PaperBLAST
PaperBLAST Hits for 74 a.a. (KRNRIPLGCT...)
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>74 a.a. (KRNRIPLGCT...)
KRNRIPLGCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELK
KLRERVKSLEKTLS
Running BLASTp...
Found 101 similar proteins in the literature:
HAP1_YEASX / P0CS82 Heme-responsive zinc finger transcription factor HAP1; CYP1 activatory protein; Heme activator protein 1 from Saccharomyces cerevisiae (Baker's yeast) (see 6 papers)
99% identity, 5% coverage
- function: Regulation of oxygen dependent gene expression. It modulates the expression of Iso-1 (CYP1) and Iso-2 (CYP3) cytochrome c. In response to heme, promotes transcription of genes encoding functions required for respiration, controlling oxidative damage and repression of anaerobic genes. Binds to the sequence 5'-CGGNNNTNNCGG-3'. Is non- functional in terms of iso-1 cytochrome c expression in strain S288c and its derivatives.
subunit: Binds DNA as a homodimer. Interacts with SRO9 and YDJ1. In the absence of heme, binds to at least four cellular proteins, including YDJ1 and SRO9, forming a high-molecular-weight complex (HMC) which results in repression of its activity and dictates its DNA-binding specificity.
HAP1_YEAST / P0CE41 Heme-responsive zinc finger transcription factor HAP1; CYP1 activatory protein; Heme activator protein 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
NP_013357 Hap1p from Saccharomyces cerevisiae S288C
YLR256W Hap1p from Saccharomyces cerevisiae
99% identity, 5% coverage
- function: Regulation of oxygen dependent gene expression. It modulates the expression of Iso-1 (CYP1) and Iso-2 (CYP3) cytochrome c. In response to heme, promotes transcription of genes encoding functions required for respiration, controlling oxidative damage and repression of anaerobic genes. Binds to the sequence 5'-CGGNNNTNNCGG-3' (By similarity). Is non-functional in terms of iso-1 cytochrome c expression in strain S288c and its derivatives.
subunit: Binds DNA as a homodimer. Interacts with SRO9 and YDJ1. In the absence of heme, binds to at least four cellular proteins, including YDJ1 and SRO9, forming a high-molecular-weight complex (HMC) which results in repression of its activity and dictates its DNA-binding specificity (By similarity). - The activator/repressor Hap1 binds to the yeast eIF5A-encoding gene TIF51A to adapt its expression to the mitochondrial functional status.
Barba-Aliaga, FEBS letters 2022 (PubMed)- GeneRIF: The activator/repressor Hap1 binds to the yeast eIF5A-encoding gene TIF51A to adapt its expression to the mitochondrial functional status.
- Regulation of the HAP1 gene involves positive actions of histone deacetylases.
Xin, Biochemical and biophysical research communications 2007 - GeneRIF: analysis of a complex mechanism of transcriptional regulation at the HAP1 promoter, involving multiple DNA elements and regulatory proteins
- Heme levels switch the function of Hap1 of Saccharomyces cerevisiae between transcriptional activator and transcriptional repressor.
Hickman, Molecular and cellular biology 2007 - GeneRIF: Hap1 also plays a significant and direct role under hypoxic conditions, not as an activator, but as a repressor.
- The heme activator protein Hap1 represses transcription by a heme-independent mechanism in Saccharomyces cerevisiae.
Hon, Genetics 2005 - GeneRIF: Hap1 binds to DNA and activates transcription of genes encoding functions required for respiration and for controlling oxidative damage.
- Control of Hap1-DNA site recognition through the interplay of multiple distinct intermolecular interactions.
Wang, Biochemistry 2004 (PubMed)- GeneRIF: A simultaneous optimization of distinct intermolecular interactions determines the DNA-binding specificity of Hap1. Perturbations to individual interactions modulate Hap1 binding affinity and, very likely, its binding geometry.
- Candida glabrata maintains two HAP1 ohnologs, HAP1A and HAP1B, for distinct roles in ergosterol gene regulation to mediate sterol homeostasis under azole and hypoxic conditions
Saha, mSphere 2024 - “...and black color indicates outgroup species. ( D ) Syntenic analysis between S. cerevisiae HAP1 (YLR256W) and C. glabrata Hap1A ( CAGL0B03421 ) and Hap1B ( CAGL0K05841 ) provided by the Yeast Gene Order Browser ( http://ygob.ucd.ie/ ). Red asterisks mark the position of the HAP1...”
- Acute ethanol stress induces sumoylation of conserved chromatin structural proteins in Saccharomyces cerevisiae
Bradley, Molecular biology of the cell 2021 - “...ENV11 1 2 9 Vacuolar function YBL097W BRN1 2 3 9 Subunit of condensin complex YLR256W HAP1 1 21 9 Zinc finger transcription factor YDR485C VPS72 1 6 8 Htz1p-binding component of the SWR1 complex YIL126W STH1 1 4 8 ATPase component of RSC chromatin remodeling...”
- Transcriptomic Insights into the Effect of Melatonin in Saccharomyces cerevisiae in the Presence and Absence of Oxidative Stress
Sunyer-Figueres, Antioxidants (Basel, Switzerland) 2020 - “...to decreased oxygen levels, which showed the highest enrichment (50%), including 4 upregulated genes ( YLR256W, FRD1, MGA2, UPC2 ) ( Figure 2 A and Dataset S13 ). Additionally, molecular functions related to transport activity and transmembrane transport were significantly overexpressed in the presence of melatonin,...”
- Gene Expression Is Not Random: Scaling, Long-Range Cross-Dependence, and Fractal Characteristics of Gene Regulatory Networks
Ghorbani, Frontiers in physiology 2018 - “...covariance function in a gene-TF link in E. coli (ihfB to ompR) and S. cerevisiae (YLR256W to YKL020C) regulatory network. (b) Generalized cross-correlation exponent of a gene-TF link in E. coli and S. cerevisiae . (c) Histogram of cross-correlation exponents of gene regulatory network links in...”
- “...pair of gene and TF (link) in E. coli (ihfB to ompR) and S. cerevisiae (YLR256W to YKL020C). We have applied the multifractal detrended cross-correlation analysis for pairs of genes and TFs (links) in the gene regulatory network of E. coli and S. cerevisiae and found...”
- The role of PCNA as a scaffold protein in cellular signaling is functionally conserved between yeast and humans
Olaisen, FEBS open bio 2018 - “...YKL176C Lst4 Protein Lst4 14, 20 YLL040C Vps13 Vacuolar protein sortingassociated protein 13 14, 20 YLR256W Hap1 Transposon Ty1LR4 GagPol polyprotein 2, 11 YML098W Taf13 Transcription initiation factor TFIID subunit 13 10, 11 YML127W Rsc9 Chromatin structureremodeling complex subunit Rsc9 10, 11 YNL248C Rpa49 DNAdirected RNA...”
- Transcriptome response to alkane biofuels in Saccharomyces cerevisiae: identification of efflux pumps involved in alkane tolerance
Ling, Biotechnology for biofuels 2013 - “...YDR207C UME6 +6 +4 +4 YOR028C CIN5 2 3 10 YPR104C FHL1 3 4 8 YLR256W HAP1 3 3 7 Note: C10-24h, cells exposed to C10 for 24h compared to cells without alkane exposure for 24h, C9- or C10-48h, cells exposed to C9 or C10 for...”
- Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks
Brion, BMC genomics 2013 - “...weak-acid-inducible multidrug transporter required for weak organic acid resistance; regulated by War1p Transcription factor HAP1 YLR256W chr12:673 6,22 Self 123 Zinc finger transcription factor involved in the complex regulation of gene expression in response to levels of heme and oxygen PDR8 YLR266C chr16:138 5,00 unknown 2...”
- Transcriptional response to mitochondrial NADH kinase deficiency in Saccharomyces cerevisiae
Stuart, Mitochondrion 2009 - “...YJR150C DAN1 12.74 2214.79 Cell wall mannoprotein expressed under anaerobic conditions; repressed during aerobic growth YLR256W HAP1 1.04 -3.51 Transcription factor involved in regulation of gene expression in response to levels of heme and oxygen YOR237W HES1 5.28 38.01 Protein implicated in the regulation of ergosterol...”
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2hapC / P0CS82 Structure of a hap1-18/DNA complex reveals that protein/DNA interactions can have direct allosteric effects on transcriptional activation (see paper)
99% identity, 97% coverage
- Ligands: dna; zinc ion (2hapC)
MAR1_CANGA / Q6FXJ5 Transcription factor MAR1; Multiple azole resistance protein 1 from Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138) (Yeast) (Nakaseomyces glabratus) (see paper)
78% identity, 5% coverage
- function: Transcription factor that contributes to plasma membrane sphingolipid incorporation and membrane permeability, decreasing fluconazole accumulation (PubMed:35050001). Regulates 337 genes under fluconazole stress, including several related to lipid biosynthesis pathways such as RSB1, encoding a sphingoid long-chain base efflux transporter (PubMed:35050001). Associates with the promoter of RSB1 in the region containing two 5'-CCCCTCC-3' motifs and increases its promoter occupancy upon fluconazole stress (PubMed:35050001).
disruption phenotype: Increases susceptibility to multiple azoles, including fluconazole.
PGUG_03333 uncharacterized protein from Meyerozyma guilliermondii ATCC 6260
52% identity, 5% coverage
- Molecular Response of Meyerozyma guilliermondii to Patulin: Transcriptomic-Based Analysis
Yang, Journal of fungi (Basel, Switzerland) 2023 - “...Mitochondrial FAD carrier protein Cell wall and membrane formation PGUG_04330 YMR244W 2.62 Beta-glucosidase (SUN family) PGUG_03333 HAP1 1.13 Heme-responsive zinc finger transcription factor PGUG_00027 RBE1 1.69 Repressed by EFG1 protein 1 Growth and reproduction PGUG_04612 MAL31 1.32 Maltose permease PGUG_03041 FOL2 1.04 GTP cyclohydrolase PGUG_03333 HAP1...”
CTRG_02696 predicted protein from Candida tropicalis MYA-3404
33% identity, 7% coverage
FGSG_01293 hypothetical protein from Fusarium graminearum PH-1
45% identity, 8% coverage
- Genome-wide functional characterization of putative peroxidases in the head blight fungus Fusarium graminearum
Lee, Molecular plant pathology 2018 (secret) - Development of a novel multiplex DNA microarray for Fusarium graminearum and analysis of azole fungicide responses
Becher, BMC genomics 2011 - “...121 FGSG_11028 GACACACTACCGACACAACTG GACTGAGAAGACGAGAAGAAG 225 FGSG_11988 GATGTAATGCTACCTGGAACAC GATGAGACCGATTGTGAGAAC 195 Transcription factors FGSG_00069 GAATCTTCTCCGGCACTCAG TTCTTCACTTCCTTCCGAGATC 139 FGSG_01293 CCCGATATAGTCGAGCCTAAC GGTATTTGTTGCTCCGTTGAC 101 FGSG_01341 ATTCTGGCATGGATGATGAAG CACCAAAGTCACTGGCATATCC 162 FGSG_01669 TTCGACTTCTCACAGCTCAGC TGCCTGCATGTTGTACTGGTC 120 FGSG_05949 TTCGGCAACCATCACTCCTAG TGCTGTTCGTTCTCTCGCACT 100 FGSG_06324 ACAGAGTGTCGAACCAGCAAC GGTTCTCGTGGGATGCTATC 173 FGSG_06810 ATACCCGTCTCATGAACATCG TCGATAACAGCCTTGGCTATG 127 FGSG_09333 CACAGCTCAACGATGCAATG CAAGATAAGCAAGGATGCTGTG 101 FGSG_09349 GCTTGATTGCCCCTCTGAGA GGTTCGCATTCTCCTGGTTC...”
- “...0.4518 FGSG_11988 MDR -1.91 0.0509 -1.63 0.0264 Transcription factors FGSG_00069 Zn2Cys6 -2.14 0.0385 -1.81 0.0207 FGSG_01293 Zn2Cys6 2.08 0.0385 1.91 0.0010 FGSG_01341 C2H2 1.62 0.0357 1.92 0.0042 FGSG_01669 Zn2Cys6 3.86 0.0392 3.30 0.0002 FGSG_05949 WING 4.16 0.0385 3.96 < 0.0001 FGSG_06324 Zn2Cys6 1.64 0.0385 1.00 <...”
rosA repressor of sexual development from Emericella nidulans (see paper)
34% identity, 10% coverage
- CharProtDB Description: Putative Zn(II)2Cys6 transcription factor; negative regulator of sexual development; Source:AspGD
RHTO_05847 Zn(2)-C6 fungal-type transcription factor from Rhodotorula toruloides NP11
35% identity, 7% coverage
CPAR2_501570 uncharacterized protein from Candida parapsilosis
38% identity, 6% coverage
CLUG_00542 Fungal Zn(2)-Cys(6) binuclear cluster domain family protein from Clavispora lusitaniae
52% identity, 3% coverage
- Balancing Positive and Negative Selection: In Vivo Evolution of Candida lusitaniae MRR1
Demers, mBio 2021 - “...heterogeneity in fluconazole (FLZ) resistance among these isolates identified numerous distinct alleles of MRR1 ( CLUG_00542 ) ( 10 ). Multiple alleles encoded gain-of-function (GOF) mutations causing constitutive Mrr1 activity, which, as in other Candida species, increased expression of MDR1 and Mdr1-dependent multidrug efflux pump activity...”
- “...license . DNA for gene knockout constructs. Gene replacement constructs for knocking out MRR1 ( CLUG_00542 , as annotated in reference 10 ), MDR1 ( CLUG_01938/9 , as annotated in reference 10 ), and CAP1 ( CLUG_02670 ) were generated by fusion PCR as described by...”
- Mrr1 regulation of methylglyoxal catabolism and methylglyoxal-induced fluconazole resistance in Candida lusitaniae
Biermann, Molecular microbiology 2021 - “...a link between FLZ resistance and specific single nucleotide polymorphisms in the MRR1 locus ( CLUG_00542 ) among twenty clinical C. lusitaniae isolates from a single patient with cystic fibrosis ( Demers et al. , 2018 ). We identified multiple MRR1 alleles containing gain-of-function mutations that...”
- Evolution of drug resistance in an antifungal-naive chronic Candida lusitaniae infection
Demers, Proceedings of the National Academy of Sciences of the United States of America 2018 - “...mutations per gene found that the most heterogeneous locus among the 20 sequenced isolates was CLUG_00542 , an ortholog of C. albicans MRR1 ( SI Appendix , Fig. S4 ). CLUG_00542 is referred to hereafter as MRR1 . Among the 20 C. lusitaniae clinical isolate genomes...”
SS1G_14383 hypothetical protein from Sclerotinia sclerotiorum 1980 UF-70
41% identity, 12% coverage
SS1G_12532 hypothetical protein from Sclerotinia sclerotiorum 1980 UF-70
28% identity, 6% coverage
SPBC530.05 transcription factor (predicted) from Schizosaccharomyces pombe
32% identity, 10% coverage
YN25_SCHPO / O59741 Uncharacterized transcriptional regulatory protein C530.05 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
32% identity, 10% coverage
- Oryzines A & B, Maleidride Congeners from Aspergillus oryzae and Their Putative Biosynthesis
Wasil, Journal of fungi (Basel, Switzerland) 2018 - “..., A0A161CLJ6 (93%/48%) oryO XP_023094060 Transcription factor Uncharacterized transcriptional regulatory protein C530.05, Schizosaccharomyces pombe , O59741 (24%/40%) oryP - Acyl-CoA ligase Acyl-CoA synthetase family member 3, Homo sapiens , Q4G176 (92%/23%) oryQ - P450 monooxygenase (truncated) Probable sterigmatocystin biosynthesis P450 monooxygenase StcF, Aspergillus nidulans , Q12609...”
FOIG_05174 uncharacterized protein from Fusarium odoratissimum NRRL 54006
27% identity, 6% coverage
- The FTF gene family regulates virulence and expression of SIX effectors in Fusarium oxysporum
Niño-Sánchez, Molecular plant pathology 2016 - “...FOWG_17814 (930) FOWG_18009 (1079) FOWG_17908 (930) FOWG_17740 (930) raphani FOQG_03479 FOQG_15325 (1071) FOQG_19052 (914) cubense FOIG_05174 FOIG_16560 (1046) FOIG_16484 (971) FOIG_16630 (969) vasinfectum FOTG_03936 FOTG_16755 (1072) FOTG_17956 (969) FOTG_18226 FOTG_17879 (1072) FOTG_18225 FOTG_18080 (1098) arabidopsis FOXB_12381 FOXB_19743 FOXB_12596 FOXB_18246 melonis FOMG_08221 FOMG_18985 (1075) FOMG_18692 (969) FOMG_18999...”
FOXG_09390 hypothetical protein from Fusarium oxysporum f. sp. lycopersici 4287
27% identity, 6% coverage
- Effects of biocontrol Bacillus sp. strain D5 on the pathogenic Fusarium oxysporum R1 at the microscopic and molecular level in Crocus sativus L. (saffron) corm
Bhagat, FEMS microbes 2024 - “...TF 3.7 .01 FOXG_10510 sge1 Gti1/Pac2 family 1.27 .0007 FOXG_10430 ren1 HSF TF 1.83 .005 FOXG_09390 ftf2 Fusarium transcription factor-2 2.80 2.04E-05 FOXG_11273 vea Velvet family 3.4 .01 FOXG_00016 velb 0.21 .4 * FOXG_08140 fmk1 MAP kinase 0.26 .08 FOXG_06318 hog1 0.11 .3 * FOXG_03107 pbs2...”
- “...expression of genes for TF Ebr1 (FOXG_05408), Xnlr (FOXG_03748), Sge1 (FOXG_10510), Snt2 (FOXG_01993), and FTF2 (FOXG_09390) were significantly downregulated in presence of Bar D5. In addition, the DEG encoding MAP kinases Pbs2 (FOXG_03107) was significantly downregulated but the expression of two other genes encoding MAP kinases...”
- The Role of the Fusarium oxysporum FTF2 Transcription Factor in Host Colonization and Virulence in Common Bean Plants (Phaseolus vulgaris L.)
Casado-Del, Pathogens (Basel, Switzerland) 2023 - “...[ 9 ] was used to obtain FOP-SP4 transformants with the FTF2 gene ( locus FOXG_09390 in strain 4287 of F. oxysporum f. sp. lycopersici ) inactivated by gene replacement with a selectable marker (the hygromycin resistance gene hph ). Fungal transformations were performed following the...”
- “...FTF2 Mutants FTF2 mutants obtained by the gene replacement of the native FTF2 locus ( FOXG_09390 in the F. oxysporum f. sp. lycopersici genome) in the highly virulent wild-type strain FOP-SP1 and weakly virulent wild-type strain FOP-SP4 were subjected to in vitro phenotypic characterization by analyzing...”
- The FTF gene family regulates virulence and expression of SIX effectors in Fusarium oxysporum
Niño-Sánchez, Molecular plant pathology 2016 - “...Fo 47 FOZG_12687 FOZG_18011 (1007) Fo human FOYG_11202 radicislycopersici FOCG_10914 FOXG_17757 (446) lycopersici r. 2 FOXG_09390 FOXG_14257 (1070) FOXG_17123 (930) Chr 9, Sc 11 Chr 14, Sc 22 Chr 6, Sc 22 FOXG_17458 (1079) FOXG_16414 (930) Chr 14, Sc 51 Chr 14, Sc 36 FOXG_14422 (1072)*...”
- “...the corresponding fungal genomes, except for the F.oxysporum f. sp. lycopersici and phaseoli ORFs, where FOXG_09390 and GenBank JN167165 were used, respectively. The scale indicates the length of branch that represents one substitution per site. On the right, the names of the species, family, order and...”
- Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes
van, PLoS genetics 2016 - “...aTF7 overexpression could also be induced by overexpression of their core homologs, strains expressing cTF1 (FOXG_09390, long gene model) or cTF7 (FOXG_17774) from the FEM1 promoter were generated and tested as described above ( S5 Fig , Fig 4 ). cTF1 can activate the SIX1 promoter...”
NCU06407 zinc finger transcription factor 1 from Neurospora crassa OR74A
27% identity, 6% coverage
- PWWP domain-containing protein Crf4-3 specifically modulates fungal azole susceptibility by regulating sterol C-14 demethylase ERG11
Yu, mSphere 2025 - “...crassa and its cost-effectiveness. The results showed that the knockout of crf4-3 (NCU02684), NCU03206, and NCU06407 genes caused the strains to grow slower on plates containing ketoconazole, compared with WT ( Fig. 2C ; Fig. S2 ). In particular, the phenotype of the crf4-3 knockout strain...”
- “...involved in the transcriptional response of erg11 to azole stress. The knockout of NCU03206 and NCU06407 did not affect the transcriptional response of erg11 to ketoconazole ( Fig. 2D ). Fig 2 DNA pulldown identifies Crf4-3 as a novel protein regulating erg11 response to azole drugs....”
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...11373 zinc finger transcription factor-9 znf-9 Transc Factors NCU06265 11245 Hyphal anastamosis-13 protein ham-13 Morph/Hyph NCU06407 11017 zinc finger transcription factor 1 vad-3 Transc Factors NCU06411 11116 vegetative asexual development-4 vad-4 Transc Factors Binding/Catalytic Activity Metabolic Process NCU06419 11319 map kinase kinase mek-1 Morph/Hyph Binding/Signal Transducer...”
- Exploring the bZIP transcription factor regulatory network in Neurospora crassa
Tian, Microbiology (Reading, England) 2011 - “...vegetative growth defects [ pp-1 (NCU00340), NCU02671, NCU06503, cre-1 (NCU08807), ada-6 (NCU04866), col-26 (NCU07788), vad-3 (NCU06407), kal-1 (NCU03593) and the bZIP TF gene, ada-1 (NCU00499)] ( Colot et al. , 2006 ). Phylogenetic analysis of N. crassa bZIP family members In S. cerevisiae , the bZIP...”
- “...Zn2Cys6 1.9 Related to cutinase TF NCU07392 Zn2Cys6 1.5 6065 adv-1 , all development altered NCU06407 Zn2Cys6 1.5 5560 vad-3 , vegetative asexual development-3 NCU02307 Zn2Cys6 1.5 7075 Conserved hypothetical protein NCU08726 Zn2Cys6 0.2 2025 fl , conidial development protein fluffy NCU03593 1.7 1015 Probable homeoprotein...”
- Transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for neurospora white collar complex
Smith, Eukaryotic cell 2010 - “...WCC binding sites in their promoters in our study (NCU06407 vad-3 and NCU03643, the gene encoding cutinase TF-1). However, both genes had a single perfect match...”
- Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism
Borkovich, Microbiology and molecular biology reviews : MMBR 2004 - “...5.00e-06 04390.1 03931.1 2307.1 07139.1 N. crassa NCU06407; 6.00e-08 N. crassa NCU09205.1; 2.00e-20 A. nidulans; 2.00e-10 N. crassa NCU01097.1 3.00e-55 N....”
NCU02307 hypothetical protein from Neurospora crassa OR74A
39% identity, 8% coverage
- A global search for novel transcription factors impacting the Neurospora crassa circadian clock
Muñoz-Guzmán, G3 (Bethesda, Md.) 2021 - “...et al. 2018 ). This gene exhibits rhythmic expression ( Hurley et al. 2014 ). NCU02307 : ( = 0.51h) is a light-responsive gene encoding for a zinc-finger TFs, up-regulated indirectly by ADV-1 ( Dekhang et al. 2017 ), with reduced expression in a csp-1 overexpressing...”
- “...starch, where it is repressed by the TF COL-26 ( Xiong et al. 2017 ). NCU02307 has been reported as exhibiting rhythmic expression, with a peak in the evening ( Hurley et al. 2014 ). NCU04773 : ( = 0.56h) encodes for a conserved fungal hypothetical...”
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...Morph/Hyph Transporter Activity/Catalytic Activity Cellular Process/Metabolic Process NCU02265 11554 period clock protein FRQ frq Morph/Hyph NCU02307 11054 hypothetical protein Transc Factors NCU02387 11219 nuclear import and export protein Msn5 Morph/Hyph Binding/Transporter Activity Biological Regulation/Localization Process/Cellular Process NCU02406 16076 nuclear protein Morph/Hyph Binding Cellular Component Organization or...”
- Exploring the bZIP transcription factor regulatory network in Neurospora crassa
Tian, Microbiology (Reading, England) 2011 - “...6065 adv-1 , all development altered NCU06407 Zn2Cys6 1.5 5560 vad-3 , vegetative asexual development-3 NCU02307 Zn2Cys6 1.5 7075 Conserved hypothetical protein NCU08726 Zn2Cys6 0.2 2025 fl , conidial development protein fluffy NCU03593 1.7 1015 Probable homeoprotein *Significance cut-off ( bagel ) of at least 1.5-fold....”
PEX2_030910 Transcription factor, fungi from Penicillium expansum
36% identity, 13% coverage
Afu8g02640 C6 transcription factor, putative from Aspergillus fumigatus Af293
51% identity, 6% coverage
AFUA_2G17860 C6 transcription factor, putative from Aspergillus fumigatus Af293
50% identity, 6% coverage
- Regulation of gliotoxin biosynthesis and protection in Aspergillus species
de, PLoS genetics 2022 - “...Table , Fig 7A7C ). The kojR (AFUA_5G06800), AFUA_5G12060, rgdA (AFUA_3G13920), AFUA_8G07360, sreA (AFUA_5G11260), and AFUA_2G17860 strains secrete significantly less GT when compared to the WT strain ( Fig 7A and 7C ). In contrast, the oefC (AFUA_3G09670), AFUA_6G09870, and AFUA_5G14390 strains secrete significantly more GT...”
- “...out of 16), with the exception of rglT , AFUA_5G12060, rgdA (AFUA_3G13920), sreA (AFUA_5G11260), and AFUA_2G17860 which produce similar concentrations of bmGT than the WT strain ( Fig 7B and 7C ). Interestingly, the kojR (AFUA_5G06800) strain is the only TF deletion strain with reduced GT...”
FDB3_GIBM7 / W7N466 Transcription factor FBD3; Fusarium detoxification of benzoxazolinone cluster 2 protein 3; FDB2 cluster protein 3 from Gibberella moniliformis (strain M3125 / FGSC 7600) (Maize ear and stalk rot fungus) (Fusarium verticillioides) (see 3 papers)
36% identity, 10% coverage
- function: Transcription factor; part of the Fusarium detoxification of benzoxazolinone cluster 2 (FDB2) involved in the degradation of benzoxazolinones produced by the host plant (PubMed:19302487, PubMed:26808652). Maize, wheat, and rye produce the 2 benzoxazinone phytoanticipins 2,4-dihy-droxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and 2,4-dihydroxy-1,4-benzoxazin-3-one (DIBOA) that, due to their inherent instability once released, spontaneously degrade to the more stable corresponding benzoxazolinones, 6-methoxy-2-benzoxazolinone (MBOA) and 2-benzoxazolinone (BOA), respectively (PubMed:11876429). FDB3 is not essentiel, but contributes to efficient BOA biotransformation (PubMed:19302487).
disruption phenotype: Decreases, but does not eliminate the ability to metabolize 2-benzoxasolinone (BOA).
NCU16667 hypothetical protein from Neurospora crassa OR74A
35% identity, 6% coverage
- Experimental Evolution of Multidrug Resistance in Neurospora crassa under Antifungal Azole Stress
Zhou, Journal of fungi (Basel, Switzerland) 2022 - “...whose mutants were tested above, and three hypothetical protein encoding genes without available mutants ( NCU16667 , NCU02014 and NCU04216 ) ( Tables S5 and S6 ). The drug susceptibilities were tested for the available knockout mutants of eight mutated genes ( NCU08055 , NCU01997 ,...”
- “...eight commonly mutated genes with the 30thK2 strain ( NCU02036 , NCU02548 , NCU03491 , NCU16667 , NCU03641 , NCU02014 , NCU02243, and NCU04216 ). In addition, NCU02051 and NCU02024 had mutations in all three evolved strains. Four genes, including NCU16302 , NCU01967 , NCU02867, and...”
NCU05051 COL-23 from Neurospora crassa OR74A
49% identity, 5% coverage
FGSG_12742 hypothetical protein from Fusarium graminearum PH-1
37% identity, 8% coverage
SS1G_06754 hypothetical protein from Sclerotinia sclerotiorum 1980 UF-70
40% identity, 9% coverage
NCU09804 C6 transcription factor from Neurospora crassa OR74A
61% identity, 4% coverage
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...Transc Factors NCU09655 11272 hypothetical protein Morph/Hyph NCU09739 11062 all development altered-7 fld Transc Factors NCU09804 11080 zinc finger transcription factor-43 znf-43 Transc Factors NCU09829 11065 hypothetical protein Transc Factors NCU09866 11264 thyroid hormone receptor interactor 12 Morph/Hyph NCU09882 11266 metacaspase-1A mcp-1 Morph/Hyph NCU10006 11396 hypothetical...”
FDB3_FUSPC / K3UIH8 Transcription factor FBD3; Fusarium detoxification of benzoxazolinone cluster protein 3; FDB cluster protein 3 from Fusarium pseudograminearum (strain CS3096) (Wheat and barley crown-rot fungus) (see 2 papers)
38% identity, 10% coverage
- function: Transcription factor; part of the Fusarium detoxification of benzoxazolinone cluster involved in the degradation of benzoxazolinones produced by the host plant (PubMed:25727347, PubMed:26828593). Maize, wheat, and rye produce the 2 benzoxazinone phytoanticipins 2,4-dihy- droxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and 2,4-dihydroxy-1,4- benzoxazin-3-one (DIBOA) that, due to their inherent instability once released, spontaneously degrade to the more stable corresponding benzoxazolinones, 6-methoxy-2-benzoxazolinone (MBOA) and 2- benzoxazolinone (BOA), respectively (By similarity). FDB3 controls the transcription of the FDB gene cluster in response to 6-methoxy-2- benzoxazolinone (MBOA) (PubMed:26828593).
disruption phenotype: Reduces significantly the induction of the FBD cluster genes in response to 6-methoxy-2-benzoxazolinone (MBOA) treatment (PubMed:26828593). Impairs the degradation of MBOA but does not affect the degradation of BOA and 2-aminophenol (2-AP) (PubMed:26828593).
FOXG_15059 hypothetical protein from Fusarium oxysporum f. sp. lycopersici 4287
FOXG_14422 hypothetical protein from Fusarium oxysporum f. sp. lycopersici 4287
32% identity, 6% coverage
- The FTF gene family regulates virulence and expression of SIX effectors in Fusarium oxysporum
Niño-Sánchez, Molecular plant pathology 2016 - “...14, Sc 36 FOXG_14422 (1072)* FOXG_14000 (930) Chr. 15, Sc 24 Chr 6, Sc 21 FOXG_15059 (1072)* FOXG_17084 (930) Chr 1, Sc 27 Chr 6, Sc 41 FOXG_12539 (930) Chr 3, Sc 18 FOXG_12589 (930) Chr 3, Sc 18 lycopersici r. 3 FOWG_05099 FOWG_17325 (1070) FOWG_17814...”
- “...the number found in strain 4287 should be approached with caution, as loci FOXG_14422 and FOXG_15059, and loci FOXG_14000, FOXG_17084, FOXG_12539 and FOXG_12589, are identical duplicates. It is worthwhile to highlight that all the copies of FTF1 in F.oxysporum f. sp. lycopersici 4287 map to chromosomes...”
- The FTF gene family regulates virulence and expression of SIX effectors in Fusarium oxysporum
Niño-Sánchez, Molecular plant pathology 2016 - “...6, Sc 22 FOXG_17458 (1079) FOXG_16414 (930) Chr 14, Sc 51 Chr 14, Sc 36 FOXG_14422 (1072)* FOXG_14000 (930) Chr. 15, Sc 24 Chr 6, Sc 21 FOXG_15059 (1072)* FOXG_17084 (930) Chr 1, Sc 27 Chr 6, Sc 41 FOXG_12539 (930) Chr 3, Sc 18 FOXG_12589...”
- “...(4287). However, the number found in strain 4287 should be approached with caution, as loci FOXG_14422 and FOXG_15059, and loci FOXG_14000, FOXG_17084, FOXG_12539 and FOXG_12589, are identical duplicates. It is worthwhile to highlight that all the copies of FTF1 in F.oxysporum f. sp. lycopersici 4287 map...”
MYCTH_2305551 uncharacterized protein from Thermothelomyces thermophilus ATCC 42464
37% identity, 12% coverage
SPAC1327.01c transcription factor (predicted) from Schizosaccharomyces pombe
55% identity, 3% coverage
SJAG_03918 transcription factor from Schizosaccharomyces japonicus yFS275
49% identity, 4% coverage
- Disruption of the Schizosaccharomyces japonicus lig4 Disturbs Several Cellular Processes and Leads to a Pleiotropic Phenotype
Acs-Szabo, Journal of fungi (Basel, Switzerland) 2023 - “...on 16 May 2022), and the 565 and 583 bp long flanking sequences of the SJAG_03918 S. japonicus gene, which encodes a hypothetical DNA-binding transcription factor ( https://www.japonicusdb.org , accessed on 13 October 2021). For PCR amplification of the flanking sequences, the 13061307 and 13051309 primers...”
- “...for additional data file. Author Contributions Research design, L.A.P., L.A.-S. and I.M.; preparation of the SJAG_03918 disrupted strain, bioinformatic tasks, and RNA isolation, L.A.P.; preparation of the lig4 disrupted strain, phylogenetic tree, BLAST, and statistical analyses, L.A.-S.; characterization of the lig4 mutant strain, S.T.; manuscriptwriting and...”
CNAG_05255 hypothetical protein from Cryptococcus neoformans var. grubii H99
33% identity, 8% coverage
ABL7_LEPMJ / E5A7E3 Abscisic acid cluster transcription factor abl7; Abscisic acid biosynthesis cluster protein 7 from Leptosphaeria maculans (strain JN3 / isolate v23.1.3 / race Av1-4-5-6-7-8) (Blackleg fungus) (Phoma lingam) (see paper)
34% identity, 12% coverage
- function: Transcription factor that regulates the expression of the gene cluster that mediates the biosynthesis of abscisic acid (ABA), a phytohormone that acts antagonistically toward salicylic acid (SA), jasmonic acid (JA) and ethylene (ETH) signaling, to impede plant defense responses.
PDR8_YEAST / Q06149 Transcription factor PDR8; Pleiotropic drug resistance protein 8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
YLR266C Pdr8p from Saccharomyces cerevisiae
33% identity, 10% coverage
- function: Up-regulates the transcription of the genes for ATP-binding cassette (ABC) transporters YOR1 and PDR15, for major facilitator superfamily transporter AZR1, for pleiotropic drug resistance SNG1, for alpha-glucosidase YJL216C and for YLL056C.
- Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks
Brion, BMC genomics 2013 - “...the complex regulation of gene expression in response to levels of heme and oxygen PDR8 YLR266C chr16:138 5,00 unknown 2 Transcription factor; targets include ATP-binding cassette (ABC) transporters, major facilitator superfamily transporters, and other genes involved in the PDR phenomenon WAR1 YML076C chr12:673 6,57 HAP1/PDR8 123...”
- “...transporter of the major facilitator superfamily, required for resistance to quinidine, ketoconazole, fluconazole, and barban YLR266C PDR8 chr16:138 0,493 0,0032 Transcription factor; targets include ATP-binding cassette (ABC) transporters, major facilitator superfamily transporters, and other genes involved in the pleiotropic drug resistance (PDR) phenomenon The gene paralog...”
- Biochemical and genetic analysis of the yeast proteome with a movable ORF collection
Gelperin, Genes & development 2005 - “...N-linked glycoproteins also include three transcription factors (YLR266C, Adr1p, and Sok2p) and a cytosolic kinase (YNR047W), suggesting that glycosylation has...”
- Theme discovery from gene lists for identification and viewing of multiple functional groups
Pehkonen, BMC bioinformatics 2005 - “...promoter. Among these genes, some of them are reported to be important for drug resistance (YLR266C, YCR106W) and to stress response (YFL031W, YMR037C) and to two associated with copper uptake (YGL166W, YMR021C). In summary, we observed with GENERATOR an amino acid biosynthesis associated group, steroid and...”
- A general strategy to uncover transcription factor properties identifies a new regulator of drug resistance in yeast
Hikkel, The Journal of biological chemistry 2003 (PubMed)- “...its target genes. The product of the unknown gene, YLR266c, was chosen because of its structural similarities with YRR1 (5). Yrr1 is a transcription factor (7,...”
- “...The functions of the genes directly controlled by YLR266c are in agreement with the observed drug-resistance phenotype of the cell expressing an activated form...”
- New insights into the pleiotropic drug resistance network from genome-wide characterization of the YRR1 transcription factor regulation system
Le, Molecular and cellular biology 2002 - “...of four genes, the others being YKL222C, YOR172W, and YLR266C. We aligned the sequences of these four genes with that of PDR1 (Fig. 1B) and identified a...”
- “...or other new genes encoding transcription factors, such as YLR266C (I. Hikkel et al., unpublished data). The complete description of such related networks is a...”
- Phenotypic analysis of genes encoding yeast zinc cluster proteins
Akache, Nucleic acids research 2001 - “...HIS3 This study YLR228C YN YPH499 ORF HIS3 This study YLR266C FS FY73 aa 25-246 HIS3 This study This study YLR278C YO YPH499 ORF HIS3 YML076C BZM BY4742 aa...”
- “...ECM22 + + + + + + + + + + + + + + + XX + + FS YLR266C - XXX XXX + + + + + + + + + + + + + XXX + + + YO YLR278C - + + + + + + + + + + + +...”
NCU04866 ADA-6 from Neurospora crassa OR74A
37% identity, 10% coverage
- The PAC-3 transcription factor critically regulates phenotype-associated genes in Neurospora crassa
Martins, Genetics and molecular biology 2020 - “...NCU00282 Zn(2)-C6 fungal-type domain-containing protein 3.89 4.34 GO:0046830 NCU07723 Norsolorinic acid reductase 3.08 2.26 GO:0006357 NCU04866 All development altered-6 2.00 2.15 GO:0033499 NCU04442 GAL10 1.73 1.77 GO:0000122 NCU08055 B-ZIP transcription factor IDI4 1.60 2.45 GO:0001080 GO:0045944 GO:1903833 GO:0007165 NCU06111 GTPase Ras2p 1.55 1.52 Unannotated NCU09629 Hypothetical...”
- The Zn(II)2Cys6-Type Transcription Factor ADA-6 Regulates Conidiation, Sexual Development, and Oxidative Stress Response in Neurospora crassa
Sun, Frontiers in microbiology 2019 - “...d RPKM WT-0 h RPKM WT-12 h RPKM WT-24 h RPKM WT-4 d Down-regulated genes NCU04866 ada-6 0 0.046 0.0883 0.0408 7.1396 40.4223 19.06 5.1192 NCU00496 hypothetical protein 1.2303 5.8881 3.8363 1.6779 2.8212 17.7147 17.029 5.7047 NCU00719 hypothetical protein, direct target of ADV-1 5.0315 3.9651 0.4172...”
- “...-24 h RPKM WT-0 h RPKM WT-12 h RPKM WT-24 h Genes positively regulating conidiation NCU04866 Ada-6 0 0.045997 0.088329 7.139561 40.42227 19.05998 NCU00116 Aab-1, TF subunit 41.0876 104.1344 177.4739 48.6871 114.6333 560.9975 NCU00269 Set-2 1.868055 2.594838 22.58605 2.667073 3.150217 6.208719 NCU00929 hypothetical protein 9.3544 4.7866...”
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...Orth NCU04834 11236 sensor histidine kinase/response regulator phy-1 Morph/Hyph NCU04851 11089 hypothetical protein Transc Factors NCU04866 11022 all development altered-6 ada-6 Transc Factors NCU05046 11237 calcium-transporting ATPase 3 ena-1 Morph/Hyph Transporter Activity/Catalytic Activity Cellular Process/Metabolic Process NCU05210 11444 postreplication repair E3 ubiquitin-protein ligase rad-18 uvs-2 Transc...”
- Identification and characterization of the glucose dual-affinity transport system in Neurospora crassa: pleiotropic roles in nutrient transport, signaling, and carbon catabolite repression
Wang, Biotechnology for biofuels 2017 - “...gene con - 10 (NCU07325) [ 54 ], the all development-altered regulator ada - 6 (NCU04866) [ 55 ], the Aspergillus flbC homolog NCU03184 [ 56 ], and the Aspergillus flbD ortholog rca - 1 (NCU01312) (Additional file 11 : Table S5). The role of rca...”
- Modulation of Circadian Gene Expression and Metabolic Compensation by the RCO-1 Corepressor of Neurospora crassa
Olivares-Yañez, Genetics 2016 - “...NCU01528 NCU02139 NCU02713 NCU03317 NCU03415 NCU04851 NCU04866 NCU05855 NCU07027 NCU07442 NCU09873 NCU10007 NCU11201 NCU06660 NCU07649 NCU05964 NCU07846...”
- “...NCU00212 NCU01634 NCU02621 NCU02713 NCU03552 NCU04851 NCU04866 NCU06095 NCU06266 NCU08055 NCU08159 NCU08594 NCU09033 NCU04414 NCU07846 Gene description...”
- Exploring the bZIP transcription factor regulatory network in Neurospora crassa
Tian, Microbiology (Reading, England) 2011 - “...), including nine with vegetative growth defects [ pp-1 (NCU00340), NCU02671, NCU06503, cre-1 (NCU08807), ada-6 (NCU04866), col-26 (NCU07788), vad-3 (NCU06407), kal-1 (NCU03593) and the bZIP TF gene, ada-1 (NCU00499)] ( Colot et al. , 2006 ). Phylogenetic analysis of N. crassa bZIP family members In S....”
- “...2.5 6570 tah-1 , tall aerial hyphae-1 NCU01097 Zn2Cys6 3.6 7075 Related to NITA protein NCU04866 Zn2Cys6 2.0 5055 Related to FacB DNA-binding protein NCU06799 Zn2Cys6 3.0 6065 Hypothetical protein NCU07139 Zn2Cys6 5.0 8085 Conserved hypothetical protein NCU07788 Zn2Cys6 2.7 5560 col-26 , colonial-26 NCU08063 Zn2Cys6...”
AFUA_6G07010 C6 transcription factor RosA from Aspergillus fumigatus Af293
36% identity, 10% coverage
- The Influence of Aspergillus fumigatus Fatty Acid Oxygenases PpoA and PpoC on Caspofungin Susceptibility
Delbaje, Journal of fungi (Basel, Switzerland) 2024 - “...respectively ( Figure 4 a,b). We observed that the TF mutants AFUA_2G02540, AFUA_5G00290, AFUA_5G07510, AFUA_4G10340, AFUA_6G07010, AFUA_1G11000, and AFUA_1G16410 were more resistant to both CAS concentrations of 0.25 g/mL and 8.0 g/mL ( Figure 4 a,b). In contrast, AFUA_2G05310 and AFUA_4G10110 were more resistant to only...”
- Fungal oxylipins direct programmed developmental switches in filamentous fungi
Niu, Nature communications 2020 - “...of branching responses (no ortholog of AFUA_3G02590 was found in CEA10, and the ortholog of AFUA_6G07010 was not in the TFKO library). A first screen using 96-well plates identified nine deletion mutants statistically less responsive to 5,8-diHODE than WT as measured by hyphal branching (Supplementary Fig....”
- Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus
Fedorova, PLoS genetics 2008 - “...was drawn using PHYML [73] . Southern Blot Analysis To detect polymorphisms in the rosA (AFUA_6G07010) gene, several hybridizations were performed using rosA gene as the probe and genomic DNA cleaved with EcoR I, ClaI , BamH I or EcoR V. For comparison, an invariable gene...”
YRM1_YEAST / Q12340 Zinc finger transcription factor YRM1; Reveromycin resistance modulator 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 4 papers)
YOR172W Yrm1p from Saccharomyces cerevisiae
36% identity, 9% coverage
Afu8g05270 C6 transcription factor, putative from Aspergillus fumigatus Af293
32% identity, 8% coverage
- Determining Aspergillus fumigatus transcription factor expression and function during invasion of the mammalian lung
Liu, PLoS pathogens 2021 - “...2.3 27841 Afu5g13790 1 29.2 1.9 2.6 815 Afu7g00130 NscR 1 21.3 209.4 308.4 3803 Afu8g05270 1 0.5 2.2 2.0 3969 RlmA is required for maximal lung fungal burden during invasive aspergillosis RlmA is a putative MADS-box transcription factor whose orthologs in many ascomycetes function in...”
- “...study afu5g13790 Af293; Afu5g13790 :: hph Present study afu7g00130 Af293; Afu7g00130 :: hph Present study afu8g05270 Af293; Afu8g05270 :: hph Present study rlmA+rlmA rlmA ; rlmA ; ble Present study sltA+sltA sltA ; sltA ; ble Present study laeA Af293.1; laeA :: pyrG1 [ 48 ]...”
FOXG_17458 hypothetical protein from Fusarium oxysporum f. sp. lycopersici 4287
27% identity, 7% coverage
- Putative Novel Effector Genes Revealed by the Genomic Analysis of the Phytopathogenic Fungus Fusarium oxysporum f. sp. physali (Foph) That Infects Cape Gooseberry Plants
Simbaqueba, Frontiers in microbiology 2020 - “...the ctg_568 in Foph _MAP5, also confirmed the presence of another highly conserved homologous gene (FOXG_17458) between Foph and Fol , including the corresponding mimp class 1 element in the 5 UTR ( Figure 3 ). The transcript FOXG_17458 in Fol , encode a transcription factor...”
- Evidence for horizontal gene transfer and separation of effector recognition from effector function revealed by analysis of effector genes shared between cape gooseberry- and tomato-infecting formae speciales of Fusarium oxysporum
Simbaqueba, Molecular plant pathology 2018 (secret) - Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes
van, PLoS genetics 2016 - “...homologs are present on the pathogenicity chromosome and one of these was selected for overexpression (FOXG_17458, long coding sequence). Also one short aTF1 gene from another accessory region was chosen for overexpression (FOXG_17084), the same gene that was used for the DNA binding site determination. To...”
- “...the DNA binding array in an independent system. For this we used the aTF1 homolog (FOXG_17458) used for overexpression and cTF1 in the in vivo transcriptional activation assay described above for Sge1. In this case, a short fragment was cloned from the promoter of the SIX1...”
- The FTF gene family regulates virulence and expression of SIX effectors in Fusarium oxysporum
Niño-Sánchez, Molecular plant pathology 2016 - “...strain 4287 (de VegaBartol etal ., 2011 ). Three of these copies (FOXG_16414, FOXG_14257 and FOXG_17458) are located in chromosome 14 close to miniclusters of SIX effectorencoding genes (Schmidt etal ., 2013 ). Recently, it has been shown that FTF1 is highly expressed in root crown...”
- “...(1070) FOXG_17123 (930) Chr 9, Sc 11 Chr 14, Sc 22 Chr 6, Sc 22 FOXG_17458 (1079) FOXG_16414 (930) Chr 14, Sc 51 Chr 14, Sc 36 FOXG_14422 (1072)* FOXG_14000 (930) Chr. 15, Sc 24 Chr 6, Sc 21 FOXG_15059 (1072)* FOXG_17084 (930) Chr 1, Sc...”
NCU00945 fungal specific transcription factor from Neurospora crassa OR74A
35% identity, 8% coverage
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...wc-2 Transc Factors NCU00923 11273 topogenesis of outer membrane beta barrel protein 37 tob37 Morph/Hyph NCU00945 11064 fungal specific transcription factor col-20 Transc Factors NCU00959 16505 succinate dehydrogenase iron-sulfur protein tca-10 E. coli CS Orth Cellular Process/Metabolic Process NCU01020 13009 hypothetical protein Morph/Hyph NCU01033 11204 hypothetical...”
NCU05308 Zn(II)2Cys6 transcription factor from Neurospora crassa OR74A
44% identity, 5% coverage
DEP6_ALTBR / D2E9X1 Depudecin biosynthesis cluster-specific transcription activator DEP6; Depudecin biosynthesis cluster protein 6 from Alternaria brassicicola (Dark leaf spot agent) (see paper)
34% identity, 10% coverage
- function: Transcription factor that positively regulates the expression of the gene cluster that mediates the biosynthesis of depudecin, a highly oxidized eleven-carbon linear polyketide that acts as a histone deacetylase (HDAC) inhibitor and makes a small contribution to pathogenesis (PubMed:19737099).
disruption phenotype: Affects the expression of all the depudecin cluster genes and impairs the production of depudecin (PubMed:19737099).
AO090011000890 uncharacterized protein from Aspergillus oryzae RIB40
36% identity, 10% coverage
CNAG_03894 hypothetical protein from Cryptococcus neoformans var. grubii H99
48% identity, 6% coverage
- Transcription Factors Fzc9 and Pdr802 Regulate ATP Levels and Metabolism in <i>Cryptococcus neoformans</i>
Ma, International journal of molecular sciences 2025 - “...verified through polymerase chain reaction (PCR) analysis. Similarly, the sequence for the Pdr802 homolog gene (CNAG_03894) was obtained from the C. neoformans var. grubii serotype A genome database ( https://www.broadinstitute.org/fungal-genome-initiative/cryptococcus-neoformans-serotype-genome-project ). To construct the pdr802 mutant, the genetic locus containing the 2087 bp open reading frame...”
- Thiazole Derivatives as Promising Candidates for Cryptococcosis Therapy
Leocádio, ACS infectious diseases 2025 - “...unknown function CNAG_03902 RDS2 regulator of drug sensitivity 2, putative CNAG_04093 YRM103 putative transcription factor CNAG_03894 PDR802 putative Zn2-Cys6 zinc-finger transcription factor CNAG_03018 ASG101 putative zinc finger transcription factor CNAG_01973 ZFC2 C2H2 zinc finger protein Zas1A CNAG_07922 FZC4 transcription factor CNAG_03366 ZNF2 C2H2 type zinc finger...”
- Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level
Rhodes, Genetics 2017 - “...GLN3 Transcription factor, deletion sensitive to organic peroxides ( Jung et al. 2015 ) 0.0155 CNAG_03894 PDR802 Transcription factor, deletion with reduced virulence ( Jung et al. 2015 ) 0.0095 CNAG_03213 UVE1 UV damage endonuclease 0.0092 CNAG_02756 CDC43 Geranylgeranyltransferase-I, essential for virulence ( Selvig et al....”
- Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans
Liu, Cell 2008 - “...STM Score Growth Score Additional Phenotypes Decreased Infectivity (STM Score < 2.5) Transcription D883 PDR802 CNAG_03894 Binuclear cluster DNA-binding regulator 7.2 * 0.08 None detected D231 LIV1 CNAG_00460 bHLH family DNA-binding regulator 6.1 * 0.35 None detected D725 HCM1 CNAG_03116 Forkhead DNA-binding regulator 4.2 * 0.46...”
TRIATDRAFT_222577 uncharacterized protein from Trichoderma atroviride
53% identity, 5% coverage
- A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride
Olivares-Yañez, Computational and structural biotechnology journal 2021 - “...TF. Sclerotial Melanin Regulator TRIATDRAFT_295411; 7.6e-14; 50.9 Bcin14g03200 95 n.a. Zn_Cluster & Fungal_TF domain TF TRIATDRAFT_222577; 7.2e-17; 55.9 Bcin11g06200 92 n.a. C2H2 domain TF TRIATDRAFT_173231; 1.1e-17; 50.8 Bcin02g09340 91 n.a. Zn_Cluster & C2H2 domain TF TRIATDRAFT_314109; 7.1e-17; 46.7 Bcin04g03280 86 n.a. C2H2 domain TF TRIATDRAFT_161626; 0.00035;...”
- “...observed in Fig. 4 A, peptidases were associated with four TFs (TRIATDRAFT_167723, TRIATDRAFT_315146, TRIATDRAFT_51934, and TRIATDRAFT_222577). Among these TFs, TRIATDRAFT_222577 was the most connected predicted regulator of peptidases (Module 8 in Fig. 4 A). This TF displays a 76.3% identity with the lscL transcriptional regulator of...”
FDB94_GIBM7 / W7MVT8 Transcription factor FVEG_08294; Fusarium detoxification of benzoxazolinone cluster 1 protein FVEG_08294; FDB1 cluster protein FVEG_08294 from Gibberella moniliformis (strain M3125 / FGSC 7600) (Maize ear and stalk rot fungus) (Fusarium verticillioides) (see 2 papers)
33% identity, 10% coverage
- function: Transcription factor; part of the Fusarium detoxification of benzoxazolinone cluster 1 (FDB1) involved in the degradation of benzoxazolinones produced by the host plant (PubMed:26808652). Maize, wheat, and rye produce the 2 benzoxazinone phytoanticipins 2,4-dihy- droxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and 2,4-dihydroxy-1,4- benzoxazin-3-one (DIBOA) that, due to their inherent instability once released, spontaneously degrade to the more stable corresponding benzoxazolinones, 6-methoxy-2-benzoxazolinone (MBOA) and 2- benzoxazolinone (BOA), respectively (PubMed:11876429). Might be involved in the regulation of the expression of the FDB1 cluster genes (Probable).
ARG81 potential ARGR fungal zinc cluster transcription factor from Candida albicans (see paper)
34% identity, 4% coverage
- CharProtDB CGD description: Putative transcription factor with zinc cluster DNA-binding motif; required for utilization of ornithine as a nitrogen source and for wild-type resistance to caffeine
OAF1_YEAST / P39720 Oleate-activated transcription factor 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 6 papers)
NP_009349 oleate-activated transcription factor OAF1 from Saccharomyces cerevisiae S288C
36% identity, 6% coverage
- function: The PIP2-OAF1 heterodimer acts as a transcriptional activator to induce the transcription of genes encoding proteins involved in fatty acid beta-oxidation, a response called oleic acid induction, when cells grow on fatty acids as sole carbon source. Recognizes and binds to the oleate response element (ORE) (or peroxisome box), two inverted CGG triplets spaced by 14 to 18 intervening nucleotides, in the promoter region of a number of genes (such as CTA1, FOX1 to FOX3, FAA2, PAS8, PAS10, etc.) for peroxisomal proteins. OAF1 acts as the sensor for oleate and inhibits PIP2 activity under non-inducing conditions. Activity is repressed by glucose.
subunit: Heterodimer of PIP2 and OAF1 - DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories.
Lutz, PLoS genetics 2019 - GeneRIF: The OAF1 and OLE1 variants showed a non-additive genetic interaction, and affected cellular lipid metabolism. These results demonstrate that the molecular basis of trans-regulatory variation is diverse, highlighting the challenges in predicting which natural genetic variants affect gene expression
- Role of the repressor Oaf3p in the recruitment of transcription factors and chromatin dynamics during the oleate response.
Wan, The Biochemical journal 2013 (PubMed)- GeneRIF: Data indicate that Oaf1p, Pip2p and Adr1p are required for the initial binding of Oaf3p before oleate induction.
- Mediator subunit Gal11p/MED15 is required for fatty acid-dependent gene activation by yeast transcription factor Oaf1p.
Thakur, The Journal of biological chemistry 2009 - GeneRIF: Mediator subunit Gal11p/MED15 is required for fatty acid-dependent gene activation by yeast transcription factor Oaf1p.
- Yeast transcription factor Oaf1 forms homodimer and induces some oleate-responsive genes in absence of Pip2.
Trzcinska-Danielewicz, Biochemical and biophysical research communications 2008 (PubMed)- GeneRIF: Oaf1 may form homodimers which apparently substitute for the Oaf1-Pip2 heterodimer.
LYS144 Lys144p from Candida albicans SC5314
52% identity, 4% coverage
- Adaptation of Candida albicans to specific host environments by gain-of-function mutations in transcription factors
Morschhäuser, PLoS pathogens 2024 - “...the LYS14 gene underwent successive gene duplications to produce 4 paralogs, Lys14, Lys142, Lys143, and Lys144, none of which regulates lysine biosynthesis genes. Instead, all 4 paralogs have acquired distinct functions by binding to different sets of genes that are important for growth and survival in...”
- A Brg1-Rme1 circuit in Candida albicans hyphal gene regulation
Kim, mBio 2024 - “...RME1 , CSP37 , orf19.1274 , ZCF5 , BMT4 , BMT9 , CFL11 , and LYS144 to create overexpression alleles. All mutant strains in the SC5314 and L26 backgrounds were then assayed for epithelial cell damage ability. Epithelial cell damage for most mutants was comparable to...”
- Reprogramming in Candida albicans Gene Expression Network under Butanol Stress Abrogates Hyphal Development
Anand, International journal of molecular sciences 2023 - “...NS 4.49 6.02 C2_00640W_A NS 2.15 3.11 UGA3 NS 3.97 3.15 ZCF25 5.8 NS 13.8 LYS144 NS 3.03 2.34 WOR2 5.73 10.45 NS C4_03160C_A NS 2.44 3.8 CTA8 3.25 3.04 NS NDT80 NS 2.19 2.38 C3_04860W_A 3.11 4.72 3.81 C2_01870C_A 2.92 2.06 2.58 Fungal-Specific Genes ATO1...”
- Overexpression approaches to advance understanding of Candida albicans
Rai, Molecular microbiology 2022 - “...than that caused by UPC2 overexpression, the other regulators identified, comprising CTA4, ARO80, AHR1, LYS14, LYS144, SUC1 , and the mostly uncharacterized transcription factors ZCF2, ZCF9, ZCF25, ZCF35 , and ZCF38 , conferred equally increased resistance levels. Detailed analysis of MRR2 revealed that hyperactive Mrr2 causes...”
- Engineering of phenylalanine dehydrogenase from Thermoactinomyces intermedius for the production of a novel homoglutamate
Tariq, PloS one 2022 - “...that were detected in the binding pocket of -Ketoadipic acid including Gly114, Thr115, Ala135, Gly136, Lys144, Asp146, Gln296, Val297, and Glu300 Fig 6c . Phenylalanine dehydrogenases from different enzymes have shown substantial resemblance particularly in the region between D58-E130. The region from D58 to E130 contains...”
- The Roles of Chromatin Accessibility in Regulating the Candida albicans White-Opaque Phenotypic Switch
Qasim, Journal of fungi (Basel, Switzerland) 2021 - “...Mating [ 90 , 91 ] LYS143 Orf19.4776 7.25 0.88 Biofilm formation [ 43 ] LYS144 Orf19.5380 1.29 0.42 Biofilm formation [ 43 ] MAC1 Orf19.7068 0.05 0.63 Copper ion homeostasis, Filamentation [ 92 ] MIG1 Orf19.4318 <0.03 1.37 Metabolism [ 93 , 94 , 95...”
- Transcriptional Circuits Regulating Developmental Processes in Candida albicans
Rodriguez, Frontiers in cellular and infection microbiology 2020 - “...Isw2 3.4 2.9 Yes Orf19.3736 Kar4 -2.0 1.2 Yes Orf19.4776 Lys143 7.3 -1.1 Yes Orf19.5380 Lys144 1.3 -2.4 Yes Orf19.7068 Mac1 -19.4 -1.6 Yes Orf19.4318 Mig1 -29.7 1.4 Yes Orf19.5326 Mig2 1.6 -1.6 Yes Orf19.4752 Msn4 1.9 -4.7 Yes Orf19.2119 Ndt80 -10.1 1.9 Yes Orf19.5910 Nto1...”
- “...Yes ( Prez etal., 2013 ) A subsequent study identified eight transcriptional regulators (Tye7, Orf19.3625, Lys144, Zcf21, Lys14, Hsm1, Rtg1, and Rtg3) that influence C. albicans proliferation in the commensal and/or pathogenic growth states ( Prez etal., 2013 ). These regulators were identified by screening a...”
- Systematic gene overexpression in Candida albicans identifies a regulator of early adaptation to the mammalian gut
Znaidi, Cellular microbiology 2018 - “...a handful number of transcription factors (TFs) with a role in GI tract colonisation ( LYS144 , TYE7 , ZCF8 , ZFU2 , and TRY4 ; Bohm et al., 2017 ; Perez, Kumamoto, & Johnson, 2013 ), establishment of systemic infection ( LYS14 , ZCF21 ,...”
- “...2011 ). The same approaches also demonstrated that RTG1 , RTG3 , TYE7 , and LYS144 mediate GI tract colonisation by controlling the expression of genes involved in the acquisition and metabolism of specific nutrients, reflecting the importance of nutrient sensing/uptake during C.albicans commensalism (Perez &...”
- More
CPAR2_405270 uncharacterized protein from Candida parapsilosis
30% identity, 7% coverage
- Transcriptional Control of Drug Resistance, Virulence and Immune System Evasion in Pathogenic Fungi: A Cross-Species Comparison
Pais, Frontiers in cellular and infection microbiology 2016 - “...) Cta4 ( C. albicans ) orf19.5133; orf19.7371 Pdr1 ( C. glabrata ) CPAR2_501570; CPAR2_405260 CPAR2_405270; CPAR2_704130 Tac1 ( C. albicans ) Mrr2 ( C. albicans ) CPAR2_807260; CTRG_02269 * CTRG_02696 * ; CTRG_02712 * CTRG_02268 * ; CTRG_05208 * CTRG_00538 * ; CTRG_02271 * CPAR2_501570;...”
- “...Mrr2 ( C. albicans ) Mrr1 ( C. parapsilosis ) Cta4 ( C. albicans ) CPAR2_405270; CPAR2_807820 Pdr1 ( C. glabrata ) CAGL0M12298g ; CTRG_05568 * Tac1 ( C. albicans ) Mrr1 ( C. albicans ) Drug resistance (ergosterol biosynthesis) Upc2 ( C. albicans ) Upc2...”
NCU05294 C6 finger domain-containing protein from Neurospora crassa OR74A
52% identity, 3% coverage
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...div-76 Transc Factors Binding Biological Regulation/Cellular Compoonent Organization or Biogenisis/Localization Process/Response to Stimulus/Cellular Process/Metabolic Process NCU05294 11074 zinc finger transcription factor-40 znf-40 Transc Factors NCU05383 11019 fungal specific transcription factor col-24 Transc Factors NCU05411 11040 pathway-specific nitrogen regulator Transc Factors NCU05637 11365 hypothetical protein Transc Factors...”
NCU09739 ADA-7 from Neurospora crassa OR74A
53% identity, 5% coverage
- RNAseq and targeted metabolomics implicate RIC8 in regulation of energy homeostasis, amino acid compartmentation, and asexual development in Neurospora crassa
Quinn, mBio 2024 - “...1.5 1.4 1.0 NCU01713 ve-1 1.0 1.0 1.0 Minor constrictions NCU00478 acon-2 1.4 1.3 1.4 NCU09739 fld 1.8 1.97 1.0 Major constrictions NCU07617 acon-3 39.8 148.9 21.1 NCU08726 fl 2.5 10.4 4.8 Conidial release NCU02713 csp-1 1.9 6.1 6.8 NCU06095 csp-2 1.3 8.7 5.5 fl regulation...”
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...Process NCU09549 11084 zinc finger transcription factor-51 znf-51 Transc Factors NCU09655 11272 hypothetical protein Morph/Hyph NCU09739 11062 all development altered-7 fld Transc Factors NCU09804 11080 zinc finger transcription factor-43 znf-43 Transc Factors NCU09829 11065 hypothetical protein Transc Factors NCU09866 11264 thyroid hormone receptor interactor 12 Morph/Hyph...”
- Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa
Wang, Eukaryotic cell 2014 - “...of TFs related to sexual development (NCU00097, NCU04561, NCU09739, NCU07392, and NCU044731) showed 5- to 20-fold changes across all time points, exhibiting...”
- A genome-wide screen for Neurospora crassa transcription factors regulating glycogen metabolism
Gonçalves, Molecular & cellular proteomics : MCP 2011 - “...2). Five strains (knocked-out in the ORFs NCU08000, NCU09739, NCU06971, NCU01154, and NCU00090) were selected because they did not show differences in their...”
- “...glycogen accumulated in the strains with deleted NCU09739, NCU06971, and NCU01154 ORFs. The strains with deleted NCU04851, NCU00808, NCU04390, NCU02713,...”
- Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa
McCluskey, G3 (Bethesda, Md.) 2011 - “...3831 ff-1 NCU01543 +1:C Frameshift PTAB 3921 tng NCU03436 572 base deletion stk-15 7022 fld NCU09739 1:G Frameshift ada-7 7035 per-1 NCU03584 1:A Frameshift PKS-7 Figure 1 Morphological characterization of FGSC 3921 and validation of the deletion detected by whole genome sequencing. (A) FGSC 2489 (wt)....”
- “...and to the left of his-5 that causes a frameshift mutation in the annotated ORF NCU09739. This deletion is found in all reads covering this region in this strain and is the only frameshift inducing indel in NCU09739 among 18 strains (there is one instance of...”
CC77DRAFT_1063927 C6 transcription factor FacB from Alternaria alternata
32% identity, 8% coverage
CPAR2_200790 uncharacterized protein from Candida parapsilosis
35% identity, 8% coverage
LEPE_ASPFN / B8NJG9 Transcription factor lepE; Leporins biosynthesis protein E from Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167) (see paper)
40% identity, 6% coverage
- function: Transcription factor involved in regulation of gene cluster 23 that mediates the biosynthesis of leporins (PubMed:20447271, PubMed:26051490).
disruption phenotype: Results in significantly reduced expression of the leporins biosynthesis gene cluster (PubMed:26051490).
BEA4_GIBF5 / S0EFU6 Beauvericin cluster-specific repressor BEA4; Beauvericin biosynthesis cluster protein 4 from Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) (Bakanae and foot rot disease fungus) (Fusarium fujikuroi) (see paper)
FFUJ_09298 uncharacterized protein from Fusarium fujikuroi IMI 58289
33% identity, 9% coverage
- function: Transcription factor that specifically represses the expression of the gene cluster involved in the biosynthesis of beauvericin (BEA), a non-ribosomal cyclic hexadepsipeptide that shows antibiotic, antifungal, insecticidal, and cancer cell antiproliferative and antihaptotactic activity (PubMed:27750383).
disruption phenotype: Leads to elevated expression of BEA1, BEA2 and BEA3 (PubMed:27750383). - Fumonisin and Beauvericin Chemotypes and Genotypes of the Sister Species Fusarium subglutinans and Fusarium temperatum
Fumero, Applied and environmental microbiology 2020 - “...Fig. 5 ). In Fusarium circinatum FSP 34, the Zn(II) 2 Cys 6 transcription factor (FFUJ_09298), encoded by Bea4 , is absent, and this gene also is missing in the other two F. circinatum genomes in GenBank (strains GL 1327 and KS 17). FIG 5 Organization...”
- “...in beauvericin and fumonisin production. Genes from the Bea cluster in F. fujikuroi (FFUJ_09294 to FFUJ_09298) ( 21 ) were used as probes in a blastn analysis of individual genome sequence databases in CLC Genomics Workbench, version 8.0 (CLC Bio-Qiagen, Aarhus, Denmark). Sequences of Bea genes...”
- Comparative transcriptome and proteome analysis reveals a global impact of the nitrogen regulators AreA and AreB on secondary metabolism in Fusarium fujikuroi
Pfannmüller, PloS one 2017 - “...2 Cys 6 4 related to STB5SIN3 binding protein carbon metabolism -8,06 -8,19 1,09 N/A FFUJ_09298 Zn 2 Cys 6 19 Bea4beauvericin cluster transcription factor beauvericin cluster -3.42 -1.75 N/A N/A FFUJ_11293 Cys 2 His 2 0 related to TRI15putative transcription factor secondary metabolism N/A 4,56...”
CTRG_02712 predicted protein from Candida tropicalis MYA-3404
28% identity, 7% coverage
PIP2_YEAST / P52960 Peroxisome proliferation transcriptional regulator; Oleate-activated transcription factor 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 5 papers)
NP_015008 oleate-activated transcription factor PIP2 from Saccharomyces cerevisiae S288C
YOR363C Autoregulatory oleate-specific transcriptional activator of peroxisome proliferation, contains Zn(2)-Cys(6) cluster domain, forms heterodimer with Oaf1p, binds oleate response elements (OREs), activates beta-oxidation genes from Saccharomyces cerevisiae
34% identity, 7% coverage
- function: The PIP2-OAF1 heterodimer acts as a transcriptional activator to induce the transcription of genes encoding proteins involved in fatty acid beta-oxidation, a response called oleic acid induction, when cells grow on fatty acids as sole carbon source. Recognizes and binds to the oleate response element (ORE) (or peroxisome box), two inverted CGG triplets spaced by 14 to 18 intervening nucleotides, in the promoter region of a number of genes (such as CTA1, FOX1 to FOX3, FAA2, PAS8, PAS10, etc.) for peroxisomal proteins. Activity is inhibited by OAF1 under non-inducing conditions. Activity is repressed by glucose.
subunit: Heterodimer of PIP2 and OAF1 - Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant.
Gupta, G3 (Bethesda, Md.) 2016 - GeneRIF: We thus uncover a meiotic functional role for TAO3, and identify ERT1 and PIP2 as novel regulators of sporulation efficiency. Our results demonstrate that studying the causal effects of genetic variation on the underlying molecular network has the potential to provide a more extensive understanding of the pathways driving a complex trait
- Role of the repressor Oaf3p in the recruitment of transcription factors and chromatin dynamics during the oleate response.
Wan, The Biochemical journal 2013 (PubMed)- GeneRIF: Data indicate that Oaf1p, Pip2p and Adr1p are required for the initial binding of Oaf3p before oleate induction.
- Yeast transcription factor Oaf1 forms homodimer and induces some oleate-responsive genes in absence of Pip2.
Trzcinska-Danielewicz, Biochemical and biophysical research communications 2008 (PubMed)- GeneRIF: In the absence of Pip2, Oaf1 may form homodimers.
- Molecular mechanisms of system responses to novel stimuli are predictable from public data
Danziger, Nucleic acids research 2014 - “...plus three known factors not present in the database (open reading frames: YIL036w, YKR064w and YOR363c). To compensate for the noise in the data and the stochasticity in Inferelator, we identified proteins that were significantly enriched ( ) as regulators for the genes in biclusters (...”
- Heterodimeric protein complex identification by naïve Bayes classifiers
Maruyama, BMC bioinformatics 2013 - “...the five trained classifiers. The following 15 instances satisfy this criteria: YPL147W YKL188C; YNL246W YLL002W; YOR363C YAL051W; YCL009C YMR108W; YJR135W-A YGR181W; YJR137C YFR030W; YBR036C YBR161W; YFL041W YBR207W; YDL099W YDR517W; YLR067C YJL209W; YIR021W Q0115; YHR079C-A YPL121C; YCL017C YER048W-A; YJR035W YKL054C; YOR321W YDL093W. Among them, the pair of...”
- Emergence of switch-like behavior in a large family of simple biochemical networks
Siegal-Gaskins, PLoS computational biology 2011 - “...(YML007W) bcdh FKH1 (YIL131C) FKH2 (YNL068C) jknptv MTH1 (YDR277C) RGT1 (YKL038W) aejknp OAF1 (YAL051W) PIP2 (YOR363C) abejp NRG1 (YDR043C) RIM101 (YHL027W) abejp IFH1 (YLR223C) RAP1 (YNL216W) bfjpv KSS1 (YGR040W) CST6 (YIL036W) bfjpv OPI1 (YHL020C) INO2 (YDR123C) *Model names refer to the constituent reactions as labeled in...”
- Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast
Chang, Molecular biology and evolution 2008 - “...HAP5 YDR216W ADR1 YOL067C RTG1 YBL103C RTG3 YAL051W OAF1 YOR363C PIP2 YMR280C CAT8 YJL089W SIP4 YGL035C MIG1 The Snf complex YDR477W SNF1 YGL115W SNF4 YER027C...”
- Global phenotype screening and transcript analysis outlines the inhibitory mode(s) of action of two amphibian-derived, alpha-helical, cationic peptides on Saccharomyces cerevisiae
Morton, Antimicrobial agents and chemotherapy 2007 - “...YKL175W YLR023C SUR2 FMS1 YOL002C YMR243C Transcription, YOR363C IZH2 ZRC1 PIP2 Telomere maintenance YLR150W YPL205C DNA modification, YOL006C ZRT3 IZH3 STM1...”
- Phenotypic analysis of genes encoding yeast zinc cluster proteins
Akache, Nucleic acids research 2001 - “...to SDS and moderately sensitive to MMS 72,45 YOR363C OAF2 (PIP2) Activator of peroxisome proliferation along with Oaf1p Impaired in growth of oleate as...”
- Global regulatory functions of Oaf1p and Pip2p (Oaf2p), transcription factors that regulate genes encoding peroxisomal proteins in Saccharomyces cerevisiae
Karpichev, Molecular and cellular biology 1998 - “...YNL035c YNL202w YNR001c YOL002c YOL147c YOR100c YOR180c YOR184w YOR349w YOR363c YOR377w YPL095c YAT1 ORF MALC3 MDH3 UGA3 TPS2 ORF PEX5 CTA1 FAA2 ORF HXK1 CUP2...”
C0NEC3 C6 finger domain transcription factor nscR from Ajellomyces capsulatus (strain G186AR / H82 / ATCC MYA-2454 / RMSCC 2432)
HCBG_01239 uncharacterized protein from Histoplasma capsulatum G186AR
61% identity, 3% coverage
- Extracellular Vesicle-Mediated RNA Release in Histoplasma capsulatum.
Alves, mSphere 2019 - “...Uncharacterized protein HCBG_05069 C0NKI6 Uncharacterized protein HCBG_03666 C0NF97 Uncharacterized protein HCBG_01563 C0NEJ1 Uncharacterized protein HCBG_01307 C0NEC3 Uncharacterized protein HCBG_01239 C0NJN9 Uncharacterized protein HCBG_03369 C0NYC3 Uncharacterized protein HCBG_07917 C0NIB5 Uncharacterized protein HCBG_03087 C0NYN4 Uncharacterized protein HCBG_08264 C0NBT4 Uncharacterized protein HCBG_00580 C0NKE4 Uncharacterized protein HCBG_03624 C0NGB7 Uncharacterized protein...”
- Extracellular Vesicle-Mediated RNA Release in Histoplasma capsulatum
Alves, mSphere 2019 - “...C0NKI6 Uncharacterized protein HCBG_03666 C0NF97 Uncharacterized protein HCBG_01563 C0NEJ1 Uncharacterized protein HCBG_01307 C0NEC3 Uncharacterized protein HCBG_01239 C0NJN9 Uncharacterized protein HCBG_03369 C0NYC3 Uncharacterized protein HCBG_07917 C0NIB5 Uncharacterized protein HCBG_03087 C0NYN4 Uncharacterized protein HCBG_08264 C0NBT4 Uncharacterized protein HCBG_00580 C0NKE4 Uncharacterized protein HCBG_03624 C0NGB7 Uncharacterized protein HCBG_02389 C0NM01 Uncharacterized...”
AFUA_4G12180 C6 transcription factor Prf, putative from Aspergillus fumigatus Af293
34% identity, 8% coverage
- The Influence of Aspergillus fumigatus Fatty Acid Oxygenases PpoA and PpoC on Caspofungin Susceptibility
Delbaje, Journal of fungi (Basel, Switzerland) 2024 - “...(HLH transcription factor GlcD gamma) 1.0999 AFUA_5G09070 (glycosyltransferase family 8 protein) 1.0634 AFUA_2G11860 (lipoprotein) 1.0475 AFUA_4G12180 (C6 transcription factor Prf) 1.076 AFUA_2G04210 (L-tyrosine degradation gene cluster protein hmgX) 1.2644 AFUA_3G00370 (phosphoketolase) 1.4249 AFUA_1G09940 (casein kinase II beta 2 subunit) 2.112 AFUA_7G08350 (alpha-1,3-glucanase) 2.4887 AFUA_7G04800 (G-protein coupled...”
An03g05500 uncharacterized protein from Aspergillus niger
35% identity, 10% coverage
FGSG_01638 hypothetical protein from Fusarium graminearum PH-1
53% identity, 4% coverage
- Compartmentalized gene regulatory network of the pathogenic fungus Fusarium graminearum
Guo, The New phytologist 2016 - “...GCGGRGN STB5 Yes Stress response 1 FGSG_04293 CNCCGMC CRZ1 Yes Stress response, calcium binding 0.97 FGSG_01638 GCGNCAN HAP1 Yes Transcription regulation 0.64 FGSG_00324 CNCCCNC SNT1 No Transcription, chromatin regulation, meiosis FGSG_05498 GANGCGN BUR6 No Transcription, chromosomal cycle TFBS, transcription factor binding site. a Score not calculated....”
DEP6_FUSLA / A0A0M9ER64 Depudecin biosynthesis cluster-specific transcription activator DEP6; Depudecin biosynthesis cluster protein 6 from Fusarium langsethiae (see paper)
33% identity, 11% coverage
- function: Transcription factor that positively regulates the expression of the gene cluster that mediates the biosynthesis of depudecin, a highly oxidized eleven-carbon linear polyketide that acts as a histone deacetylase (HDAC) inhibitor and makes a small contribution to pathogenesis (PubMed:19737099, PubMed:28460114).
CCM_09617 C6 transcription factor from Cordyceps militaris CM01
43% identity, 8% coverage
- Metabolic comparison of aerial and submerged mycelia formed in the liquid surface culture of Cordyceps militaris
Suparmin, MicrobiologyOpen 2019 - “...the transcriptome results revealed that the Gal4 transcription factor that regulates the glycolysis metabolic pathway, CCM_09617, CCM_06477, CCM_03378, CCM_07868, CCM_06621, and CCM_08260 , with fold numbers of expression of 6.065, 5.106, 4.107, 2.250, 2.518 and 2.955, was significantly upregulated in the submerged mycelia, and only CCM_08260...”
MOC3_SCHPO / Q9UT46 Transcriptional regulatory protein moc3; Multicopy suppressor of overexpressed cyr1 protein 3 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 3 papers)
NP_593160 DNA-binding transcription factor Moc3 from Schizosaccharomyces pombe
48% identity, 6% coverage
CWT1 potential fungal zinc cluster transcription factor from Candida albicans (see 2 papers)
41% identity, 7% coverage
- CharProtDB CGD description: Putative transcription factor; mutant has cell wall defects; transcription increased at stationary phase; has predicted PAS domain and Zn(II) Cys(6)-type DNA-binding region; similar to S. cerevisiae Rds2p
moc3 / RF|NP_593160.1 transcription factor Moc3 from Schizosaccharomyces pombe (see 3 papers)
SPAC821.07c transcription factor Moc3 from Schizosaccharomyces pombe
48% identity, 6% coverage
An15g02080 uncharacterized protein from Aspergillus niger
44% identity, 6% coverage
ATNN_EMENI / C8V3N0 Aspercryptin biosynthesis cluster-specific transcription regulator atnN; Aspercryptin biosynthesis cluster protein N from Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans) (see paper)
62% identity, 4% coverage
- function: Transcription factor that positively regulates the cluster that mediate the production of aspercryptins, linear lipopeptides built from six amino acids including 2 highly unusual and nonproteogenic amino acids, 2-amino-octanoic acid (2aoa) and 2-amino-dodecanol (2adol) (PubMed:26563584, PubMed:27310134).
FOXG_16414 hypothetical protein from Fusarium oxysporum f. sp. lycopersici 4287
28% identity, 8% coverage
- Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes
van, PLoS genetics 2016 - “...aTF1 14275 = FOXG_14257, both the longer version of a TF1 , aTF1 16414 = FOXG_16414, shorter version of aTF1 ), other genes are shown in black. SM- 47 to SM- 56 : putative secondary metabolite gene cluster, FOXG_174 47 to FOXG_174 56 . The majority...”
- “...Both aTf1 and cTf1 up-regulate expression of the shorter aTF1 gene on the pathogenicity chromosome (FOXG_16414), although not to the same level as during infection. Apart from this aTF1 homolog, expression of only one other transcription factor gene is significantly altered in any of the overexpressors:...”
- The FTF gene family regulates virulence and expression of SIX effectors in Fusarium oxysporum
Niño-Sánchez, Molecular plant pathology 2016 - “...f. sp. lycopersici strain 4287 (de VegaBartol etal ., 2011 ). Three of these copies (FOXG_16414, FOXG_14257 and FOXG_17458) are located in chromosome 14 close to miniclusters of SIX effectorencoding genes (Schmidt etal ., 2013 ). Recently, it has been shown that FTF1 is highly expressed...”
- “...(930) Chr 9, Sc 11 Chr 14, Sc 22 Chr 6, Sc 22 FOXG_17458 (1079) FOXG_16414 (930) Chr 14, Sc 51 Chr 14, Sc 36 FOXG_14422 (1072)* FOXG_14000 (930) Chr. 15, Sc 24 Chr 6, Sc 21 FOXG_15059 (1072)* FOXG_17084 (930) Chr 1, Sc 27 Chr...”
NCU07374 hypothetical protein from Neurospora crassa OR74A
38% identity, 8% coverage
An08g06580 acetate regulatory DNA binding protein facB-Aspergillus niger from Aspergillus niger
30% identity, 8% coverage
- Metabolic activity in dormant conidia of Aspergillus niger and developmental changes during conidial outgrowth
Novodvorska, Fungal genetics and biology : FG & B 2016 - “...factor An01g13410 9.9 43.2 Cutinase transcription factor An16g07110 39.6 242.5 Acetyl-CoA hydrolase T1, T1SA, T5SA An08g06580 42.3 145.5 Acetate regulatory protein facB An04g05620 17.2 23.2 Acetyl-CoA synthase, facA T1SA An16g05340 5.3 8.1 Enoyl reductase T5SA Plasma membrane remodeling An09g01240 12.6 80.8 Lysophospholipase T1SA An04g03830 0.5 2.0...”
- Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing
Novodvorska, BMC genomics 2013 - “...10.77 2.20 An08g04990 carnitine acetyl transferase ( A. nidulans facC ) 20.74 107.81 10.2 10.56 An08g06580 facB , acetate regulatory DNA binding protein 2.09 16.27 0.99 16.43 Metabolism of alternative carbon sources An13g00480 triacylglycerol lipase 17.13 10.83 0.36 30.08 An09g05120 triacylglycerol lipase 5.09 11.84 0.81 14.62...”
- “...) were more prevalent in dormant conidia than in conidia at T1. Transcript levels of An08g06580 encoding FacB, the transcriptional regulator of acetate metabolism [ 23 ] which plays a role in the de-repression of gluconeogenic enzymes [ 24 ], were also more highly represented in...”
facB acetate regulatory DNA binding protein FacB from Emericella nidulans (see 5 papers)
30% identity, 8% coverage
- CharProtDB Description: Transcription factor containing a Zn(II)2-Cys6 binuclear DNA-binding cluster domain; activates transcription of genes required for acetate utilization; active form is likely a dimer formed via leucine zipper-like repeats; induced by acetate; Source:AspGD
OAF3_YEAST / P36023 Oleate activated transcription factor 3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 3 papers)
YKR064W Oaf3p from Saccharomyces cerevisiae
34% identity, 8% coverage
- function: Transcriptional inhibitor with a significantly increased number of target genes in response to oleate.
- Biases in the experimental annotations of protein function and their effect on our understanding of protein function space.
Schnoes, PLoS computational biology 2013 - “...in ontology is calculated as: For example, the protein Oleate activated transcription factor 3 (UniProtID: P36023) in S. cerevisiae is annotated four times by three articles using the Cellular Component ontology, as shown in Table 5 . The annotation consistency for P36023 is therefore the maximum...”
- “...0.5. 10.1371/journal.pcbi.1003063.t005 Table 5 Annotation Consistency Example. PubMedID UniProt ID Ontology GO term description 14562095 P36023 CCO GO:0005634 nucleus 14562095 P36023 CCO GO:0005737 cytoplasm 16823961 P36023 CCO GO:0005739 mitochondrion 14576278 P36023 CCO GO:0005739 mitochondrion Example of annotation consistency of a single protein in four publications. See...”
- Molecular mechanisms of system responses to novel stimuli are predictable from public data
Danziger, Nucleic acids research 2014 - “...51 ) plus three known factors not present in the database (open reading frames: YIL036w, YKR064w and YOR363c). To compensate for the noise in the data and the stochasticity in Inferelator, we identified proteins that were significantly enriched ( ) as regulators for the genes in...”
- Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors
Cheng, Genome biology 2011 - “...RDS1 0.50 0.67 SFP1 0.59 0.74 SWI5 0.62 0.74 TYE7 0.53 0.64 YKL222C 0.57 0.69 YKR064W 0.49 0.59 a Data from Pokholok et al . [ 23 ]; b data from Pokholok et al . [ 23 ] and Kurdistani et al . [ 22 ]....”
- fREDUCE: detection of degenerate regulatory elements using correlation with expression
Wu, BMC bioinformatics 2007 - “...YDR049W AWTGAW 3.5 YER051w AKYACT 3.9 YER130C CAARTW 3.1 YFL052w WTCAAK 3.6 YGR067C TTYAAW 4.6 YKR064W WGTTRA 6.3 YLR278C KTTMAA 7.2 YML081W WCAAMT 3.7 YNR063W TCAARTA 2.4 YPR196W WTCAAW 10.3 We searched the literature for evidence supporting our motif predictions and the matching examples are highlighted....”
- Transcriptional activators in yeast
Titz, Nucleic acids research 2006 - “...uncharacterized proteins are suggested to be bona fide transcriptional regulators (namely YFL049W, YJR070C, YDR520C, YGL066W/Sgf73, YKR064W and YCR082W/Ahc2). INTRODUCTION Transcriptional regulators (TRs) that activate transcription are usually composed of a DNA-binding domain (DBD) and an activation domain (AD). The DBD targets these proteins to a specific...”
- “...and its activation properties supports a role in transcriptional regulation function. A profiles/patterns analysis of YKR064W revealed the presence of a Zn[2]-Cys[6] fungal-type binuclear cluster domain in the N-terminal region. This domain binds to DNA and is also found in ArgR2p, a component of the ARGR...”
- A fungal family of transcriptional regulators: the zinc cluster proteins
MacPherson, Microbiology and molecular biology reviews : MMBR 2006 - “...(YBR033W) TBS1 (YBR150C) YBR239C YDR520C YER184C YFL052W YJL103C YJL206C YKL222C YKR064W YLL054C YLR278C YNR063W U C, C, C, U U U U U C, C N U Expression is...”
- A two-hybrid screen of the yeast proteome for Hsp90 interactors uncovers a novel Hsp90 chaperone requirement in the activity of a stress-activated mitogen-activated protein kinase, Slt2p (Mpk1p)
Millson, Eukaryotic cell 2005 - “...kinase I isoform HAP1 2 YBL005w PDR3 2 YCR029c-a RIM1 1 YKR064w YKR064w 1 ESC5 SAP30 SIR2 2 2 1 WTM2 1 Involved in chromatin silencing, has similarity to Tof2p...”
- Isolation and characterization of new Saccharomyces cerevisiae mutants perturbed in nuclear pore complex assembly
Ryan, BMC genetics 2002 - “...temperature sensitive growth defect of npa10 was rescued by a region on chromosome XI from YKR064W to the 5' end of MET1 . The only essential gene in this region is BET3 . Invertase Assays Mutants were grown at 23 overnight in 5 ml YPD to...”
- Transcriptome profiling to identify genes involved in peroxisome assembly and function
Smith, The Journal of cell biology 2002 - “...YKR046C u 1 YMR018W u 13 SAP155 o 4 YIL057C u 2 MRS6 o 1 YKR064W u 1 PEX1 p 1 12 SDS23 o 4 YJL217W u 2 MSB1 o 1 YLR294C u N/D 1 YKR027W u 12 YBR012C u 4 YLR285W u 1 2 MYO5...”
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TERG_05497 uncharacterized protein from Trichophyton rubrum CBS 118892
53% identity, 7% coverage
FOXG_17123 hypothetical protein from Fusarium oxysporum f. sp. lycopersici 4287
27% identity, 8% coverage
UPC2_CANAL / Q59QC7 Sterol uptake control protein 2 from Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast) (see 17 papers)
UPC2 potential fungal zinc cluster transcription factor (Upc2) from Candida albicans (see 5 papers)
XP_711879 Upc2p from Candida albicans SC5314
35% identity, 8% coverage
- function: Transcription factor involved in the regulation of ergosterol biosynthetic genes such as ERG2 and ERG11 through direct binding to sterol response elements (SREs) in the promoters. Also binds to its own promoter on 2 cis-acting elements to promote autoregulation. Regulates sterol uptake across the plasma membrane. Acts as a major regulator of ascorbic acid-induced response. Plays a role in the triggering of pyroptosis, an inflammasome-mediated programmed cell death pathway in macrophages, allowing macrophages escaping.
disruption phenotype: Shows increased susceptibility to the azole drugs ketoconazole, itraconazole, and fluconazole; drugs that act on ergosterol biosynthesis such as terbinafine, fenpropimorph, and lovastatin; as well as malachite green. Leads to lower ergosterol levels. Decreases pyroptosis but has little effect on filamentation in the macrophage. - CharProtDB CGD description: Transcriptional regulator of ergosterol biosynthetic genes and sterol uptake; binds ERG2 promoter; has Zn(2)-Cys(6) binuclear cluster; induced upon ergosterol depletion, by azoles, anaerobicity; macrophage/pseudohyphal-repressed
- Two negative regulators of biofilm development exhibit functional divergence in conferring virulence potential to Candida albicans.
Kakade, FEMS yeast research 2019 (PubMed)- GeneRIF: While acting as negative regulators of biofilm formation, transcription factors Zcf32 and Upc2 target a different set of biofilm genes. A mouse model of candidiasis reveals that zcf32/zcf32 was hypervirulent, while upc2/upc2 shows compromised virulence compared to the wild-type.
- Loss of Upc2p-Inducible ERG3 Transcription Is Sufficient To Confer Niche-Specific Azole Resistance without Compromising Candida albicans Pathogenicity.
Luna-Tapia, mBio 2018 - GeneRIF: The induction of ERG3 upon azole treatment is completely dependent upon the Upc2p transcription factor.
- A gain-of-function mutation in the transcription factor Upc2p causes upregulation of ergosterol biosynthesis genes and increased fluconazole resistance in a clinical Candida albicans isolate.
Dunkel, Eukaryotic cell 2008 - GeneRIF: A gain-of-function mutation in UPC2 leads to the increased expression of ERG11 and resistance to fluconazole in clinical isolates of C. albicans.
- Candida albicans UPC2 is transcriptionally induced in response to antifungal drugs and anaerobicity through Upc2p-dependent and -independent mechanisms.
Hoot, Microbiology (Reading, England) 2008 - GeneRIF: UPC2 is transcriptionally induced in response to antifungal azoles through Upc2p-dependent and -independent mechanisms.
- A Proteomic Landscape of Candida albicans in the Stepwise Evolution to Fluconazole Resistance
Song, Antimicrobial agents and chemotherapy 2022 (secret)
YRR1_YEAST / Q12172 Zinc finger transcription factor YRR1; Pleiotropic drug-resistance protein 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 6 papers)
YOR162C Yrr1p from Saccharomyces cerevisiae
NP_014805 Yrr1p from Saccharomyces cerevisiae S288C
29% identity, 9% coverage
- function: Transcription factor involved in the regulation of multidrug resistance genes. Acts in concert with YRR1.
- Different Toxicity Mechanisms for Citrinin and Ochratoxin A Revealed by Transcriptomic Analysis in Yeast
Vanacloig-Pedros, Toxins 2016 - “...10 4 Cytoplasmic aldehyde dehydrogenase YDR132C - 7.3 1.74 10 6 Protein of unknown function YOR162C YRR1 7.2 1.24 10 7 Zn 2 -Cys 6 zinc-finger transcription factor YMR038C CCS1 6.9 6.96 10 5 Copper chaperone for superoxide dismutase Sod1p YJL219W HXT9 6.9 1.67 10 7...”
- Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks
Brion, BMC genomics 2013 - “...binds to a weak acid response element to induce transcription of PDR12 and FUN34 YRR1 YOR162C chr15:639 5,03 Self 13 Zn2-Cys6 zinc-finger transcription factor that activates genes involved in multidrug resistance; paralog of Yrm1p acting on an overlapping set of target genes FZF1 YGL254W chr7:21 4,02...”
- Identification of molecular pathways affected by pterostilbene, a natural dimethylether analog of resveratrol
Pan, BMC medical genomics 2008 - “...the PDR network YML007W YAP1 3.1 1.66 10 -5 Transcription factor required for oxidative stress YOR162C YRR1 2.5 9.44 10 -5 Transcription factor involved in MDR d. Other drug-responsive genes YOR266W PNT1 2.0 0.01 Mitochondrial protein involved in export of proteins YNL231C PDR16 6.1 3.54 10...”
- Phenotypic analysis of genes encoding yeast zinc cluster proteins
Akache, Nucleic acids research 2001 - “...This study YOL089C FZJ FY73 aa 115-319 HIS3 This study YOR162C FZU FY73 aa 28-332 HIS3 This study YOR172W YZV YPH499 ORF HIS3 This study YOR380W FZP FY73 aa...”
- “...YOL089C HAL9 + + + + + + + + + + + + + + + + + FZU YOR162C YRR1 XXX XXX + + + + + + + + + + + + + XXX + + + YZV YOR172W - + + + + + + + + + + + +...”
- Functional analysis of six genes from chromosomes XIV and XV of Saccharomyces cerevisiae reveals YOR145c as an essential gene and YNL059c/ARP5 as a strain-dependent essential gene encoding nuclear proteins
Grava, Yeast (Chichester, England) 2000 (PubMed)- “...from chromosome XIV and YOR145c, YOR152c, YOR161c and YOR162c from chromosome XV of Saccharomyces cerevisiae. ORFs were replaced with the KanMX4 resistance...”
- Global response of Saccharomyces cerevisiae to an alkylating agent
Jelinsky, Proceedings of the National Academy of Sciences of the United States of America 1999 - “...HSP YNL241C ZWF1 6.0 Glucose-6-phosphate dehydrogenase YOR162C YRR1 ;5.7** Transcription factor YML070W DAK1 5.4 Dihydroxyacetone kinase YOL052C-A DDR2...”
- “...kinases\ YDL025C -- 6.3 SeryThr protein kinase YOR162C YRR1 ;5.7 Transcription factor YLR178C TFS1 5.7 Cell-cycle regulator YML112W CTK3 5.5 Carboxy-terminal...”
- Salicylic acid resistance is conferred by a novel YRR1 mutation in Saccharomyces cerevisiae.
Kodo, Biochemical and biophysical research communications 2013 (PubMed)- GeneRIF: A novel mutation is identified in YRR1 conferring salicylic acid resistance; cells carrying the yrr1 allele (yrr1-52) activate expression of several efflux pump-encoding genes.
- Yeast adaptation to mancozeb involves the up-regulation of FLR1 under the coordinate control of Yap1, Rpn4, Pdr3, and Yrr1.
Teixeira, Biochemical and biophysical research communications 2008 (PubMed)- GeneRIF: This activation of FLR1 transcription is fully dependent on Yap1p and is reduced (by 50%) in the absence of Rpn4p, Yrr1p or Pdr3p.
O13417 FacB from Aspergillus oryzae
30% identity, 8% coverage
NCU06656 transcriptional activator protein acu-15 from Neurospora crassa OR74A
30% identity, 7% coverage
BBA_01499 nitrate assimilation regulatory protein nirA from Beauveria bassiana ARSEF 2860
34% identity, 10% coverage
- A network of transcription factors in complex with a regulating cell cycle cyclin orchestrates fungal oxidative stress responses
Kan, BMC biology 2024 - “...Bioinformatic analysis indicated that these proteins were annotated as GAL4-like Zn 2 Cys 6 proteins (BBA_01499, BBA_04239, and BBA_01981) in the B. bassiana genome, consisting of 702, 764, and 1010 amino acids that were designed as BbOsrR1, BbOsrR2, and BbOsrR3 ( O xidative s tress r...”
- “...B. bassiana genomic DNA as the template and cloned into pGADT7 to produce pGADT7-BBA_04239, -BBA_01981, -BBA_01499, -BBA_06193, -BBA_00237, -BBA_05389, and -BBA_04821, respectively. The resultant plasmids were then transformed into the Y1HGold strain harboring pAbAi-bait. Transformants were cultured on leucine-free SD agar or leucine-free SD agar containing...”
BCIN_16g03230 hypothetical protein from Botrytis cinerea B05.10
30% identity, 9% coverage
- Multidrug resistance of Botrytis cinerea associated with its adaptation to plant secondary metabolites
Wu, mBio 2024 - “...these, eleven transcription factors (BCIN_01g03660, BCIN_03g01840, BCIN_03g06600, BCIN_06g05210, BCIN_09g05540, BCIN_10g03530, BCIN_13g03910, BCIN_13g05610, BCIN_14g00770, BCIN_15g00080, and BCIN_16g03230) were found to be up-regulated in the resveratrol-induced strain compared to the non-induced strain selected from the reference, which was related to drug resistance in microorganisms including Tac1p, Mrr1, and...”
- “...BCIN_13g02900 were found to be down-regulated. Meanwhile, 13g04870, BCIN_13g03910, BCIN_03g00220, BCIN_03g00450, BCIN_03g06600, BCIN_06g05210, BCIN_10g03880, BCIN_04g03220, BCIN_16g03230, BCIN_15g00120, BCIN_01g03660, BCIN_02g01900, BCIN_02g03500, BCIN_11g05340, BCIN_16g03200, and BCIN_03g01840 were up-regulated in group D compared to group C. Fig 3 ( a and b) Volcano plots of differentially expressed genes in...”
CPAR2_803820 uncharacterized protein from Candida parapsilosis
36% identity, 8% coverage
- The Pathogenic Yeast Candida parapsilosis Forms Pseudohyphae through Different Signaling Pathways Depending on the Available Carbon Source
Rupert, mSphere 2022 - “...GZF3 GCAACAGCAGCAGCGAG GTGTTGGAACCTCTCCTGG CPAR2_501290 CZF1 CCTCATCCGTACCAACAAC GACGGCATGTGAGACATCCC CPAR2_805930 TEC1 GCCAGAACTTCGATACCCGC GACCAGCGTCCAAACCTTG CPAR2_601080 FLO8 CTTCGTCAAATGCAACGGGG GTTGCCACCACCACCAAGAC CPAR2_803820 UME6 CAAATCGACGCCGTTATTGCC CCGAACCTGACACAAGCCCC CPAR2_204370 ACE2 CGACATTTAAAGGGCCACAG CCATGCCCTTTACCCCACC CPAR2_109520 TUP1 GCTGCTGGATCTTTAGATCGC CTATCCAATGACCCTGAAGC CPAR2_300790 NRG1 CCATGGCCTACATGTGATGC CCCCATAACCAGTATGACCG CPAR2_803890 MLS1 CCAGGAGGTGTCATTACTG CACCATGAGTGACCCATTGC CPAR2_106400 GSC1 GGCAAGCTCCATTGTTGTGG GTGCCACTTGGTGTTACCTC CPAR2_403180 PGA62 CCAACCACTCAAACCACCG GAACAGACTTGGCGGCACCG CPAR2_803900 HST1 CGGAGCTACGGGAGTATAAAG...”
- The transcription factor Ndt80 is a repressor of Candida parapsilosis virulence attributes
Branco, Virulence 2021 - “...), RHR2 ( CPAR2_503990 ), ACE2 ( CPAR2_204370 ), CPH2 ( CPAR2_603440 ), UME6 ( CPAR2_803820 ) and CZF1 ( CPAR2_501290 ). For each real-time quantitative PCR, five replicates per strain were analyzed. All primers used are detailed in Table 1 . PCRs were performed using...”
CCM_05172 C6 zinc finger domain containing protein from Cordyceps militaris CM01
43% identity, 5% coverage
- Expanded Gene Regulatory Network Reveals Potential Light-Responsive Transcription Factors and Target Genes in Cordyceps militaris
Buradam, International journal of molecular sciences 2024 - “...we identified five key TFshomeobox TF (CCM_07504), FlbC (CCM_04849), FlbB (CCM_01128), C6 zinc finger TF (CCM_05172), and mcrA (CCM_06477)along with ten regulated genes within the light-responsive subnetwork. These TFs and regulated genes are likely crucial for the growth, development, and secondary metabolite production in C. militaris...”
- “...the highest number of regulated genes and highest normalized betweenness scores are CCM_07504, CCM_04849, CCM_01128, CCM_05172, and CCM_06477. The normalized betweenness scores further imply that the homeobox TF is central to the regulatory network, potentially serving as a key hub that integrates various signaling pathways to...”
MGG_04108 transcriptional activator protein acu-15 from Pyricularia oryzae 70-15
30% identity, 8% coverage
B6QAJ8 Endo-chitosanase from Talaromyces marneffei (strain ATCC 18224 / CBS 334.59 / QM 7333)
33% identity, 6% coverage
- Cloning and overexpression of a new chitosanase gene from Penicillium sp. D-1
Zhu, AMB Express 2012 - “...chitosanases (Figure 1 ) from Talaromyces stipitatus ATCC 10500 (B8M2R4, 83.6%), Penicillium marneffei ATCC 18224 (B6QAJ8, 80.8%), Aspergillus clavatus (A1CN44, 54.6%), Neosartorya fischeri NRRL 181 (A1DKV7, 54.2%), N . fumigata Af293 (Q4W904, 53.4%), A. fumigatus A1163 (B0YDW3, 53.0%), F. solani subsp. Phaseoli (Q00867, 49.0%), F. solani...”
- “...GenBank accession details are for Penicillium sp. D-1 (this study), Talaromyces stipitatus (B8M2R4), Penicillium marneffei (B6QAJ8), Aspergillus clavatus (A1CN44), Neosartorya fischeri (A1DKV7), N. fumigata (Q4W904), A. fumigatus (B0YDW3), Fusarium solani subsp. Phaseoli (Q00867), F. solani f. robiniae (Q8NK77) and Colletotrichum graminicola (E3QWY0). Purification of CSN The...”
BC1G_13551 BcfacB from Botrytis cinerea B05.10
30% identity, 8% coverage
H2AZK4 Zn(2)-C6 fungal-type domain-containing protein from Kazachstania africana (strain ATCC 22294 / BCRC 22015 / CBS 2517 / CECT 1963 / NBRC 1671 / NRRL Y-8276)
52% identity, 3% coverage
- Loss of TIP60 (KAT5) abolishes H2AZ lysine 7 acetylation and causes p53, INK4A, and ARF-independent cell cycle arrest.
Wichmann, Cell death & disease 2022 - “...deletion of Tip60 in Cdnk2a / or Trp53 / MEFs resulted in a reduction in H2AZK4, H2AZK7, and H2AZK411 acetylation (Fig. 7E ). In addition to the profound effects on H2AZ acetylation, we found a modest reduction in H4K12ac and H4K16ac in Tip60 deleted Cdkn2 /...”
- “...Loss of TIP60 results in a marked decline in H2AZK7 acetylation and a reduction in H2AZK4 acetylation, consistent with previous reports proposing that TIP60 is required for the acetylation of H2A.Z and gene activation in human and mouse cells [ 75 , 76 ]. Apart from...”
AFUA_1G13510, Afu1g13510 C6 transcription factor FacB/Cat8 from Aspergillus fumigatus Af293
30% identity, 8% coverage
- Integrated multi-omics identifies pathways governing interspecies interaction between A. fumigatus and K. pneumoniae
Bitencourt, Communications biology 2024 - “...revealed the upregulation of key players of fatty acid catabolism, including the transcription factor Cat8 (AfuA_1g13510) and Ctf1A (AfuA_4g03960) (Supplementary Table 1 ). Conversely, cell division, translation, spore formation and secondary metabolism primarily associated with conidia were downregulated (Fig. 4 and Supplementary Table 8 ). The...”
- Aspergillus fumigatus Acetate Utilization Impacts Virulence Traits and Pathogenicity
Ries, mBio 2021 - “...C at https://doi.org/10.6084/m9.figshare.14740482 ). These strains were deleted for the acuK (Afu2g05830), acuM (Afu2g12330), facB (Afu1g13510), farA (Afu4g03960), and mtfA (Afu6g02690) genes ( Fig.1B to D ; see also Fig. S1 at https://doi.org/10.6084/m9.figshare.14740482 ). AcuM, AcuK, and MtfA have been characterized in A. fumigatus and have...”
- The Transcription Factor ZafA Regulates the Homeostatic and Adaptive Response to Zinc Starvation in Aspergillus fumigatus
Vicentefranqueira, Genes 2018 - “...Induction AFUA_1G10130 NZR sahA 1.9 0.1 1.1 0.1 AFUA_1G12830 IZR niaD 1.6 0.1 5.2 0.7 AFUA_1G13510 NZR facB 4.6 0.6 1.0 0.1 AFUA_1G14550 DZR sodC / sod3 1698.7 198.2 1176.5 142.4 Induction AFUA_1G15590 NZR cybS / sdh4 2.9 0.4 1.1 0.1 AFUA_1G17190 NZR sidI 92.5 8.7...”
- Large-scale transcriptional response to hypoxia in Aspergillus fumigatus observed using RNAseq identifies a novel hypoxia regulated ncRNA
Losada, Mycopathologia 2014 - “...AFUB_022410 Afu2g05380 C6 transcription factor, putative 3.33 AFUB_080790 Afu8g02640 C6 transcription factor, putative 0.22 AFUB_013000 Afu1g13510 C6 transcription factor FacB/Cat8 0.20 AFUB_080380 Afu8g07360 C6 transcription factor, putative 0.18 AFUB_077130 Afu6g11110 C6 transcription factor, putative 0.06 1 Values below above and below one signify up or down-regulation...”
- Genes differentially expressed in conidia and hyphae of Aspergillus fumigatus upon exposure to human neutrophils
Sugui, PloS one 2008 - “...3-ketoacyl-coA thiolase peroxisomal A precursor AN5646.2 Afu2g10920 enoyl-CoA hydratase/isomerase family protein AN5916.2/ echA Acetate metabolism: Afu1g13510 C6 transcription factor (FacB/Cat8) AN0689.2/ facB Afu4g11080 acetyl-coenzyme A synthetase FacA AN5626.2/ facA Afu6g14100 mitochondrial carnitine:acyl carnitine carrier AN5356.2/ acuH Afu1g12340 carnitine acetyl transferase AN1059.2/ facC Afu2g12530 carnitine acetyl transferase...”
NCU00017 hypothetical protein from Neurospora crassa OR74A
53% identity, 4% coverage
FFUJ_12938 related to transcription activator protein acu-15 from Fusarium fujikuroi IMI 58289
34% identity, 9% coverage
RHTO_05808 C6 transcription factor from Rhodotorula toruloides NP11
31% identity, 8% coverage
XP_723152 Zcf32p from Candida albicans SC5314
32% identity, 9% coverage
RDS1_YEAST / P25611 Regulator of drug sensitivity 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
YCR106W Rds1p from Saccharomyces cerevisiae
45% identity, 5% coverage
- function: Zinc cluster transcription factor involved in resistance to cycloheximide.
- Resistance to Arsenite and Arsenate in Saccharomyces cerevisiae Arises through the Subtelomeric Expansion of a Cluster of Yeast Genes
Stefanini, International journal of environmental research and public health 2022 - “...involved in fluoride export ( FEX1 -YOR390W and FEX2 -YPL279C), a transcription factor ( RDS1 -YCR106W), a protein required for the progression of the cell cycle ( CDC4 -YFL009W), and a protein controlling telomere length ( RIF2 -YLR453C). Furthermore, two additional genes (YPR195C and YPR197C) with...”
- Nuclear pore complex acetylation regulates mRNA export and cell cycle commitment in budding yeast
Gomar-Alba, The EMBO journal 2022 - “...other. Red lines show a fold change of 1. Genes with FC>1 are YCR107W , YCR106W and YGL263W (subtelomeric); genes with FC<1 are YFL065C (subtelomeric), YLR124W and tF(GAA)F (phenylalanine tRNA). Esa1 and Nup60 acetylation promote bulk mRNA export Nuclear basket components are required for the efficient...”
- SESAME-catalyzed H3T11 phosphorylation inhibits Dot1-catalyzed H3K79me3 to regulate autophagy and telomere silencing
He, Nature communications 2022 - “...In addition, we investigated the transcription of genes near the other telomeres, including YFR057W , YCR106W , COS8 , COS4 , SEO1, and YEL077C , which are located 2kb from Tel VI-R, 3.2kb from Tel III-R, 6.2kb from Tel VIII-L, 6.2kb from Tel VI-L, 7.2kb from...”
- Metabolic regulation of telomere silencing by SESAME complex-catalyzed H3T11 phosphorylation
Zhang, Nature communications 2021 - “...shm2 mutants. c e qRT-PCR analysis of native telomere-proximal genes ( YFR057W , COS8 , YCR106W , SOR1 , SEO1 ) in WT, H3T11A ( c ), H3T11D ( c ), pyk1-ts ( d ), ser33 ( e ), and sir 2 mutants. f Effect of...”
- “...2c ). We also investigated the transcription of genes near other telomeres, including COS8 , YCR106W , SOR1 , PHO11 , and SEO1 , which locate 6.4kb from Tel VIII-L, 3.2kb from Tel III-R, 8.6kb from Tel X-R, 3.4kb from Tel I-L, and 7.2kb from Tel...”
- Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D
Salazar, FEMS yeast research 2017 - “...in assembly Daran-Lapujade etal. YAL064C-A, YAL066W, YAR047C, YHL046W-A, YIL058W, YOL013W-A YAL065C, YAL067C, YBR093C, YCR018C, YCR105W, YCR106W, YDR038C, YDR039C, YHL047C, YHL048W, YNR070W, YNR071C and YNR074C YAL069W, YDR036C, YDR037W, YJL165C, YNR004W, and YPL277C (misannotated as YOR389W ) Nijkamp et al. Q0140, YDR543C, YDR544C, YDR545W, YIL046W-A, YLR154C-H, YLR156C-A, YLR157C-C,...”
- Population structure and comparative genome hybridization of European flor yeast reveal a unique group of Saccharomyces cerevisiae strains with few gene duplications in their genome
Legras, PloS one 2014 - “.... A second subtelomeric cluster contains PAU3 / YCR104W , ADH7/ YCR105W , and RDS1/ YCR106W , AAD3/ YCR107W and a third cluster located at the right end of chromosome XIII contains YMR320W , YM321C and SNO4/YMR322C. The low hybridization of genes from the first and...”
- Yeast phospholipase C is required for normal acetyl-CoA homeostasis and global histone acetylation
Galdieri, The Journal of biological chemistry 2013 - “...YCR100C (5-TGTCATCTACGGACATCTGGAT-3 and 5CCTTCCGATAGAATCTTCACGA-3), YCR106W (5-CTCJOURNAL OF BIOLOGICAL CHEMISTRY 27987 Downloaded from http://www.jbc.org/...”
- “...(5-TGTCATCTACGGACATCTGGAT-3 and 5-CCTTCCGATAGAATCTTCACGA-3), YCR106W (5-CTCGCGATGCCAACAAAATTC-3 and 5-TGAATCCATCAGAGTCGTTTGC-3), and POL1...”
- A Whole Genome Screen for Minisatellite Stability Genes in Stationary-Phase Yeast Cells
Alver, G3 (Bethesda, Md.) 2013 - “...YAP1801 YHR161c YOL079W YOL079w FDC1 YDR539w QCR10 YHR001w-a YAT2 YER024w YOL153C YOL153c FIN1 YDR130c RDS1 YCR106w YBL096C YBL096c YOR170W YOR170w FOB1 YDR110w REC104 YHR157w YBR197C YBR197c YOR296W YOR296w GET2 YER083c RGP1 YDR137w YBR277C YBR277c YPL066W YPL066w GIT1 YCR098c RNH203 YLR154c YCR015C YCR015c YPL102C YPL102c HIR1 YBL008w...”
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PRO1_NEUCR / Q9P326 Transcriptional regulatory protein pro1; Arrested development protein 1 from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (see paper)
NCU07392, XP_958476 transcriptional regulatory protein Pro-1 from Neurospora crassa OR74A
32% identity, 10% coverage
- function: May be involved in fruiting body development.
- The Zn(II)2Cys6 putative Aspergillus nidulans transcription factor repressor of sexual development inhibits sexual development under low-carbon conditions and in submersed culture
Vienken, Genetics 2005 - “...and the homolog from N. crassa (accession no. Q9P326). Shaded background indicates amino acids that were identical in two sequences and solid background...”
- VE-1 regulation of MAPK signaling controls sexual development in Neurospora crassa
Cea-Sánchez, mBio 2024 - “...P / A Mitogen-activated protein kinase MKC1 NO NO YES NO YES ( 56 ) NCU07392 adv-1 PP / P / A Transcriptional regulatory protein pro-1 NO NO NO NO YES ( 50 , 57 ) Osmosensing pathway (OS) NCU03071 os-4 SSK22 PP / P /...”
- Dysfunctional Pro1 leads to female sterility in rice blast fungi
Uchida, iScience 2023 - “...derived from CH598 (Pro1 CH598 ) with Sordaria macrospora Pro1 (SMAC_00338) and Neurospora crassa Adv-1 (NCU07392) was 71.19% and 72.19%, respectively ( FigureS7 ). Compared with Pro1 CH598 , two mutations, S16W and frameshift after G125 (8bp deletion), which leads to protein truncation ( Figure3 B),...”
- Circadian clock control of tRNA synthetases in Neurospora crassa
Castillo, F1000Research 2022 - “...2 ). Previous RNA-seq data comparing WT to cells deleted for the transcription factor ADV-1 (NCU07392) showed that the levels of glnrs mRNA, but not asprs mRNA levels, were generally higher in adv-1 cells compared to WT grown in DD and following light treatments ( Dekhang...”
- The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassa
Herold, Frontiers in fungal biology 2021 - “...2016 ). This pathway can alter the transcription of multiple genes via the transcription-factor ADV-1 (NCU07392), encoded by a gene that is conserved among the Pezizomycotina and is essential for germling communication and fusion (Leeder et al., 2013 ; Dekhang et al., 2017 ; Fischer et...”
- “...404_Rev455 CTGTTGTGCCAGGTCCAAGC 347_For1517 NCU07347 ( gh17-2 ) CGGCACCGATTGTAACCAAA 64 105 347_Rev1622 GTGTTGCCATCCTGCCAGAC adv1_ For 1455 NCU07392 ( adv-1 ) CCTTGTTCGCGCACACCTAC 64 133 adv1_ Rev1588 TTCAGCGACTCAAGGCAAGC RNA Immunoprecipitation (RIP) and RIP-RNAseq Analysis The RIP procedures used here were conceptually based on those described by Dang et al....”
- A global search for novel transcription factors impacting the Neurospora crassa circadian clock
Muñoz-Guzmán, G3 (Bethesda, Md.) 2021 - “...with WCC upon light exposure, modulating several genes ( Sancar et al. 2015a ). ADV-1 (NCU07392) regulates NCU04001/ff-7 expression in a light dependent manner ( Dekhang et al. 2017 ). ff-7 is subjected to metabolic regulation and its expression is decreased in a col-26 (NCU07788) strain...”
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...or Biogenisis/Response to Stimulus/ Cellular Process/ Metabolic Process NCU07379 11383 transcription factor-5 tcf-5 Transc Factors NCU07392 11041 transcriptional regulatory protein pro-1 adv-1 Transc Factors NCU07420 11844 eIF4A eif4A Morph/Hyph NCU07535 11094 SAH-3 sah-3 Transc Factors Catalytic Activity Cellular Process/ Metabolic Process NCU07589 12409 acetyltransferase Morph/Hyph NCU07591...”
- A HAD family phosphatase CSP-6 regulates the circadian output pathway in Neurospora crassa
Zhou, PLoS genetics 2018 - “...weakly rhythmic in csp- 6 ( S7D Fig ) before rediscovering that deletion of adv-1 (NCU07392) results in defects similar to csp-6 ( Fig 6A ) [ 22 ]. Though deletion of csp -6 did not affect the oscillation of csp -1 and fluffy promoter activity,...”
- Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30
Borin, Frontiers in bioengineering and biotechnology 2018 - “...several orthologs had already been characterized in ascomycetes. In Neurospora crassa , the ortholog Adv-1 (NCU07392; identity: 66%) regulates cell-to-cell fusion and sexual development (Chinnici et al., 2014 ; Dekhang et al., 2017 ), and in Sordaria macrospora (CAB52588.2; identity: 66%), Pro1 has a pivotal role...”
- More
YKL222C Protein of unknown function that may interact with ribosomes, based on co-purification experiments; similar to transcriptional regulators from the zinc cluster (binuclear cluster) family; null mutant is sensitive to caffeine from Saccharomyces cerevisiae
35% identity, 10% coverage
- Brazilian industrial yeasts show high fermentative performance in high solids content for corn ethanol process
Secches, Bioresources and bioprocessing 2022 - “...gene, which encodes for monocarboxylate permease, and BG-1 and SA-1 genomes have two copies of YKL222C (unknown function). All these genes have been related to high ethanol tolerance (Nagamatsu et al. 2021 ). It is known that ethanol can affect cell viability and act negatively on...”
- Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts
Jacobus, Frontiers in microbiology 2021 - “...( Figure 4 ). Alongside the FRE2 amplification, the adjacent MCH2 region containing the genes YKL222C (unknown function) and MCH2 (specifying a monocarboxylate permease) also shows an increased copy number in many bioethanol yeasts ( Figure 4 and Supplementary Figure 8 ). At the subtelomere of...”
- Multiplex Genome Engineering Methods for Yeast Cell Factory Development
Malcı, Frontiers in bioengineering and biotechnology 2020 - “...and low down-regulation efficiencies were expressed via plasmids to down regulate several target genes including YKL222C , which interacts with ribosomes, ESBP6 , which encodes a transporter protein and ULA1 , which plays a role in protein degradation. Microfluidic single-cell screening was subsequently used to select...”
- Nuclear microtubule filaments mediate non-linear directional motion of chromatin and promote DNA repair
Oshidari, Nature communications 2018 - “...integrated under the URA3 promoter of W303a. The csURA3csa tetO 224 construct was integrated at YKL222C by transforming cells with Bmt 1-linearized pKM255. Orientation of the integrated construct was confirmed via PCR, indicating that the tetO array is located internally to the csURA3csa construct. The tetO...”
- “...Nsi I (primers: URA3-AatII-ISceI-F and URA3-NsiI-ISceI-R). To allow for homology-directed integration, a 1.28kb fragment of YKL222C harboring a unique internal Bmt I restriction site was amplified via PCR and cloned into the csURA3csa tetO 224 plasmid using Sac I and Nsi I (primers: YKL222-NsiI and YKL222-SacI)....”
- Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication
Legras, Molecular biology and evolution 2018 - “...bakery, NA oak, Med oak, sake, and W African). We observed the amplification of CUP1, YKL222C , and MCH2 , as previously reported in wine and flor strains ( Legras etal. 2014 ; Strope etal. 2015 ), and the CUP1 region was also amplified for rum...”
- Reconstructing the regulatory circuit of cell fate determination in yeast mating response
Shao, PLoS computational biology 2017 - “...significantly regulated as observed in a former study [ 28 ], including YGL252C, YNL027W, YDL080C, YKL222C, YBR289W and YML099C. The resulting profile is also in agreement with the median trajectory of all the protein synthesis rates. The protein synthesis shows a ~40% reduction after slightly up-regulation...”
- Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library
Youn, G3 (Bethesda, Md.) 2017 - “...and TFs ( MCK1 , MKK2 , FRK1 , RCK1 , YRR1 , RPB3 , YKL222C , WAR1 , DIG1 , IOC4 , MATALPHA1 , and GAL3 ) caused a range of morphological defects with little impact on cell growth. This result affirms the importance of...”
- Flor Yeast: New Perspectives Beyond Wine Aging
Legras, Frontiers in microbiology 2016 - “...when looking for amplified genes, only three genes were detected: FRE2 , MCH2 , and YKL222C ( Legras et al., 2014 ). MCH2 is annotated as a putative monocarboxylic-acid transporter, although its involvement in monocarboxylic acid transport has not been shown experimentally ( Makuc et al.,...”
- “...environment, as has been proposed previously ( Infante et al., 2003 ). However, MCH2 and YKL222C are promising targets, the roles of which need to be evaluated. Further studies, such as population genomics, have to be performed to unravel the genetics basis of flor-yeast adaptation. Specificities...”
- More
Afu7g01810 C6 transcription factor, putative from Aspergillus fumigatus Af293
34% identity, 8% coverage
CPAR2_405260 uncharacterized protein from Candida parapsilosis
39% identity, 4% coverage
UME6_YEAST / P39001 Transcriptional regulatory protein UME6; Negative transcriptional regulator of IME2; Regulator of inducer of meiosis protein 16; Unscheduled meiotic gene expression protein 6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 24 papers)
NP_010493 DNA-binding transcriptional regulator UME6 from Saccharomyces cerevisiae S288C
YDR207C Key transcriptional regulator of early meiotic genes, binds URS1 upstream regulatory sequence, couples metabolic responses to nutritional cues with initiation and progression of meiosis, forms complex with Ime1p, and also with Sin3p-Rpd3p from Saccharomyces cerevisiae
37% identity, 7% coverage
- function: Component of the RPD3C(L) histone deacetylase complex (HDAC) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Binds to the URS1 site (5'-AGCCGCCGA-3') and recruits the RPD3 histone deacetylase complex to the promoters to negatively regulate the expression of many genes including CAR1 (arginase), several required for sporulation, mating type switching, inositol metabolism, and oxidative carbon metabolism. Also recruits the ISW2 chromatin remodeling complex to promoters in a second gene repression pathway. Associates with the master regulator of meiosis IME1 in order to activate the expression of meiosis genes. Has both a positive and negative role in regulating phospholipid biosynthesis.
subunit: Component of the RPD3C(L) complex composed of at least ASH1, CTI6, DEP1, PHO23, RPD3, RXT2, RXT3, SAP30, SDS3, SIN3, UME1 and UME6. Interacts with RIM11, MCK1 and IME1. - MIP diversity from Trichoderma: Structural considerations and transcriptional modulation during mycoparasitic association with Fusarium solani olive trees
Ben, PloS one 2018 - “...1 (0,9%) 6 (4,9%) 3 (2,7%) PUT3 P25502 4 (3,8%) 0 0 0 CAR1 Repressor P39001 15 (14,4%) 12 (10,5%) 19 (15,4%) 13 (11,7%) RAP1 P11938 2 (1,9%) 1 (0,9%) 1 (0,8%) 0 STE12 Q03063 4 (3,8%) 4 (3,5%) 6 (4,9%) 8 (7,2%) PHO2 P07269 12...”
- “...to stress SMP1 P38128 1 (0,9%) 1 (0,9%) 0 0 Cellular response to stress XBP1 P39001 1 (0,9%) 1 (0,9%) 1 (0,8%) 3 (2,7%) Cellular response to oxidative stress 4/104 (0,04%) 4/107 (0,04%) 6/123 (0,05%) 4/114 (0,04%) Conclusion Our present results bring us nearer to understanding...”
- The transcriptional regulator Ume6 is a major driver of early gene expression during gametogenesis.
Harris, Genetics 2023 - GeneRIF: The transcriptional regulator Ume6 is a major driver of early gene expression during gametogenesis.
- Ume6 Acts as a Stable Platform To Coordinate Repression and Activation of Early Meiosis-Specific Genes in Saccharomyces cerevisiae.
Raithatha, Molecular and cellular biology 2021 - GeneRIF: Ume6 Acts as a Stable Platform To Coordinate Repression and Activation of Early Meiosis-Specific Genes in Saccharomyces cerevisiae.
- RPD3 and UME6 are involved in the activation of PDR5 transcription and pleiotropic drug resistance in ρ0 cells of Saccharomyces cerevisiae.
Yamada, BMC microbiology 2021 - GeneRIF: RPD3 and UME6 are involved in the activation of PDR5 transcription and pleiotropic drug resistance in rho(0) cells of Saccharomyces cerevisiae.
- GSK-3β Homolog Rim11 and the Histone Deacetylase Complex Ume6-Sin3-Rpd3 Are Involved in Replication Stress Response Caused by Defects in Dna2.
Demin, Genetics 2017 - GeneRIF: We also present evidence that indicates Rim11/Ume6 works independently but in parallel with that of checkpoint inhibition, dNTP regulation, and sister-chromatid recombination. In conclusion, our results establish Rim11, Ume6, the histone deacetylase complex Sin3-Rpd3 and Sml1 as new factors important in the events of faulty lagging strand synthesis.
- The conserved histone deacetylase Rpd3 and the DNA binding regulator Ume6 repress BOI1's meiotic transcript isoform during vegetative growth in Saccharomyces cerevisiae.
Liu, Molecular microbiology 2015 (PubMed)- GeneRIF: evidence that the Rpd3/Sin3/Ume6 histone deacetylase complex, which represses meiotic genes during mitosis, also prevents the induction of BOI1's 5'-extended isoform in mitosis by direct binding of Ume6 to its URS1 target
- Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification.
Lardenois, Molecular genetics and genomics : MGG 2015 - GeneRIF: identifies novel Ume6 repressed genes during growth and development and reveals a strong effect of the carbon source on the derepression pattern of transcripts in growing and developmentally arrested ume6/ume6 mutant cells
- Acetylation of the transcriptional repressor Ume6p allows efficient promoter release and timely induction of the meiotic transient transcription program in yeast.
Law, Molecular and cellular biology 2014 - GeneRIF: acetylation inhibits Ume6p binding by electrostatic repulsion
- Gcn5p-dependent acetylation induces degradation of the meiotic transcriptional repressor Ume6p.
Mallory, Molecular biology of the cell 2012 - GeneRIF: Gcn5p-dependent acetylation induces degradation of the meiotic transcriptional repressor Ume6p.
- More
- Transcriptome response to alkane biofuels in Saccharomyces cerevisiae: identification of efflux pumps involved in alkane tolerance
Ling, Biotechnology for biofuels 2013 - “...YDR123C INO2 +12 +18 +19 YOL108C INO4 +3 +4 +3 YGL162W SUT1 +4 +5 +5 YDR207C UME6 +6 +4 +4 YOR028C CIN5 2 3 10 YPR104C FHL1 3 4 8 YLR256W HAP1 3 3 7 Note: C10-24h, cells exposed to C10 for 24h compared to cells...”
- Molecular determinants of sporulation in Ashbya gossypii
Wasserstrom, Genetics 2013 - “...Ime2 Ime4 Ndt80 Ume6 YJR094C YJL106W YGL192W YHR124W YDR207C AGL308W AFR076W AFR173W AGR347W AGL099C None None None None Severely reduced Sporulation Dmc1 Spo1...”
- Mcm2 phosphorylation and the response to replicative stress
Stead, BMC genetics 2012 - “...factor 1,6,7 yhp1 YDR451C Transcription factor/cell cycle 2,4,6 mbp1 YDL056W Transcription factor/cell cycle 2,4,6 ume6 YDR207C Transcription factor 2,4,5,6 hrd1 YOL013C Ubiquitin ligase/ER assoc. decay 8 ssm4 YIL030C Ubiquitin ligase/ER assoc. decay 8 pac10 YGR078C Protein folding 8 sip18 YMR175W Osmotic stress 9 rpl8b YLL045C Ribosomal...”
- The Antifungal Plant Defensin HsAFP1 from Heuchera sanguinea Induces Apoptosis in Candida albicans
Aerts, Frontiers in microbiology 2011 - “...repair pathway; interacts with Mms2p to assemble ubiquitin chains at the Ub Lys-63 residue 4 YDR207C UME6 Key transcriptional regulator of early meiotic genes, binds URS1 upstream regulatory sequence, couples metabolic responses to nutritional cues with initiation and progression of meiosis, forms complex with Ime1p, and...”
- Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships
Seok, BMC bioinformatics 2010 - “...1.2911 0.0070 YJR060W (CBF1) YOR375C (GDH1) 1.2126 0.0001 YLR451W (LEU3) YOR202W (HIS3) 1.2027 < 0.0001 YDR207C (UME6) YJR048W (CYC1) 0.9489 0.0059 YEL009C (GCN4) YNL220W (ADE12) 0.9472 0.0077 YLR223C (IFH1) YMR242C (RPL20A) 0.9341 0.0079 YLR403W (SFP1) YBR189W (RPS9B) 0.8802 0.0050 YDR253C (MET32) YPR167C (MET16) 0.8625 < 0.0001...”
- Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes
Simola, Genome biology 2010 - “...0.624 0.175 33 (0.73) 73.92 YLR403W ( Sfp1 ) 0.01056* 0.653 0.200 36 (0.80) 73.46 YDR207C ( Ume6 ) 0.01626* 0.532 0.153 27 (0.60) 63.20 YPR104C ( Fhl1 ) 0.0015** 0.547 0.120 28 (0.62) 59.81 Module 2 YKL112W ( Abf1 ) 0.025* 0.629 0.201 33 (0.73)...”
- On cycles in the transcription network of Saccharomyces cerevisiae
Jeong, BMC systems biology 2008 - “...Fig. 3 node code TF node code TF 1 YBR049C REB1 14 YLR183C TOS4 2 YDR207C UME6 15 YLR256W HAP1 3 YDR259C YAP6 16 YML007W YAP1 4 YDR501W PLM2 17 YML027W YOX1 5 YER111C SWI4 18 YNL068C FKH2 6 YGL073W HSF1 19 YNL216W RAP1 7 YIL122W...”
- Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment
Shevchenko, Genome biology 2008 - “...48 DEP1 SPBC21C3.02c 55 Figure S3 SAP30 YMR263W 23 No orthologues in S. pombe UME6 YDR207C 91 No orthologues in S. pombe DOT6 YER088C 72 No orthologues in S. pombe TOD6 YBL054W 59 No orthologues in S. pombe ASH1 YKL185W 66 No orthologues in S. pombe...”
- More
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory