PaperBLAST
PaperBLAST Hits for ABID97_RS24730 (78 a.a., MSKKHIEDCV...)
Show query sequence
>ABID97_RS24730
MSKKHIEDCVRTSLDSYFRDLRGTEPDGMYEMLVRVVEKPLLDVVMTRAEGNQSKAAQWL
GLNRNTLRKKLVEHKLLK
Running BLASTp...
Found 45 similar proteins in the literature:
BCAL3335 DNA-binding protein from Burkholderia cenocepacia J2315
64% identity, 99% coverage
azo2893 putative fis-like DNA-binding protein from Azoarcus sp. BH72
51% identity, 99% coverage
LHK_03207 Fis from Laribacter hongkongensis HLHK9
52% identity, 91% coverage
PMI3622 DNA-binding protein Fis from Proteus mirabilis HI4320
43% identity, 78% coverage
A0J47_RS00510 DNA-binding transcriptional regulator Fis from Photobacterium damselae subsp. damselae
42% identity, 78% coverage
A1S_2186 DNA-binding protein from Acinetobacter baumannii ATCC 17978
ABUW_1533 DNA-binding transcriptional regulator Fis from Acinetobacter baumannii
48% identity, 82% coverage
- The Response of Acinetobacter baumannii to Hydrogen Sulfide Reveals Two Independent Persulfide-Sensing Systems and a Connection to Biofilm Regulation
Walsh, mBio 2020 - “...in untreated cells. On the other hand, the nucleoid associated, nonspecific DNA binding protein Fis (A1S_2186) is only observed in untreated cells ( Fig.4B ). In addition to these, there are several proteins whose cellular abundance significantly changes upon treatment with exogenous sulfide as depicted in...”
- Fluorescence-Based Detection of Natural Transformation in Drug-Resistant Acinetobacter baumannii
Godeux, Journal of bacteriology 2018 - “...A. baumannii AB5075. We identified three homodimeric small NAPs: HU (ABUW_2198), HNS (ABUW_3609), and Fis (ABUW_1533). Two other candidate proteins were also selected based on their abundance inferred from proteomic analysis performed in A. baumannii strain ATCC 17978 ( 28 ). In this particular strain, heat...”
- Towards the complete proteinaceous regulome of Acinetobacter baumannii
Casella, Microbial genomics 2017 - “...Regulates initiation of bacterial replication in E. coli 48% (2 e 159) [ 98 ] ABUW_1533 Fis Homeostatic regulator of DNA topology in E. coli 59% (8 e 33) [ 45, 46 ] ABUW_3813 GntR Regulator of genes involved in transport and catabolism of l -lactate...”
WP_012883002 DNA-binding transcriptional regulator Fis from Dickeya dianthicola
42% identity, 78% coverage
Fis / b3261 DNA-binding transcriptional dual regulator Fis from Escherichia coli K-12 substr. MG1655 (see 8 papers)
FIS_ECOLI / P0A6R3 DNA-binding protein Fis; Factor-for-inversion stimulation protein; Hin recombinational enhancer-binding protein from Escherichia coli (strain K12) (see 4 papers)
Fis / P0A6R3 Transcription factor Fis (activator/repressor) from Escherichia coli K12 MG1655 (see 25 papers)
Fis / FIS_SALTI Transcription factor Fis (repressor) from Salmonella enterica
5ds9B / P0A6R3 Crystal structure of fis bound to 27bp DNA f1-8a (aaattagtttgaattttgagctaattt) (see paper)
fis / GB|AAN44763.1 DNA-binding protein fis from Shigella sonnei Ss046 (see 13 papers)
STM3385 site-specific DNA inversion stimulation factor from Salmonella typhimurium LT2
B5R1C8 DNA-binding protein Fis from Salmonella enteritidis PT4 (strain P125109)
NP_417727 DNA-binding transcriptional dual regulator Fis from Escherichia coli str. K-12 substr. MG1655
NP_462295 site-specific DNA inversion stimulation factor from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
AP_003801 global DNA-binding transcriptional dual regulator from Escherichia coli W3110
b3261 DNA-binding protein Fis from Escherichia coli str. K-12 substr. MG1655
t3300 Fis DNA-binding protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
KP1_4989 DNA-binding protein from Klebsiella pneumoniae NTUH-K2044
ECs4133 site-specific DNA inversion stimulation factor from Escherichia coli O157:H7 str. Sakai
BN49_RS03455, ECL_04646, KP1_RS23255, SENTW_3516, STM14_4083, T_RS16745 DNA-binding transcriptional regulator Fis from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
KPHS_48020 DNA-binding protein Fis from Klebsiella pneumoniae subsp. pneumoniae HS11286
42% identity, 78% coverage
- function: Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin- mediated DNA inversion. Prevents initiation of DNA replication from oriC. Binds to hundreds of transcriptionally active and inactive AT- rich sites, approximately half its binding sites are in non-coding DNA, which only accounts for about 10% of the genome (PubMed:16963779).
subunit: Homodimer - Ligand: dna (5ds9B)
- Inorganic Polyphosphate Is Essential for Salmonella Typhimurium Virulence and Survival in Dictyostelium discoideum
Varas, Frontiers in cellular and infection microbiology 2018 - “...Putative cytoplasmic protein STM14_4067 STM3373 mreC Cell wall structural complex MreBCD transmembrane component MreC STM14_4083 STM3385 fis DNA-binding protein Fis STM14_4435 STM3678 Putative regulatory protein (AraC family) STM14_4568 STM3787 uhpT Sugar phosphate antiporter STM14_4599 STM3808 ibpB Heat shock chaperone IbpB STM14_4982 STM4146 tuf_2 Elongation factor Tu...”
- Regulatory principles governing Salmonella and Yersinia virulence
Erhardt, Frontiers in microbiology 2015 - “...host defense FimZ STM0549 YPK_2269 98 48 Transcription Colonization FimZ STM0549 YPK_2499 98 31 Fis STM3385 Fis YPK_0452 100 98 Transcription Colonization, invasion, host defense FlhC STM1924.S FlhC YPK_1746 100 82 Transcription Colonization FlhD STM1925 FlhD YPK_1745 97 76 Transcription Colonization FliA STM1956 FliA YPK_2380 99...”
- Ethanol Adaptation Strategies in Salmonella enterica Serovar Enteritidis Revealed by Global Proteomic and Mutagenic Analyses
He, Applied and environmental microbiology 2019 (secret) - Negative feedback for DARS2-Fis complex by ATP-DnaA supports the cell cycle-coordinated regulation for chromosome replication.
Miyoshi, Nucleic acids research 2021 - GeneRIF: Negative feedback for DARS2-Fis complex by ATP-DnaA supports the cell cycle-coordinated regulation for chromosome replication.
- Fis protein forms DNA topological barriers to confine transcription-coupled DNA supercoiling in Escherichia coli.
Dages, FEBS letters 2020 - GeneRIF: Fis protein forms DNA topological barriers to confine transcription-coupled DNA supercoiling in Escherichia coli.
- Cooperative DNA binding by proteins through DNA shape complementarity.
Hancock, Nucleic acids research 2019 - GeneRIF: Comparisons with structures of DNA complexes containing only Fis or Xis, together with mutant protein and DNA binding studies, support a mechanism for cooperative protein binding solely by DNA allostery.
- Influence of Nucleoid-Associated Proteins on DNA Supercoiling.
Dahlke, The journal of physical chemistry. B 2019 (PubMed)- GeneRIF: Influence of Nucleoid-Associated Proteins on DNA Supercoiling.
- Facilitated Dissociation of a Nucleoid Protein from the Bacterial Chromosome.
Hadizadeh, Journal of bacteriology 2016 - GeneRIF: The prolific transcription factor and chromosome packaging protein Fis displays a strong dependence of its off-rate from the bacterial chromosome on Fis concentration.
- Building the bacterial orisome: high-affinity DnaA recognition plays a role in setting the conformation of oriC DNA.
Kaur, Molecular microbiology 2014 - GeneRIF: Authors found that, although oligomers were assembled in the absence of any individual high-affinity DnaA binding site, loss of DnaA binding at peripheral sites eliminated Fis repression, and made binding of both Fis and IHF essential.
- Timely binding of IHF and Fis to DARS2 regulates ATP-DnaA production and replication initiation.
Kasho, Nucleic acids research 2014 - GeneRIF: Simultaneous binding of IHF and Fis to specific sites within the DARS2 chromosomal site promoted regeneration of ATP-DnaA.
- E. coli Fis protein insulates the cbpA gene from uncontrolled transcription.
Chintakayala, PLoS genetics 2013 - GeneRIF: our work identifies a novel role for Fis and incorporates CbpA into the growing network of factors that mediate bacterial chromosome structure.
- More
- Dynamic Transcriptional Regulation of Fis in Salmonella During the Exponential Phase.
Wang, Current microbiology 2015 (PubMed)- GeneRIF: A total of 1495 Fis-regulated genes were successfully identified, including 987 Fis-repressed genes and 508 Fis-activated genes.
- Genome-wide analysis of the salmonella Fis regulon and its regulatory mechanism on pathogenicity islands.
Wang, PloS one 2013 - GeneRIF: Fis regulates 63 of the 94 Salmonella pathogenicity island (SPI)-1 and SPI-2 genes, by three regulatory modes.
- Multiple interfaces between a serine recombinase and an enhancer control site-specific DNA inversion.
McLean, eLife 2013 - GeneRIF: Hin is a member of the DNA invertase subclass of serine recombinases that are regulated by a remote recombinational enhancer element containing two binding sites for the protein Fis.
- Expression of the Fis protein is sustained in late-exponential- and stationary-phase cultures of Salmonella enterica serovar Typhimurium grown in the absence of aeration.
O, Molecular microbiology 2007 (PubMed)- GeneRIF: In Salmonella enterica serovar Typhimurium cultures grown in non-aerated SPI1-inducing conditions, Fis can be detected readily in stationary phase.while cultures grown with standard aeration showed the classic Fis expression pattern.
- Roles for DNA supercoiling and the Fis protein in modulating expression of virulence genes during intracellular growth of Salmonella enterica serovar Typhimurium.
O, Molecular microbiology 2006 (PubMed)- GeneRIF: Fis protein modulated both the level of DNA supercoiling and ssrA transcription.
- Fis regulates transcriptional induction of RpoS in Salmonella enterica.
Hirsch, Journal of bacteriology 2005 - GeneRIF: We characterized the activity of promoters serving rpoS in Salmonella enterica serovar Typhimurium and report that regulation of transcription during growth into stationary phase depends on Fis.
- Biodistribution of 89Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
Li, Poultry science 2023 - “...DPS Inorganic ion transport and metabolism Cytoplasm 168 P17169 GLMS Cell wall/membrane/envelope biogenesis Cytoplasm 169 P0A6R3 FIS Function unknown Cytoplasm 170 P0A7G6 RECA Replication, recombination and repair Cytoplasm 171 P0A8N5 SYK2 Translation, ribosomal structure and biogenesis Cytoplasm 172 P0A715 KDSA Cell wall/membrane/envelope biogenesis Cytoplasm 173 P21889...”
- Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom.
Amemiya, Transcription 2021 (no snippet) - A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS
Midha, Scientific data 2020 - “...sample compared to the control. A significantly down-regulated protein is the DNA-binding protein Fis (UniProt P0A6R3) which plays an important role in DNA metabolism, chromosome replication and repair mechanisms 55 . The effect of prolonged IPTG treatment has resulted in its decreased expression by nearly 10-fold...”
- A bacteriophage mimic of the bacterial nucleoid-associated protein Fis
Chakraborti, The Biochemical journal 2020 - “...Fis as a template. The sequences of NinH (UniProt ID P03771) and Fis (UniProt ID P0A6R3) protein were aligned using Clustal Omega by creating two separate sequence alignments (aligning NinH residues 144 to the C-terminal region of Fis and NinH residues 4569 to the N-terminal region...”
- Endogenous and Foreign Nucleoid-Associated Proteins of Bacteria: Occurrence, Interactions and Effects on Mobile Genetic Elements and Host's Biology
Flores-Ríos, Computational and structural biotechnology journal 2019 - “...11 P0A6X7/P0A6Y1 Escherichia coli Y DNA transposition, recombination, plasmid replication Fis family proteins Fis 11 P0A6R3 Escherichia coli ND Gene regulation, nucleoid architecture, DNA remodeling Other Lrp 19 P0ACJ0 Escherichia coli Y Gene regulation EbfC 11 O51418 Borrelia burgdorferi ND Gene regulation NdpA 37 A0A024L1K9 Escherichia...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...P06971 Ferrichrome-iron receptor 5.13/78,742.19 Fis P0A6R3 DNA-binding protein 9.34/11,239.93 FklB P0A9L3 FKBP-type 22-kDa peptidylprolyl cis-trans isomerase...”
- Mutational analysis of the C-terminal domain of the Rhodobacter sphaeroides response regulator PrrA
Jones, Microbiology (Reading, England) 2005 (secret) - Distribution of genes encoding nucleoid-associated protein homologs in plasmids
Takeda, International journal of evolutionary biology 2011 - “...identity and 70% query coverage). The complete amino acid sequences of Fis (DDBJ/EMBL/GenBank accession no. AP_003801), H-NS (AP_001863), Hha (AP_001109), HU (AP_003818), HU (AP_001090), IHF (AP_002332), IHF (AP_001542), Lrp (AP_001519), and NdpA (P33920) from E. coli K-12 W3110 and MvaT (AAP33788) from Pseudomonas aeruginosa PAO1 were...”
- The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model
Frick-Cheng, mBio 2020 - “...4.3 b3556 dsdX d -Serine transporter 2.7 b2365 fis DNA-binding transcriptional dual regulator Fis 2.4 b3261 ftsB Cell division protein FtsB 2.3 b2748 gntK d -Gluconate kinase, thermostable 2.7 b3437 gpt Xanthine-guanine phsophoribosyltransferase 2.4 b0238 gspH Hypothetical type II secretion protein GspH 3.0 UTI89_C3381 gspL Hypothetical...”
- An integrated approach to reconstructing genome-scale transcriptional regulatory networks
Imam, PLoS computational biology 2015 - “...NA NA 11.1 25 20 25 b1040 (CsgD) 23 0 0 33 13 12.1 17.4 b3261 (Fis) 227 0 0 10.5 0.9 6.7 4 E b1130 (PhoP) 55 NA NA 20 1.8 NA NA b4324 (UxuR) 7 NA NA 16.66 12.5 NA NA F b1988 (Nac)...”
- Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome
Ying, BMC genomics 2013 - “...lrp 83 0.0038 b3461 rpoH 150 0.0065 b0761 modE 45 0.0061 b1237 hns 136 0.0145 b3261 fis 216 0.0513 b2193 narP 49 0.0870 b1221 narL 113 0.1043 b3912 cpxR 51 0.0972 b2531 iscR 26 0.1580 b0399 phoB 36 0.1572 b1712 ihfA 191 0.1477 b2741 rpoS 215...”
- Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella
Skippington, BMC genomics 2011 - “...breakpoint(s)? CRP crp b3357 435 Concordant No FNR fnr b1334 282 Concordant No Fis fis b3261 225 Concordant No IHF ihfA b1712 217 Concordant No IHF ihfB b0912 217 Discordant No ArcA arcA b4401 158 Concordant No H-NS hns b1237 144 Concordant No NarL narL b1221...”
- “...breakpoint(s)? CRP crp b3357 435 Concordant No FNR fnr b1334 282 Concordant No Fis fis b3261 225 Concordant No IHF ihfA b1712 217 Concordant No IHF ihfB b0912 217 Discordant No ArcA arcA b4401 158 Concordant No H-NS hns b1237 144 Concordant No Lrp lrp b0889...”
- Overexpression of cloned RhsA sequences perturbs the cellular translational machinery in Escherichia coli
Aggarwal, Journal of bacteriology 2011 - “...change) in cells induced with IPTG at:b 0.1 mM b3704 b3261 b0472 b4201 b1863 b3740 b2567 3.7 (0.8) 3.6 (0.8) 1.4 (0.5) 2.9 (1.1) 1.1 (0.7) 1.5 (0.5) 1.3...”
- Remaining flexible in old alliances: functional plasticity in constrained mutualisms
Wernegreen, DNA and cell biology 2009 - “...BUsg012 Bbp012 Transcriptional dual regulator HU-alpha; (HU-2) fis b3261 - - - BU400 BUsg387 - DNA-binding protein; a trans activator for transcription flhC...”
- MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations
Keilwagen, Genome biology 2009 - “...Percentage b3357 crp 218 22 20 31 23.4% b1221 narL 74 7 2 11 17.6% b3261 fis 68 21 13 17 44.1% b1334 fnr 54 14 2 3 9.3% b0683 fur 46 15 1 43 95.7% b0889 lrp 43 12 4 23 62.8% b3912 cpxR 33...”
- Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
Lee, Applied and environmental microbiology 2009 - “...phnB mutL isrB isrC micF b0797 b0953 b0991 b1004 b1569 b2018 b3261 b3506 b3864 b4107 b4170 b4434 b4435 b4439 6.5 9.8 4.9 16.0 2.3 2.3 4.3 14.9 4.9 9.8 1.3 6.1...”
- More
- Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue
Nickerson, EBioMedicine 2018 - “...t0157 2.34 0.0004 Pyruvate dehydrogenase complex repressor T_RS17570 t3461 2.31 0.0004 DNA-binding protein HU-alpha T_RS16745 t3300 2.31 0.0004 Fis family transcriptional regulator T_RS12085 t2377 2.31 0.0004 Adenine phosphoribosyltransferase T_RS00330 t0067 2.3 0.0004 Carbamoyl-phosphate synthase small subunit T_RS00865 t0172 2.29 0.0004 Hypothetical protein T_RS03955 t0785 2.27 0.0004...”
- The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort
Dorman, mBio 2018 - “..._ 4976 ( csrD ) csrB regulatory protein CsrD 0.95 KP1_4976 fis DNA-binding protein 1.00 KP1_4989 pitA Putative low-affinity inorganic phosphate transporter 0.84 KP1_5198 a A list of all statistically significant genes from this TraDIS screen which, when disrupted by transposon insertion, increase capsule production in...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...accB -2.57 1 ECs4427 O157 2.20 2 ECs4128 accC -3.51 1 ECs4433 yhjY 3.88 2 ECs4133 fis -3.76 1 ECs4438 yiaE -2.49 1 ECs4159 rplQ -3.99 1 ECs4440 yiaG 2.73 2 ECs4160 rpoA -4.11 1 ECs4449 xylF 2.34 2 ECs4163 rpsM -3.05 1 ECs4463 yiaW 2.75...”
- Aminoglycoside heteroresistance in Enterobacter cloacae is driven by the cell envelope stress response
Choi, mBio 2024 - “...( Table S1 ). Additionally, fnr (ECL_02259), csgD (ECL_02600), narL (ECL_01619), cra (ECL_00876), and fis (ECL_04646) targets were enriched among downregulated genes in SCVs. Gentamicin treatment led to enrichment of puuR (ECL_02228), glnG (ECL_05113), fadR (ECL_01510), rob (ECL_00809), and arcA (ECL_00811) targets among upregulated genes, whereas...”
- Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation
Barbosa, BMC genomics 2019 - “...be involved in KP T6SS regulation Transcriptional regulator Locus-Tag T6SS relationship* Kp52.145 HS11286 NTUH-K2044 Fis BN49_RS03455 KPHS_48020 KP1_RS23255 Binding sites predicted at 17, 12, 12 promoters OxyR BN49_RS25290 KPHS_01030 KP1_RS00535 Binding sites predicted at 15, 10, 12 promoters H-NS BN49_RS18480 KPHS_31980 KP1_RS15455 Binding sites predicted at...”
- “...in KP T6SS regulation Transcriptional regulator Locus-Tag T6SS relationship* Kp52.145 HS11286 NTUH-K2044 Fis BN49_RS03455 KPHS_48020 KP1_RS23255 Binding sites predicted at 17, 12, 12 promoters OxyR BN49_RS25290 KPHS_01030 KP1_RS00535 Binding sites predicted at 15, 10, 12 promoters H-NS BN49_RS18480 KPHS_31980 KP1_RS15455 Binding sites predicted at 13, 8,...”
- Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue
Nickerson, EBioMedicine 2018 - “...T_RS00790 t0157 2.34 0.0004 Pyruvate dehydrogenase complex repressor T_RS17570 t3461 2.31 0.0004 DNA-binding protein HU-alpha T_RS16745 t3300 2.31 0.0004 Fis family transcriptional regulator T_RS12085 t2377 2.31 0.0004 Adenine phosphoribosyltransferase T_RS00330 t0067 2.3 0.0004 Carbamoyl-phosphate synthase small subunit T_RS00865 t0172 2.29 0.0004 Hypothetical protein T_RS03955 t0785 2.27...”
- Inorganic Polyphosphate Is Essential for Salmonella Typhimurium Virulence and Survival in Dictyostelium discoideum
Varas, Frontiers in cellular and infection microbiology 2018 - “...yhcG Putative cytoplasmic protein STM14_4067 STM3373 mreC Cell wall structural complex MreBCD transmembrane component MreC STM14_4083 STM3385 fis DNA-binding protein Fis STM14_4435 STM3678 Putative regulatory protein (AraC family) STM14_4568 STM3787 uhpT Sugar phosphate antiporter STM14_4599 STM3808 ibpB Heat shock chaperone IbpB STM14_4982 STM4146 tuf_2 Elongation factor...”
- Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization
Brankatschk, Microbial biotechnology 2014 - “...and F) metF SENTW_4195 6.17 Methylenetrahydrofolate reductase atpG SENTW_3971 4.42 Membrane-bound ATP synthase Regulators fis SENTW_3516 37.55 DNA binding protein yiaG SENTW_3750 13.86 Transcriptional regulator metR SENTW_4054 13.81 Transcriptional regulator rcsA SENTW_1101 9.30 Regulator of capsular polysaccharide synthesis ydcI SENTW_1576 6.26 Probable RuBisCO transcriptional regulator ydhM...”
- “...thiazole. Regulators Altogether, eight regulatory genes were more transcribed in presence of sprouts, with fis (SENTW_3516) being the regulatory gene with highest fold expression ratio (38-fold). In S. Typhimurium, this DNA-binding protein is involved in coordinating the expression of metabolic, flagella and type III secretion factors...”
- Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation
Barbosa, BMC genomics 2019 - “...involved in KP T6SS regulation Transcriptional regulator Locus-Tag T6SS relationship* Kp52.145 HS11286 NTUH-K2044 Fis BN49_RS03455 KPHS_48020 KP1_RS23255 Binding sites predicted at 17, 12, 12 promoters OxyR BN49_RS25290 KPHS_01030 KP1_RS00535 Binding sites predicted at 15, 10, 12 promoters H-NS BN49_RS18480 KPHS_31980 KP1_RS15455 Binding sites predicted at 13,...”
VC0290 factor-for-inversion stimulation protein from Vibrio cholerae O1 biovar eltor str. N16961
VP2885 factor-for-inversion stimulation protein from Vibrio parahaemolyticus RIMD 2210633
42% identity, 78% coverage
- CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species
McDonald, BMC genomics 2019 - “...Type I-E CRISPR-Cas island characterized in classical V. cholerae strains (O395) inserted between VC0289 and VC0290 relative to the El Tor biotype strain N16961 that lacked the island. b These type I-E systems have a conserved PAM of 3 NTT 5 and c a canonical type...”
- Functional Analysis of Bacteriophage Immunity through a Type I-E CRISPR-Cas System in Vibrio cholerae and Its Application in Bacteriophage Genome Engineering
Box, Journal of bacteriology 2016 - “...genomic island integrated between genes equivalent to VC0289 and VC0290 in the V. cholerae El Tor strain N16961. The colored arrows indicate the genes of the...”
- Post-Genomic Analysis of Members of the Family Vibrionaceae
Boyd, Microbiology spectrum 2015 - “...No. XXR No. ORF 5-flanking ORF 3-flanking ORF V. cholerae N16961 125 42/48 177 216 VC0290 (L20) VC0507 (Tnp) IEC224 125 42/48 177 218 O3Y_14818 (L20) O3Y_15923 (Tnp) MJ-1236 119 42/47 137 163 VCD_000985 (L20) VCD_000819 (Tnp) 2010EL-1786 99 42/48 136 160 Vch1786_II0036 (L20) Vch1786_II0197 (Tnp)...”
- A systems biology approach to modeling vibrio cholerae gene expression under virulence-inducing conditions
Kanjilal, Journal of bacteriology 2010 - “...protein RstB1 (VC1453), a factor-forinversion stimulation protein (VC0290), a heat shock gene (VC1663), and the flagellar assembly protein MinD (VC2067)....”
- “...VC1483 VC1827 VC1995 VC2021 VC2484 VCA0678 VC0196 VC0290 VC0612 VC1663 VC2055 VC2067 VC2368 Cholera enterotoxin, A subunit Hypothetical protein VC1457 VCA0435...”
- Differences in gene expression between the classical and El Tor biotypes of Vibrio cholerae O1
Beyhan, Infection and immunity 2006 - “...to encode regulatory proteins, VC0072, VC0278 (cadC), VC0290 (fis), VC1222 (himA), VC1286, VC1713, VC2485, VC2749 (ntrC), VCA0532, VCA0850, and VCA0952 (vpsT),...”
- Characterization of the small untranslated RNA RyhB and its regulon in Vibrio cholerae
Davis, Journal of bacteriology 2005 - “...3 samples) VC0001 VC0099 VC0108 VC0122 VC0132 VC0151 VC0290 VC0291 VC0452 VC0492 VC0574a VC0988 VC1016 VC1169 VC1170 VC1203 VC1260 VC1304a VC1806 VC2045a VC2090...”
- Regulatory Small RNA Qrr2 Is Expressed Independently of Sigma Factor-54 and Can Function as the Sole Qrr Small RNA To Control Quorum Sensing in Vibrio parahaemolyticus
Tague, Journal of bacteriology 2022 (secret) - Fis Connects Two Sensory Pathways, Quorum Sensing and Surface Sensing, to Control Motility in Vibrio parahaemolyticus
Tague, Frontiers in microbiology 2021 - “...et al., 1989 ) were used to construct an in-frame, non-polar deletion mutant of fis (VP2885) in V. parahaemolyticus RIMD2210633. Briefly, primers were designed using V. parahaemolyticus RIMD2210633 genomic DNA as a template. All primers used in this study are listed in Supplementary Table S2 ....”
- “...Supplementary Table S2 ) and V. parahaemolyticus RIMD2210633 genomic DNA were used to amplify fis (VP2885). The fis PCR product along with purified pMAL-c5x, were digested with NcoI and BamHI, ligated with T4 ligase, and transformed into DH5. The vector pMAL-c5x fis was purified, sequenced, and...”
- Quorum Sensing Regulators Are Required for Metabolic Fitness in Vibrio parahaemolyticus
Kalburge, Infection and immunity 2017 - “...we also found that the DNA-binding protein Fis (VP2885) was slightly upregulated in the luxO mutant (1.62-fold; Padj 0.0001). Fis is a known global...”
ECA0255 DNA-binding transcriptional regulator Fis from Pectobacterium atrosepticum SCRI1043
42% identity, 78% coverage
- Global Gene Expression Analysis of Cross-Protected Phenotype of Pectobacterium atrosepticum
Gorshkov, PloS one 2017 - “...ECA1540, ECA2013, ECA2873, ECA2226; down-regulatedECA3054, ECA3682, ECA4006, ECA4513, ECA1141, ECA1232, ECA4461, ECA1407, ECA2651, ECA4079, ECA0260, ECA0255, ECA0238, ECA3343, ECA3814. Total RNA was extracted from Pba cells and digested with DNAze as described above and used for cDNA synthesis. The reaction mixture for reverse transcription contained 1...”
YPTB3577 DNA-binding protein Fis from Yersinia pseudotuberculosis IP 32953
YPK_0452 Fis family transcriptional regulator from Yersinia pseudotuberculosis YPIII
42% identity, 78% coverage
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPO3570 BolA-like protein 1.315 (0.035) YPTB3538 (rnk) YPO3695 regulator of nucleoside diphosphate kinase 0.564 (0.016) YPTB3577 (fiS) or2359 DNA-binding protein Fis 0.611 (0.034) 0.58 (0.02) YPTB3579 YPO3651 Transcriptional regulator (pseudogene. inframe deletion) 0.675 (0.017) YPTB3764 (greB) YPO0136 transcription elongation factor 0.69 (0.004) YPTB3779 (glpR) YPO0120 glycerol-3-phosphate...”
- “...(xseA) YPO2872 exodeoxyribonuclease VII large subunit 0.639 (0.01) YPTB3389 YPO0674 putative MutT-family protein 1.299 (0.044) YPTB3577 (fiS) or2359 DNA-binding protein Fis 0.611 (0.034) 0.58 (0.02) YPTB3757 YPO0144 putative hydrolase 1.58 (0.013) M: cell envelope biogenesis, outer membrane YPTB0051 (kdtX) YPO0054 lipopolysaccharide core biosynthesis glycosyl transferase 0.592...”
- Fis Is Essential for Yersinia pseudotuberculosis Virulence and Protects against Reactive Oxygen Species Produced by Phagocytic Cells during Infection
Green, PLoS pathogens 2016 - “...YPK_1253; rfaH , YPK_3937; wecC , YPK_4030; arnDT , YPK_1834-YPK_1835; dusB , YPK_0453; fis , YPK_0452; flgD , YPK_2423; psaEFABC , YPK_2761-YPK_2757; katG , YPK_3388; ahpC , YPK_3267; grxA , YPK_2733; recA , YPK_3375; rpoC , YPK_0341. Supporting Information S1 Fig Mini-TnSeq assay schematic. (A) Mutants...”
- Regulatory principles governing Salmonella and Yersinia virulence
Erhardt, Frontiers in microbiology 2015 - “...FimZ STM0549 YPK_2269 98 48 Transcription Colonization FimZ STM0549 YPK_2499 98 31 Fis STM3385 Fis YPK_0452 100 98 Transcription Colonization, invasion, host defense FlhC STM1924.S FlhC YPK_1746 100 82 Transcription Colonization FlhD STM1925 FlhD YPK_1745 97 76 Transcription Colonization FliA STM1956 FliA YPK_2380 99 83 Transcription...”
SO0393, SO_0393 DNA-binding protein Fis from Shewanella oneidensis MR-1
K3G22_17135 DNA-binding transcriptional regulator Fis from Shewanella putrefaciens
47% identity, 65% coverage
HD0449 DNA-binding protein from Haemophilus ducreyi 35000HP
42% identity, 74% coverage
APL_0190 DNA-binding protein Fis from Actinobacillus pleuropneumoniae L20
42% identity, 74% coverage
PA14_64190 DNA-binding protein Fis from Pseudomonas aeruginosa UCBPP-PA14
NP_253540 Fis family transcriptional regulator from Pseudomonas aeruginosa PAO1
PA4853 DNA-binding protein Fis from Pseudomonas aeruginosa PAO1
47% identity, 67% coverage
- Genomewide identification of genetic determinants of antimicrobial drug resistance in Pseudomonas aeruginosa
Dötsch, Antimicrobial agents and chemotherapy 2009 - “...PA14_57880 PA14_57910 PA14_62560 PA14_62770 PA14_62880 PA14_64190 PA14_68670 PA14_69810 PA14_70980 PA14_15750 PA0425 PA0426 PA0572 PA0595 PA0764 PA0770e...”
- Fis Contributes to Resistance of Pseudomonas aeruginosa to Ciprofloxacin by Regulating Pyocin Synthesis.
Long, Journal of bacteriology 2020 - GeneRIF: Fis Contributes to Resistance of Pseudomonas aeruginosa to Ciprofloxacin by Regulating Pyocin Synthesis.
- Virtual Screening and Meta-Analysis Approach Identifies Factors for Inversion Stimulation (Fis) and Other Genes Responsible for Biofilm Production in <i>Pseudomonas aeruginosa</i>: A Corneal Pathogen
Emeka, Current issues in molecular biology 2024 - “...PqsC, PqsD, PhzA, and PhzB ( Figure 6 ). Since the pathway associated with fis (PA4853) has not yet been reported in P. aeruginosa , adaptation of the biofilm pathway from Vibrio cholera revealed the up-regulated fis gene is an important contributor to biofilm formation in...”
- “...Zhou J. Gao Z. Zhang H. Dong Y. Crystal Structure of the Nucleoid-Associated Protein Fis (PA4853) from Pseudomonas aeruginosa Acta Crystallogr. Sect. F Struct. Biol. Commun. 2020 76 209 215 10.1107/S2053230X20005427 32356522 32. Pettersen E.F. Goddard T.D. Huang C.C. Couch G.S. Greenblatt D.M. Meng E.C. Ferrin...”
- Peptide 1018 inhibits swarming and influences Anr-regulated gene expression downstream of the stringent stress response in Pseudomonas aeruginosa
Wilkinson, PloS one 2021 - “...regulator, CupD activation 1.7 -1.6 Regulators of swarming (of 20 total in S5 Table ) PA4853 ( fis ) 1 D DNA-binding protein -1.8 -2.1 PA0905 ( rsmA ) 1 D RNA binding protein translational regulator 1.6 NC PA4725 ( cbrA ) 1 D two-component sensor...”
- Crystal structure of the nucleoid-associated protein Fis (PA4853) from Pseudomonas aeruginosa
Zhou, Acta crystallographica. Section F, Structural biology communications 2020 - “...Fis (PA4853) from Pseudomonas aeruginosa ISSN 2053-230X Juan Zhou,a Zengqiang Gao,b Heng Zhangb* and Yuhui Dongb* Received 26 February 2020 Accepted 18 April...”
- “...adaptation to various environments. Fis from Pseudomonas aeruginosa (PA4853, referred to as PaFis) has recently been found to be required for virulence by...”
- Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
Rubio-Gómez, Frontiers in microbiology 2020 - “...Secretion protein 0.6 0.003 0.7 0.001 PA4844 ctpL Methyl-accepting chemotaxis protein 0.7 0.001 0.6 0.002 PA4853 fis Putative Fis-like DNA-binding protein 0.7 0.006 1.0 0.000 PA4945 miaA Delta 2-isopentenylpyrophosphate 0.8 0.000 0.6 0.004 PA4960 serB Probable phosphoserine phosphatase 0.9 0.000 0.7 0.000 PA4961 Uncharacterized protein 0.7...”
- “...0.002 PA4747 secG Secretion protein 0.8 0.000 PA4844 ctpL Chemoreceptor for inorganic phosphate 0.6 0.005 PA4853 fis Putative Fis-like DNA-binding protein 0.9 0.000 PA4941 hflC Protease 0.5 0.004 PA4944 hfq Motilities and Quorum sensing 0.6 0.001 PA4945 miaA Delta 2-isopentenylpyrophosphate 1.0 0.000 PA4960 serB Probable phosphoserine...”
- PvrA is a novel regulator that contributes to Pseudomonas aeruginosa pathogenesis by controlling bacterial utilization of long chain fatty acids
Pan, Nucleic acids research 2020 - “...10.32 transcriptional regulator PchR PA4776 pmrA 3.44 14.05 8.68 two-component regulator system response regulator PmrA PA4853 fis 5.16 4.37 3.44 Fis family transcriptional regulator PA5117 typA 6.93 3.08 4.79 regulatory protein TypA PA5550 glmR 2.82 3.14 4.88 GlmR transcriptional regulator Roles of the regulatory genes in...”
- Pseudomonas aeruginosa Aggregate Formation in an Alginate Bead Model System Exhibits In Vivo-Like Characteristics
Sønderholm, Applied and environmental microbiology 2017 - “...( 45 ) indicates low metabolic activity, which is further supported by the downregulation of PA4853 ( fis ) ( 43 ), a gene associated with early exponential growth. One of the most notable findings was the broad repression of genes associated with iron regulation, which...”
- Identification of a small molecule that simultaneously suppresses virulence and antibiotic resistance of Pseudomonas aeruginosa
Guo, Scientific reports 2016 - “...Cip PA3351 flgM 4 PA3050 pyrD 4 4 4 2 2 PA5288 glnK PA4441 PA4781 PA4853 fis 2 PA2128 cupA1 2 2 PA1195 PA1098 fleS 2 PA4745 nusA 2 2 2 2 PA5198 2 2 PA0871 phhB PA0770 rnc 4 2 2 Sm, streptomycin; Tob, tobramycin;...”
- Phosphate starvation promotes swarming motility and cytotoxicity of Pseudomonas aeruginosa
Bains, Applied and environmental microbiology 2012 - “...PA4290 PA4292 PA4302 PA4350 PA4351 PA4551 PA4555 PA4723 PA4844 PA4853 PA4915 PA5261 PA5360 PA5361 PA5365 PA5366 PA5367 rhlB rhlA algD algF algA rpoS eddB eddA...”
- More
PP4821 DNA-binding protein Fis from Pseudomonas putida KT2440
46% identity, 68% coverage
- LapF and Its Regulation by Fis Affect the Cell Surface Hydrophobicity of Pseudomonas putida
Lahesaare, PloS one 2016 - “...TTACAACAAGTCGTACTGC-3 positions 321 to 303 in relation to the initiator codon of the fis gene (PP4821) Km0 5-GTGCAATGTAACATCAGAGATTTT -3 positions -68 to -92 in relation to the initiator codon of the Km r gene LapF-fw (BglII) 5-T AGATCT TTCGCTGAGGCTTTTCTAC-3 positions 198 to 180 in relation to...”
- “...Ni-NTA agarose matrix (Qiagen) as previously described [ 37 ]. The polyclonal antibodies against Fis (PP4821) were produced and purified by LabAs. Western immunoblot analysis was carried out to detect the amount of Fis from the crude lysates of P . putida . Bacteria were grown...”
HI0980 Hin recombinational enhancer binding protein (fis) from Haemophilus influenzae Rd KW20
39% identity, 77% coverage
- Suppression of Alternative Lipooligosaccharide Glycosyltransferase Activity by UDP-Galactose Epimerase Enhances Murine Lung Infection and Evasion of Serum IgM
Wong, Frontiers in cellular and infection microbiology 2019 - “...Site-specific tyrosine recombinase 0.6 1.5E-01 0.06 3.6E-04 HI0718 vacJ (mlaA) Lipoprotein 1.1 8.8E-01 0.06 8.8E-04 HI0980 fis Factor for inversion stimulation DNA binding protein 0.3 2.1E-04 0.05 3.0E-04 HI1084 yrbC (mlaC) ABC transporter; substrate-binding protein 0.7 1.8E-01 0.06 3.5E-04 HI1085 yrbD (mlaD) ABC transporter periplasmic protein...”
- Comparison of transcription of the Haemophilus influenzae iron/heme modulon genes in vitro and in vivo in the chinchilla middle ear
Whitby, BMC genomics 2013 - “...+1.68 +2.17 HI0348 Periplasmic nitrate reductase, cytochrome C-type subunit NapC +3.20 ns +1.71 +1.69 +2.34 HI0980 DNA architectural protein Fis +4.67 +2.56 +2.06 +1.66 +1.15 HI1066 Nitrite reductase complex, transmembrane protein NrfD +6.34 +2.24 +1.88 +3.84 ns HI1067 Nitrite reductase complex, Fe-S subunit NrfC +6.99 +1.70...”
- “...1.15 -3.84 1.81 HI0185 adhC -4.48 -1.42 -5.35 -1.42 HI0343 napD -1.38 1.56 1.00 12.4 HI0980 fis -1.05 1.26 -1.18 2.36 HI1069 nrfA -5.08 2.28 -5.06 9.69 HI1078 tcyC -1.92 2.58 -1.01 3.79 HI1094 ccmF -1.51 9.74 -2.01 4.68 HI1384 ftnA -4.27 -7.88 -6.89 -5.41 a...”
- The iron/heme regulated genes of Haemophilus influenzae: comparative transcriptional profiling as a tool to define the species core modulon
Whitby, BMC genomics 2009 - “...FeHm supplementation (FeHm+ve) were: HI0007 which encodes a putative formate dehydrogenase, HI0185 encoding alcohol dehydrogenase, HI0980 encoding the DNA architectural protein Fis, HI1384 encoding the ferritin subunit A1 and HI1706 which encodes the osmoprotection-related protein BetT. Genes selected for validation which failed to show significant fold...”
- “...-4.03 -12.12 HI0502 rbsA ns +1.08 ns c +1.13 HI0591 potE -11.40 -13.39 -13.78 -2.91 HI0980 fis +4.67 +5.99 +2.56 +5.19 HI0994 tbp1 -9.56 -10.87 -8.16 -16.53 HI0997m ompU -15.68 -4.43 -14.61 -4.21 HI1349 dps -4.12 -3.03 -3.70 -4.81 HI1368 pqqL ns +1.67 ns -1.60 HI1384...”
- Transcriptional profile of Haemophilus influenzae: effects of iron and heme
Whitby, Journal of bacteriology 2006 - “...and valine biosynthesis Translation factor for Fis (HI0980) Putative ribosome-associated GTPase (cgtA) Methyltransferase for 50S ribosomal protein L11 (prmA)...”
- In vivo transposon mutagenesis in Haemophilus influenzae
Kraiss, Applied and environmental microbiology 1998 - “...frames, designated HI0246, HI0219, and a fis gene homologue, HI0980. The fis gene product of E. coli is a global DNAbinding protein involved in DNA...”
PMCN03_0067, PmCQ2_004565, WP_005723276 DNA-binding transcriptional regulator Fis from Pasteurella multocida
41% identity, 77% coverage
- Attenuated vaccine PmCQ2Δ4555-4580 effectively protects mice against Pasteurella multocida infection
He, BMC veterinary research 2024 - “...Whole genome resequencing and PCR analysis showed that PmCQ245554580 missed six genes, including PmCQ2_004555, PmCQ2_004560, PmCQ2_004565, PmCQ2_004570, PmCQ2_004575, and PmCQ2_004580. Importantly, the virulence of PmCQ245554580 was reduced by approximately 2.810 9 times in mice. Notably, live PmCQ245554580 could provide 100%, 100% and 40% protection against PmA,...”
- “...Table 4 ), including PmCQ2_004555 (50S ribosomal protein L11 methyltransferase), PmCQ2_004560 (tRNA dihydrouridine synthase DusB), PmCQ2_004565 (Fis family transcriptional regulator), PmCQ2_004570 (phosphorribosylformyl-glycinamidine synthase), PmCQ2_004575 (hypothetical protein), and PmCQ2_004580 (DUF 26-containing protein) (Fig. 2 B). Then, the 6 missing genes were identified by PCR and RT-qPCR, which...”
- Genomic and transcriptomics analysis reveal putative secreted proteins expressed of <i>Pasteurella multocida</i> during 18β-glycyrrhetinic acid treatment
Wu, Frontiers in veterinary science 2024 - “...multocida HB03 genome. Numbers Putative proteins Description 1 PMCN03_0012 50S ribosomal protein L33, rpl33 2 PMCN03_0067 DNA-binding protein Fis, Fis 3 PMCN03_0121 Galactose-1-phohate uridylyltransferase, galT 4 PMCN03_0141 Polysaccharide export protein Wza 5 PMCN03_0287 Hypothetical protein 6 PMCN03_0519 30S ribosomal protein S9, rps9 7 PMCN03_0521 Stringent starvation...”
- Fis is essential for capsule production in Pasteurella multocida and regulates expression of other important virulence factors.
Steen, PLoS pathogens 2010 - GeneRIF: Fis as a critical regulator of capsule expression and is involved in the regulation of a range of other P. multocida genes including important virulence factors.
XC_0520 DNA-binding protein from Xanthomonas campestris pv. campestris str. 8004
46% identity, 82% coverage
AKJ12_RS16695 DNA-binding transcriptional regulator Fis from Xanthomonas arboricola pv. juglandis
46% identity, 82% coverage
- Proteome Analysis of Walnut Bacterial Blight Disease
H, International journal of molecular sciences 2020 - “...PM-Alpha Helix 15 AKU51052.1 AKJ12_RS15520 ATP F0F1 synthase subunit alpha OTHER PM-Alpha Helix 16 AKU50723.1 AKJ12_RS16695 Succinyl-CoA synthetase subunit alpha OTHER Cytoplasm 17 AKU49376.1 AKJ12_RS06020 DNA-binding protein HU OTHER Cytoplasm 18 AKU49010.1 AKJ12_RS03895 Cold-shock protein SP(Sec/SPI) SP-Extracellular space 19 AKU50240.1 AKJ12_RS10980 Peptidylprolyl isomerase OTHER Cytoplasm 20...”
BU400 factor-for-inversion stimulation protein from Buchnera aphidicola str. APS (Acyrthosiphon pisum)
41% identity, 76% coverage
BUE60_07695 DNA-binding transcriptional regulator Fis from Pseudomonas syringae pv. actinidiae ICMP 19099
46% identity, 65% coverage
PmVP161_0076 DNA-binding transcriptional regulator Fis from Pasteurella multocida
41% identity, 77% coverage
ACP86_06670 DNA-binding transcriptional regulator Fis from Marinobacter sp. CP1
44% identity, 69% coverage
- Marinobacter atlanticus electrode biofilms differentially regulate gene expression depending on electrode potential and lifestyle
Eddie, Biofilm 2021 - “...transcription factors had increased expression which were annotated as ArsR (ACP86_04765), LuxR (ACP86_06460), and Fis (ACP86_06670) family transcriptional regulators ( Fig. 4 ). The ArsR protein contains a helix-turn-helix motif as is typical of DNA-binding proteins, but also contains an S-adenosylmethionine dependent methyltransferase domain not typically...”
- “...to those of its targets [ 34 ], suggesting that the increase in expression of ACP86_06670 is a factor in promoting motility in M. atlanticus CP1 as well. Thirty-five genes were significantly more highly expressed in electrode-attached cells relative to planktonic, including many encoding hypothetical proteins....”
XF_RS13495 DNA-binding transcriptional regulator Fis from Xylella fastidiosa 9a5c
44% identity, 83% coverage
A1B9J9 DNA-binding transcriptional regulator NtrC from Paracoccus denitrificans (strain Pd 1222)
Pden_4129 two component, sigma54 specific, transcriptional regulator, Fis family from Paracoccus denitrificans PD1222
47% identity, 13% coverage
- Exploring the Denitrification Proteome of Paracoccus denitrificans PD1222
Olaya-Abril, Frontiers in microbiology 2018 - “...functionally associated with the nitrogen starvation response, such as the global regulatory proteins NtrBC (A1B9K0, A1B9J9), NtrYX (A1B9J8, A1B9J7) and PII-GlnB (A1BAI1), glutamine synthetase GlnA (A1BAI2), glutamate synthase large and small subunits (A1AZA6 and A1AZA8), urease structural and accessory proteins (A1B1B6, A1B1B8, A1B1B9, and A1B1C2), and...”
- Transcriptional and translational adaptation to aerobic nitrate anabolism in the denitrifier Paracoccus denitrificans
Luque-Almagro, The Biochemical journal 2017 - “...Pden_0794 bztB 1.90.4 Pden_1212 ureD 5.11.8 Pden_2032 amtB 5.31.7 Pden_2151 potD 2.60.2 Pden_4019 urtC 6.20.4 Pden_4129 ntrC 4.60.5 Pden_4130 ntrB 1.60.2 Pden_4234 narJ 24.311.1 Pden_4236 narG 100.523.3 Pden_4450 nasH 185.79.8 Pden_4453 nasA 385.011.9 Pden_4454 nasS 7.71.5 Pden_4455 nasT 23.36.3 Pden_4461 glnB 2.60.6 Pden_4462 glnA 3.40.7 Qualitative...”
- “...1.80.1 Pden_2032 amtB 0.40.0 0.60.1 0.30.1 Pden_2151 potD 0.50.1 0.60.1 Pden_4019 urtC 0.50. 1 0.50.1 Pden_4129 ntrC 0.40.1 0.50.1 0.80.2 Pden_4130 ntrB 0.70.1 0.60.2 0.60.1 Pden_4234 narJ 7.71.2 57.014.4 Pden_4236 narG 2.50.2 67.512.2 173.812.3 Pden_4450 nasH 0.60.2 0.90.1 0.20.1 Pden_4453 nasA 0.90.3 0.30.1 0.20.1 Pden_4454 nasS...”
SPO2087 nitrogen regulation protein NtrC from Silicibacter pomeroyi DSS-3
SPO2087 sigma-54-dependent transcriptional regulator from Ruegeria pomeroyi DSS-3
47% identity, 13% coverage
lpp0606 hypothetical protein from Legionella pneumophila str. Paris
lpg0542 DNA binding protein Fis from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
41% identity, 71% coverage
- The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system
Sahr, PLoS genetics 2017 - “...RNA polymerase sigma factor 62.5 1.80 / lpp1255 PmrA, TCS response regulator 25.68 / / lpp0606 Fis1, Global DNA-binding transcriptional regulator 51.2 / / lpp1324 Fis2, Global DNA-binding transcriptional regulator 50.83 3.42 4.52 lpp1707 Fis3, Global DNA-binding transcriptional regulator 15.42 0.35 0.47 lpp1826 HU-beta, DNA-binding protein...”
- The LetA/S two-component system regulates transcriptomic changes that are essential for the culturability of Legionella pneumophila in water
Mendis, Scientific reports 2018 - “...factor rho 1.52 1.68 Lpg0232 transcriptional regulator np20 (Fur family) (ferric uptake) np20 2.26 2.39 Lpg0542 DNA binding protein Fis (recombinational enhancer binding protein; factor-for-inversion stimulation protein) fis 2.15 2.63 Lpg1743 Fis transcriptional activator (factor for inversion stimulation) (DNA-binding protein) fis 1.05 1.00 Lpg2361 RNA polymerase...”
- Two Fis regulators directly repress the expression of numerous effector-encoding genes in Legionella pneumophila
Zusman, Journal of bacteriology 2014 - “...encoding the three Fis regulators revealed that Fis1 (lpg0542 gene) and Fis3 (lpg1743) but not Fis2 (lpg1370) are partially required for intracellular growth of...”
- “...instead of the icmT gene (GS3011) (39), the fis1 (lpg0542) gene (ZT-Fis1) (this study), the fis2 (lpg1370) gene (ZT-Fis2) (this study), and the fis3 (lpg1743)...”
Atu1446 two component response regulator from Agrobacterium tumefaciens str. C58 (Cereon)
AGRO_4553, ATU_RS07125 nitrogen regulation protein NR(I) from Agrobacterium sp. ATCC 31749
45% identity, 14% coverage
Bd0039 site-specific DNA inversion stimulation factor from Bdellovibrio bacteriovorus HD100
40% identity, 72% coverage
- Quantitative proteome of bacterial periplasmic predation reveals a prey damaging protease
Lai, 2024 - Chromosome structure and DNA replication dynamics during the life cycle of the predatory bacterium Bdellovibrio bacteriovorus
Pląskowska, FEMS microbiology reviews 2023 - “...2021 ). Genes encoding homologs of classic bacterial NAPs, including HU (Bd2104), IHF (Bd1639), Fis (Bd0039), and Dps (Bd2620), have been identified within the B. bacteriovorus genome (The Bdellovibrio viewer: B. bacteriovorus transcriptome 2023 ). Additionally, B. bacteriovorus was recently shown to encode two histones (Bd0055...”
- The first bite--profiling the predatosome in the bacterial pathogen Bdellovibrio
Lambert, PloS one 2010 - “...DNA replication encoding genes are up-regulated in the HI-specific gene set. It is interesting that Bd0039 encoding a site-specific invertase is induced in both HI and predatory datasets, possibly indicating the role of invertible promoters in the exit from attack-phase [19] . Transporters, both exporters of...”
RSP_2838 nitrogen metabolism transcriptional regulator, NtrC from Rhodobacter sphaeroides 2.4.1
43% identity, 15% coverage
ntrC / CAA86065.1 Nitrogen assimilation regulatory protein from Azospirillum brasilense (see paper)
P45671 DNA-binding transcriptional regulator NtrC from Azospirillum brasilense
48% identity, 13% coverage
AZOLI_1343 nitrogen regulation protein NR(I) from Azospirillum lipoferum 4B
43% identity, 14% coverage
A6A40_05215 nitrogen regulation protein NR(I) from Azospirillum humicireducens
43% identity, 14% coverage
- Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5T
Yu, Standards in genomic sciences 2018 - “...A6A40_07685 339 glnB Nitrogen regulatory protein P-II A6A40_05220 1200 ntrB Nitrogen regulation sensor histidine kinase A6A40_05215 1146 ntrC Nitrogen regulation response regulator A6A40_05205 1401 ntrX Sigma-54-dependent transcriptional regulator A6A40_05210 2319 ntrY Nitrogen regulation sensor histidine kinase Organization of the nitrogen fixation gene cluster in A. humicireducens...”
AZC_3086 nitrogen assimilation regulatory protein ntrC from Azorhizobium caulinodans ORS 571
48% identity, 13% coverage
- The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571
Lee, BMC genomics 2008 - “...of nif A AZC_3083 ntr X Transcriptional regulator AZC_3084 ntr Y Signal transduction histidine kinase AZC_3086 ntr C Transcriptional regulator AZC_3087 ntr B Signal transduction histidine kinase AZC_3088 nif R3 Nitrogen assimilation-regulatory protein AZC_3410 nif U Mobilization of Fe for Fe-S cluster synthesis and repair AZC_3411...”
blr4488 two-component response regulator from Bradyrhizobium japonicum USDA 110
44% identity, 13% coverage
P10576 DNA-binding transcriptional regulator NtrC from Bradyrhizobium sp. (strain RP501 Parasponia)
44% identity, 13% coverage
BMEI0866 NITROGEN ASSIMILATION REGULATORY PROTEIN from Brucella melitensis 16M
43% identity, 14% coverage
- Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales
Dombrecht, Genome biology 2002 - “...Re NGR Bj R7A Ml Sm At Bm NtrC Mlr0389 (14021374) SMc01043 (15074392) Atu1446 (17739866) BmeI0866 (17987149) NtrX Mlr0400 (14021376) SMc01045 (15074394) Atu1448 (17739869) BmeI0868 (17987151) DctD-1 Msi357 (20804186) Mlr5842 (14025622) SMb20613 (15141413) Atu3296 (17741681) DctD-2 Mlr7239 (14026791) SMb21200 (15140751) Atu0114 (17738434) NifA RE1SP0000735 (21492735) Y4uN...”
CCNA_01815 nitrogen assimilation regulatory protein from Caulobacter crescentus NA1000
CC1741 nitrogen regulation protein NR(I) from Caulobacter crescentus CB15
44% identity, 13% coverage
- Phosphotransferase-dependent accumulation of (p)ppGpp in response to glutamine deprivation in Caulobacter crescentus
Ronneau, Nature communications 2016 - “...glnA CCNA_02047, glnA 2 CCNA_03230 and glnA 3 CCNA_03240) and two NtrC homologues ( ntrC CCNA_01815, and ntrX CCNA_01817). Single in-frame deletions of each of these genes were created and tested for growth, motility and G1 accumulation in complex PYE medium. We found that only glnB...”
- Global regulation of gene expression and cell differentiation in Caulobacter crescentus in response to nutrient availability
England, Journal of bacteriology 2010 - “...P-II-2 glnK CC1089 transcriptional regulator, endoribonuclease CC1741 nitrogen regulation protein ntrC CC0521 nitrogen regulatory protein P-II family CC1968...”
- Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus
Badger, Journal of bacteriology 2006 - “...CC0289 CC0294 CC0530 CC0744 CC1063 CC1078 CC1114 CC1740 CC1741 CC1743 CC2462 CC2463 CC2482 CC2755 CC2931 CC2932 CC3035 CC3315 CC3471 CC3474 CC3477 CC3484 CC3743...”
- Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus
Hu, Journal of bacteriology 2005 - “...in metabolism Ammonium transport CC1338 CC1339 CC1740 CC1741 Glutamate sysnthesis CC3606 CC3607 Phosphate starvation response CC2644 PHB synthesis CC0510 CC0511...”
- Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis
Skerker, PLoS biology 2005 - “...for its known substrate or the substrate encoded within its own operon, CC0294 (PhoB), CC0758, CC1741, CC2766, and CC3325, respectively (data not shown). Figure 5 Phosphotransfer Profiling of C. crescentus Histidine Kinases Profiles for four purified C. crescentus kinases versus 44 purified response regulators were obtained...”
RL2257 two component response regulator nitrogen regulation protein NR(I) from Rhizobium leguminosarum bv. viciae 3841
43% identity, 14% coverage
SAMCFNEI73_Ch1589 nitrogen regulation protein NR(I) from Sinorhizobium americanum
42% identity, 14% coverage
P10577 DNA-binding transcriptional regulator NtrC from Rhizobium meliloti (strain 1021)
SMc01043 NITROGEN ASSIMILATION REGULATORY PROTEIN from Sinorhizobium meliloti 1021
42% identity, 14% coverage
lpg1370 Hypothetical protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
lpp1324 hypothetical protein from Legionella pneumophila str. Paris
35% identity, 70% coverage
- Life Stage-specific Proteomes of Legionella pneumophila Reveal a Highly Differential Abundance of Virulence-associated Dot/Icm effectors
Aurass, Molecular & cellular proteomics : MCP 2016 - “...lpg1190 lpg1198 lpg1200 lpg1215 lpg1334 lpg1343 lpg1370 polypeptide deformylase hypothetical protein lpg1106 hypothetical protein lpg1121 amine oxidase...”
- “...hypothetical protein lpg1343 hypothetical protein lpg1370 thiol-disulfide oxidoreductase hemagglutinin/protease, zinc metalloprotease GAR synthetase ATP-grasp...”
- Two Fis regulators directly repress the expression of numerous effector-encoding genes in Legionella pneumophila
Zusman, Journal of bacteriology 2014 - “...(lpg0542 gene) and Fis3 (lpg1743) but not Fis2 (lpg1370) are partially required for intracellular growth of L. pneumophila in Acanthamoeba castellanii. To...”
- “...the fis1 (lpg0542) gene (ZT-Fis1) (this study), the fis2 (lpg1370) gene (ZT-Fis2) (this study), and the fis3 (lpg1743) gene (ZTFis3) (this study) were used. The...”
- Loss of RNase R induces competence development in Legionella pneumophila
Charpentier, Journal of bacteriology 2008 - “...putative lpg1340; flagellin lpg0938; lipoprotein signal peptidase lpg1370; DNA binding protein Fis lpg0066; carbamoyl phosphate synthase large chain lpg0952...”
- The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system
Sahr, PLoS genetics 2017 - “...and FleR, the alternative sigma factor RpoS ( lpp1247 ), the nucleoid-associated proteins Fis2 ( lpp1324 ), Fis3 ( lpp1707 ) and HU-beta ( lpp1826 ) or the transmission trait enhancer protein LetE. As it is well known, transcriptome and proteome data overlap only partially and...”
- “...TCS response regulator 25.68 / / lpp0606 Fis1, Global DNA-binding transcriptional regulator 51.2 / / lpp1324 Fis2, Global DNA-binding transcriptional regulator 50.83 3.42 4.52 lpp1707 Fis3, Global DNA-binding transcriptional regulator 15.42 0.35 0.47 lpp1826 HU-beta, DNA-binding protein 5.52 1.78 2.84 lpp1413 RelA, GTP pyrophosphokinase 25.75 /...”
- Two small ncRNAs jointly govern virulence and transmission in Legionella pneumophila
Sahr, Molecular microbiology 2009 - “...LqsR, a protein involved in phagocytosis and cytotoxicity ( Tiaden et al ., 2007 ), lpp1324 , coding a protein similar to a DNA-binding protein Fis, and lpp2675 which exhibits similarity to Papain-like cysteine peptidases. Weak induction of fleQ ( lpp0915 ), coding for the regulator...”
- “...system B protein B 0.30 - lpp2363 Chemiosmotic efflux system B protein C 0.30 - lpp1324 Similar to DNA-binding protein Fis 0.31 6.75 lpp2266 MotA2 0.31 0.62 lpp2888 PatA/VipD 0.31 0.23 lpp0351 Regulatory protein (EAL domain) 0.34 - lpp0352 Regulatory protein (GGDEF domain) 0.34 0.42 lpp1745...”
lpp1707 hypothetical protein from Legionella pneumophila str. Paris
lpg1743 Fis transcriptional activator from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
51% identity, 45% coverage
- The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system
Sahr, PLoS genetics 2017 - “...sigma factor RpoS ( lpp1247 ), the nucleoid-associated proteins Fis2 ( lpp1324 ), Fis3 ( lpp1707 ) and HU-beta ( lpp1826 ) or the transmission trait enhancer protein LetE. As it is well known, transcriptome and proteome data overlap only partially and they do not allow...”
- “...DNA-binding transcriptional regulator 51.2 / / lpp1324 Fis2, Global DNA-binding transcriptional regulator 50.83 3.42 4.52 lpp1707 Fis3, Global DNA-binding transcriptional regulator 15.42 0.35 0.47 lpp1826 HU-beta, DNA-binding protein 5.52 1.78 2.84 lpp1413 RelA, GTP pyrophosphokinase 25.75 / 0.62 lpp1002 LidA, Dot/Icm effector protein 25.23 1.88 /...”
- The LetA/S two-component system regulates transcriptomic changes that are essential for the culturability of Legionella pneumophila in water
Mendis, Scientific reports 2018 - “...Lpg0542 DNA binding protein Fis (recombinational enhancer binding protein; factor-for-inversion stimulation protein) fis 2.15 2.63 Lpg1743 Fis transcriptional activator (factor for inversion stimulation) (DNA-binding protein) fis 1.05 1.00 Lpg2361 RNA polymerase sigma 70 factor (sigma factor RpoD) rpoD 1.45 2.00 Translation Lpg0287 translation elongation factor P...”
- Two Fis regulators directly repress the expression of numerous effector-encoding genes in Legionella pneumophila
Zusman, Journal of bacteriology 2014 - “...regulators revealed that Fis1 (lpg0542 gene) and Fis3 (lpg1743) but not Fis2 (lpg1370) are partially required for intracellular growth of L. pneumophila in...”
- “...fis2 (lpg1370) gene (ZT-Fis2) (this study), and the fis3 (lpg1743) gene (ZTFis3) (this study) were used. The E. coli strains used in this work were MC1022 and...”
- Synergistic contribution of the Legionella pneumophila lqs genes to pathogen-host interactions
Tiaden, Journal of bacteriology 2008 - “...lpg1698 lqs-29 lqs-34 lqs-2 lqs-7 lqs-10 lqs-31 lpg2755 lpg1743 lpg1836 lpg2874 lpg2577 lpg1520 SdcA, paralog of SidC, binds to host cell PtdIns(4)P SidC, binds...”
Adeh_1992 two component, sigma54 specific, transcriptional regulator, Fis family from Anaeromyxobacter dehalogenans 2CP-C
52% identity, 9% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory