence of sodium and citrate as substrates were also proposed. Citrate binding induces a defined movement of alpha helices within the distal helical cluster. Kebbel et al. 2013 proposed a substrate translocation site and conformational changes that are in agreement with the "alternating access" model. The loop between TMSs VIII and IX folds into an amphipathic surface helix (Sobczak and Lolkema 2005)

CITN_SALPU / P0A2G0 Citrate/sodium symporter; Citrate carrier; Citrate transporter CitS from Salmonella pullorum (see paper)
STM0057 putative citrate-sodium symport from Salmonella typhimurium LT2
32% identity, 96% coverage

• function: Secondary active transporter that catalyzes the uptake of citrate across the membrane with the concomitant uptake of sodium (PubMed:1374406). Is specific for citrate (PubMed:1374406).
  catalytic activity: citrate(out) + 2 Na(+)(out) = citrate(in) + 2 Na(+)(in) (RHEA:79471)
  subunit: Homodimer.
• The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium
  Colgan, PLoS genetics 2016
  • “...< > 0.98 Yes STnc3730 yfcC pta > < > 0.89 - c STnc3090 oadG STM0057 < > < 0.87 - STnc470 (InvS) STM0082 STM0081 > < < 0.85 - STnc3020 prgJ prgH as to prgI 0.84 Yes STnc3180 ybdO dsbG < > < 0.83 -...”
• In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection
  Marchal, Genome biology 2004
  • “...The intergenic sequences of these paralogs showed an overall low degree of conservation (for example, STM0057) with the original intergenic sequence in S. typhimurium (data not shown). In some of the datasets, a local alignment of the respective intergenic regions could be detected, but the putative...”
• Identification and characterization of Helicobacter pylori genes essential for gastric colonization
  Kavermann, The Journal of experimental medicine 2003
  • “...fliI 4 Flagellar export protein ATP synthase STM0244 0685 fliP 2 Flagellar biosynthetic protein <0.0149 STM0057 0753 a fliS >5 Flagellar protein STM0019 0797 a hpaA 2 Flagellar sheath adhesin hpaA STM0327 0232 a 2 Secreted protein involved in flagellar motility STM0357 0392 a cheA 2...”

CITN_SALDU / P31603 Citrate/sodium symporter; Citrate carrier; Citrate transporter CitS from Salmonella dublin (see paper)
32% identity, 96% coverage

• function: Secondary active transporter that catalyzes the uptake of citrate across the membrane with the concomitant uptake of sodium (PubMed:1374406). Is specific for citrate (PubMed:1374406).
  catalytic activity: citrate(out) + 2 Na(+)(out) = citrate(in) + 2 Na(+)(in) (RHEA:79471)
  subunit: Homodimer.

WP_000183608 citrate/sodium symporter CitS from Salmonella enterica subsp. enterica serovar Montevideo
32% identity, 96% coverage

• Mechanism of Na(+)-dependent citrate transport from the structure of an asymmetrical CitS dimer
  Wöhlert, eLife 2015
  • “...Materials and methods Protein expression and purification A gene coding for CitS from Salmonella enterica (WP_000183608) was cloned into a pET21d plasmid harboring an N-terminal His 10 -Tag and a thrombin cleavage site between tag and target protein. The resulting plasmid was used to transform E....”

5a1sD Crystal structure of the sodium-dependent citrate symporter secits form salmonella enterica. (see paper)
33% identity, 91% coverage

• Ligands: sodium ion; citrate anion (5a1sD)

GALLO_2048 Putative malate transporter from Streptococcus gallolyticus UCN34
SGGBAA2069_c20060, SGGB_2031 2-hydroxycarboxylate transporter family protein from Streptococcus gallolyticus subsp. gallolyticus ATCC 43143
34% identity, 94% coverage

• The Road to Infection: Host-Microbe Interactions Defining the Pathogenicity of Streptococcus bovis/Streptococcus equinus Complex Members
  Jans, Frontiers in microbiology 2018
  • “...SGG is the only Streptococcus known so far to use malate via the malolactic enzyme (Gallo_2048) and a malate transporter (Gallo_2049) as well as degrade tannins encoded by tanA , that are otherwise toxic to many bacteria (Rusniok et al., 2010 ; Papadimitriou et al., 2014...”
• Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex
  Papadimitriou, BMC genomics 2014
  • “...GALLO_1578 SGGB_1577 SGGBAA2069_c16060 SGPB_1461 (p) SMA_1582 (p) - SMA_1583 (s) SMA_1584 (s) Malate transporter mleP GALLO_2048 SGGB_2031 SGGBAA2069_c20060 SGPB_1855 SMA_1945 Sinf_1750 Malate dehydrogenase mleS GALLO_2049 SGGB_2032 SGGBAA2069_c20070 SGPB_1856 SMA_1946 Sinf_1751 PTS system, mannitol-specific IIBC component mtlA GALLO_0993 SGGB_0982 SGGBAA2069_c09680 - SMA_0905 (p) - Mannitol operon transcriptional...”
• Genome sequence of Streptococcus gallolyticus: insights into its adaptation to the bovine rumen and its ability to cause endocarditis
  Rusniok, Journal of bacteriology 2010
  • “...UCN34 expresses a malolactic enzyme (encoded by gallo_2048) associated with a malate transporter (encoded by gallo_2049). Taken together, the specific catabolic...”
• Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex
  Papadimitriou, BMC genomics 2014
  • “...SGGBAA2069_c16060 SGPB_1461 (p) SMA_1582 (p) - SMA_1583 (s) SMA_1584 (s) Malate transporter mleP GALLO_2048 SGGB_2031 SGGBAA2069_c20060 SGPB_1855 SMA_1945 Sinf_1750 Malate dehydrogenase mleS GALLO_2049 SGGB_2032 SGGBAA2069_c20070 SGPB_1856 SMA_1946 Sinf_1751 PTS system, mannitol-specific IIBC component mtlA GALLO_0993 SGGB_0982 SGGBAA2069_c09680 - SMA_0905 (p) - Mannitol operon transcriptional antiterminator mtlR...”
  • “...SGGB_1577 SGGBAA2069_c16060 SGPB_1461 (p) SMA_1582 (p) - SMA_1583 (s) SMA_1584 (s) Malate transporter mleP GALLO_2048 SGGB_2031 SGGBAA2069_c20060 SGPB_1855 SMA_1945 Sinf_1750 Malate dehydrogenase mleS GALLO_2049 SGGB_2032 SGGBAA2069_c20070 SGPB_1856 SMA_1946 Sinf_1751 PTS system, mannitol-specific IIBC component mtlA GALLO_0993 SGGB_0982 SGGBAA2069_c09680 - SMA_0905 (p) - Mannitol operon transcriptional antiterminator...”

SGPB_1855 2-hydroxycarboxylate transporter family protein from Streptococcus pasteurianus ATCC 43144
34% identity, 94% coverage

• Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex
  Papadimitriou, BMC genomics 2014
  • “...SGPB_1461 (p) SMA_1582 (p) - SMA_1583 (s) SMA_1584 (s) Malate transporter mleP GALLO_2048 SGGB_2031 SGGBAA2069_c20060 SGPB_1855 SMA_1945 Sinf_1750 Malate dehydrogenase mleS GALLO_2049 SGGB_2032 SGGBAA2069_c20070 SGPB_1856 SMA_1946 Sinf_1751 PTS system, mannitol-specific IIBC component mtlA GALLO_0993 SGGB_0982 SGGBAA2069_c09680 - SMA_0905 (p) - Mannitol operon transcriptional antiterminator mtlR GALLO_0994...”

LLMG_RS08245 2-hydroxycarboxylate transporter family protein from Lactococcus cremoris subsp. cremoris MG1363
llmg_1637 malate transporter from Lactococcus lactis subsp. cremoris MG1363
36% identity, 94% coverage

• Resistance to the Bacteriocin Lcn972 Deciphered by Genome Sequencing
  Escobedo, Microorganisms 2023
  • “...(-60/+63) LLMG_RS08235/LLMG_RS08240 ABC transporter ATP-binding protein/EamA family transporter - * 1,614,130 +T coding (1149/1278 nt) LLMG_RS08245 citrate:sodium symporter * * 1,660,056 (T) 78 intergenic (-14/+100) LLMG_RS08475/LLMG_RS08480 hypothetical protein/DNA repair protein RecN * * 1,826,465 (T) 67 intergenic (-23/+300) LLMG_RS09240/LLMG_RS09245 metal-dependent hydrolase/cold-shock protein * * 1,968,674 GA...”
• Genome sequences of Lactococcus lactis MG1363 (revised) and NZ9000 and comparative physiological studies
  Linares, Journal of bacteriology 2010
  • “...llmg_1616 llmg_1616 llmg_1616 llmg_1616 llmg_1634 llmg_1637 Glu3Gly Synonymous Synonymous llmg_1706 llmg_1749 llmg_1845 Thr3Ala Met3Ile Synonymous Trp3Leu...”

MLEP_LACLA / O07032 Malate transporter MleP; Malate/lactate antiporter from Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis) (see 4 papers)
TC 2.A.24.2.2 / O07032 Malate:lactate antiporter (substrates include: S-lactate, R-lactate, S-malate and S-citramalate) from Lactococcus lactis (subsp. lactis) (Streptococcus lactis) (see paper)
36% identity, 94% coverage

• function: Secondary transporter involved in malolactic fermentation (PubMed:1917837, PubMed:9218448). Catalyzes the uptake of divalent malate into the cell coupled to the exit of monovalent lactate, a product of malate degradation (precursor/product exchange) (PubMed:10441129, PubMed:1917837, PubMed:9218448). The malate/lactate exchange is electrogenic and results in the generation of a membrane potential (PubMed:1917837, PubMed:9218448). Is highly selective for the S-enantiomer of malate (PubMed:10441129). In the absence of lactate, MleP can also catalyze the proton-dependent transport of malate (PubMed:1917837). In vitro, transports a range of substrates that contain the 2-hydroxycarboxylate motif, HO-CR(2)-COO(-), with a preference for malate, lactate and glycolate (PubMed:10441129, PubMed:9218448). Modification of the OH or the COO(-) groups of the 2- hydroxycarboxylate motif drastically reduces the affinity of the transporter for the substrates, indicating their relevance in substrate recognition (PubMed:10441129). Significant activity is also observed with some 2-oxocarboxylates (PubMed:9218448). Transports only poorly citromalate (PubMed:10441129, PubMed:9218448). Citrate binds to MleP but is not translocated (PubMed:10441129, PubMed:9218448).
  catalytic activity: (S)-lactate(in) + (S)-malate(out) = (S)-lactate(out) + (S)- malate(in) (RHEA:79475)
  catalytic activity: (R)-lactate(in) + (S)-malate(out) = (R)-lactate(out) + (S)- malate(in) (RHEA:79479)
  catalytic activity: glycolate(in) + (S)-malate(out) = glycolate(out) + (S)- malate(in) (RHEA:79483)
• substrates: Citramalate, Lactate, malate

5xarD / P31602 Structural insights into the elevator-like mechanism of the sodium/citrate symporter cits (see paper)
32% identity, 91% coverage

• Ligand: sodium ion (5xarD)

FN1375 Citrate-sodium symport from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
32% identity, 96% coverage

• The 2-hydroxycarboxylate transporter family: physiology, structure, and mechanism
  Sobczak, Microbiology and molecular biology reviews : MMBR 2005
  • “...local alignment was observed between the N-terminal half of FN1375 of F. nucleatum and the C-terminal half of NP973298 of T. denticola. The span of 148...”
• Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586
  Kapatral, Journal of bacteriology 2002
  • “...Resistance to -lactams is due to the presence of-lactamase (FN1375), which is similar to that of Clostridium spp. (10, 32). There is a second -lactamase similar...”

VC0795 / Q9KTU3 citrate:Na⁺ symporter from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (see paper)
VC0795 citrate/sodium symporter from Vibrio cholerae O1 biovar eltor str. N16961
33% identity, 89% coverage

• Vibrio cholerae Alkalizes Its Environment via Citrate Metabolism to Inhibit Enteric Growth <i>In Vitro</i>
  Kostiuk, Microbiology spectrum 2023
  • “...( 54 ) and OptFlux ( 55 ). Although V. cholerae carries a sodium/citrate symporter (VC0795), there was no reaction for citrate transport in this model ( 54 ), so citrate exchange was modified to be cytoplasmic. We removed external boundary metabolites and used the core...”
• Transcriptional profiling of Vibrio cholerae O1 following exposure to human anti- lipopolysaccharide monoclonal antibodies
  Baranova, Pathogens and disease 2020
  • “...VCA0944 VC0606 VCA0136 VCA0137 VC0089 VC1778 VC0795 VC0797 VC0796 VCA0684 VCA0685 VCA0687 VC0713 VCA0686 Maltoporin (OmpS) Trehalose-6-phosphate hydrolase...”
• CitAB Two-Component System-Regulated Citrate Utilization Contributes to Vibrio cholerae Competitiveness with the Gut Microbiota
  Liu, Infection and immunity 2019
  • “...promoter sequences of citA (VC0791), citC (VC0796), citS (VC0795), and tcpA (VC0828) (35) into the pBBR-lux vector, which contains a promoterless luxCDABE...”

CITP_LACLL / P21608 Citrate transporter CitP; Citrate carrier; Citrate permease P; Citrate/lactate antiporter from Lactococcus lactis subsp. lactis (Streptococcus lactis) (see 8 papers)
TC 2.A.24.3.1 / P21608 Electrogenic citrate:L-lactate exchanger, CitP or CitN from Lactococcus lactis (subsp. lactis) (Streptococcus lactis) (see paper)
NP_258266 citrate transporter from Lactococcus lactis
29% identity, 97% coverage

• function: Secondary transporter involved in citrate metabolism (PubMed:10049375, PubMed:2120190, PubMed:9572922, Ref.2). During cometabolism of citrate and glucose, catalyzes the uptake of divalent citrate into the cell coupled to the exit of monovalent lactate, the end product of glycolysis in L.lactis (PubMed:10049375, PubMed:9572922). The citrate/lactate exchange is electrogenic and results in the generation of a membrane potential (PubMed:10049375, PubMed:9572922). Plays an important role in resistance against lactate toxicity at low pH (PubMed:10049375). In the absence of glucose, i.e. when no lactate is produced, CitP catalyzes the uptake of citrate in exchange with the citrate metabolism intermediates pyruvate and alpha- acetolactate, and the end product acetate (PubMed:21115655). In the absence of glucose, CitP can also catalyze the proton-dependent transport of citrate (PubMed:2120190, PubMed:22563050). In vitro, shows a broad substrate specificity (PubMed:22563050). Can transport a wide variety of mono- and dicarboxylates of the form X-CR(2)-COO(-), where X represents OH (2-hydroxy acid), O (2-keto acid), or H (acid) and R groups differ in size, hydrophobicity and composition (PubMed:22563050). Many of the substrates are intermediates or products of amino acid metabolism, suggesting that CitP may have a broader physiological function than its role in citrate metabolism (PubMed:22563050).
  catalytic activity: (R)-lactate(in) + citrate(out) = (R)-lactate(out) + citrate(in) (RHEA:79491)
  catalytic activity: (S)-lactate(in) + citrate(out) = (S)-lactate(out) + citrate(in) (RHEA:79487)
  catalytic activity: citrate(in) + H(+)(in) = citrate(out) + H(+)(out) (RHEA:32123)
• substrates: Citrate, L-lactate
• Adaptative potential of the Lactococcus lactis IL594 strain encoded in its 7 plasmids
  Górecki, PloS one 2011
  • “...on pIL2 shares 100% identity with the protein product of citP of the pCRL1127 plasmid (NP_258266). Upstream of citP , there are putative regulator genes citQ and citR . The citP gene encodes the citrate permease responsible for the uptake of divalent citrate with simultaneous transport...”

CITP_LEUMS / Q48769 Citrate transporter CitP; Citrate carrier; Citrate/lactate antiporter from Leuconostoc mesenteroides subsp. mesenteroides (see 7 papers)
29% identity, 97% coverage

• function: Secondary transporter involved in citrate metabolism (PubMed:7592702, PubMed:8636016, PubMed:9572922). During cometabolism of citrate and glucose, catalyzes the uptake of divalent citrate into the cell coupled to the exit of monovalent lactate, a product of citrate fermentation during citrate-glucose cometabolism (precursor/product exchange) (PubMed:7592702, PubMed:8636016, PubMed:9572922). The citrate/lactate exchange is electrogenic and results in the generation of a membrane potential (PubMed:7592702, PubMed:8636016, PubMed:9572922). In the absence of glucose, i.e. when no lactate is produced, CitP catalyzes the proton-dependent transport of citrate and malate (PubMed:7592702). Transports the divalent form of citrate and malate with the concomitant uptake of one proton, therefore translocating a single unit of negative charge across the membrane (PubMed:7592702). In vitro, transports a range of substrates that contain the 2-hydroxycarboxylate motif, HO-CR(2)-COO(-), with a preference for malate, citrate and monovalent 2-hydroxyisobutyrate (PubMed:10441129, PubMed:9218448). Modification of the OH or the COO(-) groups of the 2-hydroxycarboxylate motif drastically reduces the affinity of the transporter for the substrates, indicating their relevance in substrate recognition (PubMed:10441129). Significant activity is also observed with some 2-oxocarboxylates and a 3- hydroxycarboxylate (PubMed:9218448).
  catalytic activity: (R)-lactate(in) + citrate(out) = (R)-lactate(out) + citrate(in) (RHEA:79491)
  catalytic activity: (S)-lactate(in) + citrate(out) = (S)-lactate(out) + citrate(in) (RHEA:79487)
  catalytic activity: citrate(in) + H(+)(in) = citrate(out) + H(+)(out) (RHEA:32123)

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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.