PaperBLAST

PaperBLAST Hits for AZOBR_RS07475 (67 a.a., MADTYKVGGM...)

Show query sequence

>AZOBR_RS07475
MADTYKVGGMTCGGCARSVTNAIGKLAPGAAVTVDLDAGTVAVEGGVAPETVKKAVEGAG
FDFGGQA

Running BLASTp...

Found 46 similar proteins in the literature:

A3LVL5 Copper-transporting ATPase (Cu(2+)-ATPase) from Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545)
40% identity, 5% coverage

• Amino Acid Features of P1B-ATPase Heavy Metal Transporters Enabling Small Numbers of Organisms to Cope with Heavy Metal Pollution.
  Ashrafi, Bioinformatics and biology insights 2011
  • “...YJM789, Bakers yeast) A5E2U1 Cu T Lodderomyces elongisporus (yeast) A5E1L1 Cu T Lodderomyces elongisporus (yeast) A3LVL5 Cu T Pichia stipitis (yeast) A3LRS8 Cu T Pichia stipitis (yeast) A3GG72 Cu T Pichia stipitis (yeast) A3BI12 Zn/Cd/pb T Oryza sativa subspecies japonica (rice) A3BF39 Zn/Cd/pb T Oryza sativa...”

PSPPH_4641 YccA from Pseudomonas syringae pv. phaseolicola 1448A
40% identity, 87% coverage

• Transcriptional profile of P. syringae pv. phaseolicola NPS3121 at low temperature: physiology of phytopathogenic bacteria
  Arvizu-Gómez, BMC microbiology 2013
  • “...PSPPH_4332 DNA repair protein RadA 1.76 PSPPH_4372 RNA 2'-phosphotransferase 1.55 PSPPH_4634 bmp family protein 2.99 PSPPH_4641 YccA 1.68 PSPPH_4717 dethiobiotin synthetase 2.09 PSPPH_4866 proline-specific permease proY 1.54 PSPPH_4925 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit 1.62 PSPPH_5142 oxaloacetate decarboxylase alpha subunit 2.35 The described functions were...”

SMU_427 copper chaperone CopZ from Streptococcus mutans UA159
33% identity, 99% coverage

• Cnm of Streptococcus mutans is important for cell surface structure and membrane permeability
  Naka, Frontiers in cellular and infection microbiology 2022
  • “...1029569 SMU_410 4.619 SMU_1657c Nitrogen regulatory protein PII 1028889 SMU_1657c 3.904 copZ Copper chaperone 1027946 SMU_427 2.545 SMU_1548c Histidine kinase 1028787 SMU_1548c 2.398 Table4 List of genes whose expression was downregulated (>2-fold) in strain SN74CND compared with parental strain SN74 by RNA-Sequencing. Cell surface protein-related genes...”
• Graphene Oxide-Copper Nanocomposites Suppress Cariogenic Streptococcus mutans Biofilm Formation
  Mao, International journal of nanomedicine 2021
  • “...without treatment ( Figure 6B ). In particular, the expression of copZ (encoding copper chaperone, SMU_427), copY (encoding negative transcriptional regulator CopY, SMU_424) were up-regulated by 2.69-, 2.35-folds, while the expression of mreD (encoding cell shape-determining protein MreD, SMU_21) was down-regulated by 0.40-folds in GO-Cu_vs_WT comparison...”
• Streptococcus mutans copper chaperone, CopZ, is critical for biofilm formation and competitiveness
  Garcia, Molecular oral microbiology 2016
  • “...Biomass was quantified using O.D. 562 . Protein Expression & Isothermal Titration Calorimetry The copZ (SMU_427) coding region from S. mutans UA159 was cloned into the pET28a-hisSUMO vector in E. coli BL21 Gold (DE3) cells to make the copZpET28a-hisSUMO expression plasmid. Primers used to make the...”
• The copYAZ Operon Functions in Copper Efflux, Biofilm Formation, Genetic Transformation, and Stress Tolerance in Streptococcus mutans
  Singh, Journal of bacteriology 2015
  • “...operon (NCBI database gene annotations, SMU_424, SMU_426, and SMU_427) in the S. mutans UA159 wild-type background was constructed for this study. Briefly, a...”
• A five-species transcriptome array for oral mixed-biofilm studies
  Redanz, PloS one 2011
  • “...SMU_387 putative glycoprotein endopeptidase 2.06 down SMU_424 copY - negative transcriptional regulator, CopY 4.25 up SMU_427 copZ - putative copper chaperone 3.74 up SMU_772 gbpD - glucan-binding protein D with lipase activity; BglB-like protein 2.8 down Genetic information processing,Environmental Information Processing SMU_498 comF - putative late...”

NCgl2860 heavy-metal-associated domain-containing protein from Corynebacterium glutamicum ATCC 13032
49% identity, 74% coverage

• The two-component signal transduction system CopRS of Corynebacterium glutamicum is required for adaptation to copper-excess stress
  Schelder, PloS one 2011
  • “...product Cu /Cu s Copper-related proteins cg3281 NCgl2859 copB probable cation-transporting ATPasetransmembrane protein 11.22 cg3282 NCgl2860 heavy metal binding transport protein 14.91 cg3283 protein of unknown function 12.36 cg3284 NCgl2862 copS two component sensor kinase 545.93 cg3285 NCgl2863 copR two component response regulator 38.68 cg3286 NCgl2864...”
• Two-component systems of Corynebacterium glutamicum: deletion analysis and involvement of the PhoS-PhoR system in the phosphate starvation response
  Kocan, Journal of bacteriology 2006
  • “...NCgl2717 NCgl2718 NCgl2731 NCgl2787 NCgl2817 NCgl2859 NCgl2860 NCgl2864 NCgl2865 NCgl2877 NCgl2897 NCgl2904 NCgl2952 NCgl2953 NCgl2956 NCgl2957 NCgl2970...”

W6QTN1 Heavy metal transport/detoxification protein from Ectopseudomonas oleovorans (strain CECT 5344)
40% identity, 90% coverage

• Alternative Pathway for 3-Cyanoalanine Assimilation in Pseudomonas pseudoalcaligenes CECT5344 under Noncyanotrophic Conditions.
  Pérez, Microbiology spectrum 2021
  • “...MerR family transcriptional regulator R R W6QYV6 BN5_0702 Heavy metal translocating P-type ATPase 453.86 130.94 W6QTN1 BN5_0704 Heavy metal transport/detoxification protein R R W6RBV5 BN5_0715 Oligopeptide/dipeptide ABC transporter, ATPase CNA CNA W6QZ51 BN5_0842 Beta-alanine-pyruvate transaminase 2.01 W6QUE9 BN5_1006 Putative amino-acid ABC transporter-binding protein 6.92 4.24 W6QZK3...”

EP10_000121 copper chaperone CopZ from Geobacillus icigianus
43% identity, 93% coverage

• The Transcriptomic Response of Cells of the Thermophilic Bacterium <i>Geobacillus icigianus</i> to Terahertz Irradiation
  Peltek, International journal of molecular sciences 2024
  • “...least five operons. One of them governs copper homeostasis in the cell (EP10_000119, EP10_000120, and EP10_000121) and encodes proteins that ensure the export of copper in case of its excess within the cell. The four others ensure the entry of iron into the cell from different...”
  • “...10 16 Copper-sensing transcriptional repressor CsoR EP10_000120 3.90026 4.68006 1.25 10 25 Copper-exporting P-type ATPase EP10_000121 4.45124 5.08835 1.09 10 32 Copper chaperone CopZ EP10_000626 1.46412 2.53572 0.00823 Petrobactin import system permease protein YclN EP10_000627 1.50607 2.64895 0.008339 Petrobactin import system permease protein YclO EP10_000628 1.78528...”

WP_058616432 heavy-metal-associated domain-containing protein from Tepidimonas taiwanensis
36% identity, 91% coverage

• Identification of Gold Sensing Peptide by Integrative Proteomics and a Bacterial Two-Component System
  Ng, Frontiers in chemistry 2017
  • “...9.98 16 2 Iron donor protein (CyaY) WP_043703651 181 12,257 5.06 19 3 Hypothetical protein_65aa WP_058616432 28 7,299 5.16 5 As shown in Figure 1 , the predicted metal binding site in 65aa peptide was analyzed using the Basic Local Alignment Search Tool (BLAST). The MSCGHC...”

T303_08745 copper chaperone CopZ from Streptococcus thermophilus ASCC 1275
35% identity, 99% coverage

• Functional Genomic Analyses of Exopolysaccharide-Producing Streptococcus thermophilus ASCC 1275 in Response to Milk Fermentation Conditions
  Wu, Frontiers in microbiology 2019
  • “...hydratase T303_07275 0.63 Isocitrate dehydrogenase T303_01900 2.59 Hypothetical protein T303_04110 4.02 Branched-chain amino acid aminotransferase T303_08745 2.85 Copper-binding protein T303_04795 2.24 Cytoplasmic membrane protein T303_01820 0.35 Hypothetical protein T303_03875 2.05 Sulfurtransferase T303_04595 1.70 Hypothetical protein As shown in Table 1 , we also observed that expression...”

GY20_RS0110545 heavy-metal-associated domain-containing protein from Corynebacterium glutamicum
49% identity, 53% coverage

• Copper Resistance Mechanism and Copper Response Genes in Corynebacterium crenatum
  Huang, Microorganisms 2024
  • “...further study. Among them, GY20_RS0100790 and GY20_RS0110535 belong to transcription factors, and GY20_RS0110270, GY20_RS0100790, and GY20_RS0110545 belong to copper-binding peptides. The two transcription factors were studied for the function of regulatory gene expression. The three copper-binding peptides were displayed on the C. crenatum surface for a...”
  • “...using PCR. The three open reading frames of copper-binding peptide (locus_tags are GY20_RS0110270, GY20_RS0100790, and GY20_RS0110545) were amplified using PCR extension with PrimeSTAR Max DNA Polymerase (Takara, Beijing, China), with the PCR steps being 35 cycles of 10 s at 98 C, 10 s at 55...”

H16_A3669 copper chaperone, heavy metal ion binding from Ralstonia eutropha H16
H16_A3669 heavy-metal-associated domain-containing protein from Cupriavidus necator H16
37% identity, 85% coverage

• Detection of phase-dependent transcriptomic changes and Rubisco-mediated CO2 fixation into poly (3-hydroxybutyrate) under heterotrophic condition in Ralstonia eutropha H16 based on RNA-seq and gene deletion analyses
  Shimizu, BMC microbiology 2013
  • “...transporter subunits, were highly up-regulated in the growth phase along with copDCBA (H16_B2182-B2185) and copZ (H16_A3669) (Additional file 1 : Table S3), which confer resistance to copper. The up-regulation of these genes was estimated to be due to formation of active copper-containing enzymes, such as cytochrome...”

FRAAL0988 putative regulator from Frankia alni ACN14a
44% identity, 85% coverage

• Identification and evolution of nsLTPs in the root nodule nitrogen fixation clade and molecular response of Frankia to AgLTP24
  Gasser, Scientific reports 2023
  • “...2.79 7.90E03 Copper resistance membrane protein FRAAL2326 2.76 2.55E02 Hypothetical protein; putative serine-threonine protein kinase FRAAL0988 2.69 5.06E03 Putative regulator FRAAL6807 2.62 4.62E03 Conserved hypothetical protein FRAAL6813 nifH 2.62 1.11E02 Nitrogenase iron protein (NITROGENASE component II) (nitrogenase Fe protein) (nitrogenase reductase, dinitrogenase reductase) FRAAL1134 groL 2.61...”
• The possible two operons cadCA and cadB/DX are induced in cadmium resistance Mechanism by Frankia alni ACN14a
  Rehan, Electronic journal of biotechnology : EJB 2022

G8E09_12835 heavy-metal-associated domain-containing protein from Acinetobacter pittii
44% identity, 82% coverage

• Phenotypic Variation and Carbapenem Resistance Potential in OXA-499-Producing Acinetobacter pittii
  Zhang, Frontiers in microbiology 2020
  • “...family stress response membrane protein 1.71 0.0020 0.0463 G8E09_01795 Hemerythrin domain-containing protein 1.71 0.0008 0.0244 G8E09_12835 Heavy-metal-associated domain-containing protein -1.70 0.0002 0.0091 G8E09_07185 Hypothetical protein 1.67 0.0008 0.0229 G8E09_18175 Flavodoxin family protein -1.65 0.0001 0.0044 G8E09_12485 Hypothetical protein 1.64 0.0000 0.0033 G8E09_08655 Flavin reductase family protein...”

PFLU0660 putative substrate-binding periplasmic protein from Pseudomonas fluorescens SBW25
42% identity, 85% coverage

• Regulation of copper homeostasis in Pseudomonas fluorescens SBW25
  Zhang, Environmental microbiology 2008 (PubMed)
  • “...activation of the copper chaperone protein encoded by cueZ (pflu0660). The promoters of cueA and cueZ are also responsive to the metal salts of gold, silver and...”
  • “...we identify a putative copper chaperone protein CueZ (Pflu0660) that depends on CueR for expression. We provide genetic evidence suggesting that the chromosomal...”

BDGL_000478 putative copper chaperone from Acinetobacter pittii PHEA-2
42% identity, 82% coverage

• Analysis of Phenol Biodegradation in Antibiotic and Heavy Metal Resistant Acinetobacter lwoffii NL1
  Xu, Frontiers in microbiology 2021
  • “...of phenol degradation operon were putative transposases for insertion elements in A. lwoffii NL1. Genes BDGL_000478 and BDGL_000468 positioned before and after mphR and mphX in A. calcoaceticus PHEA-2 were putative copper chaperone and LysR family regulatory protein, respectively. Different from three gene sets of two-component...”
  • “...for phenol hydroxylase and catechol 1,2-dioxygenase, respectively. Transcriptional regulators are present yellow arrows. BDGL_000475 and BDGL_000478 , respectively, encode hypothetical protein and copper chaperone in A. calcoaceticus PHEA-2. Putative transposases for insertion sequence elements are represented using quadrilateral meshes in A. lwoffii NL1. The LSNL_2981 gene...”

Q1LHH9 Copper chaperone, heavy metal ion binding (Modular protein) from Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)
35% identity, 43% coverage

• Antisense transcription is associated with expression of metal resistance determinants in Cupriavidus metallidurans CH34
  Große, Metallomics : integrated biometal science 2024
  • “...Rmet_3525 cupC 184 334 0.55 42.9 0.77 5.00 b 0.79 0.92 0.86 0.60 0.79 1.06 Q1LHH9 Heavy metal transport/detoxification protein Rmet_6119 copF 41.3 10.0 4.13 13.5 8.97 1.00 2.00 Q58AE3 Heavy metal translocating P-type ATPase cop2, cop1 Rmet_5668 copD 2 4.3 12.3 0.35 25.5 0.16 1.40...”

IYO_003325 heavy-metal-associated domain-containing protein from Pseudomonas syringae pv. actinidiae ICMP 18884
44% identity, 72% coverage

• Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit
  McAtee, BMC genomics 2018
  • “...in metal transport (IYO_00331025); included in these is the highly expressed copper resistance/binding protein copZ (IYO_003325). Very high expression of the chemotaxis protein IYO_006420 was also observed; while not a membrane-bound chemoreceptor, it is predicted to contain a 4-helix bundle, which is a common chemoreceptor sensor...”

Aave_0033 Heavy metal transport/detoxification protein from Acidovorax avenae subsp. citrulli AAC00-1
38% identity, 91% coverage

• Comparison of Copper-Tolerance Genes between Different Groups of Acidovorax citrulli
  Zhang, Microorganisms 2024
  • “...in A. citrulli , including copA ( Aave_0034 ), cueO ( Aave_1810 ), copZ ( Aave_0033 ), and cusA ( Aave_0038 ) in Aac5 (group II) [ 10 , 14 , 15 ]; copA ( Aave_0034 ) in pslb3 (group I) [ 10 ]; cusA -like...”
  • “...cusC -like ( Aave_0387 ), zneB ( Aave_0039 ), cueR ( Aave_0032 ), copZ ( Aave_0033 ), cusB ( Aave_4663 ), tolC ( Aave_1811 ), and gntR ( Aave_2798 ) in FC440 (group I) [ 16 , 17 , 18 , 19 ]. Previous studies using...”

ABUW_2708, ABUW_RS13140 heavy-metal-associated domain-containing protein from Acinetobacter baumannii
44% identity, 82% coverage

• Correlative proteomics identify the key roles of stress tolerance strategies in Acinetobacter baumannii in response to polymyxin and human macrophages
  Kho, PLoS pathogens 2022
  • “...log 2 FC, -3.00) and abrogated infection-specific upregulation in the heavy-metal associated domain-containing protein CopZ (ABUW_RS13140) observed in the AB + THP-1-dMs group ( S1 S3 Tables ). Interestingly, nickel and cobalt homeostasis associated RcnB family protein (ABUW_RS02965) was upregulated (log 2 FC, 3.16) solely in...”
  • “...A . baumannii cells likely utilized glutaredoxins (GrxC, GrxD) and a putative copper chaperone CopZ (ABUW_RS13140) as a copper tolerance strategy to survive within macrophages. Glutaredoxin minimizes the incorrect formation of disulfide bonds in cellular proteins resulting from copper-induced oxidation of sulfhydryl groups [ 67 ,...”
• Essential Gene Clusters Involved in Copper Tolerance Identified in Acinetobacter baumannii Clinical and Environmental Isolates
  Thummeepak, Pathogens (Basel, Switzerland) 2020
  • “...the putative copper regulator ( copR ) and the putative copper-binding proteins ( copD and ABUW_2708) [ 11 , 12 ]. Recently, a functional analysis by Alquethamy et al. [ 14 ] showed that the copper efflux P-type ATPases mediates copper tolerance, and interestingly, this efflux...”
• Characterization of Acinetobacter baumannii Copper Resistance Reveals a Role in Virulence
  Williams, Frontiers in microbiology 2020
  • “...are encoded as an operon; divergently transcribed from that operon is a putative copper chaperone, ABUW_2708, recently named CopZ ( Alquethamy et al., 2019 ). CueR has been well-studied in E. coli and is a cytoplasmic transcription factor that binds copper ions with exquisite sensitivity (...”
  • “...copper resistance genes in AB5075 ( Williams et al., 2016 ); only one small ORF, ABUW_2708, was not represented in the available mutant strain library. To assess the role of the remaining 21 genes in copper resistance, each of the mutant strains was individually grown in...”
• Copper Resistance of the Emerging Pathogen Acinetobacter baumannii
  Williams, Applied and environmental microbiology 2016
  • “...Quantitative real-time PCR actP2/copA1 RT up actP2/copA1 RT dw ABUW_2708 RT up ABUW_2708 RT dw ABUW_3322 RT up ABUW_3322 RT dw copR/cusR RT up copR/cusR RT dw...”
  • “...ABUW_3324/ABUW_RS16150 ABUW_3325/ABUW_RS16155 ABUW_2708/ABUW_RS13140 ABUW_2708 ABUW_3322c CopR/CusR CopS/CusS ActP1/CopA2 ABUW_2707/ABUW_RS13135 ActP2/CopA1...”

PSPTO0752 copZ protein, putative from Pseudomonas syringae pv. tomato str. DC3000
40% identity, 75% coverage

• Survival and growth in the presence of elevated copper: transcriptional profiling of copper-stressed Pseudomonas aeruginosa
  Teitzel, Journal of bacteriology 2006
  • “...on the P. putida (PP0588) and P. syringae (PSPTO0752) chromosomes. Regulation of outer membrane permeability appears to be a feature of adaptation to copper....”

BAB1_0960 Heavy metal transport/detoxification protein:Heavy metal binding from Brucella melitensis biovar Abortus 2308
47% identity, 85% coverage

• Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
  Lamontagne, BMC genomics 2010
  • “...BAB1_1655 GabD subfamily IIA BAB1_0215 ThiE BAB1_0955 DeaD BAB1_1669 PAS domain BAB2_0198 Pseudouridine BAB1_0216 ThiG BAB1_0960 Trs heavy metal BAB1_1671 TcaR synthase BAB1_0242 ManR BAB1_1014 MetG BAB1_1687 Dut BAB2_0216 3-hydroxybutyryl-CoA BAB1_0285 HisD BAB1_1030 Gor BAB1_1695 PurA dehydrogenase BAB1_0317 Trs arginine/ornithine BAB1_1037 Mandelate racemase; BAB1_1702 Phosphoglucosamine BAB2_0246...”

BP1727 putative exported protein from Bordetella pertussis Tohama I
43% identity, 91% coverage

• Streamlined copper defenses make Bordetella pertussis reliant on custom-made operon
  Rivera-Millot, Communications biology 2021
  • “...bp2722 that code for P IB -type ATPases, the latter being Zn-specific 22 , and bp1727, bp1728, and bp1729 that form an operon (Supplementary Figure S2 ) and code for a CopZ-like copper chaperone, a putative glutaredoxin and a putative oxidoreductase, respectively. Copper-repressed bp2921 and bp2922...”
  • “...pertussis . a Lysates of wild type B. pertussis (wt) or the deletion mutant ( bp1727 ) grown in SS medium supplemented (+ Cu) or not with 2mM CuSO 4 were subjected to SDS-PAGE electrophoresis in Tris-tricine gels for the detection of CopZ. The gel was...”

JJQ59_18480 heavy-metal-associated domain-containing protein from Cupriavidus necator
37% identity, 85% coverage

• Whole Genome Sequence Analysis of Cupriavidus necator C39, a Multiple Heavy Metal(loid) and Antibiotic Resistant Bacterium Isolated from a Gold/Copper Mine
  Xie, Microorganisms 2023
  • “...transcriptional regulator Cu JJQ59_18470 ctpA copper-translocating P-type ATPase Cu JJQ59_18475 copZ heavy-metal-associated domain-containing protein Cu JJQ59_18480 atpX heavy metal translocating P-type ATPase JJQ59_35770 czcB efflux RND transporter periplasmic adaptor subunit Co/Zn/Cd JJQ59_31505 czcC TolC family protein Co/Zn/Cd JJQ59_31510 czcI cobalt-zinc-cadmium resistance protein Co/Zn/Cd JJQ59_31515 czcA efflux...”

A7J09_03980, DP111_07130 heavy metal translocating P-type ATPase from Streptococcus suis
38% identity, 7% coverage

• CopA Protects Streptococcus suis against Copper Toxicity
  Zheng, International journal of molecular sciences 2019
  • “...CR541_06915 97 T15 T15_0568 97 SC070731 NJAUSS_1288 97 JS14 SSUJS14_1360 97 ST1 SSUST1_0574 96 ISU2812 A7J09_03980 96 SH1510 DP111_07130 96 GZ0565 BFP66_02780 95 DN13 A6M16_02880 95 6407 ID09_03115 95 TL13 TL13_0615 95 CZ130302 CVO91_03355 95 HN105 DF184_07440 95 HN136 CWM22_09360 95 SRD478 A7J08_03040 92 1081 BKM67_07590...”
  • “...T15_0568 97 SC070731 NJAUSS_1288 97 JS14 SSUJS14_1360 97 ST1 SSUST1_0574 96 ISU2812 A7J09_03980 96 SH1510 DP111_07130 96 GZ0565 BFP66_02780 95 DN13 A6M16_02880 95 6407 ID09_03115 95 TL13 TL13_0615 95 CZ130302 CVO91_03355 95 HN105 DF184_07440 95 HN136 CWM22_09360 95 SRD478 A7J08_03040 92 1081 BKM67_07590 93 0061 BKM66_07040...”

SSUST1_0574 heavy metal translocating P-type ATPase from Streptococcus suis ST1
38% identity, 7% coverage

• CopA Protects Streptococcus suis against Copper Toxicity
  Zheng, International journal of molecular sciences 2019
  • “...SSUST3_0597 97 CS100322 CR541_06915 97 T15 T15_0568 97 SC070731 NJAUSS_1288 97 JS14 SSUJS14_1360 97 ST1 SSUST1_0574 96 ISU2812 A7J09_03980 96 SH1510 DP111_07130 96 GZ0565 BFP66_02780 95 DN13 A6M16_02880 95 6407 ID09_03115 95 TL13 TL13_0615 95 CZ130302 CVO91_03355 95 HN105 DF184_07440 95 HN136 CWM22_09360 95 SRD478 A7J08_03040...”

SPy1714 putative copper chaperone - copper transport operon from Streptococcus pyogenes M1 GAS
35% identity, 94% coverage

• Novel Tyrosine Kinase-Mediated Phosphorylation With Dual Specificity Plays a Key Role in the Modulation of Streptococcus pyogenes Physiology and Virulence
  Kant, Frontiers in microbiology 2021
  • “...Streptokinase 0.8729 1.8313404 0.01577 0.079648 Spy1318 rocA Sensory transduction protein kinase 0.9818 1.97493 0.01527 0.078922 Spy1714 - Cell surface protein 1.0042 2.00583 0.04635 0.16478 Spy1715 scpA C5A peptidase 1.0364 2.0511 0.19829 0.4143 Spy1718 sic1.01 Inhibitor of complement protein 1.5132 2.85442 3.60E05 0.001046 Spy1719 emm1.0 M protein...”
• New Pathogenesis Mechanisms and Translational Leads Identified by Multidimensional Analysis of Necrotizing Myositis in Primates
  Kachroo, mBio 2020
  • “...3.5 Spy1734 spi Streptopain protease inhibitor Spy1713 1,080.7 NS Spy1735 speB Streptococcal pyrogenic exotoxin B Spy1714 912.3 NS Spy1738 spd Phage-associated deoxyribonuclease Spy1717 70.5 NS Superantigens Spy0182 speG Exotoxin type G precursor Spy0222 2.1 3.8 Spy1702 smeZ Mitogenic exotoxin Z Spy0238 NS 2.6 Spy0356 speJ Exotoxin...”
• Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A Streptococcus Biofilms
  Freiberg, mSystems 2016
  • “...reductase [NAD(P)H] V Downregulated Spy1709 1.66 1.64 2.59 1.42 2.84 2.82 3.77 Hypothetical protein S Spy1714 3.43 3.68 3.13 3.33 3.58 3.03 3.07 3.32 2.77 Fibronectin-binding protein D Spy1719 emm1.0 3.05 4.26 5.72 3.45 4.66 6.12 3.3 4.51 5.98 M protein D a Upregulated and Downregulated...”

BC351_38480 copper ion binding protein from Paenibacillus ferrarius
45% identity, 88% coverage

• High-quality-draft genomic sequence of Paenibacillus ferrarius CY1^T with the potential to bioremediate Cd, Cr and Se contamination
  Li, Standards in genomic sciences 2017
  • “...transport protein BC351_15720 Copper-translocating P-type ATPase BC351_26145 Copper-translocating P-type ATPase BC351_38485 Copper-transporting P-type ATPase CopZ BC351_38480 Manganese Manganese transport protein MntH BC351_25600 Manganese transport protein MntH BC351_14100 Conclusions The genome of 10.1601/nm.26197 CY1 T harbors various genes responsible for sulfate transport and reduction, chromate and selenite...”

PF0740 heavy-metal transporting cpx-type atpase from Pyrococcus furiosus DSM 3638
Q8TH11 Heavy-metal transporting cpx-type atpase from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
37% identity, 8% coverage

• CopR, a Global Regulator of Transcription to Maintain Copper Homeostasis in Pyrococcus furiosus
  Grünberger, Frontiers in microbiology 2020
  • “...al., 2012 ). In short, the DNA template containing the promoter regions of pf0739 and pf0740 was obtained from genomic DNA by PCR amplification (see Supplementary Table 1 ). HEX-labeled primers were used in two separate reactions for strand-specific labeling. 4.4 nM template DNA was assembled...”
  • “...(C) Bioinformatical analysis of conserved amino acids in transmembrane helices 4, 5 and 6 classify PF0740 as the copper exporter CopA. FIGURE 2 Growth analysis of the P. furiosus parental strain (MURPf52) and CopR-knockout strain (MURPf74) in the presence of CuSO 4 . Triplicates of 40...”
• Metabolic and evolutionary relationships among Pyrococcus Species: genetic exchange within a hydrothermal vent environment
  Hamilton-Brehm, Journal of bacteriology 2005
  • “...transporter No InterPRO entry PF0735 PF0737 PF0738 PF0739 PF0740 PF0742 PF0743 PF0744 PF0758 PF0760 PF0762 PF0763 PF0764 PF0765 PF0766 PF0767 PF0768 PF0769...”
• A P-type ATPase importer that discriminates between essential and toxic transition metals
  Lewinson, Proceedings of the National Academy of Sciences of the United States of America 2009
  • “...aeruginosa P. aeruginosa Accession no. Q0P9A1 Q0P995 Q0PAK1 Q8TH11 O26033 Q7D0J8 A9CJE3 A9CJP7 A9CIZ1 Q97RR4 Q97NE2 Q97PQ2 P35597 Q9HXV0 Q9HX93 Q9I147 Q9I3G8...”
  • “...could be established for 6 of the tested proteins (Q8TH11, Q7D0J8, A9CJE3, A9CJP7, Q9HXV0, and Q9I147), all of which contained the CPX motif. Putative functions...”
• The funnel approach to the precrystallization production of membrane proteins
  Lewinson, Journal of molecular biology 2008
  • “...Q7AR91 Pseudomonas aeruginosa ** Q9HUY5 Pyrococcus furiosus Q8TH11 Archaeoglobus fulgidus ** O29777 Helicobacter pylori P55989 Archaeoglobus fulgidus ** O30085...”

TL13_0615 heavy metal translocating P-type ATPase from Streptococcus suis TL13
38% identity, 7% coverage

• CopA Protects Streptococcus suis against Copper Toxicity
  Zheng, International journal of molecular sciences 2019
  • “...A7J09_03980 96 SH1510 DP111_07130 96 GZ0565 BFP66_02780 95 DN13 A6M16_02880 95 6407 ID09_03115 95 TL13 TL13_0615 95 CZ130302 CVO91_03355 95 HN105 DF184_07440 95 HN136 CWM22_09360 95 SRD478 A7J08_03040 92 1081 BKM67_07590 93 0061 BKM66_07040 93 D12 SSUD12_0568 92 HA1003 DP112_07660 92 AH681 CWI26_08525 92 1 Gene...”

ID09_03115 heavy metal translocating P-type ATPase from Streptococcus suis 6407
38% identity, 7% coverage

• CopA Protects Streptococcus suis against Copper Toxicity
  Zheng, International journal of molecular sciences 2019
  • “...SSUST1_0574 96 ISU2812 A7J09_03980 96 SH1510 DP111_07130 96 GZ0565 BFP66_02780 95 DN13 A6M16_02880 95 6407 ID09_03115 95 TL13 TL13_0615 95 CZ130302 CVO91_03355 95 HN105 DF184_07440 95 HN136 CWM22_09360 95 SRD478 A7J08_03040 92 1081 BKM67_07590 93 0061 BKM66_07040 93 D12 SSUD12_0568 92 HA1003 DP112_07660 92 AH681 CWI26_08525...”

A6M16_02880, BFP66_02780 heavy metal translocating P-type ATPase from Streptococcus suis
38% identity, 7% coverage

• CopA Protects Streptococcus suis against Copper Toxicity
  Zheng, International journal of molecular sciences 2019
  • “...SSUJS14_1360 97 ST1 SSUST1_0574 96 ISU2812 A7J09_03980 96 SH1510 DP111_07130 96 GZ0565 BFP66_02780 95 DN13 A6M16_02880 95 6407 ID09_03115 95 TL13 TL13_0615 95 CZ130302 CVO91_03355 95 HN105 DF184_07440 95 HN136 CWM22_09360 95 SRD478 A7J08_03040 92 1081 BKM67_07590 93 0061 BKM66_07040 93 D12 SSUD12_0568 92 HA1003 DP112_07660...”
  • “...NJAUSS_1288 97 JS14 SSUJS14_1360 97 ST1 SSUST1_0574 96 ISU2812 A7J09_03980 96 SH1510 DP111_07130 96 GZ0565 BFP66_02780 95 DN13 A6M16_02880 95 6407 ID09_03115 95 TL13 TL13_0615 95 CZ130302 CVO91_03355 95 HN105 DF184_07440 95 HN136 CWM22_09360 95 SRD478 A7J08_03040 92 1081 BKM67_07590 93 0061 BKM66_07040 93 D12 SSUD12_0568...”

Q6BIS6 DEHA2G07986p from Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 / JCM 1990 / NBRC 0083 / IGC 2968)
40% identity, 5% coverage

• Amino Acid Features of P1B-ATPase Heavy Metal Transporters Enabling Small Numbers of Organisms to Cope with Heavy Metal Pollution
  Ashrafi, Bioinformatics and biology insights 2011
  • “...Kluyveromyces lactis (yeast, Candida sphaerica ) Q6BVG6 Cu T Debaryomyces hansenii (yeast, Torulaspora hansenii ) Q6BIS6 Cu T Debaryomyces hansenii (yeast, Torulaspora hansenii ) Q654Y9 co T Oryza sativa subspecies Japonica (rice) Q5K722 Cu T Cryptococcus neoformans ( Filobasidiella neoformans ) Q58AE3 Cu/Ag/Zn/Cd/pb T Ralstonia metallidurans...”

PP0588, PP_0588 copper-binding protein, putative from Pseudomonas putida KT2440
36% identity, 87% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023
• The Cellular Response to Lanthanum Is Substrate Specific and Reveals a Novel Route for Glycerol Metabolism in Pseudomonas putida KT2440
  Wehrmann, mBio 2020
  • “...2.41 2.33 PP_3603 Transcriptional regulator, GntR family 2.46 2.73 PP_4313 Putative peptidylprolyl isomerase 2.55 2.50 PP_0588 Putative copper-binding chaperone 2.75 2.62 PP_2674 PedE Quinoprotein ethanol dehydrogenase 4.25 3.78 PP_2673 Pentapeptide repeat family protein 5.37 3.71 PP_3732 Enoyl-CoA hydratase/isomerase family protein 5.78 3.07 a CoA, coenzyme A;...”
• Mechanisms of resistance to chloramphenicol in Pseudomonas putida KT2440
  Fernández, Antimicrobial agents and chemotherapy 2012
  • “...PP0185 PP0205 PP0323 PP0339 PP0368 PP0504 PP0529 PP0586 PP0588 PP0613 PP0620 PP0741 PP0742 PP0765 PP0766 PP0951 PP1018 PP1514 PP1516 PP2284 PP2310 PP2512 PP2736...”
• Antimicrobial activities of commercial nanoparticles against an environmental soil microbe, Pseudomonas putida KT2440
  Gajjar, Journal of biological engineering 2009
  • “...500 bps 5' to 100 bps 3' downstream of the translational start site at locus PP_0588 in wild type P. putida KT2440. The primers were: For, CGATGCGGTATTTGTTGATCT and Rev, AATCGCAGTGAGGATCTGCT. PCR products containing the PP_0588 promoter region were ligated to the promoterless luxAB :: npt cassette...”
  • “...the reverse orientation and identifying PCR products when used with the 5' promoter primer of PP_0588, 5'-CGATGCGGTATTTGTTGATCT-3'. The luxA primer sequence was 5'-CAACCAAATTTTCCCCAAGA-3'. Positive clones were ultimately confirmed by the presence of Lux activity and ability to grow on kanamycin at 20 g/ml. The PP_0588 lux...”
• Survival and growth in the presence of elevated copper: transcriptional profiling of copper-stressed Pseudomonas aeruginosa
  Teitzel, Journal of bacteriology 2006
  • “...Homologous genes are found on the P. putida (PP0588) and P. syringae (PSPTO0752) chromosomes. Regulation of outer membrane permeability appears to be a feature...”

T1E_3759 heavy-metal-associated domain-containing protein from Pseudomonas putida DOT-T1E
36% identity, 87% coverage

• Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome
  Udaondo, Microbial biotechnology 2013
  • “...transcriptional regulaor 1e-075 T1E_3757 PacS Cu P-type Cooper uptake Heavy metal translocating P-type ATPase 0.0 T1E_3759 PacZ(CopZ) Cu HMA Activator heavy metal transport/detoxification protein 7e-031 T1E_3760 Cu Cooper homeostasis Multidrug resistance transporter, Bcr/CflA family 1e-163 T1E_4452 MfpII Me 2 /drug RND MFP/HlyD Me2+/drug efflux efflux transporter,...”

IS492_27185 heavy-metal-associated domain-containing protein from Pseudomonas aeruginosa
40% identity, 85% coverage

• Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
  Valzano, Microbiology spectrum 2022
  • “...3.2E03 0.2 IS492_27180 PA3574 PA14_18080 nalD Transcriptional regulator NalD (second repressor of MexAB-OprM) 1.5E19 1.3 IS492_27185 PA3574a PA14_18070 copZ Copper chaperone CopZ (copper efflux) 9.1E11 1.0 IS492_27760 PA3690 PA14_16660 Heavy metal-translocating P-type ATPase (efflux) 1.1E08 1.0 IS492_28975 PA3920 PA14_13170 copA Copper-translocating P-type ATPase CopA1 (copper efflux)...”

PA14_18070 putative periplasmic metal-binding protein from Pseudomonas aeruginosa UCBPP-PA14
40% identity, 85% coverage

• Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
  Valzano, Microbiology spectrum 2022
  • “...IS492_27180 PA3574 PA14_18080 nalD Transcriptional regulator NalD (second repressor of MexAB-OprM) 1.5E19 1.3 IS492_27185 PA3574a PA14_18070 copZ Copper chaperone CopZ (copper efflux) 9.1E11 1.0 IS492_27760 PA3690 PA14_16660 Heavy metal-translocating P-type ATPase (efflux) 1.1E08 1.0 IS492_28975 PA3920 PA14_13170 copA Copper-translocating P-type ATPase CopA1 (copper efflux) 1.2E27 1.2...”
• Quorum-sensing regulation of a copper toxicity system in Pseudomonas aeruginosa
  Thaden, Journal of bacteriology 2010
  • “...is a 198-bp gene that is homologous to the PA14_18070 locus in P. aeruginosa PA14. A BLAST analysis of PA3574.1 indicated it is a putative periplasmic metal...”
• Genomewide identification of genetic determinants of antimicrobial drug resistance in Pseudomonas aeruginosa
  Dötsch, Antimicrobial agents and chemotherapy 2009
  • “...PA14_73370 PA14_73410 PA14_14420 PA14_15540 PA14_15600 PA14_18070 PA14_23420 PA14_23430 PA14_23460 PA14_28520 PA14_43090 PA14_44230 PA14_51950 PA14_54750...”
  • “...PA14_57540 PA14_57570 PA14_58260 PA14_60860 PA14_66600 PA14_68610 PA14_18070 PA14_30210 PA0090 PA0958 PA1095 PA1348 PA1549 PA2023 PA2693 PA3224 PA3702 PA3831...”

CWI26_08525 heavy metal translocating P-type ATPase from Streptococcus suis
40% identity, 7% coverage

• CopA Protects Streptococcus suis against Copper Toxicity
  Zheng, International journal of molecular sciences 2019
  • “...A7J08_03040 92 1081 BKM67_07590 93 0061 BKM66_07040 93 D12 SSUD12_0568 92 HA1003 DP112_07660 92 AH681 CWI26_08525 92 1 Gene sequence identity is compared with the copA gene of SC19 strain. ijms-20-02969-t002_Table 2 Table 2 Bacterial strains and plasmids used in this study. Strain or Plasmid Relevant...”

DP112_07660 heavy metal translocating P-type ATPase from Streptococcus suis
36% identity, 7% coverage

• CopA Protects Streptococcus suis against Copper Toxicity
  Zheng, International journal of molecular sciences 2019
  • “...CWM22_09360 95 SRD478 A7J08_03040 92 1081 BKM67_07590 93 0061 BKM66_07040 93 D12 SSUD12_0568 92 HA1003 DP112_07660 92 AH681 CWI26_08525 92 1 Gene sequence identity is compared with the copA gene of SC19 strain. ijms-20-02969-t002_Table 2 Table 2 Bacterial strains and plasmids used in this study. Strain...”

FAY30_11165 copper chaperone CopZ from Bacillus sp. S3
39% identity, 87% coverage

• Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium
  Li, BMC microbiology 2020
  • “...copA_1234 Copper-exporting P-type ATPase; Lead, cadmium, zinc and mercury transporting ATPase Cation translocation P-type ATPase FAY30_11165 FAY30_16840 copZ_12 Copper chaperone FAY30_05265 cutC Copper homeostasis protein Chromate detoxification FAY30_22440 chrR Chromate reductase FAY30_11465 FAY30_20185 FAY30_20190 chrA_123 Chromate transport protein Cadmium, zinc, cobalt, mercury detoxification FAY30_09760 cadC Cadmium...”

Q9WYF3 P-type Cu+ transporter (EC 7.2.2.8) from Thermotoga maritima (see paper)
TC 3.A.3.5.33 / Q9WYF3 Ca2+ from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
TM0317 cation-transporting ATPase, P-type from Thermotoga maritima MSB8
38% identity, 8% coverage

• substrates: Cu2+
  tcdb comment: exporting ATPase, CopA. The domain organization and mechanism have been studied (Hatori et al., 2009, Hatori et al., 2008, Hatori et al., 2007). Residues involved in catalysis have been defined (Hatori et al. 2009)
• Solubilization of native integral membrane proteins in aqueous buffer by noncovalent chelation with monomethoxy poly(ethylene glycol) (mPEG) polymers
  Janaratne, Bioconjugate chemistry 2011
  • “...++ TM0407 Cymal-5 4 20 - ++ ++ TM1122 OG 6 32 - ++ ++ TM0317 Cymal-5 7 72 - ++ ++ - protein started precipitating in less than two weeks; + protein started precipitating after two weeks; ++ protein didn't precipitate after two months. 1...”
• Intermediate phosphorylation reactions in the mechanism of ATP utilization by the copper ATPase (CopA) of Thermotoga maritima
  Hatori, The Journal of biological chemistry 2008
  • “...(H479Q mutant), 70,922 (NMBD). MATERIALS AND METHODS Preparations of Proteins Overexpression of T. maritima CopA (TM0317) in Escherichia coli and purification of the expressed protein was previously described ( 35 ). The CopA constructs used in this study are shown in Fig. 1 . The purified...”
• The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture
  Johnson, Applied and environmental microbiology 2006
  • “...in pure culture growth Annotation Fold changea TM_rnpB TM0317 TM0373 TM0374 TM0456 TM0504 TM0505 TM0506 TM0571 TM0729 TM0807 TM0849 TM1286 TM1369 TM1370 TM1371...”
• Transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium Thermotoga maritima
  Pysz, Applied and environmental microbiology 2004
  • “...11.9 Cellobiose phosphorylase Cation-transporting ATPase, P-type TM1848 TM0317 6.9 6.6 12.9 14.1 SufD homolog, similar to ABC permease components SufB homolog,...”
  • “...5.7 2.7 5.5 2.8 3.6 12.2 9.1 TM0317 TM0318 TM0319 TM0320 Predicted membrane protein Uncharacterized homolog of -carboxymuconolactone decarboxylase subunit...”

JK_RS07345 heavy-metal-associated domain-containing protein from Corynebacterium jeikeium K411
47% identity, 53% coverage

• An Integrated Database of Small RNAs and Their Interplay With Transcriptional Gene Regulatory Networks in Corynebacteria
  Parise, Frontiers in microbiology 2021
  • “...( Pao and Saier, 1995 ). TscR4 is also predicted to regulate the copper chaperone JK_RS07345 alongside the sRNA Cj-K411-sRNA-3. Likewise, this sRNA potentially co-regulates the heat shock protein groES and the flavin-dependent oxidoreductase JK_RS00955, which are also regulated by the hrcA and JK_RS10540 ( maR1...”

cg3402 copper chaperone from Corynebacterium glutamicum ATCC 13032
41% identity, 88% coverage

• Physiological Response of Corynebacterium glutamicum to Indole
  Walter, Microorganisms 2020
  • “...htaB , htaC , ripA ), copper-related genes (e.g., copB , copO , cg0464 , cg3402 ), and the operons for p -cresol catabolism and cytochrome bd ( cydABCD ) ( Table 2 ). Since the cydABCD operon and the operon for p -cresol catabolism are...”
  • “...a putative copper ion transporting P-type ATPase), cg2962 (encoding a putative enzyme synthesizing extracellular polysaccharides), cg3402 (coding for a copper chaperone), phenol oxygenase gene phe , and DNA protection gene dps (compare Table 2 and Table 3 ). This led us to the speculation that the...”
• Function of L-Pipecolic Acid as Compatible Solute in Corynebacterium glutamicum as Basis for Its Production Under Hyperosmolar Conditions
  Pérez-García, Frontiers in microbiology 2019
  • “...cg3326 Hypothetical protein 1.1 0.8 mez Malic enzyme 0.9 0.3 proP Proline/betaine permease -1.2 -1.2 cg3402 Putative Hg 2+ permease, MerTP-family 1.2 0.0 cg3404 ABC-type putative iron(III) dicitrate transporter, substrate-binding lipoprotein -2.1 -0.4 cg4014 Conserved hypothetical protein, possibly involved in stress response 0.3 -1.0 cg4019 0.8...”
  • “...uptake system, genes for divalent metal transporter proteins ( ctpA , cg0569, cg3281, cg3282, and cg3402), for transcriptional regulators ( glyR, whiB3 , and whcE ) and for enzymes of central carbon metabolism ( pck, ldh and mez ) showed higher RNA levels than in the...”
• The MarR-Type Regulator MalR Is Involved in Stress-Responsive Cell Envelope Remodeling in Corynebacterium glutamicum
  Hünnefeld, Frontiers in microbiology 2019
  • “...vitro approach ( Supplementary Figure S2 ). As a negative control, the promoter region of cg3402 (a putative copper chaperone) was used. Here, no shift was detectable. In vitro , different migration patterns were observed for the tested MalR targets, which likely reflect differences in binding...”
• Physiology and Transcriptional Analysis of (p)ppGpp-Related Regulatory Effects in Corynebacterium glutamicum
  Ruwe, Frontiers in microbiology 2019
  • “...5.49 0 4.67 0 cg0464 5.31 0 5.63 0 cg3392 idhA2 5.31 2.2E107 4.68 9.48E25 cg3402 5.29 0 5.16 0 cg1376 ssuD1 5.17 1.97E37 1.24 0.003146 R A cg0759 prpD2 5.15 0 1.84 0.010373 A cg3279 5.14 0 4.66 9.3E196 cg1377 ssuC 5.14 7.08E95 0.22 0.753393...”

cg3282 cation transport ATPase from Corynebacterium glutamicum ATCC 13032
47% identity, 78% coverage

• Function of L-Pipecolic Acid as Compatible Solute in Corynebacterium glutamicum as Basis for Its Production Under Hyperosmolar Conditions
  Pérez-García, Frontiers in microbiology 2019
  • “...GCTGCCAACTCTGCAACCTC CCATTCGGGCCTTCTTCCAC 245 cg2677 GGCTCTGCCTCCATTCTTTG GGTTGTGCCTTGACCTCTTC 210 cg2851 CAACGTGAACACGGTGTATC CACATCGTCGAATCCGTTTG 210 cg3254 ATGCTTGCCCTAGGTTGG CCGAGTGAAGAACTGCACG 255 cg3282 ATGACCTGCGGACACTGC TCAGGACAAGACGGTGTAG 180 gntV TCCGTCGGTAAAGCCCTAGC CGGTTCCTGGGCATTTGGTG 238 proC CGCGGCCAACATGAATCCAC GGCCATGCTGACCACAACAC 232 proP TCGACTGGTGGTGAATATGC GAATACGCCAACCGAAATCC 202 pstC AATGCGAACTCCTCTCAGAC AATCCGCCAATACCTTCAGC 206 pstS TCCGCAATGGACTACTTTGG AACTGGGCCGATAACGAATG 222 Results C. glutamicum Can Use L -PA...”
  • “...-0.9 cg3271 SAM-dependent methyltransferase 0.3 -1.1 cg3281 Putative Cu 2+ transporting P-type ATPase 1.2 -0.4 cg3282 Putative Cu 2+ transporting P-type ATPase 1.4 0.0 cg3326 Hypothetical protein 1.1 0.8 mez Malic enzyme 0.9 0.3 proP Proline/betaine permease -1.2 -1.2 cg3402 Putative Hg 2+ permease, MerTP-family 1.2...”
• Physiology and Transcriptional Analysis of (p)ppGpp-Related Regulatory Effects in Corynebacterium glutamicum
  Ruwe, Frontiers in microbiology 2019
  • “...4.66 9.3E196 cg1377 ssuC 5.14 7.08E95 0.22 0.753393 R A cg4028 5.12 2.99E78 2.2 0.00013 cg3282 5.11 3.37E73 4.72 0 cg3281 5.04 2.1E119 4.42 0 cg2678 4.99 0 0.43 0.561184 R cg1379 ssuB 4.88 1.98E71 0.58 0.371168 R A cg3411 4.83 0 4.6 1.5E292 cg0018 4.76...”
• Two-component signal transduction in Corynebacterium glutamicum and other corynebacteria: on the way towards stimuli and targets
  Bott, Applied microbiology and biotechnology 2012
  • “...the less toxic and less membrane-permeable Cu(II). The function of the putative secreted copper-binding protein Cg3282 in copper homeostasis could be sequestration of excess copper ions or delivery of copper ions from CopB to the multicopper oxidase. The function of the other encoded proteins is still...”
• The two-component signal transduction system CopRS of Corynebacterium glutamicum is required for adaptation to copper-excess stress
  Schelder, PloS one 2011
  • “...gene product Cu /Cu s Copper-related proteins cg3281 NCgl2859 copB probable cation-transporting ATPasetransmembrane protein 11.22 cg3282 NCgl2860 heavy metal binding transport protein 14.91 cg3283 protein of unknown function 12.36 cg3284 NCgl2862 copS two component sensor kinase 545.93 cg3285 NCgl2863 copR two component response regulator 38.68 cg3286...”
  • “...probable cation-transporting ATPase transmembrane protein ( copB , cg3281), a heavy metal binding transport protein (cg3282), a protein of unknown function (cg3283), a secreted protein of unknown function (cg3286), a secreted multicopper oxidase ( copO , cg3287), a protein of unknown function (cg3288) and a thioredoxin-like...”
• Two-component systems of Corynebacterium glutamicum: deletion analysis and involvement of the PhoS-PhoR system in the phosphate starvation response
  Kocan, Journal of bacteriology 2006
  • “...Berkeley cg2925 cg3116 cg3118 cg3132 cg3195 cg3227 cg3281 cg3282 cg3286 cg3287 cg3303 cg3327 cg3335 cg3386 cg3387 cg3390 cg3391 cg3404 NCBI no. c 730 KOCAN...”

APL_1264 putative cation transport ATPase from Actinobacillus pleuropneumoniae L20
37% identity, 93% coverage

• Transcriptional portrait of Actinobacillus pleuropneumoniae during acute disease--potential strategies for survival and persistence in the host
  Klitgaard, PloS one 2012
  • “...of copA (APL_1265) and the putative cation transport ATPase, most likely involved in copper detoxification (APL_1264). CopA has earlier been found to be important for survival in necrotic porcine lung tissue [18] . Urease activity may increase intracellular survival and impair macrophage function through the production...”
• Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential
  Klitgaard, BMC genomics 2010
  • “...dehydrogenase (part of oxidative phosphorylation pathway) C 0.37 APL_1265 copA Copper-transporting P-type ATPase P 1.46 APL_1264 - Cation transport ATPase P 1.81 APL_1263 - Predicted metal-binding protein R 1.60 APL_1048 + hugZ Putative heme utilization protein P 2.41 APL_1047 + hgbA Probable haemoglobin-and-haptoglobin binding protein 4...”
  • “...operon consisting of the copper-transporting P-type ATPase, copA gene (APL_1265), a putative cation transport ATPase (APL_1264), and a predicted metal-binding protein (APL_1263). In eukaryotes, several interdependent connections between copper and iron homeostasis have been described. Knowledge of such processes in bacterial systems is still limited [...”

Francci3_0489 Heavy metal transport/detoxification protein from Frankia sp. CcI3
41% identity, 82% coverage

• Transcriptomes of Frankia sp. strain CcI3 in growth transitions
  Bickhart, BMC microbiology 2011
  • “...824 STAS Francci3_4302 1405 hypothetical protein Francci3_1615 775 transcriptional regulator Francci3_0908 816 Heavy metal transportprotein Francci3_0489 1368 hypothetical protein Francci3_2179 775 hypothetical protein Francci3_4129 809 sigma-24 Francci3_3768 1353 hypothetical protein Francci3_1534 773 transposase, IS4 Francci3_4227 803 transcriptional regulator, TetR Francci3_2758 1349 hypothetical protein Francci3_2329 767 Antibiotic...”

GSU1338 heavy-metal-associated domain protein from Geobacter sulfurreducens PCA
44% identity, 42% coverage

• Adaptation to disruption of the electron transfer pathway for Fe(III) reduction in Geobacter sulfurreducens
  Leang, Journal of bacteriology 2005
  • “...GSU2006 GSU2007 GSU2008 GSU2352 GSU2490 GSU2886 GSU0711 GSU0930 GSU1338 GSU1398 GSU2010 GSU3059 GSU3157 GSU3435 a 0.774 0.144 1.938 0.395 1.776 0.312 1.540...”

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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.