Family Search for PF04461 (DUF520)

PF04461.13 hits 36 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

OFBG_01674 YajQ family cyclic di-GMP-binding protein from Oxalobacter formigenes OXCC13
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 223.9 bits

• Proteome Dynamics of the Specialist Oxalate Degrader Oxalobacter formigenes
  Ellis, Journal of proteomics & bioinformatics 2016
  • “...exposure to stress, three universal stress proteins encoded by genes at loci OFBG_00781, OFBG_00128 and OFBG_01674, which have been shown to provide general stress endurance activity, an Abi family protein (OFBG_00600), which is involved in resisting bacteriophage infection, an esterase (OFBG_01018) with predicted beta-lactamase activity, and...”

plu3881 No description from Photorhabdus luminescens subsp. laumondii TTO1
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 223.8 bits

• Genetic and proteomic characterization of rpoB mutations and their effect on nematicidal activity in Photorhabdus luminescens LN2
  Qiu, PloS one 2012
  • “...dksA DnaK transcriptional regulator DksA 5.04 17415.8 1 0 0.05 0.65 0 20 Nucleotide-binding protein, plu3881 P. luminescens TT01 Similar to Unknown protein YajQ of E. coli 5.77 18311.4 1 1.47 0.89 1.48 1.09 22 Transcriptional repressor MprA, plu1277 P. luminescens TT01 mprA DNA-binding transcriptional repressor...”

Bmul_0741 YajQ family cyclic di-GMP-binding protein from Burkholderia multivorans ATCC 17616
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 221.9 bits

• Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress
  Agarwal, Cells 2018
  • “...coq7 1.7 SRS-46 Glycosyl transferase Uracil phosphoribosyltransferase upp 2.1 SRS-46 Poorly characterized UPF0234 protein Bmul_0741/BMUL1_02519 Bmul_0741 1.9 SRS-46 UPF0307 protein Bcep18194_A4194 Bcep18194_A4194 6.4 SRS-46 Probable transcriptional regulatory protein Bphyt_1301 Bphyt_1301 2.1 SRS-46 UPF0234 protein Bphy_0527 Bphy_0527 1.7 SRS-46 Probable transcriptional regulatory protein Bamb_2332 Bamb_2332 2.3 SRS-46...”

Bphy_0527 putative nucleotide-binding protein (RefSeq) from Burkholderia phymatum STM815
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 220.1 bits

• Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress
  Agarwal, Cells 2018
  • “...protein Bcep18194_A4194 Bcep18194_A4194 6.4 SRS-46 Probable transcriptional regulatory protein Bphyt_1301 Bphyt_1301 2.1 SRS-46 UPF0234 protein Bphy_0527 Bphy_0527 1.7 SRS-46 Probable transcriptional regulatory protein Bamb_2332 Bamb_2332 2.3 SRS-46 UPF0301 protein Bamb_0737 Bamb_0737 5.1 SRS-46...”

YPO3170 nucleotide-binding protein (RefSeq) from Yersinia pestis CO92
YPC_3455 YajQ family cyclic di-GMP-binding protein from Yersinia pestis biovar Medievalis str. Harbin 35
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 219.9 bits

• Inhibition of Yersinia pestis DNA adenine methyltransferase in vitro by a stibonic acid compound: identification of a potential novel class of antimicrobial agents
  McKelvie, British journal of pharmacology 2013
  • “...3.11E-04 1.40 pPMT1-85 - 3.26E-02 6.48E-04 1.36 YPO3170 Conserved hypothetical protein 4.36E-02 1.35E-03 1.35 YPO3857 Conserved hypothetical protein 3.53E-02...”
• Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
  An, PLoS pathogens 2014
  • “...(MT0592), Pseudomonas aeruginosa (PA4395), Pseudomonas syringae (PSPPH_4093), Stenotrophomonas maltophilia (Smlt4090), Vibrio cholerae (VC_1508), Yersinia pestis (YPC_3455). Sequence alignment of proteins from the YajQ family. Consensus residues are listed below the alignment. The sequence logo illustrates the conservation between sequences. Where the height of each letter reflects...”

HI1034 conserved hypothetical protein (NCBI ptt file) from Haemophilus influenzae Rd KW20
P44096 UPF0234 protein HI_1034 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 219.6 bits

• Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris
  Zhao, Acta crystallographica. Section F, Structural biology communications 2016
  • “...solved by molecular replacement using another YajQ-family protein (HI1034; PDB entry 1in0; Teplyakov et al., 2003) from Haemophilus influenzae as the search...”
  • “...bind RNA in the same manner as classical RRM proteins. HI1034 from H. influenzae was the first protein structure to be solved from the YajQ family (Teplyakov et...”
• Identification of biofilm proteins in non-typeable Haemophilus Influenzae
  Gallaher, BMC microbiology 2006
  • “...protector protein - n n HI0847 1573861 all 3085 S Uncharacterized BCR - n y HI1034 1574067 1 3 4 1666 S Uncharacterized BCR - y y HI1168 68057915 all 2926 S Uncharacterized BCR - y y HI1333 1574791 All 1534 J Predicted RNA-binding protein containing...”
• Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
  Kolker, Nucleic acids research 2004
  • “...a model of the native tetrameric structure of the HI1034 protein was shown to dock well with DNA, suggesting a DNA- or RNA-binding function (40). Although these...”
  • “...1j8b 1j7h nanRATEK ruvCAB, mutT recR, dnaX tdcB HI0828 HI1034 P44887 P44096 98 163 2350 1666 1mwq 1in0 ispA, yciA, slt, bolA apbA, serB Sugar...”
• Structural and nucleotide-binding properties of YajQ and YnaF, two Escherichia coli proteins of unknown function
  Saveanu, Protein science : a publication of the Protein Society 2002
  • “...and Salmonella dublin. The Haemophilus influenzae yajQ gene (HI1034) is flanked by serB, encoding a phosphoserine phosphatase, and by corA, encoding a metal...”
• Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
  Kolker, Nucleic acids research 2004
  • “...ruvCAB, mutT recR, dnaX tdcB HI0828 HI1034 P44887 P44096 98 163 2350 1666 1mwq 1in0 ispA, yciA, slt, bolA apbA, serB Sugar (N-acetylneuraminate?)-binding...”

YajQ / b0426 nucleotide binding protein YajQ from Escherichia coli K-12 substr. MG1655 (see 6 papers)
YAJQ_ECOLI / P0A8E7 UPF0234 protein YajQ from Escherichia coli (strain K12) (see paper)
yajQ / MB|P0A8E7 UPF0234 protein yajQ from Escherichia coli K12 (see 6 papers)
c0537 nucleotide-binding protein (RefSeq) from Escherichia coli CFT073
NP_414960 nucleotide binding protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 219.5 bits

• function: Binds nucleotides, may bind tRNA
  subunit: Monomer.
• Identification of in vivo-induced antigens including an RTX family exoprotein required for uropathogenic Escherichia coli virulence
  Vigil, Infection and immunity 2011
  • “...c4487 c2179 c3068 c2085 c4682 c2051 c0875 c4901 c0537 c2661 Function of gene product Hypothetical dipeptide ABC transporter, permease subunit Glycine betaine...”
• Structural and nucleotide-binding properties of YajQ and YnaF, two Escherichia coli proteins of unknown function.
  Saveanu, Protein science : a publication of the Protein Society 2002
  • GeneRIF: N-terminus verified by Edman degradation on mature peptide
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...YajD YajG YajO YajQ YbbL P0AAQ2 P0ADA5 P77735 P0A8E7 P77279 YbbN YbdQ P77395 YbeZ YbfF P0A9K3 P75736 PhoH-like protein Esterase 6.24/40,654.52 5.86/28,437.26...”

AL538_RS00950 YajQ family cyclic di-GMP-binding protein from Vibrio harveyi
Aligns to 2:159 / 160 (98.8%), covers 100.0% of PF04461, 218.4 bits

• Analysis of Vibrio harveyi adaptation in sea water microcosms at elevated temperature provides insights into the putative mechanisms of its persistence and spread in the time of global warming
  Montánchez, Scientific reports 2019
  • “...substrate-binding protein 2.683 4.749 3.279 2 AL538_RS19380 Amino acid ABC transporter 1.236 1.698 1.907 3 AL538_RS00950 Amino acid ABC transporter substrate-binding protein 1.188 2.888 2.524 3 AL538_RS01680 Peptide ABC transporter substrate-binding protein 2.146 4.524 3.021 3 AL538_RS01780 Polyamine ABC transporter ATP-binding protein 2.676 3.963 3.018 2...”

BCAL2769 hypothetical protein (RefSeq) from Burkholderia cenocepacia J2315
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 218.1 bits

• High confidence prediction of essential genes in Burkholderia cenocepacia
  Juhas, PloS one 2012
  • “...ubiB , and valS , as well as the so far uncharacterized genes BCAL1882 , BCAL2769 , BCAL3142 and BCAL3369 has been confirmed experimentally in B. cenocepacia . Conclusions/Significance We report on the identification of essential genes using a novel bioinformatics strategy and provide bioinformatics and...”
  • “...infB , H111 gyrB , H111 uniB , H111 valS , H111 BCAL1882 , H111 BCAL2769 , H111 BCAL3142 and H111 BCAL3369 grew on LB plates supplemented with rhamnose but not with glucose as expected for mutants with essential genes under the control of rhamnose promoter....”

Clocel_3875 YajQ family cyclic di-GMP-binding protein from Clostridium cellulovorans 743B
Aligns to 5:163 / 163 (97.5%), covers 99.4% of PF04461, 217.1 bits

• Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
  An, PLoS pathogens 2014
  • “...(XC_3703), Escherichia coli (YajQ), Bacillus cereus (BCK_02545), Bordetella pertussis (BP1193_10170), Bacillus subtilis (YitK), Clostridium cellulovorans (Clocel_3875), C. jejuni (BN867_03480), Enterococcus faecalis (EFD32_0973), Haemophilus influenzae (R2846_1298), Legionella pneumophila (LPE509_01999), Mycobacterium tuberculosis (MT0592), Pseudomonas aeruginosa (PA4395), Pseudomonas syringae (PSPPH_4093), Stenotrophomonas maltophilia (Smlt4090), Vibrio cholerae (VC_1508), Yersinia pestis (YPC_3455)....”

R2846_1298 YajQ family cyclic di-GMP-binding protein from Haemophilus influenzae R2846
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 216.7 bits

• Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
  An, PLoS pathogens 2014
  • “...(BP1193_10170), Bacillus subtilis (YitK), Clostridium cellulovorans (Clocel_3875), C. jejuni (BN867_03480), Enterococcus faecalis (EFD32_0973), Haemophilus influenzae (R2846_1298), Legionella pneumophila (LPE509_01999), Mycobacterium tuberculosis (MT0592), Pseudomonas aeruginosa (PA4395), Pseudomonas syringae (PSPPH_4093), Stenotrophomonas maltophilia (Smlt4090), Vibrio cholerae (VC_1508), Yersinia pestis (YPC_3455). Sequence alignment of proteins from the YajQ family. Consensus...”

STM0435 nucleotide-binding protein (RefSeq) from Salmonella typhimurium LT2
Q8ZRC9 UPF0234 protein YajQ from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 216.3 bits

• Comparative proteomic analysis of Salmonella enterica serovar Typhimurium ppGpp-deficient mutant to identify a novel virulence protein required for intracellular survival in macrophages
  Haneda, BMC microbiology 2010
  • “...EC 062 STM1091 sopB 0.2 0.036 ND 064 STM4319 phoN 0.1 0.014 0.54 0.22 108 STM0435 yajQ 0.5 0.038 0.12 0.05 c 108-2 STM1440 sodC1 0.5 0.038 ND 153 STM3318 yhbN 0.6 0.047 0.28 0.12 c 154 STM4405 ytfJ 0.2 0.049 0.30 0.02 c 184 STM3348...”
• Mass spectrometry-based quantitative proteomic analysis of Salmonella enterica serovar Enteritidis protein expression upon exposure to hydrogen peroxide
  Kim, BMC microbiology 2010
  • “...41% STM0316 Aminoacyl-histidine dipeptidase pepD 52.69 5.17 15% STM0432 Phosphonoacetaldehyde hydrolase phnX 28.57 5.58 41% STM0435 Nucleotide-binding protein yajQ 18.31 5.6 52% STM0447 Trigger factor tig 48.02 4.84 23% STM0488 Adenylate kinase adk 23.49 5.53 51% STM0536 Peptidyl-prolyl cis-trans isomerase B ppiB 18.13 5.52 45% STM0608...”
  • “...tsf 21 4% STM0316 Aminoacyl-histidine dipeptidase pepD 9 1% STM0432 Phosphonoacetaldehyde hydrolase phnX 31 3% STM0435 Nucleotide-binding protein yajQ 0% STM0447 Trigger factor tig 11 2% STM0488 Adenylate kinase adk 0% STM0536 Peptidyl-prolyl cis-trans isomerase B ppiB 0% STM0608 Chain T, crystal structure of Ahpc ahpC...”
• N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
  de, PloS one 2018
  • “...to stress -7.772 1.761 ND ND 8.250 1.368 ND ND ND ND UPF0234 protein YajQ Q8ZRC9 yajQ Response to stress -7.420 2.808 8.948 0.625 ND ND ND ND ND ND Universal stress protein G P67093 uspG Response to stress ND ND 9.407 2.079 0.013 0.039 1.175...”

PP1352 conserved hypothetical protein (NCBI ptt file) from Pseudomonas putida KT2440
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 212.8 bits

• Cloning of the genes involved in synthesis of coenzyme pyrrolo-quinoline-quinone from Acinetobacter calcoaceticus
  Goosen, Journal of bacteriology 1987
  • “...PP1361 PP1333 PP1351 PP1355 PP1357 PP1358 PP1360 PP1335 PP1350 PP1352 PP1353 PP1354 PP1359 M2 M3 M6 M7 M8 M11 TnS-14 TnS-18 TnS-7 TnS-20 TnS-17 TnS-9 Tn5-2 +...”

BCK_02545 YajQ family cyclic di-GMP-binding protein from Bacillus cereus FRI-35
Aligns to 5:163 / 163 (97.5%), covers 100.0% of PF04461, 212.1 bits

• Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris
  Zhao, Acta crystallographica. Section F, Structural biology communications 2016
  • “...of homologues, such as HI1034 from H. influenzae and BCK_02545 from Bacillus cereus (Figs. 3 and 4), which makes it a candidate for a c-diGMP-binding residue....”
• Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
  An, PLoS pathogens 2014
  • “...are boxed within the same color. Key: Xanthomonas campestris (XC_3703), Escherichia coli (YajQ), Bacillus cereus (BCK_02545), Bordetella pertussis (BP1193_10170), Bacillus subtilis (YitK), Clostridium cellulovorans (Clocel_3875), C. jejuni (BN867_03480), Enterococcus faecalis (EFD32_0973), Haemophilus influenzae (R2846_1298), Legionella pneumophila (LPE509_01999), Mycobacterium tuberculosis (MT0592), Pseudomonas aeruginosa (PA4395), Pseudomonas syringae (PSPPH_4093),...”

VC_1508 YajQ family cyclic di-GMP-binding protein from Vibrio cholerae O1 biovar El Tor str. N16961
Aligns to 2:159 / 160 (98.8%), covers 100.0% of PF04461, 212.0 bits

• Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
  An, PLoS pathogens 2014
  • “...(LPE509_01999), Mycobacterium tuberculosis (MT0592), Pseudomonas aeruginosa (PA4395), Pseudomonas syringae (PSPPH_4093), Stenotrophomonas maltophilia (Smlt4090), Vibrio cholerae (VC_1508), Yersinia pestis (YPC_3455). Sequence alignment of proteins from the YajQ family. Consensus residues are listed below the alignment. The sequence logo illustrates the conservation between sequences. Where the height of...”

Q81GN2 UPF0234 protein BC_1159 from Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Aligns to 5:163 / 163 (97.5%), covers 100.0% of PF04461, 210.9 bits

• Sporulation Temperature Reveals a Requirement for CotE in the Assembly of both the Coat and Exosporium Layers of Bacillus cereus Spores
  Bressuire-Isoard, Applied and environmental microbiology 2016
  • “...Q814N4 Q816F2 Q81IY1 Q81IK9 Q81HI7 Q81IJ6 Q81FV0 Q817V9 Q81GN2 Q817Z6 Q819C5 Q819D8 Q819D7 Q81IT9 Q81A21 Q815K7 BC_0821 BC_0390 BC_1468 BC_4419 (yhcN) BC_1159...”

Rv0566c hypothetical protein (NCBI) from Mycobacterium tuberculosis H37Rv
MT0592 hypothetical protein (NCBI) from Mycobacterium tuberculosis CDC1551
Aligns to 4:163 / 163 (98.2%), covers 100.0% of PF04461, 209.6 bits

• Integrative proteomic and glycoproteomic profiling of Mycobacterium tuberculosis culture filtrate
  Tucci, PloS one 2020
  • “...Rv3273 Rv3273 S735 NO 10 This work Conserved hypotheticals Rv0311 Rv0311 S10 NO This work Rv0566c Rv0566c T52, S53 & T55 NO This work Rv1352 Rv1352 T23 SP(Sec/SPI) 1 This work Rv1466 Rv1466 S5 NO This work Rv2166c Rv2166c S39 NO This work Rv2558 Rv2558 T82...”
• Computational Identification of the Proteins Associated With Quorum Sensing and Biofilm Formation in Mycobacterium tuberculosis
  Hegde, Frontiers in microbiology 2019
  • “...Rv0199, Rv0359, Rv1258c, Rv2136c, Rv3312A, SapM, SecA2, SugA, SugB, SugC Conserved hypotheticals 14 Rv0021c, Rv0038, Rv0566c, Rv0574c, Rv1176c, Rv1354c, Rv1357c, Rv1991c, Rv1996, Rv2216, Rv2298, Rv2300c, Rv3237c, Rv3519 Information pathways 9 Fmt, HelY, Hns, Mfd, MutT3, NrdH, RplM, SigB, TypA Intermediary metabolism and respiration 29 AckA, AroK,...”
  • “...E secA2 , lpqY , sugA , sugB , sugC 0 0 1 1 1 Rv0566c , pks16 , Rv3519 , ltp3 0 0 0 1 0 Rv0195 , ceoB 0 0 1 0 0 Rv1176c , dacB2 0 1 0 0 0 Rv0199 0 0...”
• Investigating function roles of hypothetical proteins encoded by the Mycobacterium tuberculosis H37Rv genome
  Yang, BMC genomics 2019
  • “...this study No. ORF Accession number Annotated gene Description Widen value % Supporting number 1 Rv0566c NP_215080.1 yajQ Protein YajQ 94.15 3 2 Rv0190 NP_214704.1 rcnR Transcriptional repressor RcnR 92.89 4 3 Rv0587 NP_215101.1 yciC Membrane protein YciC 91.12 3 4 Rv2377c NP_216893.1 ybdZ Enterobactin biosynthesis...”
• Using a Label Free Quantitative Proteomics Approach to Identify Changes in Protein Abundance in Multidrug-Resistant Mycobacterium tuberculosis
  Phong, Indian journal of microbiology 2015
  • “...536 Rv3133c Transcriptional regulatory protein devR 9 2.6 Rv0566c UPF0234 protein 10 2.2 Rv1156 Conserved protein 10 2.6 Rv1770 Conserved protein 10 3.0 Rv0577...”
• Descriptive proteomic analysis shows protein variability between closely related clinical isolates of Mycobacterium tuberculosis
  Mehaffy, Proteomics 2010
  • “...levels within the S75 strains but differ significantly from CDC1551. Mpt83, Rv0398c, Wag31, Rv0854, Isr2, Rv0566c, AcpP, Rv2111c, and Cfp2 presented higher levels in CDC1551. From these, Mpt83, and Cfp2 were at least two fold more abundant in CDC1551, while Rv2111c was four times more abundant...”
  • “...21 , 23 25 ] 57116727 Rv0379 secE2 0.79 0.65 0.78 3 4 60.56 15607706 Rv0566c -- 1.49 0.94 1.12 10 4 28.83 [ 21 , 24 , 25 ] 15607776 Rv0636 hadB 0.74 1.46 1.03 7 1 8.45 [ 17 , 25 ] 15607780 Rv0640...”
• Biomarkers of lung-related diseases: current knowledge by proteomic approaches
  Lau, Journal of cellular physiology 2009
  • “...from the M. tuberculosis H37Rv and CDC1551 strains. Eleven proteins, Rv0652, Rv1636, Rv2818c, Rv3369, Rv3865, Rv0566c, MT3304, Rv3160, Rv3874, Rv0560c, and Rv3648c, were identified by MALDITOFMS or LCESIMS. All these proteins were cloned and expressed in E. coli and affinity purified. By using three of these...”
• In vivo inactivation of the mycobacterial integral membrane stearoyl coenzyme A desaturase DesA3 by a C-terminus-specific degradation process
  Chang, Journal of bacteriology 2008
  • “...proteins identified are Rv0100, Rv0176, Rv0204c, Rv0218, Rv0566c, Rv0687, Rv1128c, Rv1144, Rv1183, Rv1184c, Rv1405c, Rv1422, Rv1560, Rv1710, Rv1930c, Rv2038c,...”
• Antigens secreted from Mycobacterium tuberculosis: identification by proteomics approach and test for diagnostic marker
  Bahk, Proteomics 2004 (PubMed)
  • “...proteins, Rv0652, Rv1636, Rv2818c, Rv3369, Rv3865, Rv0566c, MT3304, and Rv3160, were identified by matrix-assisted laser desorption/ionization-time of...”
  • “...only the K strain (Rv0652, Rv1636, Rv2818c, Rv3369, Rv3865, Rv0566c, MT3304, and Rv3160) were shown on the gels, Rv3845 appeared on the gels from the K strain...”
• More
• Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
  An, PLoS pathogens 2014
  • “...(Clocel_3875), C. jejuni (BN867_03480), Enterococcus faecalis (EFD32_0973), Haemophilus influenzae (R2846_1298), Legionella pneumophila (LPE509_01999), Mycobacterium tuberculosis (MT0592), Pseudomonas aeruginosa (PA4395), Pseudomonas syringae (PSPPH_4093), Stenotrophomonas maltophilia (Smlt4090), Vibrio cholerae (VC_1508), Yersinia pestis (YPC_3455). Sequence alignment of proteins from the YajQ family. Consensus residues are listed below the alignment....”

MSMEG_1165 hypothetical protein (NCBI) from Mycobacterium smegmatis str. MC2 155
Aligns to 4:163 / 163 (98.2%), covers 100.0% of PF04461, 209.1 bits

• Identifying nucleic acid-associated proteins in Mycobacterium smegmatis by mass spectrometry-based proteomics
  Kriel, BMC molecular and cell biology 2020
  • “...proteins (Additional file 2 : Table S2), of which 12 (MSMEG_0067, MSMEG_0243, MSMEG_0754, MSMEG_0824, MSMEG_0948, MSMEG_1165, MSMEG_1342, MSMEG_1680, MSMEG_2782, MSMEG_3020, MSMEG_3595, MSMEG_4306) had no identifying GO terms and are not known to be associated with nucleic acids or nucleic acid-associated proteins. Gene ontology enrichment analysis demonstrated...”

MAP4063c hypothetical protein (NCBI) from Mycobacterium avium subsp. paratuberculosis str. k10
Aligns to 4:163 / 163 (98.2%), covers 100.0% of PF04461, 209.1 bits

• Proteome and differential expression analysis of membrane and cytosolic proteins from Mycobacterium avium subsp. paratuberculosis strains K-10 and 187
  Radosevich, Journal of bacteriology 2007
  • “...MAP2997c MAP2450c MAP1325 MAP2506c MAP2451c MAP2267c MAP0150c MAP4063c MAP0470 MAP1123 MAP2281c MAP0349 MAP3551c MAP34340 184.54 357.16 82.60 383.10 351.82...”

Q9F2U7 UPF0234 protein SCO4614 from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
Aligns to 4:162 / 162 (98.1%), covers 100.0% of PF04461, 208.4 bits

• Proteomic survey of the Streptomyces coelicolor nucleoid
  Bradshaw, Journal of proteomics 2013
  • “...sIHF * D 1480 Q9KXR9 n/a 11.5 10.4 3.49 2 6.4 7 YajQ D 4614 Q9F2U7 n/a 18 5.5 3.4 3 9.02 4 HupA * D 2950 P0A3H5 n/a 9.9 9.5 3.24 4 9.1 3 Uncharacterised U 5783 O69959 0.59 17.1 7.1 2.95 5 1.36 25...”

ACIAD3137 conserved hypothetical protein (NCBI) from Acinetobacter sp. ADP1
Aligns to 2:161 / 162 (98.8%), covers 100.0% of PF04461, 208.2 bits

• Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach
  Stuani, Metabolomics : Official journal of the Metabolomic Society 2014
  • “...glnE (ACIAD0596) and alkK (ACIAD1818), transport proteins (ACIAD1590 and 1601) or proteins of unknown function (ACIAD3137, 2741, 2176, and 2066) were also necessary for growth on quinate. The growth of all these mutants was not affected on other carbon sources such as acetate or glucose (de...”

PflSS101_4316 YajQ family cyclic di-GMP-binding protein from Pseudomonas lactis
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 208.2 bits

• Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP
  Song, BMC microbiology 2015
  • “...hypothetical protein 1.2 1.2 PflSS101_4298 tolB Tol-Pal system beta propeller repeat protein TolB 1.33 1.29 PflSS101_4316 PF04461 family protein 1.21 1.55 PflSS101_4394 thrC threonine synthase 1.29 1.43 PflSS101_4600 cbrB two-component response regulator CbrB 1.25 1.5 PflSS101_4631 dapB dihydrodipicolinate reductase 1.5 1.55 PflSS101_4632 dnaJ chaperone protein DnaJ...”

PA4395 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 2:158 / 159 (98.7%), covers 100.0% of PF04461, 208.0 bits

• Transcriptomic Analysis Reveals the Dependency of Pseudomonas aeruginosa Genes for Double-Stranded RNA Bacteriophage phiYY Infection Cycle
  Zhong, iScience 2020
  • “...and the initiation of L segment transcription might require a host protein(s), such as YajQ (PA4395), which results in delayed transcription of theLsegment. Bacterial Transcriptomic Profile The bacterial gene expression level was measured by FPKM (Reads Per Kilobase Per Million Read), and genes with log2 fold...”
• A Cyclic di-GMP-binding Adaptor Protein Interacts with Histidine Kinase to Regulate Two-component Signaling
  Xu, The Journal of biological chemistry 2016
  • “...effectors include FleQ, PelD, FimX, BrlR, PA4395, and seven PilZ-domain-containing proteins. The transcriptional regulator FleQ controls flagellar biosynthesis...”
  • “...IV pili biosynthesis, respectively (23-27). The c-di-GMPbinding PA4395, a member of the YajQ family proteins, interacts with a transcriptional regulator for...”
• Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris
  Zhao, Acta crystallographica. Section F, Structural biology communications 2016
  • “...(An et al., 2014). Besides XC_3703, its homologues PA4395 from Pseudomonas aeruginosa and Smlt4090 from Stenotrophomonas maltophilia are also reported to be...”
• Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique
  Rahmani-Badi, Frontiers in microbiology 2015
  • “...PA3070, PA3143, PA3216, PA3219, PA3229, PA3273, PA3402, PA3762, PA3772, PA3793, PA3869, PA3962, PA4149, PA4202, PA4298-PA4299, PA4395, PA4399, PA4404-PA4405, PA4510, PA4562,PA4884, PA4962, PA5237, PA5463, PA5492, PA5536 * The detailed information is provided in Tables S2, S3 . Figure 2 Functional classifications of DE genes in P. aeruginosa...”
• Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
  An, PLoS pathogens 2014
  • “...affinity for cyclic di-GMP binding was only seen in YajQ family proteins from P. aeruginosa (PA4395) and S. maltophilia (Smlt4090) ( Table S1 ). YajQ family proteins from E. coli , Clostridium sp. and B. cereus by contrast exhibited a greater affinity for ATP and/or GTP...”
  • “...The finding that XC_3703 can influence the virulence of Xcc prompted us to test whether PA4395 and Smlt4090 have a role in the virulence of P. aeruginosa and S. maltophilia respectively. Previous studies have established a correlation between the ability of strains of P. aeruginosa and...”

LPE509_01999 YajQ family cyclic di-GMP-binding protein from Legionella pneumophila subsp. pneumophila LPE509
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 207.5 bits

• Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
  An, PLoS pathogens 2014
  • “...(YitK), Clostridium cellulovorans (Clocel_3875), C. jejuni (BN867_03480), Enterococcus faecalis (EFD32_0973), Haemophilus influenzae (R2846_1298), Legionella pneumophila (LPE509_01999), Mycobacterium tuberculosis (MT0592), Pseudomonas aeruginosa (PA4395), Pseudomonas syringae (PSPPH_4093), Stenotrophomonas maltophilia (Smlt4090), Vibrio cholerae (VC_1508), Yersinia pestis (YPC_3455). Sequence alignment of proteins from the YajQ family. Consensus residues are listed...”

XAC3671 conserved hypothetical protein (NCBI ptt file) from Xanthomonas axonopodis pv. citri str. 306
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 206.8 bits

• Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection
  Moreira, BMC microbiology 2017
  • “...it has been previously annotated as a hypothetical protein, the protein encoded by the gene XAC3671 actually corresponds to YajQ protein. In a recent study in X. campestris it was demonstrated that YajQ belongs to a new class of effector binding proteins of c-di-GMP which contributes...”

PSPPH_4093 hypothetical protein (NCBI) from Pseudomonas syringae pv. phaseolicola 1448A
Aligns to 2:158 / 159 (98.7%), covers 100.0% of PF04461, 206.1 bits

• Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
  An, PLoS pathogens 2014
  • “...(EFD32_0973), Haemophilus influenzae (R2846_1298), Legionella pneumophila (LPE509_01999), Mycobacterium tuberculosis (MT0592), Pseudomonas aeruginosa (PA4395), Pseudomonas syringae (PSPPH_4093), Stenotrophomonas maltophilia (Smlt4090), Vibrio cholerae (VC_1508), Yersinia pestis (YPC_3455). Sequence alignment of proteins from the YajQ family. Consensus residues are listed below the alignment. The sequence logo illustrates the conservation...”

XOO0711 hypothetical protein (NCBI) from Xanthomonas oryzae pv. oryzae KACC10331
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 204.7 bits

• DgcA, a diguanylate cyclase from Xanthomonas oryzae pv. oryzae regulates bacterial pathogenicity on rice
  Su, Scientific reports 2016
  • “...In this study, we found that the homologous receptors Clp (XOO4158), a YajQ family protein XOO0711, and three PilZ domain proteins XOO0887, XOO2849 and XOO1138 were existent in Xoo . Among them, only XOO2849 was significantly down-regulated, which might affect the sliding motility of dgcA as...”

PXO_03091 protein YajQ (RefSeq) from Xanthomonas oryzae pv. oryzae PXO99A
Aligns to 13:171 / 172 (92.4%), covers 100.0% of PF04461, 204.4 bits

• Identification of c-di-GMP Signaling Components in Xanthomonas oryzae and Their Orthologs in Xanthomonads Involved in Regulation of Bacterial Virulence Expression
  Yang, Frontiers in microbiology 2019
  • “...(An et al., 2014 ; Zhao et al., 2016 ). YajQ showed 96% identity with PXO_03091, and XOC_4190 displayed 97.4% similarity with GEdpX9, suggesting that PXO_03091 and GEdpX9 might be two new c-di-GMP receptors in Xoo . In addition, a Differential Radial Capillary Action of Ligand...”

XC_3703 hypothetical protein (NCBI) from Xanthomonas campestris pv. campestris str. 8004
Q4UQD0 UPF0234 protein XC_3703 from Xanthomonas campestris pv. campestris (strain 8004)
WP_011038715 YajQ family cyclic di-GMP-binding protein from Xanthomonas campestris pv. campestris str. 8004
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 204.3 bits

• Structural Conservation and Diversity of PilZ-Related Domains
  Galperin, Journal of bacteriology 2020 (secret)
• A YajQ-LysR-like, cyclic di-GMP-dependent system regulating biosynthesis of an antifungal antibiotic in a crop-protecting bacterium, Lysobacter enzymogenes
  Han, Molecular plant pathology 2020
  • “...OH11. Results CdgL is a cdiGMPbinding protein that affects gene expression in Lysobacter The YajQ (Xc_3703) protein from X. campestris has recently been described as a cdiGMP receptor that affects the virulence of this plant pathogen (An et al. , 2014 ). Because Lysobacter is phylogenetically...”
• Evaluating Eucalyptus leaf colonization by Brasilonema octagenarum (Cyanobacteria, Scytonemataceae) using in planta experiments and genomics
  Alvarenga, PeerJ 2020
  • “...+ + + + + Q2LK92 BcPIC5/BcFKBP12 rapamycin sensitivity + + + + + Q4UQD0 XC_3703 cyclic di-GMP effector + + + + Q4UTV7 XC_2466 aspartate alpha-decarboxylase + + + + + Q4UUL4 XC_2203 nucleotide diphosphate kinase + + + + + Q58PW8 HsvA hrp-associated systemic...”
• Identification of c-di-GMP Signaling Components in Xanthomonas oryzae and Their Orthologs in Xanthomonads Involved in Regulation of Bacterial Virulence Expression
  Yang, Frontiers in microbiology 2019
  • “...and effectors has been recently identified in Xanthomonads and other bacteria. One example is YajQ (XC_3703), a PNPase from Xcc, and XOC_4190 from Xoc, which was well-conserved in Xanthomonas spp (An et al., 2014 ; Zhao et al., 2016 ). YajQ showed 96% identity with PXO_03091,...”
  • “...Zhao Z. Wu Z. Zhang J. ( 2016 ). Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris . Acta Crystallogr. F Struct. Biol. Commun . 72 , 720 725 . 10.1107/S2053230X16013017 27599864 Zheng D. Constantinidou C. Hobman J. L. Minchin S. D....”
• Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris
  Zhao, Acta crystallographica. Section F, Structural biology communications 2016
  • “...YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris Zhixin Zhao,* Zhen Wu and Jun Zhang Received 20 June 2016 Accepted 11 August 2016 Edited...”
  • “...Terwilliger, Los Alamos National Laboratory, USA Keywords: XC_3703; YajQ; c-di-GMP; receptor. PDB reference: XC_3703, 5b7w Supporting information: this article...”
• Bacterial pathogenesis of plants: future challenges from a microbial perspective: Challenges in Bacterial Molecular Plant Pathology
  Pfeilmeier, Molecular plant pathology 2016
  • “...to expand, with the discovery of new cdGbinding targets, such as the YajQ family protein XC_3703 in Xcc (An et al ., 2014b ) and the type III injectisome ATPase HrcN in P. syringae (Trampari et al ., 2015 ). Plantpathogenic bacteria display evolved cellcell signalling...”
• DgcA, a diguanylate cyclase from Xanthomonas oryzae pv. oryzae regulates bacterial pathogenicity on rice
  Su, Scientific reports 2016
  • “...PXO_00049, PXO_02374 33 , and XCC6012 46 , and a recently discovered YajQ family protein XC_3703 47 . In this study, we found that the homologous receptors Clp (XOO4158), a YajQ family protein XOO0711, and three PilZ domain proteins XOO0887, XOO2849 and XOO1138 were existent in...”
• Bacterial Signal Transduction by Cyclic Di-GMP and Other Nucleotide Second Messengers
  Hengge, Journal of bacteriology 2016
  • “...Xanthomonas campestris pv. campestris. Of particular interest was XC_3703, which encodes a member of the YajQ family of bacterial proteins that has...”
• More
• Evaluating Eucalyptus leaf colonization by Brasilonema octagenarum (Cyanobacteria, Scytonemataceae) using in planta experiments and genomics
  Alvarenga, PeerJ 2020
  • “...undefined + + + + + Q2LK92 BcPIC5/BcFKBP12 rapamycin sensitivity + + + + + Q4UQD0 XC_3703 cyclic di-GMP effector + + + + Q4UTV7 XC_2466 aspartate alpha-decarboxylase + + + + + Q4UUL4 XC_2203 nucleotide diphosphate kinase + + + + + Q58PW8 HsvA hrp-associated...”
  • “...presented similarity with proteins involved in regulatory cascades for virulence ( D4HUY4 , D4HX24 , Q4UQD0 , Q58PW8 and Q5H3K9 ) ( Oh, Kim & Beer, 2005 ; Subramoni et al., 2012 ; An et al., 2014 ; Ancona, Li & Zhao, 2014 ; Santander etal.,...”
• Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms
  Chou, Journal of bacteriology 2016
  • “...Q9HUT5 H7C7G9 P22260 G3XCV0 Q9KQ66 A0R6A5 P75905, P69432 P05055 Q9KU59 Q4UQD0 Q9UJV9 Q9Y3Q4 Structurea Kd (M) NAc NA NA 3IAO 4Q20 3IWZ NA NA NA NA 11.7 10 2.4...”
• Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris.
  Zhao, Acta crystallographica. Section F, Structural biology communications 2016
  • GeneRIF: Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. Campestris has been reported.

all4662 hypothetical protein (NCBI ptt file) from Nostoc sp. PCC 7120
Aligns to 5:163 / 163 (97.5%), covers 99.4% of PF04461, 203.0 bits

• The First Proteomics Study of Nostoc sp. PCC 7120 Exposed to Cyanotoxin BMAA under Nitrogen Starvation
  Koksharova, Toxins 2020
  • “...of NtcA ( alr0608 , all2319 , all1454 , alr0599 , alr4380 , alr0140 , all4662 , all5263 , alr1524 , alr5275 , alr4566 , alr4505 , all1411 , asl4547 , alr2889 , asr3294 , all4662 ) ( Table 2 , Supplementary Table S2 ). 2.3....”
  • “...42 AhpC/TSA family protein alr4404 This family includes peroxiredoxin proteins 0.39 0.035 43 cyclic-di-GMP-binding protein all4662 signaling and cellular processes 0.73 0.05 44 EC:3.4.24. | ftsH cell division protease all4936 cell division protease FtsH 1.89 0.015 Translation (4 proteins) 45 GTP-binding protein LepA all2508 elongation factor...”

VAS14_01951 YajQ family cyclic di-GMP-binding protein from Photobacterium angustum S14
VAS14_01951 hypothetical protein (NCBI) from Vibrio angustum S14
Aligns to 2:159 / 160 (98.8%), covers 100.0% of PF04461, 202.7 bits

• Shotgun redox proteomics: identification and quantitation of carbonylated proteins in the UVB-resistant marine bacterium, Photobacterium angustum S14
  Matallana-Surget, PloS one 2013
  • “...1 GVKIGVQRAT T HDKYLTDNFGESVEIVR VAS14_06513 formate acetyltransferase C 19 TPEYDELFSGD P IWATESMGGMGLDGR TPEYDELFSGDPIWA T ESMGGMGLDGR VAS14_01951 hypothetical protein S 1 A T MSLVREQELGQPFQFDNFRD VAS14_17071 flagellin N 1 H T MSNLANINENVNASNSR VAS14_18001 putative alcohol dehydrogenase/acetaldehyde dehydrogenase 1 SDLEGKKRAFLVTD R FLFNNGYADEIVSLLK VAS14_19986 putative Pyruvate dehydrogenase complex C 1...”

EFD32_0973 YajQ family cyclic di-GMP-binding protein from Enterococcus faecalis D32
Aligns to 6:164 / 164 (97.0%), covers 99.4% of PF04461, 199.6 bits

• Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
  An, PLoS pathogens 2014
  • “...(BCK_02545), Bordetella pertussis (BP1193_10170), Bacillus subtilis (YitK), Clostridium cellulovorans (Clocel_3875), C. jejuni (BN867_03480), Enterococcus faecalis (EFD32_0973), Haemophilus influenzae (R2846_1298), Legionella pneumophila (LPE509_01999), Mycobacterium tuberculosis (MT0592), Pseudomonas aeruginosa (PA4395), Pseudomonas syringae (PSPPH_4093), Stenotrophomonas maltophilia (Smlt4090), Vibrio cholerae (VC_1508), Yersinia pestis (YPC_3455). Sequence alignment of proteins from the...”

AMK58_18090 YajQ family cyclic di-GMP-binding protein from Azospirillum brasilense
Aligns to 2:161 / 162 (98.8%), covers 100.0% of PF04461, 199.2 bits

• Transcriptome analysis of Azospirillum brasilense vegetative and cyst states reveals large-scale alterations in metabolic and replicative gene expression
  Malinich, Microbial genomics 2018
  • “...also observed that two additional di-guanylyl cyclases (AMK58_02945 and AMK58_12665) and one di-cyclic-GMP binding protein (AMK58_18090) were also differentially regulated, as was also the case for an adenyl cyclase (AMK58_04750). A. brasilenses close neighbor, R. centenum , also differentially regulates several di-guanylyl cyclases during induction of...”

Smlt4090 hypothetical protein (RefSeq) from Stenotrophomonas maltophilia K279a
Aligns to 2:159 / 160 (98.8%), covers 100.0% of PF04461, 198.7 bits

• Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris
  Zhao, Acta crystallographica. Section F, Structural biology communications 2016
  • “...its homologues PA4395 from Pseudomonas aeruginosa and Smlt4090 from Stenotrophomonas maltophilia are also reported to be potential c-di-GMP receptors from the...”
• Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
  An, PLoS pathogens 2014
  • “...binding was only seen in YajQ family proteins from P. aeruginosa (PA4395) and S. maltophilia (Smlt4090) ( Table S1 ). YajQ family proteins from E. coli , Clostridium sp. and B. cereus by contrast exhibited a greater affinity for ATP and/or GTP than for any cyclic...”
  • “...that XC_3703 can influence the virulence of Xcc prompted us to test whether PA4395 and Smlt4090 have a role in the virulence of P. aeruginosa and S. maltophilia respectively. Previous studies have established a correlation between the ability of strains of P. aeruginosa and S. maltophilia...”

SynWH7803_1823 hypothetical protein (RefSeq) from Synechococcus sp. WH 7803
Aligns to 4:164 / 164 (98.2%), covers 99.4% of PF04461, 195.4 bits

• 100 Days of marine Synechococcus-Ruegeria pomeroyi interaction: A detailed analysis of the exoproteome
  Kaur, Environmental microbiology 2018
  • “...others (Grossowicz et al ., 2017 ). One of these proteins is the nucleotidebinding protein SynWH7803_1823, a protein predicted to be involved in the temporal control of bacteriophage gene transcription, which represents 2.4% of Synechococcus exoproteome (almost 12% of the predicted cytoplasmic proteins in this fraction),...”

SAR11_0692 hypothetical protein (NCBI) from Candidatus Pelagibacter ubique HTCC1062
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 180.4 bits

• Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'
  Meyer, BMC genomics 2009
  • “...hyp. protein (+) SAR11_1249 hyp. protein (+) 676100676308 208 28.7 193 SAR11_0691 hyp. protein (-) SAR11_0692 yajQ (-) 12127571212865 109 29.36 22 SAR11_1279 membrane prot. (-) SAR11_1280 hyp. protein (+) 732778732938 161 29.19 446 SAM-V (-) SAR11_0750 mmuM (-) SAR11_0751 hyp. protein. (-) 5772058035 316 29.11...”

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