Family Search for PF04461 (DUF520)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF04461 hits 39 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
plu3881 No description from Photorhabdus luminescens subsp. laumondii TTO1
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 224.0 bits
VY92_RS09790 YajQ family cyclic di-GMP-binding protein from Avibacterium paragallinarum
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 224.0 bits
- The Transcriptomic and Bioinformatic Characterizations of Iron Acquisition and Heme Utilization in Avibacterium paragallinarum in Response to Iron-Starvation
Huo, Frontiers in microbiology 2021 - “...the primers is listed in Supplementary Table 1 . The qPCR programs for VY92_RS06600, VY92_RS09125, VY92_RS09790, VY92_RS03730, and VY92_RS03735 were as follows: 1 cycle of 95C for 3 min; 35 cycles of 95C for 30 s, 60C for 30 s, and 72C for 40 s. The...”
- “...condition. Here, three upregulated genes (VY92_RS03730, VY92_RS03735, and VY92_RS00335) and four downregulated genes (VY92_RS06600, VY92_RS09125, VY92_RS09790, and VY92_RS01655) were selected as representative DEGs for qPCR. Among them, VY92_RS03730, VY92_RS03735, and VY92_RS00335 were annotated as the heme utilization protein HutZ, heme utilization cystosolic carrier protein HutX, and...”
BVG93_01845 YajQ family cyclic di-GMP-binding protein from Serratia marcescens
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 223.6 bits
- Microbial Reduction of Fumonisin B1 by the New Isolate Serratia marcescens 329-2
Keawmanee, Toxins 2021 - “...glgS 3.89 A0A1Q5WEW3 Antibiotic biosynthesis monooxygenase A8A12_06980 3.87 A0A6I4GZS8 Hydrolase GMA22_24835 3.80 A0A221FKL4 UPF0234 protein BVG93_01845 BVG93_01845 3.75 A0A6H3S2C0 ATP-dependent protease subunit HslV hslV 3.71 A0A6M5I193 MBL fold metallo-hydrolase HMI62_20840 3.64 A0A6N0DB57 Protein deglycase HchA hchA 3.62 A0A2V4G7I4 Amino acid ABC transporter substrate-binding protein glnH 3.62...”
YPC_3455 YajQ family cyclic di-GMP-binding protein from Yersinia pestis biovar Medievalis str. Harbin 35
YPO3170 nucleotide-binding protein from Yersinia pestis CO92
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 220.0 bits
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 from Escherichia coli CFT073
NP_414960 nucleotide binding protein YajQ from Escherichia coli str. K-12 substr. MG1655
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 220.0 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...”
1in0B / P44096 Yajq protein (hi1034) (see paper)
Aligns to 1:161 / 162 (99.4%), covers 100.0% of PF04461, 219.9 bits
- Ligand: mercury (ii) ion (1in0B)
P44096 UPF0234 protein HI_1034 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI1034 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 219.8 bits
- 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...”
- 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...”
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
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, 218.1 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...”
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, 218.0 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)....”
Q8ZRC9 UPF0234 protein YajQ from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
STM0435 nucleotide-binding protein from Salmonella typhimurium LT2
Aligns to 2:162 / 163 (98.8%), covers 100.0% of PF04461, 217.0 bits
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, 216.9 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...”
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, 216.3 bits
Bphy_0527 putative nucleotide-binding protein from Burkholderia phymatum STM815
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 214.5 bits
PP1352 conserved hypothetical protein from Pseudomonas putida KT2440
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 213.3 bits
Q81GN2 UPF0234 protein BC_1159 from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)
Aligns to 5:163 / 163 (97.5%), covers 100.0% of PF04461, 212.5 bits
BCAL2769 hypothetical protein from Burkholderia cenocepacia J2315
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 212.2 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....”
P9WFK9 UPF0234 protein Rv0566c from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
MT0592 hypothetical protein from Mycobacterium tuberculosis CDC1551
Rv0566c hypothetical protein from Mycobacterium tuberculosis H37Rv
Aligns to 4:163 / 163 (98.2%), covers 100.0% of PF04461, 212.0 bits
- The unfoldase ClpC1 of Mycobacterium tuberculosis regulates the expression of a distinct subset of proteins having intrinsically disordered termini
Lunge, The Journal of biological chemistry 2020 (secret) - 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....”
- Mycobacterium tuberculosis Small RNA MTS1338 Confers Pathogenic Properties to Non-Pathogenic Mycobacterium smegmatis
Bychenko, Microorganisms 2021 - “...MSMEG_3580 Rv0129c Lipid metabolism A0QR29 3,3 Porin MspA MSMEG_0965 no A0QRM0 3 UPF0234 protein MSMEG_1165 Rv0566c Conserved hypotheticals A0R4A7 3 DUF732 domain-containing protein MSMEG_5766 no A0QV51 2,7 Methylmalonate-semialdehyde dehydrogenase MSMEG_2449 no A0R061 2,3 HesB/YadR/YfhF family protein MSMEG_4272 Rv2204c Conserved hypotheticals...”
- 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...”
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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, 211.8 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...”
MAP4063c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
Aligns to 4:163 / 163 (98.2%), covers 100.0% of PF04461, 211.6 bits
A0QRM0 UPF0234 protein MSMEG_1165/MSMEI_1134 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_1165 hypothetical protein from Mycobacterium smegmatis str. MC2 155
MSMEG_1165 YajQ family cyclic di-GMP-binding protein from Mycolicibacterium smegmatis MC2 155
Aligns to 4:163 / 163 (98.2%), covers 100.0% of PF04461, 211.4 bits
- Mycobacterium tuberculosis Small RNA MTS1338 Confers Pathogenic Properties to Non-Pathogenic Mycobacterium smegmatis
Bychenko, Microorganisms 2021 - “...5,0 Secreted antigen 85-C FbpC MSMEG_3580 Rv0129c Lipid metabolism A0QR29 3,3 Porin MspA MSMEG_0965 no A0QRM0 3 UPF0234 protein MSMEG_1165 Rv0566c Conserved hypotheticals A0R4A7 3 DUF732 domain-containing protein MSMEG_5766 no A0QV51 2,7 Methylmalonate-semialdehyde dehydrogenase MSMEG_2449 no A0R061 2,3 HesB/YadR/YfhF family protein MSMEG_4272 Rv2204c Conserved hypotheticals...”
- Mycobacterium tuberculosis Small RNA MTS1338 Confers Pathogenic Properties to Non-Pathogenic Mycobacterium smegmatis
Bychenko, Microorganisms 2021 - “...FbpC MSMEG_3580 Rv0129c Lipid metabolism A0QR29 3,3 Porin MspA MSMEG_0965 no A0QRM0 3 UPF0234 protein MSMEG_1165 Rv0566c Conserved hypotheticals A0R4A7 3 DUF732 domain-containing protein MSMEG_5766 no A0QV51 2,7 Methylmalonate-semialdehyde dehydrogenase MSMEG_2449 no A0R061 2,3 HesB/YadR/YfhF family protein MSMEG_4272 Rv2204c Conserved hypotheticals...”
- 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...”
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, 209.5 bits
ACIAD3137 conserved hypothetical protein from Acinetobacter sp. ADP1
Aligns to 2:161 / 162 (98.8%), covers 100.0% of PF04461, 209.0 bits
PflSS101_4316 YajQ family cyclic di-GMP-binding protein from Pseudomonas lactis
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 208.4 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...”
Q9HW11 UPF0234 protein PA4395 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA4395 hypothetical protein from Pseudomonas aeruginosa PAO1
Aligns to 2:158 / 159 (98.7%), covers 100.0% of PF04461, 208.2 bits
- Adsorption of extracellular proteases and pyocyanin produced by Pseudomonas aeruginosa using a macroporous magnesium oxide-templated carbon decreases cytotoxicity
Hirakawa, Current research in microbial sciences 2022 - “...1.02.E+06 5.00.E+06 Q9I6J1 Putrescine-binding protein (SpuD) 61.373 3.67.E+06 5.48.E+06 Q9I5W4 Metalloprotease (ImpA) 61.116 1.17.E+07 9.64.E+06 Q9HW11 UPF0234 protein (PA4395) 59.911 3.33.E+07 1.58.E+06 Q9I457 Glutathione peroxidase (PA1287) 59.694 1.08.E+08 1.14.E+08 Q9HV46 Transcription elongation factor (GreA) 58.009 1.26.E+07 4.30.E+06 *1 : Proteins from a supernatant of PAO1 grown...”
- Adsorption of extracellular proteases and pyocyanin produced by Pseudomonas aeruginosa using a macroporous magnesium oxide-templated carbon decreases cytotoxicity
Hirakawa, Current research in microbial sciences 2022 - “...Putrescine-binding protein (SpuD) 61.373 3.67.E+06 5.48.E+06 Q9I5W4 Metalloprotease (ImpA) 61.116 1.17.E+07 9.64.E+06 Q9HW11 UPF0234 protein (PA4395) 59.911 3.33.E+07 1.58.E+06 Q9I457 Glutathione peroxidase (PA1287) 59.694 1.08.E+08 1.14.E+08 Q9HV46 Transcription elongation factor (GreA) 58.009 1.26.E+07 4.30.E+06 *1 : Proteins from a supernatant of PAO1 grown without MgOC150 2...”
- Cysteamine Inhibits Glycine Utilisation and Disrupts Virulence in Pseudomonas aeruginosa
Fraser-Pitt, Frontiers in cellular and infection microbiology 2021 - “...RNA metabolic processes NP_251543.1 outer membrane lipoprotein PA2853 oprI Outer membrane protein NP_253085.1 nucleotide-binding protein PA4395 yajQ Unknown NP_253132.1 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase PA4442 cysNC hydrogen sulfide biosynthesis NP_250493.1 ATP-dependent protease ATP-binding subunit ClpX PA1802 clpX Protein folding NP_251342.1 chemotaxis transducer PA2652 Cellular response...”
- 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...”
XAC3671 conserved hypothetical protein from Xanthomonas axonopodis pv. citri str. 306
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 206.7 bits
PSPPH_4093 hypothetical protein from Pseudomonas syringae pv. phaseolicola 1448A
Aligns to 2:158 / 159 (98.7%), covers 100.0% of PF04461, 206.3 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...”
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, 205.7 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...”
XOO0711 hypothetical protein from Xanthomonas oryzae pv. oryzae KACC10331
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 204.6 bits
WP_011038715 YajQ family cyclic di-GMP-binding protein from Xanthomonas campestris pv. campestris str. CFBP 1712
Q4UQD0 UPF0234 protein XC_3703 from Xanthomonas campestris pv. campestris (strain 8004)
XC_3703 hypothetical protein from Xanthomonas campestris pv. campestris str. 8004
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 204.4 bits
- 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.
- 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...”
- Functional diversity of c-di-GMP receptors in prokaryotic and eukaryotic systems
Khan, Cell communication and signaling : CCS 2023 - “...115 ] CLP X. campestris - 3.5M Regulated bacterial virulence gene expression [ 116 ] XC_3703 X. campestris pv. campestris - 2M Activated virulence-related genes [ 117 ] PXO_00049 PXO_02374 PXO_02715 X. oryzae pv. oryzae PilZ domain 0.139M for PXO_00049 0.102M for PXO_02374 Regulated virulence [...”
- “...Biol. 2010;396:64662. 117. Zhao Z, Wu Z, Zhang J. Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris . Acta Crystallogr F Struct Biol Commun. 2016;72:7205. 118. Yang F, Tian F, Chen H, Hutchins W, Yang CH, He C. The Xanthomonas oryzae pv....”
- Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas
An, FEMS microbiology reviews 2020 - “...identified in Xcc (An etal . 2013b ; Zhao etal . 2016 ). This protein (XC_3703) acts to influence the transcription of genes that contribute to virulence in plants and biofilm formation. The available evidence suggests that XC_3703 exerts its action through proteinprotein interactions with the...”
- “..., Wu Z , Zhang J et al . Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris . Acta Crystallogr Sect F Struct Biol Commun . 2016 ; 72 : 720 5 . 27599864 Zhou L , Huang T-W , Wang J-Y...”
- 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...”
- 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
PXO_03091 protein YajQ from Xanthomonas oryzae pv. oryzae PXO99A
Aligns to 13:171 / 172 (92.4%), covers 100.0% of PF04461, 204.3 bits
all4662 hypothetical protein from Nostoc sp. PCC 7120
Aligns to 5:163 / 163 (97.5%), covers 99.4% of PF04461, 203.9 bits
- β-N-Methylamino-L-Alanine (BMAA) Causes Severe Stress in Nostoc sp. PCC 7120 Cells under Diazotrophic Conditions: A Proteomic Study
Koksharova, Toxins 2021 - “...ABC transporter alr3938 ABC transporter iron binding protein high-affinity iron ion transport Regulatory proteins Signaling all4662 cyclic-di-GMP-binding protein all0089 Uncharacterized conserved protein YggE, contains kinase-interacting SIMPL domain all0129 two-component system, OmpR family, response regulator RpaA Stress response all1541 peroxi- redoxin 2 family protein/ glutaredoxin Transcription all5263...”
- “...Secondary metabolites alr0599 1-deoxy- xylulose 5-phosphate synthase EC:2.2.1.7 Hypothetical proteins alr4505 all1411 asl4547 alr2889 asr3294 all4662 alr4505 all1411 asr1156 alr4505 alr4504 all1411 asl4547 all3826...”
- 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
Aligns to 2:159 / 160 (98.8%), covers 100.0% of PF04461, 203.3 bits
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, 200.1 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
Smlt4090 hypothetical protein from Stenotrophomonas maltophilia K279a
Aligns to 2:159 / 160 (98.8%), covers 100.0% of PF04461, 198.5 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 from Synechococcus sp. WH 7803
Aligns to 4:164 / 164 (98.2%), covers 99.4% of PF04461, 194.1 bits
SYNW1816 conserved hypothetical protein from Synechococcus sp. WH 8102
Aligns to 5:165 / 165 (97.6%), covers 100.0% of PF04461, 192.0 bits
SAR11_0692 hypothetical protein from Candidatus Pelagibacter ubique HTCC1062
Aligns to 2:160 / 161 (98.8%), covers 100.0% of PF04461, 182.0 bits
Or search for genetic data about PF04461 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory