PaperBLAST
PaperBLAST Hits for tr|Q9HVX3|Q9HVX3_PSEAE Soluble and membrane-bound lytic transglycosylase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=mltB1 PE=4 SV=1 (367 a.a., MRRTALALPL...)
Show query sequence
>tr|Q9HVX3|Q9HVX3_PSEAE Soluble and membrane-bound lytic transglycosylase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=mltB1 PE=4 SV=1
MRRTALALPLFLLVSACSSEPTPPPKPAAKPQARTVISPRPVRQSVQPILPLRGDYANNP
AAQHFIDRMVSQHGFNRQQLHDLFAQTQRLDWVIRLMDRQAPTYTPPSGPNGAWLRYRKK
FVTPGNVQNGVLFWDQYETDLQRASRVYGVPPEIIVGIIGVETRWGRVMGKTRIIDALST
LSFSYPRRAEFFSGELEQFLLQARKEGTDPLALRGSYAGAMGYGQFMPSSFTKYAVDFDG
DGHIDLWNPRDAIGSVANYFKQHGWVSGDRVAVPASGRAPSLEDGFKTLYPLDVLASAGL
RPQGPLGGHRQASLLRLDMGRNYQYWYGLPNFYVITRYNHSTHYAMAVWELGKEVDRVRH
RSVVRQD
Running BLASTp...
Found 85 similar proteins in the literature:
AAG07832.1 membrane-bound lytic transglycosylase B (MltB;Mltb1;PA4444;sMltB) (EC 4.2.2.n1) (see protein)
PA4444 membrane-bound lytic transglycosylase from Pseudomonas aeruginosa PAO1
NP_253134 murein hydrolase B from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- From Genome to Proteome to Elucidation of Reactions for All Eleven Known Lytic Transglycosylases from Pseudomonas aeruginosa
Lee, Angewandte Chemie (International ed. in English) 2017 - “...MltB MltD MltF MltF2 MltG RlpA Slt SltB1 SltB2 (SltG) SltB3 (SltH) Locus tag PA1222 PA4444 PA1812 PA3764 PA2865 PA2963 PA4000 PA3020 PA4001 PA1171 PA3992 1 NR 100 NR NR NR NR NR NR 100 100 100 2 100 100 10 6 5 17 4 41...”
- Lytic transglycosylases: concinnity in concision of the bacterial cell wall
Dik, Critical reviews in biochemistry and molecular biology 2017 - “...Rechenberg et al. , 1996 ). The other Family 3A LTs include P. aeruginosa MltB (PA4444) and SltB1 (PA4001), N. gonorrhoeae LtgD (NGO0626), and S. maltophilia MltB1 (Smlt4052). These four have, respectively, 68%, 47%, 35%, and 41% sequence identity (and, respectively, 89%, 77%, 90%, and 74%...”
- “...Bulgecin A & (GLCNAC) 2 ) ( van Asselt et al. , 2000 ) MltB (PA4444) 367 41404.1 SltB1 (PA4001) 340 37835.6 4ANR (Apo) ( Nikolaidis et al. , 2012 ) MltB1 (Smlt4052) 381 41821.6 LtgD (NGO0626) 363 39821.2 Family 3B SltB2 (PA1171) 398 42682.5 SltB3...”
- Deciphering the Resistome of the Widespread Pseudomonas aeruginosa Sequence Type 175 International High-Risk Clone through Whole-Genome Sequencing
Cabot, Antimicrobial agents and chemotherapy 2016 - “...oprM creB creC creD PA4218 PA4270 PA4381 PA4393 PA4418 PA4444 PA4462 PA4522 ampP rpoB colR ampG ftsI mltB1 rpoN ampD PA4597 PA4598 PA4599 oprJ mexD mexC PA4700...”
- Loss of membrane-bound lytic transglycosylases increases outer membrane permeability and β-lactam sensitivity in Pseudomonas aeruginosa
Lamers, MicrobiologyOpen 2015 - “...WT with mltA deletion (PA1222) This study Family 2 PAO1 mltB WT with mltB deletion (PA4444) This study Family 3 PAO1 mltD WT with mltD deletion (PA1812) This study Family 1D PAO1 mltF WT with mltF deletion (PA3764) This study Family 1E PAO1 mltF2 WT with...”
- Genome-wide patterns of recombination in the opportunistic human pathogen Pseudomonas aeruginosa
Dettman, Genome biology and evolution 2014 - “...protein PA1475 PALES_39381 ccmA , cytochrome c biogenesis ATP-binding export protein PA0671 PALES_46581 Hypothetical protein PA4444 PALES_48231 mltB1 , lytic transglycosylase, murein hydrolase, peptidoglycan metabolism PA4523 PALES_49041 Thymidine phosphorylase PA4543 PALES_49261 Multicopper polyphenol oxidoreductase PA4571 PALES_49541 Cytochrome c PA4700 PALES_50851 mrcB , penicillin-binding protein 1B, membrane...”
- Changes to its peptidoglycan-remodeling enzyme repertoire modulate β-lactam resistance in Pseudomonas aeruginosa
Cavallari, Antimicrobial agents and chemotherapy 2013 - “...transposon ISphoA/hah insertion at nucleotide 358 of mltB (PA4444) WT with transposon ISphoA/hah insertion at nucleotide 1573 of ponA (PBP1a, PA5045) WT with...”
- Beta-lactam antibiotics: from antibiosis to resistance and bacteriology
Kong, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2010 - “...MltE AmiA mltC mltD mltE emtA amiA PA3020? PA1222 PA4444 mltB1 sltB PA4001 sltB1 mltB2 PA3020? PA1812 PA3764 PA5538 AmiB amiB PA4947 AmiC amiC MepA mepA PA4947?...”
- Role of arginine residues in the active site of the membrane-bound lytic transglycosylase B from Pseudomonas aeruginosa.
Reid, Biochemistry 2006 (PubMed)- GeneRIF: Arg187 and Arg188 are vital for proper orientation of the substrate in the active site, and furthermore this supports the proposed role of the stem peptide at binding subsite -2 in catalysis.
YPTB2681 putative membrane-bound lytic murein transglycosylase B from Yersinia pseudotuberculosis IP 32953
70% identity, 100% coverage
YPO2957 putative membrane-bound lytic murein transglycosylase B from Yersinia pestis CO92
69% identity, 99% coverage
AEX15_21995, SeKA_A2343 lytic murein transglycosylase B from Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188
68% identity, 98% coverage
- Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America
Haley, PloS one 2016 - “...NS Lys Glu 156 AEX15_21540 SeKA_A2229 phospho-2-dehydro-3-deoxyheptonate aldolase 2169354 G A S Asn Asn 149 AEX15_21995 SeKA_A2343 murein hydrolase effector LrgB 2282024 G A S Gly Gly 38 AEX15_22185 SeKA_A2383 putative type III secretion system effector protein OrgC 2317497 G A NS Ser Leu 98 AEX15_22530...”
- “...Lys Glu 156 AEX15_21540 SeKA_A2229 phospho-2-dehydro-3-deoxyheptonate aldolase 2169354 G A S Asn Asn 149 AEX15_21995 SeKA_A2343 murein hydrolase effector LrgB 2282024 G A S Gly Gly 38 AEX15_22185 SeKA_A2383 putative type III secretion system effector protein OrgC 2317497 G A NS Ser Leu 98 AEX15_22530 SeKA_A2451...”
MltB / b2701 membrane-bound lytic murein transglycosylase B from Escherichia coli K-12 substr. MG1655 (see 30 papers)
mltB / P41052 membrane-bound lytic murein transglycosylase B from Escherichia coli (strain K12) (see 31 papers)
AAB60060.1 lytic murein transglycosylase B (MltB;b2701;Slt35) (EC 4.2.2.n1) (see protein)
mltB / AAB60060.1 membrane-bound lytic transglycosylase precursor from Escherichia coli (see 4 papers)
P41052 Membrane-bound lytic murein transglycosylase B from Escherichia coli (strain K12)
b2701 membrane-bound lytic murein transglycosylase B from Escherichia coli str. K-12 substr. MG1655
68% identity, 98% coverage
c3255 Membrane-bound lytic murein transglycosylase B precursor from Escherichia coli CFT073
68% identity, 90% coverage
1d0kA / P41052 The escherichia coli lytic transglycosylase slt35 in complex with two murodipeptides (glcnac-murnac-l-ala-d-glu) (see paper)
73% identity, 85% coverage
- Ligands: n-acetyl-beta-muramic acid; calcium ion; d-glutamic acid; alanine (1d0kA)
U876_15120 lytic murein transglycosylase B from Aeromonas hydrophila NJ-35
62% identity, 98% coverage
Q9HX24 Soluble lytic transglycosylase B from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
NP_252690 soluble lytic transglycosylase B from Pseudomonas aeruginosa PAO1
PA14_12080 soluble lytic transglycosylase B from Pseudomonas aeruginosa UCBPP-PA14
PA4001 soluble lytic transglycosylase B from Pseudomonas aeruginosa PAO1
48% identity, 83% coverage
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - A potential space-making role in cell wall biogenesis for SltB1and DacB revealed by a beta-lactamase induction phenotype in Pseudomonas aeruginosa.
Gyger, mBio 2024 - GeneRIF: A potential space-making role in cell wall biogenesis for SltB1and DacB revealed by a beta-lactamase induction phenotype in Pseudomonas aeruginosa.
- Interaction of penicillin-binding protein 2 with soluble lytic transglycosylase B1 in Pseudomonas aeruginosa.
Legaree, Journal of bacteriology 2008 - GeneRIF: Penicillin-binding protein 2 (PBP2) was identified as a binding partner of SltB1, suggesting that the two proteins function together in the biosynthesis of peptidoglycan.
- The role of peptidoglycan hydrolases in the formation and toxicity of Pseudomonas aeruginosa membrane vesicles
Chen, microLife 2022 - “...of the pbpG (PA14_53020), dacB (PA14_24690), sltB1 (PA14_12080) and pbpA (PA14_12060) mutants (Fig. S3A). Nanoparticle tracking analysis (NTA) revealed that the...”
- Identification of Genes Required for Resistance to Peptidomimetic Antibiotics by Transposon Sequencing
Vitale, Frontiers in microbiology 2020 - “...in the recycling of peptidoglycan ( Sonnabend et al., 2020 ). The lytic transglycosylase SltB1 (PA14_12080) and the murein endopeptidase MepM1 (PA14_08540), which cleave peptidoglycan cross-connections, and the AmpG permease (PA14_57100), which imports peptidoglycan catabolites into the cytoplasm where they are degraded. To verify a role...”
- “...a L27-11 a 4 a 3 a PA14_08540 mepM1 PMB/COL/4 4 2 1 2 2 PA14_12080 sltB1 All (ex. L27-11) 4 2 1 1 1 PA14_57100 ampG PMB/COL/4 4 4 1 1 1 PA14_58090 asmA All 8 16 1 1 2 PA14_18370 arnB All 64 32...”
- A potential space-making role in cell wall biogenesis for SltB1and DacB revealed by a beta-lactamase induction phenotype in Pseudomonas aeruginosa
Gyger, mBio 2024 - “...induction. PCR-based mapping revealed that this isolate had a transposon inserted in the sltB1 ( PA4001 ) gene ( Fig. 2A ), encoding the LT enzyme SltB1 that is related to E. coli MltB ( 43 ). Fig 2 Inactivation of SltB1 promotes P ampC ::lacZ...”
- Ceftazidime resistance in Pseudomonas aeruginosa is multigenic and complex
Ramsay, PloS one 2023 - “...PBP4, D-alanyl-D-alanine carboxypeptidase 15 mpl PA4020 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase 12 ampC PA4110 -lactamase precursor 7 sltB1 PA4001 soluble lytic transglycosylase B 3 MexAB-OprM efflux pump and its regulation nalD PA3574 NalD repressor 5 Lipopolysaccharide synthesis wapH PA5004 WapH 10 wbpL PA3145 glycosyltransferase WbpL 3 ssg PA5001 cell...”
- Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics
Salvà-Serra, Frontiers in microbiology 2022 - “...rlpA Endolytic peptidoglycan transglycosylase RplA 5 10 1.10 0.94 1.30 0.45 16.68 0.00 Up WP_003132500.1 PA4001 sltB1 Soluble lytic transglycosylase B 6 14 1.17 0.27 1.34 0.12 1.64 0.02 Up 1.16 0.51 WP_003093601.1 PA4201 ddlA D-alanine-D-alanine ligase A 7 25 1.07 0.13 1.14 0.02 1.69 0.00...”
- The role of peptidoglycan hydrolases in the formation and toxicity of Pseudomonas aeruginosa membrane vesicles
Chen, microLife 2022 - “...erfK mltG mltC dacB (PBP4) tse3 mltF PA3992 PA4000 PA4001 PA4003 PA4412 sltB3 (sltH) rlpA sltB1 pbpA murG PA4413 ftsW PA4414 murD PA4417 murE PA4418 PA4450 ftsI...”
- From Genome to Proteome to Elucidation of Reactions for All Eleven Known Lytic Transglycosylases from Pseudomonas aeruginosa
Lee, Angewandte Chemie (International ed. in English) 2017 - “...SltB1 SltB2 (SltG) SltB3 (SltH) Locus tag PA1222 PA4444 PA1812 PA3764 PA2865 PA2963 PA4000 PA3020 PA4001 PA1171 PA3992 1 NR 100 NR NR NR NR NR NR 100 100 100 2 100 100 10 6 5 17 4 41 100 100 100 3 NR NR NR...”
- Lytic transglycosylases: concinnity in concision of the bacterial cell wall
Dik, Critical reviews in biochemistry and molecular biology 2017 - “..., 1996 ). The other Family 3A LTs include P. aeruginosa MltB (PA4444) and SltB1 (PA4001), N. gonorrhoeae LtgD (NGO0626), and S. maltophilia MltB1 (Smlt4052). These four have, respectively, 68%, 47%, 35%, and 41% sequence identity (and, respectively, 89%, 77%, 90%, and 74% query coverage) to...”
- “...2 ) ( van Asselt et al. , 2000 ) MltB (PA4444) 367 41404.1 SltB1 (PA4001) 340 37835.6 4ANR (Apo) ( Nikolaidis et al. , 2012 ) MltB1 (Smlt4052) 381 41821.6 LtgD (NGO0626) 363 39821.2 Family 3B SltB2 (PA1171) 398 42682.5 SltB3 (PA3992) 448 47760.9 5ANZ...”
- Deciphering the Resistome of the Widespread Pseudomonas aeruginosa Sequence Type 175 International High-Risk Clone through Whole-Genome Sequencing
Cabot, Antimicrobial agents and chemotherapy 2016 - “...PA2809 PA2810 PA3047 PA3078 PA3168 PA3677 PA3678 PA3721 PA3999 PA4001 PA4109 PA4119 PA4207 prtN prtR ampDh3 pbpG oprD pagP gshB pdxB aphA oprF folD parS parR...”
- Loss of membrane-bound lytic transglycosylases increases outer membrane permeability and β-lactam sensitivity in Pseudomonas aeruginosa
Lamers, MicrobiologyOpen 2015 - “...This study Family 1A PAO1 sltB1 WT with FRT scar at nucleotide 577 of sltB1 (PA4001) Cavallari etal. ( 2013 ) Family 3 PAO1 sltG WT with sltG deletion (PA1171) This study Family 3 PAO1 sltH WT with sltH deletion (PA3992) This study Family 3 PAO1...”
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5o8xA / Q9HX24 The x-ray structure of catenated lytic transglycosylase sltb1 from pseudomonas aeruginosa (see paper)
47% identity, 83% coverage
- Ligand: calcium ion (5o8xA)
AUP74_01707 lytic murein transglycosylase B from Microbulbifer aggregans
41% identity, 97% coverage
BPSL2506 putative exported transglycosylase from Burkholderia pseudomallei K96243
43% identity, 69% coverage
ACIAD2264 membrane-bound lytic murein transglycosylase B from Acinetobacter sp. ADP1
40% identity, 82% coverage
XC_0706 membrane-bound lytic transglycosylase from Xanthomonas campestris pv. campestris str. 8004
38% identity, 78% coverage
NGO0626 putative murein hydrolase from Neisseria gonorrhoeae FA 1090
Q5F8Y3 Murein transglycosylase from Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)
NGO_0626 lytic murein transglycosylase B from Neisseria gonorrhoeae FA 1090
36% identity, 96% coverage
- Inactivation of Genes Encoding MutL and MutS Proteins Influences Adhesion and Biofilm Formation by Neisseria gonorrhoeae
Płaczkiewicz, Microorganisms 2019 - “...ngo1535 , and ngo1822 ( secY ), and in N. gonorrhoeae mutS::km , they are ngo0626 and ngo0834 ( Figure S1 and Table S2 ). The ngo0206 gene, which expression was increased by 2.17-fold ( p = 2.95 10 5 ) encodes a polyamine ABC transporter...”
- “...46 , 47 , 48 , 49 , 50 , 51 , 52 ]. The ngo0626 gene, overexpressed 1.89-fold in N. gonorrhoeae mutS::km ( p = 3.36 10 6 ) encodes lytic transglycosylase (LT), and recently, it was demonstrated that in addition to the role of...”
- Lytic transglycosylases: concinnity in concision of the bacterial cell wall
Dik, Critical reviews in biochemistry and molecular biology 2017 - “...other Family 3A LTs include P. aeruginosa MltB (PA4444) and SltB1 (PA4001), N. gonorrhoeae LtgD (NGO0626), and S. maltophilia MltB1 (Smlt4052). These four have, respectively, 68%, 47%, 35%, and 41% sequence identity (and, respectively, 89%, 77%, 90%, and 74% query coverage) to MltB of E. coli....”
- “...37835.6 4ANR (Apo) ( Nikolaidis et al. , 2012 ) MltB1 (Smlt4052) 381 41821.6 LtgD (NGO0626) 363 39821.2 Family 3B SltB2 (PA1171) 398 42682.5 SltB3 (PA3992) 448 47760.9 5ANZ (Apo) ( Lee et al. , 2016b ) 5AO7 (NAG-anhNAM-pentapeptide) ( Lee et al. , 2016b )...”
- The lytic transglycosylases of Neisseria gonorrhoeae
Chan, Microbial drug resistance (Larchmont, N.Y.) 2012 - “...grew without any apparent growth or morphological defects. LtgD (NGO0626) is predicted to be 363-amino-acid long with a molecular weight of 38.5 kDa. LtgD is...”
- Neisseria gonorrhoeae uses two lytic transglycosylases to produce cytotoxic peptidoglycan monomers
Cloud-Hansen, Journal of bacteriology 2008 - “...LtgA (NGO2135) LtgB (NGO1033) LtgC (NGO2048) LtgD (NGO0626) LtgE (NGO0608) LtgXb (NGO5004) AtlAb (NGO5025) PG monomer production Unknown Cell separation PG...”
- Quantitative proteomics of the Neisseria gonorrhoeae cell envelope and membrane vesicles for the discovery of potential therapeutic targets
Zielke, Molecular & cellular proteomics : MCP 2014 - “...Q5F9M1 Q5F6Q5 Q5F7C5 Q5FA28 Q5F574 Q5FAB9 Q5F718 Q5F598 Q5F8Y3 Q5FA91 Q5F515 Q5F5C7 Q5F6P4 Q5F7W0 Q5F7X1 Q5F7X2 Q5F8C4 Q5F571 Q5F649 Q5F6V7 Q5F505 Q5F912 Inner...”
- The Pathogenic Neisseria Use a Streamlined Set of Peptidoglycan Degradation Proteins for Peptidoglycan Remodeling, Recycling, and Toxic Fragment Release
Schaub, Frontiers in microbiology 2019 - “...LtgB NGO_1033 Y SpI MltC Y SpII+2=S LtgC NGO_2048 Y SpII+2=Q MltA Y SpII+2=S LtgD NGO_0626 Y SpII+2=T MltB Y SpII+2=S LtgE NGO_0608 Y SpI MltD Y SpII+2=Q LtgG NGO_0238 Y SpI MltG Y SpI RlpA NGO_1728 Y SpI RlpA Y SpII+2=T GGI LTs AtlA NGrG_00979...”
NMB1279 putative membrane-bound lytic murein transglycosylase B from Neisseria meningitidis MC58
35% identity, 96% coverage
SO1166 membrane-bound lytic transglycosylase, putative from Shewanella oneidensis MR-1
36% identity, 96% coverage
- Deletion of Lytic Transglycosylases Increases Beta-Lactam Resistance in Shewanella oneidensis
Yin, Frontiers in microbiology 2018 - “...groups. Results LTs in S. oneidensis MR-1 According to genome annotation, seven genes [ mltB (SO1166), SO1994, sltY (SO2040), SO2564, mltF (SO3288), mltD (SO4017), and SO4660 ] are predicted to encode LTs in S. oneidensis MR-1. Except for SO4660, all LTs have a homolog in E....”
- “...or P. aeruginosa counterparts a Similarity (%) Identity (%) Query Cover (%) E -Value Family SO1166 mltB MltB 50 36 96 5e-60 3 SO1994 mltB2 MltB 50 35 66 6e-33 3 SO2040 sltY Slt70 50 29 95 5e-90 1A SO2564 mltD2 MltD 56 34 95 1e-83...”
XAC_RS03435 lytic murein transglycosylase B from Xanthomonas citri pv. citri str. 306
38% identity, 78% coverage
- Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness
Oliveira, PeerJ 2018 - “...assembly XAC_RS02185 hpaH/etgA 487,771..488,334 187 1G Insertion of the type III and IV secretion system XAC_RS03435 mltB 785,110..786,249 379 3A Cell-wall recycling and resistance XAC_RS16355 mltB2.2 3,798,986..3,800,263 425 3B Related to XccA virulence and fitness XAC_RS22275 mltB2.1 3,862..5,088 (pXAC64) XAC_RS05780 mltG 1,281,557..1,282,630 357 5A Regulates peptidoglycan...”
SSKA14_RS05295 lytic murein transglycosylase B from Stenotrophomonas sp. SKA14
40% identity, 77% coverage
- Bacterial transcriptional response to labile exometabolites from photosynthetic picoeukaryote Micromonas commoda
Ferrer-González, ISME communications 2023 - “...Xanthine/Uracil Family Permease SSKA14_1406 WP_006461445.1 2.2 arginine/agmatine antiporter CAZymes SSKA14_2639 WP_008267014.1 2.7 lytic transglycosylase (CBM50+GH23) SSKA14_RS05295 WP_040007079.1 2.2 lytic murein transglycosylase B (GH103) SSKA14_3712 WP_008268057.1 2.1 lytic murein transglycosylase (GH23) SSKA14_1720 WP_008266069.1 1.9 LysM peptidoglycan-binding domain-containing protein (CBM50) SSKA14_2822 WP_040007055.1 5.3 glucans biosynthesis glucosyltransferase MdoH (GT2)...”
Smlt4052 putative murein hydrolase from Stenotrophomonas maltophilia K279a
40% identity, 77% coverage
- Lytic transglycosylases: concinnity in concision of the bacterial cell wall
Dik, Critical reviews in biochemistry and molecular biology 2017 - “...P. aeruginosa MltB (PA4444) and SltB1 (PA4001), N. gonorrhoeae LtgD (NGO0626), and S. maltophilia MltB1 (Smlt4052). These four have, respectively, 68%, 47%, 35%, and 41% sequence identity (and, respectively, 89%, 77%, 90%, and 74% query coverage) to MltB of E. coli. The structure of SltB1 was...”
- “...41404.1 SltB1 (PA4001) 340 37835.6 4ANR (Apo) ( Nikolaidis et al. , 2012 ) MltB1 (Smlt4052) 381 41821.6 LtgD (NGO0626) 363 39821.2 Family 3B SltB2 (PA1171) 398 42682.5 SltB3 (PA3992) 448 47760.9 5ANZ (Apo) ( Lee et al. , 2016b ) 5AO7 (NAG-anhNAM-pentapeptide) ( Lee et...”
- Interplay among membrane-bound lytic transglycosylase D1, the CreBC two-component regulatory system, the AmpNG-AmpDI-NagZ-AmpR regulatory circuit, and L1/L2 β-lactamase expression in Stenotrophomonas maltophilia
Huang, Antimicrobial agents and chemotherapy 2015 - “...soluble LT (slt), including mltA (Smlt0155), two mltB genes (Smlt4052 and Smlt4650), two mltD genes (Smlt0994 and Smlt3434), and slt (Smlt4007) (see Table S2 in...”
- “...determined before and after induction. mologues of Smlt0155, Smlt4052, Smlt4650, Smlt0994, Smlt3434, and Smlt4007 in S. maltophilia KJ were named mltA, mltB1,...”
NMA1488 murein hydrolase from Neisseria meningitidis Z2491
38% identity, 82% coverage
PD1235 membrane-bound lytic transglycosylase from Xylella fastidiosa Temecula1
35% identity, 93% coverage
D0CC83 Lytic murein transglycosylase B from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)
AB57_2749 lytic murein transglycosylase B from Acinetobacter baumannii AB0057
ABUW_1243 lytic murein transglycosylase B from Acinetobacter baumannii
39% identity, 82% coverage
- Loss of Lipooligosaccharide Synthesis in Acinetobacter baumannii Produces Changes in Outer Membrane Vesicle Protein Content
Cano-Castaño, International journal of molecular sciences 2024 - “...D0C5L6). An M23 family peptidase and a lytic murein transglycosylase B had two epitopes (D0CBZ2; D0CC83). Only three proteins contained three and four epitopes, including a Tat pathway signal sequence domain protein (D0CDN5), and a Type VI secretion system effector, Hcp1 family (D0C8P3; D0CD52). The subcellular...”
- “...0.01 D0CDE5 gcd Quinoprotein glucose dehydrogenase 2.45 <0.01 D0CEV8 HMPREF0010_03288 Polysaccharide biosynthesis/export protein 2.06 <0.01 D0CC83 mltB Lytic murein transglycosylase B 1.67 <0.01 D0CBZ2 HMPREF0010_02272 Peptidase, M23 family 1.62 <0.01 D0CDN5 HMPREF0010_02865 Tat pathway signal sequence domain protein 1.53 <0.01 D0C6H8 HMPREF0010_00358 Uncharacterized protein 3.66 <0.01...”
- The lytic transglycosylase MltB connects membrane homeostasis and in vivo fitness of Acinetobacter baumannii
Crépin, Molecular microbiology 2018 - “...0.0044 AB57_1154 hypothetical protein 9.48 0.0075 AB57_2881 diadenosine tetraphosphatase 9.47 0.0031 AB57_3680 acetyltransferase 9.37 0.0062 AB57_2749 lytic transglycosylase 9.36 0.0000 AB57_2865 NUDIX hydrolase 9.24 0.0022 AB57_0530 50S ribosomal protein L33 9.24 0.0001 AB57_0531 50S ribosomal protein L28 9.24 0.0001 AB57_0459 hypothetical protein 9.21 0.0052 AB57_0336 glutamylQ...”
- “...as candidate fitness factors (Supporting Information Table S3 ), where the lytic transglycosylase mltB ( AB57_2749 ) showed the greatest fitness defect in the spleen, 655fold, and overall, has the 13 th greatest fitness defect among all candidate fitness factors (Table 1 ). An in silico...”
- Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach
Scribano, International journal of molecular sciences 2019 - “...0.103 CYT score = 0.200913 Response to oxidative stress 0.270 V5VBL0 Lytic murein transglycosylase B ABUW_1243 mltB Sec SP MLCS: 128 [AQA-ND]. Rs: 0.999 0.826 0.783 SpI score = 15.767 Cell envelope 0.571 A0A090C137 3-phosphoshikimate 1-carboxyvinyltransferase ABUW_1366 aroA Sec SP MLCS: 127 [IVA-EK]. Rs: 0.978 0.077...”
XF2184 membrane-bound lytic transglycosylase from Xylella fastidiosa 9a5c
37% identity, 79% coverage
SO1994, SO_1994 membrane-bound lytic transglycolase-related protein from Shewanella oneidensis MR-1
32% identity, 74% coverage
- Deletion of Lytic Transglycosylases Increases Beta-Lactam Resistance in Shewanella oneidensis
Yin, Frontiers in microbiology 2018 - “...Results LTs in S. oneidensis MR-1 According to genome annotation, seven genes [ mltB (SO1166), SO1994, sltY (SO2040), SO2564, mltF (SO3288), mltD (SO4017), and SO4660 ] are predicted to encode LTs in S. oneidensis MR-1. Except for SO4660, all LTs have a homolog in E. coli...”
- “...and 41% sequence identity with E. coli Slt70 and MltF, respectively. Interestingly, both MltB and SO1994 are E. coli MltB homologs (36 and 35% identity respectively); both SO2564 and MltD are homologous with E. coli MltD (34 and 33% identity respectively). These results indicate that S....”
- Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level
Rodrigues, Applied and environmental microbiology 2011 - “...W3181_0530, and Sama_0379), and a cold-adapted lipase (SO_1994, MR4_2269, MR7_2341, W3181_1692, and Sama_2029), were conserved among the strains. The last gene...”
PP4798 membrane-bound lytic murein transglycosylase, putative from Pseudomonas putida KT2440
30% identity, 80% coverage
PsyrB_22625 lytic murein transglycosylase from Pseudomonas syringae pv. syringae B301D
32% identity, 78% coverage
Psyr_4357 transglycosylase, putative from Pseudomonas syringae pv. syringae B728a
32% identity, 78% coverage
PsyrH_04450 lytic murein transglycosylase from Pseudomonas syringae pv. syringae HS191
32% identity, 78% coverage
PSPPH_4398 type III effector HopAJ2 from Pseudomonas syringae pv. phaseolicola 1448A
32% identity, 78% coverage
VC1956 lytic murein transglycosylase, putative from Vibrio cholerae O1 biovar eltor str. N16961
36% identity, 63% coverage
- Impact of Gene Repression on Biofilm Formation of Vibrio cholerae
Pombo, Frontiers in microbiology 2022 - “...1 VC1832 Hypothetical protein 2 VC1911 Orotidine 5-phosphate decarboxylase 1 VC1931 Hypothetical protein 1 VC1956-1957 VC1956 Lytic murein transglycosylase, membrane-bound lytic murein transglycosylase B 1 VC1965-1966 VC1966 Hypothetical protein 1 VC2037 Na + /H + antiporter, NhaC 1 VC2058-2069 VC2067 MinD-like protein; flagellar assembly protein FlhG...”
- Exploration of the effects of a degS mutant on the growth of Vibrio cholerae and the global regulatory function of degS by RNA sequencing
Huang, PeerJ 2019 - “...In addition, according to the GO analysis, the downregulated genes VC0263 (galactosyl-transferase), VC2217 (beta-N-acetylhexosaminidase) and VC1956 (lytic murein transglycosylase) were involved in the polysaccharide biosynthetic process, peptidoglycan turnover and peptidoglycan-based cell wall biogenesis, respectively. The synthesis of peptidoglycans is closely associated with bacterial cell division and...”
- Transcriptomics reveals a cross-modulatory effect between riboflavin and iron and outlines responses to riboflavin biosynthesis and uptake in Vibrio cholerae
Sepúlveda-Cisternas, Scientific reports 2018 - “...pvcA protein 1.021 VC1950 biotin sulfoxide reductase 1.785 VC1951 yecK cytochrome c-type protein YecK 1.854 VC1956 mltB lytic murein transglycosylase putative 1.242 VC1957 conserved hypothetical protein 1.314 VC1958 hypothetical protein 1.144 VC1962 lipoprotein 1.070 1.215 VC1971 menE o-succinylbenzoic acidCoA ligase 1.181 VC1972 menA o-succinylbenzoate-CoA synthase 1.587...”
Atu0092 lytic murein transglycosylase from Agrobacterium tumefaciens str. C58 (Cereon)
36% identity, 53% coverage
PSPTO_4817 transglycosylase, putative from Pseudomonas syringae pv. tomato str. DC3000
31% identity, 78% coverage
SMc02909 PUTATIVE TRANSGLYCOSYLASE TRANSMEMBRANE PROTEIN from Sinorhizobium meliloti 1021
33% identity, 66% coverage
PA1171 probable transglycolase from Pseudomonas aeruginosa PAO1
Q9I4G6 Probable transglycolase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
32% identity, 77% coverage
- A novel virulent Litunavirus phage possesses therapeutic value against multidrug resistant Pseudomonas aeruginosa
Lerdsittikul, Scientific reports 2022 - “...(High) PA1170 AMP AMC CL FOX CRO CPD CTX SXT TE DO OT Urine/Cat ND PA1171 AMP AMC CL FOX CRO CPD CTX SXT TE DO OT Wound swab/Dog + 0.850.05 (High) PA729 AMP AMC CL FOX CPD CTX SXT TE DO OT Ear swab/Cat +...”
- The role of peptidoglycan hydrolases in the formation and toxicity of Pseudomonas aeruginosa membrane vesicles
Chen, microLife 2022 - “...Gene number Gene name PA0378 PA0629 PA0807 PA0869 PA1171 PA1222 mtgA lys ampDh3 pbpG (PBP7) sltB2 (sltG) mltA PA2854 PA2963 PA3020 PA3047 PA3484 PA3764...”
- Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
Rubio-Gómez, Frontiers in microbiology 2020 - “...Citrate synthase 2 1.1 0.001 0.9 0.002 PA1069 nd Hypothetical protein 0.7 0.000 0.5 0.003 PA1171 sltB2 Soluble lytic transglycolase 0.7 0.010 0.6 0.008 PA1183 dctA C4-dicarboxylate transport protein 1.5 0.000 1.2 0.000 PA1342 aatj Probable binding protein component of ABC transporter 1.0 0.000 1.1 0.000...”
- “...DNA damage stimulus 1.4 0.000 PA0912 Uncharacterized protein 2.4 0.000 PA1069 Uncharacterized protein 0.5 0.003 PA1171 sltB2 Soluble lytic transglycolase 0.6 0.008 PA1183 dctA C4-dicarboxylate transport protein 1.2 0.000 PA1337 ansB Glutaminase-asparaginase 0.9 0.002 PA1342 aatj Probable binding protein component of ABC transport 1.1 0.000 PA1585...”
- Proteomic Analysis of Vesicle-Producing Pseudomonas aeruginosa PAO1 Exposed to X-Ray Irradiation
Zhang, Frontiers in microbiology 2020 - “...PA0953 1.215 0.439 2.768 Probable thioredoxin Q9I4Y4 PA0985 PyoS5 1.363 0.347 3.928 Pyocin S5 Q9I4G6 PA1171 SltB2 1.677 0.419 4.002 Probable lytic murein transglycosylase Q9I4B6 PA1222 MltA 1.367 0.524 2.609 Membrane-bound lytic murein trans-glycosylase A Q9I457 PA1287 1.577 0.733 2.151 Glutathione peroxidase Q9I398 PA1624 1.455 0.658...”
- From Genome to Proteome to Elucidation of Reactions for All Eleven Known Lytic Transglycosylases from Pseudomonas aeruginosa
Lee, Angewandte Chemie (International ed. in English) 2017 - “...SltB2 (SltG) SltB3 (SltH) Locus tag PA1222 PA4444 PA1812 PA3764 PA2865 PA2963 PA4000 PA3020 PA4001 PA1171 PA3992 1 NR 100 NR NR NR NR NR NR 100 100 100 2 100 100 10 6 5 17 4 41 100 100 100 3 NR NR NR NR...”
- Lytic transglycosylases: concinnity in concision of the bacterial cell wall
Dik, Critical reviews in biochemistry and molecular biology 2017 - “...Ragland et al. , 2017 ). Family 3B Blackburn and Clarke discovered the enzymes SltB2 (PA1171) and SltB3 (PA3992) in P. aeruginosa in 2002, marking a second subfamily of the Family 3 LTs ( Blackburn & Clarke, 2002 ). Although Family 3B lacks a counterpart protein...”
- “...al. , 2012 ) MltB1 (Smlt4052) 381 41821.6 LtgD (NGO0626) 363 39821.2 Family 3B SltB2 (PA1171) 398 42682.5 SltB3 (PA3992) 448 47760.9 5ANZ (Apo) ( Lee et al. , 2016b ) 5AO7 (NAG-anhNAM-pentapeptide) ( Lee et al. , 2016b ) 5AO8 (NAG-NAM-pentapeptide) ( Lee et al....”
- Within-Host Evolution of the Dutch High-Prevalent Pseudomonas aeruginosa Clone ST406 during Chronic Colonization of a Patient with Cystic Fibrosis
van, PloS one 2016 - “...GTG[V] 15 PA4562 General function prediction only [ 13 ] 0321 GGC[G] > GTC[V] 118 PA1171 Cell wall/membrane/envelope biogenesis [ 13 ] 4666 GTC[V] > ATC[I] 204 PA2346 Lipid transport and metabolism [ 13 ] 4610 GTC[V] > GCC[A] 1523 PA2402 Secondary metabolites biosynthesis, transport and...”
- Loss of membrane-bound lytic transglycosylases increases outer membrane permeability and β-lactam sensitivity in Pseudomonas aeruginosa
Lamers, MicrobiologyOpen 2015 - “...sltB1 (PA4001) Cavallari etal. ( 2013 ) Family 3 PAO1 sltG WT with sltG deletion (PA1171) This study Family 3 PAO1 sltH WT with sltH deletion (PA3992) This study Family 3 PAO1 sltB1 / slt sltB1 mutant with slt deletion This study PAO1 sltB1 / G...”
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- Proteomic Analysis of Vesicle-Producing Pseudomonas aeruginosa PAO1 Exposed to X-Ray Irradiation
Zhang, Frontiers in microbiology 2020 - “...Q9I505 PA0953 1.215 0.439 2.768 Probable thioredoxin Q9I4Y4 PA0985 PyoS5 1.363 0.347 3.928 Pyocin S5 Q9I4G6 PA1171 SltB2 1.677 0.419 4.002 Probable lytic murein transglycosylase Q9I4B6 PA1222 MltA 1.367 0.524 2.609 Membrane-bound lytic murein trans-glycosylase A Q9I457 PA1287 1.577 0.733 2.151 Glutathione peroxidase Q9I398 PA1624 1.455...”
PA14_49280 probable transglycolase from Pseudomonas aeruginosa UCBPP-PA14
32% identity, 77% coverage
7qvdAAA 7qvdAAA
32% identity, 81% coverage
PA14_12160 putative murein transglycosylase from Pseudomonas aeruginosa UCBPP-PA14
35% identity, 61% coverage
CBU_0925 lytic murein transglycosylase, putative from Coxiella burnetii RSA 493
35% identity, 66% coverage
- Quantitative Proteome Profiling of Coxiella burnetii Reveals Major Metabolic and Stress Differences Under Axenic and Cell Culture Cultivation
Dresler, Frontiers in microbiology 2019 - “...was upregulated. Further, several peptidoglycan and cell wall biogenesis proteins, including the previously described CBU_0419, CBU_0925, EnhB.1, EnhC, EnhA.4, and EnhA.5, were upregulated in NMI compared to NMII in ACCM-D (Sandoz et al., 2016b ). Three out of 16 LCV-associated proteins, CBU_0658 (unknown function), Bcp, and...”
- “...629.51 0.07 0.19 81.28 0.01 CBU_0915 EnhB.1 Enhanced entry protein 19.05 0.17 6.76 26.48 0.23 CBU_0925 Membrane-bound lytic murein transglycosylase B 2133.04 0.06 8.83 521.19 0.01 CBU_1136 EnhC Enhanced entry protein 492039.54 0.00 10.69 2157744.41 0.00 CBU_1138 EnhA.4 Enhanced entry protein 13997.48 0.02 8.57 4324.11 0.01...”
PA3992 hypothetical protein from Pseudomonas aeruginosa PAO1
35% identity, 61% coverage
- The role of peptidoglycan hydrolases in the formation and toxicity of Pseudomonas aeruginosa membrane vesicles
Chen, microLife 2022 - “...PA3484 PA3764 erfK mltG mltC dacB (PBP4) tse3 mltF PA3992 PA4000 PA4001 PA4003 PA4412 sltB3 (sltH) rlpA sltB1 pbpA murG PA4413 ftsW PA4414 murD PA4417 murE...”
- Polygenic Adaptation and Clonal Interference Enable Sustained Diversity in Experimental Pseudomonas aeruginosa Populations
Harris, Molecular biology and evolution 2021 - “...unclassified, unknown PA14_13150 PA3921 Transcriptional regulators PA14_43150</>PA14_43160 intergenic pscQ pscQ Protein secretion/export apparatus O PA14_12160 PA3992 Putative enzymes PA14_14390</>PA14_14400 intergenic PA14_27610>/>PA14_27620 intergenic PA14_27770 PA2812 Transport of small molecules PA14_51510 PA0988 Hypothetical, unclassified, unknown pstA pstA Transport of small molecules spuF spuF Transport of small molecules str...”
- From Genome to Proteome to Elucidation of Reactions for All Eleven Known Lytic Transglycosylases from Pseudomonas aeruginosa
Lee, Angewandte Chemie (International ed. in English) 2017 - “...(SltG) SltB3 (SltH) Locus tag PA1222 PA4444 PA1812 PA3764 PA2865 PA2963 PA4000 PA3020 PA4001 PA1171 PA3992 1 NR 100 NR NR NR NR NR NR 100 100 100 2 100 100 10 6 5 17 4 41 100 100 100 3 NR NR NR NR NR...”
- Lytic transglycosylases: concinnity in concision of the bacterial cell wall
Dik, Critical reviews in biochemistry and molecular biology 2017 - “..., 2017 ). Family 3B Blackburn and Clarke discovered the enzymes SltB2 (PA1171) and SltB3 (PA3992) in P. aeruginosa in 2002, marking a second subfamily of the Family 3 LTs ( Blackburn & Clarke, 2002 ). Although Family 3B lacks a counterpart protein in either E....”
- “...MltB1 (Smlt4052) 381 41821.6 LtgD (NGO0626) 363 39821.2 Family 3B SltB2 (PA1171) 398 42682.5 SltB3 (PA3992) 448 47760.9 5ANZ (Apo) ( Lee et al. , 2016b ) 5AO7 (NAG-anhNAM-pentapeptide) ( Lee et al. , 2016b ) 5AO8 (NAG-NAM-pentapeptide) ( Lee et al. , 2016b ) MltB2...”
- Turnover of Bacterial Cell Wall by SltB3, a Multidomain Lytic Transglycosylase of Pseudomonas aeruginosa
Lee, ACS chemical biology 2016 - “...properties of SltB3 (also referred to as SltH; the gene for which is annotated as PA3992), a soluble LT of P. aeruginosa . Our analysis of the reaction of this enzyme reveals it to be an exolytic enzyme. We also disclose three high-resolution X-ray structures for...”
- “...is a first step toward this goal. Methods Cloning and Protein Purification The sltB3 gene (PA3992) was cloned according to the methodology reported earlier. 16 The construct was cloned in pET28a(+) (Novagen) using NdeI and XhoI restriction enzymes to generate an N-terminal His-tagged protein lacking the...”
- Structural and Molecular Mechanism of CdpR Involved in Quorum-Sensing and Bacterial Virulence in Pseudomonas aeruginosa
Zhao, PLoS biology 2016 - “...pscC , PA5146 , and PA1271valS , PA0159 , PA4541 , selB , serS , PA3992 , PA5114 , and PA4513 ) and EMSA analyses are described in Materials and Methods. PCR products containing the indicated fragments were added to the reaction mixtures at approximately 40...”
- Loss of membrane-bound lytic transglycosylases increases outer membrane permeability and β-lactam sensitivity in Pseudomonas aeruginosa
Lamers, MicrobiologyOpen 2015 - “...WT with sltG deletion (PA1171) This study Family 3 PAO1 sltH WT with sltH deletion (PA3992) This study Family 3 PAO1 sltB1 / slt sltB1 mutant with slt deletion This study PAO1 sltB1 / G sltB1 mutant with sltG deletion This study PAO1 sltB1 / H...”
- Changes to its peptidoglycan-remodeling enzyme repertoire modulate β-lactam resistance in Pseudomonas aeruginosa
Cavallari, Antimicrobial agents and chemotherapy 2013 - “...transposon ISlacZ/hah insertion at nucleotide 415 of sltH (PA3992) WT with transposon ISlacZ/hah insertion at nucleotide 549 of dacC (PBP6, PA3999) WT with...”
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Aave_3237 lytic murein transglycosylase from Acidovorax avenae subsp. citrulli AAC00-1
34% identity, 60% coverage
MCR_0196 lytic murein transglycosylase from Moraxella catarrhalis BBH18
33% identity, 51% coverage
- Comprehensive antigen screening identifies Moraxella catarrhalis proteins that induce protection in a mouse pulmonary clearance model
Smidt, PloS one 2013 - “...10.1371/journal.pone.0064422.g001 Figure 1 Structural features of 8 potential M. catarrhalis vaccine candidates. MCR_0076, TonB-dependent receptor; MCR_0196, MltB; lytic murein transglycosylase; MCR_0686, peptide methionine sulfoxide reductase MsrA/MsrB; MCR_0996, hypothetical protein; MCR_1003, LysM domain protein; MCR_1010, D-alanyl-D-alanine carboxypeptidase; MCR_1303, oligopeptide ABC transport system substrate binding protein; MCR_1416, cytochrome...”
- “...aa Start-Stop Length No. of non-synonymous/deleted aa No. of isolates MCR_0076 21160 140 10 62 MCR_0196 36485 450 32 63 MCR_0686 28558 531 28 64 MCR_0996 27148 122 21 64 MCR_1003 30375 346 7# 64 MCR_1010 27386 360 21 64 MCR_1303 24679 656 31 64 MCR_1416...”
XAUB_14690 lytic murein transglycosylase from Xanthomonas citri pv. aurantifolii str. ICPB 11122
36% identity, 60% coverage
- Periplasm-enriched fractions from Xanthomonas citri subsp. citri type A and X. fuscans subsp. aurantifolii type B present distinct proteomic profiles under in vitro pathogenicity induction
Zandonadi, PloS one 2020 - “...in the XauB genome, by the respective ORFs XAUB_38360, XAUB_35470, XAUB_35460 and XAUB_22380, XAUB_19220, XAUB_050050, XAUB_14690, XAUB_27370, XAUB_40270, XAUB_05860, XAUB_32540. These XauB proteins are more than 98% identical to XACs homologue proteins. XI is also codified in XauB genome by ORF XAUB_09030. With the exception for...”
5anzA / Q9HX28 Crystal structure of sltb3 from pseudomonas aeruginosa. (see paper)
35% identity, 73% coverage
- Ligand: calcium ion (5anzA)
hpaJ / AAR23828.1 putative murein transglycosylase precursor from Xanthomonas euvesicatoria (see paper)
XCV2440 Lytic murein transglycosylase precursor from Xanthomonas campestris pv. vesicatoria str. 85-10
36% identity, 59% coverage
- The Predicted Lytic Transglycosylase HpaH from Xanthomonas campestris pv. vesicatoria Associates with the Type III Secretion System and Promotes Effector Protein Translocation
Hausner, Infection and immunity 2017 - “...85-10 contains an additional predicted LT gene, hpaJ (XCV2440), which is coregulated with T3S genes and might share functional redundancy with hpaH (15, 45,...”
- Whole-Genome Sequences of Xanthomonas euvesicatoria Strains Clarify Taxonomy and Reveal a Stepwise Erosion of Type 3 Effectors
Barak, Frontiers in plant science 2016 - “...xopAQ locus, we found a corresponding region in the reference strain 85-10, harboring XCV2439 and XCV2440 ( hpaJ ), in one of the two flanking sequences (2 kb). Similarly, for the xopAF2 locus, only one of the two flanking sequences has a counterpart in strain 85-10,...”
XACb0007 lytic murein transglycosylase from Xanthomonas axonopodis pv. citri str. 306
XAC_RS22275 lytic murein transglycosylase from Xanthomonas citri pv. citri str. 306
36% identity, 59% coverage
- Periplasm-enriched fractions from Xanthomonas citri subsp. citri type A and X. fuscans subsp. aurantifolii type B present distinct proteomic profiles under in vitro pathogenicity induction
Zandonadi, PloS one 2020 - “...2018 61 65 VII P XAC1719 Enolase (16) 46.0 5.0 161 4 8 I C XACb0007 Lytic murein transglycosylase (2) 46.2 5.9 128 5 14 IV M+ XAC0957 Elongation factor Tu (4) 43.3 5.5 88 4 10 III C XAC1776 Xylose isomerase (2) 48.5 5.3 71...”
- “...proteins (XAC0223 and XAC0901), succinyl-CoA synthetase -subunit (SucCD, XAC3236), adenylosuccinate synthetase (XAC1158), lytic murein transglycosylase (XACb0007), enolase (XAC1719), elongation factor Tu (XAC0957), phosphoglucomutase/phosphomannomutase (PGM, XAC3579), and TolC (XAC3463). Xylose isomerase (XI) was also detected for XAC (XAC1776, Table 1 ). All these mentioned proteins detected for...”
- Comparative proteomic analysis of Xanthomonas citri ssp. citri periplasmic proteins reveals changes in cellular envelope metabolism during in vitro pathogenicity induction
Artier, Molecular plant pathology 2018 (secret) - Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection
Moreira, BMC microbiology 2017 - “...Up 1.93 21.98 96.64 A/B/LPS 11 XAC3579 Phosphoglucomutase xanA Up 0.19 3.91 7.29 A/B/LPS 13 XACb0007 XAC3225 Lytic mureintransglycosylase Transglycosylase mlt mltB Up 8.11 71.06 113.00 A/B/LPS 17 XAC3602 Cystathionine gamma-lyase-like protein metB Up 0.00 2.67 12.91 A/B/LPS 18 XAC2504 Regulator of pathogenicity factors rpfN Up...”
- “...plant tissue, compensating the lack of sugar caused by the mutation. The gene encoding Mlt (XACb0007), a transglycosylase protein, is located in the pXAC64 plasmid in a region of 7260bp. A gene with 95% of sequence similarity ( mltB XAC3225) can be found in the chromosome....”
- Unravelling potential virulence factor candidates in Xanthomonas citri. subsp. citri by secretome analysis
Ferreira, PeerJ 2016 - “...name Product Cat. NCBI ID hrpB4 (NB) Xac (NB) hrpB4 (XAM1) Xac (XAM1) SP PIP XACb0007 mlt Lytic murein transglycosylase IV 1158494 + Y N XAC4344 vacJ Lipoprotein III 1158415 + Y N XAC3664 ompW Outer membrane protein IV 1157735 + Y N XAC1761 Hypothetical protein...”
- “...is a lytic murein transglycosylase. Xac has two copies of the mlt gene, XAC3225 and XACb0007, which are located on the chromosome and on the pXAC64 plasmid, respectively. The chromosomal copy of the gene is flanked by genes that encode the T3SS, XopE3 and XopAI effector...”
- Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness
Oliveira, PeerJ 2018 - “...arsenal, in particular, is limited. Previous studies had investigated the plasmid pXAC64 LT copy ( XAC_RS22275 ; mltB2 .1) in XccA using functional assays. The results suggested a role in XccA interaction with the citrus host ( Laia et al., 2009 ). XAC_RS22275 has a paralogue...”
- “...and the plant-pathogen interaction virulence process, we generated site-directed deletion mutants of Tn Xax1.1 ( XAC_RS22275 ) and Tn Xax1 .2 ( XAC_RS16355 ) LT passenger genes in various combinations and examined the effects on a number of properties associated with virulence and pathogenicity. Materials and...”
XAC_RS16355 lytic murein transglycosylase from Xanthomonas citri pv. citri str. 306
XAC3225 transglycosylase from Xanthomonas axonopodis pv. citri str. 306
36% identity, 59% coverage
- Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness
Oliveira, PeerJ 2018 - “...with the citrus host ( Laia et al., 2009 ). XAC_RS22275 has a paralogue copy, XAC_RS16355 ( mltB2 .2), situated on the XccA chromosome, with 99% identity to the plasmid copy. Both copies are passenger genes of derivatives of a Tn 3 family transposon, Tn Xax1...”
- “...generated site-directed deletion mutants of Tn Xax1.1 ( XAC_RS22275 ) and Tn Xax1 .2 ( XAC_RS16355 ) LT passenger genes in various combinations and examined the effects on a number of properties associated with virulence and pathogenicity. Materials and Methods Identification and in silico analysis of...”
- Comparative proteomic analysis of Xanthomonas citri ssp. citri periplasmic proteins reveals changes in cellular envelope metabolism during in vitro pathogenicity induction
Artier, Molecular plant pathology 2018 (secret) - Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection
Moreira, BMC microbiology 2017 - “...1.93 21.98 96.64 A/B/LPS 11 XAC3579 Phosphoglucomutase xanA Up 0.19 3.91 7.29 A/B/LPS 13 XACb0007 XAC3225 Lytic mureintransglycosylase Transglycosylase mlt mltB Up 8.11 71.06 113.00 A/B/LPS 17 XAC3602 Cystathionine gamma-lyase-like protein metB Up 0.00 2.67 12.91 A/B/LPS 18 XAC2504 Regulator of pathogenicity factors rpfN Up 354.75...”
- “...plasmid in a region of 7260bp. A gene with 95% of sequence similarity ( mltB XAC3225) can be found in the chromosome. This region in the plasmid is flanked downstream by xopE2 , while the same region on the chromosome is flanked upstream by xopE3 and...”
- Unravelling potential virulence factor candidates in Xanthomonas citri. subsp. citri by secretome analysis
Ferreira, PeerJ 2016 - “...Mlt, which is a lytic murein transglycosylase. Xac has two copies of the mlt gene, XAC3225 and XACb0007, which are located on the chromosome and on the pXAC64 plasmid, respectively. The chromosomal copy of the gene is flanked by genes that encode the T3SS, XopE3 and...”
- The type III protein secretion system contributes to Xanthomonas citri subsp. citri biofilm formation
Zimaro, BMC microbiology 2014 - “...4,6-dehydratase 235 Q8PGN1_XANAC 38.6/5.86 48.0/4.7 12/17% 2.1 XAC0612 Cellulase 245 Q8PPS3_XANAC 51.6/5.76 57.0/4.9 23/32% 2.6 XAC3225 Transglycosylase 178 Q8PHM6_XANAC 46.2/5.89 53.0/4.8 14/22% 1.6 01.06 Lipid, fatty acid and isoprenoid metabolism XAC3300 Putative esterase precursor (EstA) 96 Q8PHF7_XANAC 35.9/6.03 62.0/6.2 3/4% 3.1 XAC1484 Short chain dehydrogenase precursor...”
- Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii
Moreira, BMC genomics 2010 - “...important elements of this region (Fig. 4 ). Next to xopE3 (XAC3224) we find gene XAC3225, whose product is annotated as tranglycosylase mltB . This gene has strong similarity (e-value 10 -133 , 100% coverage) to hopAJ1 from P. syringae pv. tomato strain DC3000, where it...”
- “...substrate, it contributes to effector translocation [ 50 ]. A mutant with a deletion of XAC3225 has reduced ability to cause canker (mutant phenotypes include a reduction in water soaking, hyperplasia, and necrosis compared to wild type) [ 31 ]. We thus conclude that the effector...”
- New genes of Xanthomonas citri subsp. citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library
Laia, BMC microbiology 2009 - “...results indicated that the ORFs XAC0102, XAC1495, XAC2053, XAC3263, XAC3285, XAC0340, XAC0095, XAC1927, XAC2047 and XAC3225 are only expressed when Xcc is multiplied in vivo ; it was not possible to identify expression of these ORFs when cells were multiplied in vitro . A single ORF,...”
- “...exclusive to Xcc. However, regions 2, 3 and 5, which contain respective knockout ORFs XAC2639, XAC3225 and XAC3320, are present in at least one of the other studied genomes, but not in all (Fig. 5 ). In addition, some characteristics of these regions, such as abnormal...”
Smlt4650 putative transglycosylase protein from Stenotrophomonas maltophilia K279a
37% identity, 62% coverage
- Lytic transglycosylases: concinnity in concision of the bacterial cell wall
Dik, Critical reviews in biochemistry and molecular biology 2017 - “...or N. gonorrhoeae , sequence analysis reveals a Family 3B representative in S. maltophilia (MltB2, Smlt4650) ( Wu et al. , 2016 ). Family 3B LTs have the following sequence identity (query coverage) to E. coli MltB: P. aeruginosa SltB2 33% (75%), P. aeruginosa SltB3 34%...”
- “...et al. , 2016b ) 5AO8 (NAG-NAM-pentapeptide) ( Lee et al. , 2016b ) MltB2 (Smlt4650) 422 44588.4 Table 4 Summary of the Gram-negative Family 4 LTs. Length (AA) MW (Da) Apo Structure Complex Structure Family 4A LAL (Bacteriophage ) 154 17368.7 1AM7 ( Evrard et...”
- Interplay among membrane-bound lytic transglycosylase D1, the CreBC two-component regulatory system, the AmpNG-AmpDI-NagZ-AmpR regulatory circuit, and L1/L2 β-lactamase expression in Stenotrophomonas maltophilia
Huang, Antimicrobial agents and chemotherapy 2015 - “...including mltA (Smlt0155), two mltB genes (Smlt4052 and Smlt4650), two mltD genes (Smlt0994 and Smlt3434), and slt (Smlt4007) (see Table S2 in the supplemental...”
- “...before and after induction. mologues of Smlt0155, Smlt4052, Smlt4650, Smlt0994, Smlt3434, and Smlt4007 in S. maltophilia KJ were named mltA, mltB1, mltB2,...”
ABZJ_00028 lytic murein transglycosylase from Acinetobacter baumannii MDR-ZJ06
36% identity, 52% coverage
- Colistin Resistance in Acinetobacter baumannii MDR-ZJ06 Revealed by a Multiomics Approach
Hua, Frontiers in cellular and infection microbiology 2017 - “...0.029905 ABZJ_01829 Acyl-CoA dehydrogenase 1.402255 6.594396 4.45E-06 3.56E-05 ABZJ_01150 hypothetical protein 1.321675 3.205499 0.000936 0.003799 ABZJ_00028 lytic murein transglycosylase family protein 1.296752 10.96489 3.46E-14 9.79E-13 ABZJ_00976 hypothetical protein 1.295503 5.552053 1.46E-07 1.57E-06 ABZJ_01855 hypothetical protein 1.290522 2.587494 0.016132 0.044395 ABZJ_01186 hypothetical protein 1.249298 2.481015 0.013475 0.038054...”
- “...1.09309 ABZJ_01133 heat shock protein 2.180888936 0.532117 ABZJ_00060 Thiol-disulfide isomerase and thioredoxin 1.894317881 a 0.65529 ABZJ_00028 lytic murein transglycosylase family protein 1.296751692 a 0.57293 ABZJ_01078 hypothetical protein 1.081092562 0.44448 ABZJ_03720 UDP-3-O-acyl-N-acetylglucosamine deacetylase 1.144287283 0.48378 ABZJ_03859 putative RND type efflux pump involved in aminoglycoside resistance (AdeT) 1.173634714...”
ABAYE3869 putative membrane-bound lytic murein transglycosylase from Acinetobacter baumannii AYE
AB57_0044 transglycolase from Acinetobacter baumannii AB0057
36% identity, 52% coverage
- A subtractive proteomics approach for the identification of immunodominant Acinetobacter baumannii vaccine candidate proteins
Acar, Frontiers in immunology 2022 - “...B0VB25 Uncharacterized protein 15,778 144 ABAYE2389 26. B0V5U8 Putative membrane-bound lytic murein transglycosylase 46,973 430 ABAYE3869 27. B0VDR4 Uncharacterized protein 366,110 3,369 ABAYE0821 Calcium ion binding 28. A0A0R4J8Q3 Peptidyl-prolyl cis-trans isomerase 25,601 235 fklB Membrane Peptidyl-prolyl cis-trans isomerase activity 29. B0V9U0 Uncharacterized protein 27,620 241 ABAYE0130...”
- The lytic transglycosylase MltB connects membrane homeostasis and in vivo fitness of Acinetobacter baumannii
Crépin, Molecular microbiology 2018 - “...compensatory mechanism that might explain the increase membrane permeability of the mltB mutant. Expression of AB57_0044 , AB57_1136 and AB57_3476 was quantified by qRTPCR and was compared between the WT, the mltB mutant and the complemented strain. Genes AB57_1136 and AB57_3476 were induced 2.52 and 2.93fold...”
AUP74_01186 lytic murein transglycosylase from Microbulbifer aggregans
32% identity, 54% coverage
Dd586_1899 lytic murein transglycosylase from Dickeya dadantii Ech586
32% identity, 56% coverage
Dd1591_1902 lytic murein transglycosylase from Dickeya zeae Ech1591
31% identity, 60% coverage
M892_06105 lytic transglycosylase domain-containing protein from Vibrio campbellii ATCC BAA-1116
35% identity, 62% coverage
- Vibrio campbellii hmgA-mediated pyomelanization impairs quorum sensing, virulence, and cellular fitness
Wang, Frontiers in microbiology 2013 - “...protein 2.08E-07 1.37 0.13 10.54 L M892_12540 Replicative DNA helicase 7.48E-05 1.11 0.63 1.76 L M892_06105 Membrane-bound lytic murein transglycosylase B 2.70E-05 1.36 0.85 1.60 M M892_08355 UDP-3-O-3-hydroxymyristoyl N-acetylglucosamine deacetylase 5.65E-04 2.28 1.56 1.46 M M892_08935 UDP-N-acetylmuramate-L-alanyl-gamma-D-glutamyl-m eso-diaminopimelate ligase 1.23E-04 1.05 0.48 2.19 M M892_12935 UDP-N-acetylglucosamine...”
SPO3617 lytic murein transglycosylase from Ruegeria pomeroyi DSS-3
37% identity, 58% coverage
- Aminolipids elicit functional trade-offs between competitiveness and bacteriophage attachment in Ruegeria pomeroyi
Stirrup, The ISME journal 2023 - “...0.2 0.509 0.191 SPO1330 ( hflC ) Protein HflC 291 1.3 1.2 + 0.005 2.285 SPO3617 Peptidoglycan-binding protein 385 1.3 0.3 + 0.003 1.509 SPO0398 Uncharacterized protein 391 1.1 0.4 0.273 0.261 SPO3165 ( atpH ) ATP synthase subunit delta 186 0.9 1.0 0.278 0.513 SPO1329...”
- “...1.3 0.009 0.808 SPO1670 Outer membrane protein assembly factor BamA 787 3.1 1.8 0.012 0.480 SPO3617 Peptidoglycan-binding protein, putative 385 2.8 2.0 + 0.002 1.373 SPO0504 Uncharacterized protein 207 2.2 0.8 0.210 0.211 SPO1240 ( tolC ) Type I secretion outer membrane protein, TolC 472 1.9...”
- Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3
Rivers, Frontiers in microbiology 2016 - “...2-oxoacid ferredoxin oxidoreductase Amino acid metabolism 0.001 SPO2180 Hypothetical protein 0.002 SPO0940 Hypothetical protein 0.005 SPO3617 Peptidoglycan-binding protein, putative Cell-cell interaction 0.005 SPO1609 Polyamine ABC transporter, ATP-binding Transport 0.008 SPO0831 Xanthine dehydrogenase family, medium subunit Nucleic acid metabolism 0.009 SPO0937 Hypothetical protein 0.009 trans21 264 SPO1144...”
Dshi_1864 lytic murein transglycosylase from Dinoroseobacter shibae DFL 12
36% identity, 59% coverage
- Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif
Wang, mSystems 2021 - “...Iron metabolism 8.29E03 6.96E03 0.83 Dshi_1122 Tetratricopeptide region OM lipoprotein Not assigned 7.82E03 1.20E03 0.78 Dshi_1864 Putative membrane-bound lytic murein transglycosylase OM lipoprotein Not assigned 7.21E03 1.02E03 0.72 Dshi_2254 Putative polysaccharide export protein OM lipoprotein Transporter 7.06E03 2.85E03 0.71 Dshi_1499 Hypothetical protein OM-associated/OM -barrel protein Hypothetical...”
- “...in Pseudomonas aeruginosa ( 63 ). Finally, the putative membrane bound lytic murein transglycosylase (LMT) (Dshi_1864) (0.7%) divides the septal murein into separate peptidoglycan layers by reducing cross-links and is required for septum formation and OMV biogenesis ( 4 ). To identify proteins that may be...”
B1917_RS10525 lytic murein transglycosylase from Bordetella pertussis B1917
32% identity, 59% coverage
SMc04024 PUTATIVE MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE PROTEIN from Sinorhizobium meliloti 1021
Q92M47 Membrane-bound lytic murein transglycosylase from Rhizobium meliloti (strain 1021)
35% identity, 53% coverage
- Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides
Arnold, mBio 2017 - “...( smc00716 , ftsX ), an amidase ( smc01854 , ampD ), a transglycosylase ( smc04024 ), and a hydrolase ( smc04025 ). While most of these genes are not characterized, smc01188 , encoding a putative d -alanyl- d -alanine-carboxypeptidase is 49% similar to the Bradyrhizobium...”
- The twin arginine transport system appears to be essential for viability in Sinorhizobium meliloti
Pickering, Journal of bacteriology 2010 - “...determined from the database of essential genes (DEG), smc04024 and smc04449 were homologous with two genes annotated to be essential in Haemophilus influenzae....”
- Comparative Proteomic Analysis Revealing ActJ-Regulated Proteins in Sinorhizobium meliloti.
Albicoro, Journal of proteome research 2023
Q889A9 Type III helper protein HopAJ1 from Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)
PSPTO_0852 type III helper protein HopPmaG(Pto) from Pseudomonas syringae pv. tomato str. DC3000
33% identity, 65% coverage
- Genome Wide Analysis of the Potato Soft Rot Pathogen Pectobacterium carotovorum Strain ICMP 5702 to Predict Novel Insights into Its Genetic Features.
Mallick, The plant pathology journal 2022 - “...DspE (type III effector protein AvrE1) Peg.1620 268 blr1656 Q89TW7 Blr1656 protein Peg.1939 413 hopAJ1 Q889A9 Type III helper protein HopAJ1 Peg.2009 442 yscN Q9Z7J8 H(+)-transporting two-sector ATPase Peg.479 363 XOO4042 Q5GVH7 Uncharacterized protein Peg.3984 3,056 aroK Q989M4 Shikimate kinase (SK) Peg.2376 208 hrpW Q60236 Harpin...”
- Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000
Filiatrault, PloS one 2011 - “...recognizable promoter motifs associated with them. Genes exhibiting antisense activity include PSPTO_0044 ( hopK1 ), PSPTO_0852 ( hopAJ1 ), PSPTO_2862, and PSPTO_4302 ( Figure 6A ). Interestingly, Swingle et al. previously detected a predicted a PvdS binding site antisense to PSPTO_2862 [19] . Many other (100)...”
- “...PSPTO_2227 (2) motif2 PSPTO_2194 gltA PSPTO_1938 PSPTO_1935 flgD motif9 PSPTO_1595 motif1 PSPTO_1591 motif1 PSPTO_1321 motif3 PSPTO_0852 hopAJ1 PSPTO_0848 PSPTO_0803 (2) motif1 PSPTO_0607 motif5 PSPTO_0416 motif5 PSPTO_0336 motif9 PSPTO_0044 (4) hopK1 5-ends in selected genes colored green PSPTO_5391 PSPTO_5345 PSPTO_5331 PSPTO_5251 hemB motif 1 PSPTO_5133 motif 3...”
- Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity
Filiatrault, Journal of bacteriology 2010 - “...of the T3S system: hopK1 (PSPTO_0044), hopAJ1 (PSPTO_0852), and hopAK1 (PSPTO_4101), as well as the transcriptional regulator aefR (PSPTO_3549) (60, 61)....”
WN72_26565 lytic murein transglycosylase from Bradyrhizobium arachidis
41% identity, 40% coverage
- Bacteroid Development, Transcriptome, and Symbiotic Nitrogen-Fixing Comparison of Bradyrhizobium arachidis in Nodules of Peanut (Arachis hypogaea) and Medicinal Legume Sophora flavescens
Chen, Microbiology spectrum 2023 - “...S. flavescens , except for the genes encoding FtsW (WN72_33790), MltB (lytic murein transglycosylase [WN72_06590, WN72_26565, WN72_12370, and WN72_38260]), Pbp (peptidoglycan-binding protein [WN72_00345 and WN72_06690]), and Pbl (LysM peptidoglycan-binding domain-containing protein [WN72_37580]). Extremely significant differences ( q < 0.001) between the bacteroids of the two hosts...”
BAW_20069 lytic murein transglycosylase from Brucella abortus
Q2YIT4 Putative peptidoglycan binding domain 1 from Brucella abortus (strain 2308)
BAB2_0069 Putative peptidoglycan binding domain 1 from Brucella melitensis biovar Abortus 2308
31% identity, 58% coverage
- The regulon of Brucella abortus two-component system BvrR/BvrS reveals the coordination of metabolic pathways required for intracellular life
Rivas-Solano, PloS one 2022 - “...significant ChIP-Seq signals dataset. B. Schematic non-scale representation of the virB operon and upstream gene BAW_20069. Orange numbers represent each of the three significant ChIP-Seq signals in this region. The zoomed area represents a 226bp virB1 upstream region, with a promoter region previously reported [ 42...”
- “...of the location of the five ChIP-Seq signals found within the vicinity of virB1 and BAW_20069, the four putative DNA binding motifs found within the virB promoter, and the BvrR-P binding site confirmed by EMSA and Dnase I footprinting. Fig 5F also shows the location of...”
- Brucella abortus Encodes an Active Rhomboid Protease: Proteome Response after Rhomboid Gene Deletion
Marchesini, Microorganisms 2022 - “...in secretory proteins were also addressed. Differentially represented proteins included a putative lytic murein transglycosylase (Q2YIT4), nitrous-oxide reductase NosZ (Q2YJW2) and high oxygen affinity Cbb3-type cytochrome c oxidase subunit (Q2YM85). Deletion of rhomboid had no obvious effect in B. abortus virulence. However, rhomboid overexpression had a...”
- Increased Brucella abortus asRNA_0067 expression under intraphagocytic stressors is associated with enhanced virB2 transcription
Muñoz-Bucio, Archives of microbiology 2024 - “...of the virB operon. The RNA_0069 is located in the antisense strand between the genes BAB2_0069 and virB1 . Meanwhile, the asRNA_0067 is situated antisense and between the virB1 and virB2 genes, exhibiting high sequence complementarity with the virB2 gene, leading to its designation as asRNA_0067...”
XAC_RS21660 lytic murein transglycosylase from Xanthomonas citri pv. citri str. 306
XAC4296 epimerase from Xanthomonas axonopodis pv. citri str. 306
35% identity, 37% coverage
- XAC4296 Is a Multifunctional and Exclusive Xanthomonadaceae Gene Containing a Fusion of Lytic Transglycosylase and Epimerase Domains
de, Microorganisms 2022 - “...citri fitness [ 24 ]. We also identified another 3B-like LT named XAC4296 (NCBI locus_tag: XAC_RS21660). Notably, apart from the Transglycosylase SLT 2 (IPR031304) and Peptidoglycan binding-like (IPR002477) domains, XAC4296 contains an additional and unexpected aldose 1-epimerase domain (IPR015443) linked to carbohydrate metabolism, and potentially showing...”
- Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness
Oliveira, PeerJ 2018 - “...357 5A Regulates peptidoglycan strand length XAC_RS03440 rlpA 786,246..787,673 475 6A Cell division and/or morphogenesis XAC_RS21660 n/a 5,077,186..5,079,348 828 Unclassified/related to 3B Carbohydrate metabolic process/peptidoglycan binding function XAC_RS15470 mtgA 3,564,980..3,565,720 246 Biosynthetic peptidoglycan transglycosylase Peptidoglycan biosynthesis Notes: citri 306 genome and pXAC64 plasmid classification and proposed...”
- “...a general function related to the rearrangement of the peptidoglycan layer. The non-categorized LT ( XAC_RS21660 ) is exclusive to the Xanthomonas genus. It is related to the 3B subfamily, but contains an additional glycoside hydrolase-type carbohydrate-binding domain (IPR014718) linked to carbohydrate metabolism ( Fig. S2...”
- XAC4296 Is a Multifunctional and Exclusive Xanthomonadaceae Gene Containing a Fusion of Lytic Transglycosylase and Epimerase Domains
de, Microorganisms 2022 - “...pmc Microorganisms Microorganisms microorganisms Microorganisms 2076-2607 MDPI 9143381 10.3390/microorganisms10051008 microorganisms-10-01008 Article XAC4296 Is a Multifunctional and Exclusive Xanthomonadaceae Gene Containing a Fusion of Lytic Transglycosylase and Epimerase Domains https://orcid.org/0000-0002-7898-9707 de Oliveira Amanda C. P. 1 2 Ferreira Rafael M. 2 3 Ferro...”
- “...(LTs) superfamily, play an essential role in X. citri biology. One of these LTs, named XAC4296, apart from the Transglycosylase SLT_2 and Peptidoglycan binding-like domains, contains an unexpected aldose 1-epimerase domain linked to the central metabolism; therefore, resembling a canonical MFE. In this work, we experimentally...”
APL_0642 membrane-bound lytic murein transglycosylase B from Actinobacillus pleuropneumoniae L20
31% identity, 61% coverage
BM28_RS10610 lytic murein transglycosylase from Brucella melitensis M28
31% identity, 58% coverage
E2P69_RS14605 lytic murein transglycosylase from Xanthomonas perforans
34% identity, 37% coverage
WN72_12370 lytic murein transglycosylase from Bradyrhizobium arachidis
31% identity, 55% coverage
- Bacteroid Development, Transcriptome, and Symbiotic Nitrogen-Fixing Comparison of Bradyrhizobium arachidis in Nodules of Peanut (Arachis hypogaea) and Medicinal Legume Sophora flavescens
Chen, Microbiology spectrum 2023 - “...flavescens , except for the genes encoding FtsW (WN72_33790), MltB (lytic murein transglycosylase [WN72_06590, WN72_26565, WN72_12370, and WN72_38260]), Pbp (peptidoglycan-binding protein [WN72_00345 and WN72_06690]), and Pbl (LysM peptidoglycan-binding domain-containing protein [WN72_37580]). Extremely significant differences ( q < 0.001) between the bacteroids of the two hosts were...”
Atu3779 lytic murein transglycosylase from Agrobacterium tumefaciens str. C58 (Cereon)
34% identity, 58% coverage
- A peptidoglycan N-deacetylase specific for anhydroMurNAc chain termini in Agrobacterium tumefaciens
Gilmore, The Journal of biological chemistry 2024 - “...anhydro- and deacetylated anhydromuropeptides by UPLCMS in a 6 LT mutant (Atu0009Atu0092Atu1022Atu2112Atu2117Atu3779), which includes mltB (Atu3779), previously shown to be the most active in -lactamase induction ( 8 ) indicating a significant PG turnover activity that is not compensated for by the other LTs. If the...”
- Transcription Factor PecS Mediates Agrobacterium fabrum Fitness and Survival
Nwokocha, Journal of bacteriology 2023 (secret) - Induction of AmpC-Mediated β-Lactam Resistance Requires a Single Lytic Transglycosylase in Agrobacterium tumefaciens
Figueroa-Cuilan, Applied and environmental microbiology 2022 - “...generation of cell lysates. Data represent one of two biological replicates. Absence of MltB3 ( atu3779 ) leads to a failure of AmpC-dependent induction of -lactamases. Lytic transglycosylases (LTs) are likely to function as the enzymes that generate the AmpR-activating fragments. Different families of LTs have...”
- “...redundancy, we found that deletion of a single, family 3, membrane-bound lytic transglycosylase, MltB3 ( atu3779 ), causes ampicillin hypersensitivity (Fig. S4B). Treatment of mltB3 cells with AMP 25 for 2 h causes a cell lysis defect (28.8%) ( Fig. 4A and B ) and results...”
- Peptidoglycan recycling mediated by an ABC transporter in the plant pathogen Agrobacterium tumefaciens
Gilmore, Nature communications 2022 - “...detrimental mutants included a putative LD-transpeptidase (Atu1615), bifunctional PBP1b (Atu0931), DD-carboxypeptidase (Atu1499), and LTs MltB (Atu3779), MltG (Atu1099) and RlpA (Atu1500), suggesting that additive effects caused by the loss of these PG synthesis and remodelling proteins in combination with PG recycling results in loss of fitness...”
- Glycoside Hydrolase Genes Are Required for Virulence of Agrobacterium tumefaciens on Bryophyllum daigremontiana and Tomato
Mathews, Applied and environmental microbiology 2019 - “...site), Atu2489 (membrane-bound lytic murein transglycosylase B), Atu3779 (lytic murein transglycosylase), and Atu8140 (lysozyme-like) (22). Four of the genes...”
CLIBASIA_00965 lytic murein transglycosylase from Candidatus Liberibacter asiaticus str. psy62
33% identity, 53% coverage
G293_01215 lytic transglycosylase domain-containing protein from Candidatus Liberibacter africanus PTSAPSY
31% identity, 53% coverage
- The flagella of 'Candidatus Liberibacter asiaticus' and its movement in planta
Andrade, Molecular plant pathology 2020 - “...SLT domain is indicated in green. CLas, Ca. Liberibacter asiaticus (CLIBASIA_00965); CLaf, Ca. Liberibacter africanus (G293_01215); CLam, Ca. Liberibacter americanus (Lam_376); CLso, Ca. Liberibacter solanacearum (CKC_02595); Lcc, Liberibacter crescens BT1 (B488_10490). Click here for additional data file. Fig. S2 Swimming motility assay of the Agrobacterium tumefaciens...”
RSP_2163 lytic murein transglycosylase, putative from Rhodobacter sphaeroides 2.4.1
38% identity, 34% coverage
- Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
Dufour, PLoS genetics 2012 - “...RSP_3722 Fatty acid and cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides RSP_1491, RSP_2163, RSP_3721 Degradation RSP_0119 Other RSP_0422, RSP_0595, RSP_0855 Regulatory functions DNA interactions RSP_1083, RSP_4210 Other RSP_0148, RSP_2631, RSP_3430, RSP_3431 Transcription factors RSP_0601 Cellular processes Detoxification RSP_1057, RSP_2389, RSP_2693, RSP_3263 Toxin production...”
SMc04411 PUTATIVE MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE SIGNAL PEPTIDE PROTEIN from Sinorhizobium meliloti 1021
37% identity, 34% coverage
B488_10490 lytic transglycosylase domain-containing protein from Liberibacter crescens BT-1
37% identity, 39% coverage
- The flagella of 'Candidatus Liberibacter asiaticus' and its movement in planta
Andrade, Molecular plant pathology 2020 - “...(G293_01215); CLam, Ca. Liberibacter americanus (Lam_376); CLso, Ca. Liberibacter solanacearum (CKC_02595); Lcc, Liberibacter crescens BT1 (B488_10490). Click here for additional data file. Fig. S2 Swimming motility assay of the Agrobacterium tumefaciens wildtype, flaAD and flaABCD mutant strains, and the mutant strains complemented with Candidatus Liberibacter asiaticus...”
SPO2296 lytic transglycosylase domain-containing protein from Ruegeria pomeroyi DSS-3
36% identity, 34% coverage
Atu2489 hypothetical protein from Agrobacterium tumefaciens str. C58 (Cereon)
40% identity, 34% coverage
BMEI0223 MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE B from Brucella melitensis 16M
36% identity, 38% coverage
- Immuno-profiling of Brucella proteins for developing improved vaccines and DIVA capable serodiagnostic assays for brucellosis
Nandini, Frontiers in microbiology 2023 - “...Flagellar motor protein MotB BMEII0154 Oligopeptide-binding protein appa precursor BMEII0859 Membrane-bound lytic murein transglycosylase B BMEI0223 Hypothetical protein BMEI0051 Hypothetical protein BMEI0063 Alkaline phosphatase BMEI0790 Hypothetical protein BMEI1865 tRNA (guanine-N(1)-)-methyltransferase BMEI0149 Ribosome biogenesis GTP-binding protein YsxC BMEII0274 Membrane metalloprotease BMEI0829 Cytoplasmic protein BMEII0772 D-ribose-binding periplasmic protein...”
- Global analysis of quorum sensing targets in the intracellular pathogen Brucella melitensis 16 M
Uzureau, Journal of proteome research 2010 - “...AAL53120.1 0.60 GSLQNEPDILAALDR 4 121 806,4188 2+ Q-TOF vjbR , pH 711 NL Cell wall/envelope BMEI0223 Membrane-bound lytic murein transglycosylase B AAL51405.1 2.56 YAQATINADR 3 79 561,8065 2+ Q-TOF a A. Proteins identified in the 2D-DIGE analysis of babR and vjbR mutant strains. B. Proteins identified...”
- “...LSU Ribosomal Protein L28P 2.27 1.34 BMEI0195 ATP-Dependent Clp Protease, ATP-Binding Subunit ClpB 1.26 1.57 BMEI0223 Membrane Bound Lytic Murein Transglycolase 2.56 1.38 BMEI0742 Protein Translation Elongation Factor Tu (EF-Tu) 1.81 1.30 BMEI0753 SSU Ribosomal Protein S7P 1.37 1.26 BMEI0754 Protein Translation Elongation Factor G (EF-G)...”
RL4716 hypothetical protein from Rhizobium leguminosarum bv. viciae 3841
38% identity, 34% coverage
- Bacteroid Development, Transcriptome, and Symbiotic Nitrogen-Fixing Comparison of Bradyrhizobium arachidis in Nodules of Peanut (Arachis hypogaea) and Medicinal Legume Sophora flavescens
Chen, Microbiology spectrum 2023 - “...bacteroids might be another determinant factor for the formation of swollen bacteroids. Lytic transglycosylase domain (RL4716) was required for proper cell envelope function in R. leguminosarum , while the mutation of RL4716 domain influenced only the shape of free-living cells ( 50 ), and the differentiation...”
- “..., Yost CK . 2017 . An uncharacterized gene coding a conserved lytic transglycosylase domain (RL4716) is required for proper cell envelope function in Rhizobium leguminosarum . FEMS Microbiol Lett 364 : fnx035 . doi: 10.1093/femsle/fnx035 . 51 Glazebrook J , Ichige A , Walker GC...”
- An uncharacterized gene coding a conserved lytic transglycosylase domain (RL4716) is required for proper cell envelope function in Rhizobium leguminosarum
Neudorf, FEMS microbiology letters 2017 (PubMed)- “...gene coding a conserved lytic transglycosylase domain (RL4716) is required for proper cell envelope function in Rhizobium leguminosarum Kara D. Neudorf...”
- “...of growth on peptide-rich media, this study identified RL4716 as being required for proper cell envelope function in R. leguminosarum. Mutation of RL4716...”
- The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum
Perry, Frontiers in microbiology 2016 - “...protein RL4065 TGI 3 0.67 1 NE 3 0 0 NE 0.0.1 Conserved hypothetical protein RL4716 TGI 18 1 37.17 NE 18 0.61 6.55 GD 0.0.1 Conserved hypothetical exported protein RL0109 TGI 8 0.75 8.5 NE 8 0.25 2.5 GD 0.0.2 Conserved hypothetical protein RL0890 TGI...”
- “...transmembrane domains (RL1526, RL2641), AAAATPase domain (RL2625), or N-terminal secretion signals (RL3761, RL1528, RL1618A, RL2086, RL4716) that were GI on TY medium (Supplementary File 1 ). These findings suggest that the TGI phenotype collectively may be centered around cell sensing and stress response at the cell...”
RHE_CH04101 putative membrane-bound lytic murein transglycosylase protein from Rhizobium etli CFN 42
37% identity, 34% coverage
- Impact of c-di-GMP on the Extracellular Proteome of Rhizobium etli
Lorite, Biology 2022 - “...were both RA. The peptidoglycan-binding YkuD-like protein RHE_CH01507 and two putative murein transglycosidases (RHE_CH02869 and RHE_CH04101) also displayed RA in the supernatants of the cdG strain LR101 ( Table 1 ). The largest functional group (63) of DA proteins in the supernatants of the cdG strain...”
- “...RapB1, RapB2 Flagella/Motility FlaCch2, FlaCch3, FlaCch4, FlaCch5, FlaCe, FlgKch, FlgEch, FlgD, FlgG, FlgL Peptidoglycan RHE_CH02869, RHE_CH04101, RHE_CH01507 Polysaccharide RkpK, PssP PlyA1, PssO Conjugation TrbB, TrbE Protein Synthesis and Modifications Chaperones GroL1 , GroL2 , GroL4 , Tig , YidC, DnaK , PpiD2 Proteases ClpA,ClpP2 , ClpP3...”
SMc01845 PUTATIVE TRANSGLYCOSYLASE TRANSMEMBRANE PROTEIN from Sinorhizobium meliloti 1021
Q92NK3 Membrane-bound lytic murein transglycosylase B from Rhizobium meliloti (strain 1021)
29% identity, 57% coverage
RL3329 putative lytic transglycosylase from Rhizobium leguminosarum bv. viciae 3841
28% identity, 59% coverage
- Identification of protein secretion systems and novel secreted proteins in Rhizobium leguminosarum bv. viciae
Krehenbrink, BMC genomics 2008 - “...44.4 flagellar hook 8 38.5 174 14 RL4218 47.6 sorbitol-binding protein 9 37.5 76 8 RL3329 43.4 membrane bound lytic tranglycosylase 10 35.6 77 7 RL3745 38.9 Leu/Ile/Val-binding protein (BraC) 11a 34.1 60 6 RL0720 33.6 flagellin 11b 34.1 96 9 RL2375 38.9 basic membrane lipoprotein...”
- “...RL2697 0.999 0.933 28 MMNIAGLGRLAAATVVLSGLAFGSAVKA GEP COG3184 RL2753 1.000 1.000 25 MLNSTRIFAAASIAAMSLFAGSAMA GEP arginine/ornithine-binding protein RL3329 1.000 0.975 25 MHRSLASCSALALLFALALAGGAAA GEP membrane bound lytic tranglycosylase RL3745 1.000 0.999 23 MKKSLLSAVALTAMVAFSGNAWA GEP Leu/Ile/Val-binding protein (BraC) RL4218 1.000 0.998 22 MTLRTFLLGACSALAFAGMASA GEP sorbitol-binding protein RL4651 1.000 1.000 29...”
RHE_CH02869 probable membrane-bound lytic murein transglycosylase protein from Rhizobium etli CFN 42
28% identity, 58% coverage
- Impact of c-di-GMP on the Extracellular Proteome of Rhizobium etli
Lorite, Biology 2022 - “...48 ]) were both RA. The peptidoglycan-binding YkuD-like protein RHE_CH01507 and two putative murein transglycosidases (RHE_CH02869 and RHE_CH04101) also displayed RA in the supernatants of the cdG strain LR101 ( Table 1 ). The largest functional group (63) of DA proteins in the supernatants of the...”
- “...RHE_CH02634 RapB1, RapB2 Flagella/Motility FlaCch2, FlaCch3, FlaCch4, FlaCch5, FlaCe, FlgKch, FlgEch, FlgD, FlgG, FlgL Peptidoglycan RHE_CH02869, RHE_CH04101, RHE_CH01507 Polysaccharide RkpK, PssP PlyA1, PssO Conjugation TrbB, TrbE Protein Synthesis and Modifications Chaperones GroL1 , GroL2 , GroL4 , Tig , YidC, DnaK , PpiD2 Proteases ClpA,ClpP2 ,...”
BAB_RS22915 lytic murein transglycosylase from Brucella abortus 2308
27% identity, 57% coverage
- Evaluation of Brucellosis Vaccines: A Comprehensive Review
Heidary, Frontiers in veterinary science 2022 - “...B. abortus S2308 mutant strain 22915 is constructed by deleting the putative lytic transglycosylase gene BAB_RS22915 . This mutant induces an effective immune response with fewer inflammatory responses. Higher levels of antibody and better protection against B. abortus S2308 are induced by 22915 mutant compared with...”
- Development of new generation of vaccines for Brucella abortus
Gheibi, Heliyon 2018 - “...studies of B. abortus 2308 mutant produced through deletion within the putative lytic transglycosylase gene BAB_RS22915 has shown rapid clearance of the mutant with minimal pathological damage and effective immunity [88] . Studies in cattle with B. abortus 2308 mutant comprising a double deletion of htrA....”
- Characterization of Brucella abortus mutant strain Δ22915, a potential vaccine candidate
Bao, Veterinary research 2017 - “...( B. abortus ) S2308 mutant strain 22915, in which the putative lytic transglycosylase gene BAB_RS22915 was deleted. The biological properties of mutant strain 22915 were characterized and protection of mice against virulent S2308 challenge was evaluated. The mutant strain 22915 showed reduced survival within RAW264.7...”
- “...B. abortus S2308 virulence using miniTn5 transposon mutagenesis (unpublished data). One mutant with the gene BAB_RS22915 interrupted by miniTn5 showed highly attenuated virulence in BALB/c mice. BAB_RS22915 encodes a putative lytic transglycosylase that is a homolog of membrane-bound lytic transglycosylase B (MltB). MltB cleaves the -(14)-glycosidic...”
Atu2122 lytic murein transglycosylase from Agrobacterium tumefaciens str. C58 (Cereon)
27% identity, 57% coverage
BJ6T_59850 lytic transglycosylase domain-containing protein from Bradyrhizobium japonicum USDA 6
36% identity, 33% coverage
MMSR116_RS14565 lytic transglycosylase domain-containing protein from Methylobacterium mesophilicum SR1.6/6
36% identity, 38% coverage
WP_176453824 NlpC/P60 family protein from Cutibacterium acnes
51% identity, 8% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory