PaperBLAST
PaperBLAST Hits for VIMSS1225960 ferredoxin (638 a.a., MEKYQVKFMP...)
Show query sequence
>VIMSS1225960 ferredoxin
MEKYQVKFMPDQQVIEVEKGTSLLKAASQAGIFIKSSCGGKGTCGACKVTVISGEAKSER
TGNLSPEQLSRGVRLSCHTFVEGDLTVEVPPESRLQAHQVLLENANAALLTETSKDLLTY
YGYHPLARKVNIRCSEPTLTDNAGDWARLSLELKRVLQSDKPLTIPLSVLQTLPETLRQA
HWDLSVILTDLELGYTVLHVEPANDRPCYGLAIDVGTTTVVVYLVDLDSGEIVDKQGSYN
KQAQFGDDVISRIVYAVDSKENMAEIQKAVVDTVNALIDGILERQSLTSQDIASAVIAGN
TTMSQLFLGINPRYIRLEPYIPTVNSTPAVSAREIGLRLLPEALIHTYPSVASYVGGDIV
SGALATDMANSDEIILFIDIGTNGEIVLGNKDWLVSCACSAGPCFEGGGILFGMRAMPGA
IERVDIDPESLDVKLKVVGKIAPVGICGSGLVDCLAKLRKAGIIDRAGNFQLEHPSQSAR
IRATEDDKEFVLAWAHQAGGDKDIVISENDVKNLIRAKGAIYAGIRSLLQTVALEIDMIE
RIVIGGGFGNYLNVHDSVEIGLLPDLPQEKFEFIGNSSVKGARLALLSQKAWNEAADLAR
KMTYIELSIGTTFMDEFVSALFLPHTDLSLFPSVEGTF
Running BLASTp...
Found 113 similar proteins in the literature:
Dhaf_2795 ferredoxin from Desulfitobacterium hafniense DCB-2
DSY1650 ferredoxin from Desulfitobacterium hafniense Y51
100% identity, 100% coverage
- Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
Studenik, Journal of bacteriology 2012 - “...cassettes for the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank accession no. CP001336.1)...”
- “...on March 3, 2017 by University of California, Berkeley Dhaf_2795 2 Studenik et al. oriented in the reverse direction in comparison to the orientation in the...”
- Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195
Nonaka, Journal of bacteriology 2006 - “...DSY0391 DSY0393 DSY1228 DSY1247 DSY1596 DSY1598 DSY1648 DSY1650 DSY1651 DSY1652 DSY1671 DSY1890 DSY2085 DSY2558 DSY2585 DSY3715 DSY4099 DSY4876 Predicted...”
3zyyX / Q3ACS2 Reductive activator for corrinoid,iron-sulfur protein (see paper)
51% identity, 99% coverage
- Ligands: fe2/s2 (inorganic) cluster; (r,r)-2,3-butanediol (3zyyX)
Dtox_1273 ferredoxin from Desulfotomaculum acetoxidans DSM 771
49% identity, 99% coverage
TepiRe1_0615 corrinoid activation/regeneration protein AcsV from Tepidanaerobacter acetatoxydans Re1
41% identity, 99% coverage
CD0730 putative iron-sulfur protein from Clostridium difficile 630
41% identity, 98% coverage
Ccar_18775 corrinoid activation/regeneration protein AcsV from Clostridium carboxidivorans P7
41% identity, 98% coverage
DET0670 iron-sulfur cluster binding protein from Dehalococcoides ethenogenes 195
DET0704 iron-sulfur cluster binding protein from Dehalococcoides ethenogenes 195
41% identity, 99% coverage
CAETHG_1606 corrinoid activation/regeneration protein AcsV from Clostridium autoethanogenum DSM 10061
40% identity, 98% coverage
Awo_c10680 corrinoid activation/regeneration protein AcsV from Acetobacterium woodii DSM 1030
38% identity, 96% coverage
BP07_RS03235, WP_042685513 ASKHA domain-containing protein from Methermicoccus shengliensis
37% identity, 97% coverage
- Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds
Kurth, The ISME journal 2021 - “...and MtoD The gene encoding the corrinoid protein MtoC (BP07_RS03260) and the corrinoid activating enzyme (BP07_RS03235) were amplified from genomic M. shengliensis DNA with primers 3235fw/3235Srev (CTCATATGAGCGTCAGAGTAACGTTCGAGC, CTGCGGCCGCTTATTTTTCGAACTGCGGGTGGCTCCAGCTAGCTGAAGAGAGTTTTTCTCC) and 3260fw/3260Srev (CTCATATGACGGACGTAAGAGAAGAGCTC/CTGCGGCCGCTTATTTTTCGAACTGCGGGTGGCTCCAGCTAGCCTCCACCCCCACCAGAGC) for cloning in expression vector pET-30a inserting an N-terminal Strep tag via the reverse primer....”
- “...plasmid transformation. For production of the corrinoid protein MtoC (BP07_RS03260) and the corrinoid activating enzyme (BP07_RS03235) the plasmids pET-30a_BP07_RS03260 and pET-30a_BP07_RS03235 were used for transformation into E. coli Bl21 (DE3). For protein overexpression, one colony was inoculated in 600ml LB-medium containing 50g/ml kanamycin and incubated at...”
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...MtvB O-demethylase BP07_RS03250 WP_042685515 Corrinoid protein BP07_RS03260 WP_042685521 MtrH-like methyltransferase BP07_RS03240 WP_042685937 Corrinoid activation protein BP07_RS03235 WP_042685513 Methanococcoides Tertiary amines ? ? ? Methanolobus vulcani Quaternary amines MtgB methyltransferase FKV42_RS08545 WP_154809802 Corrinoid protein FKV42_RS08550 WP_154809803 Corrinoid activator FKV42_RS10455 WP_154810143 CoM methyltransferase FKV42_RS10480 WP_154810148 For the organisms...”
- “...O-demethylase BP07_RS03250 WP_042685515 Corrinoid protein BP07_RS03260 WP_042685521 MtrH-like methyltransferase BP07_RS03240 WP_042685937 Corrinoid activation protein BP07_RS03235 WP_042685513 Methanococcoides Tertiary amines ? ? ? Methanolobus vulcani Quaternary amines MtgB methyltransferase FKV42_RS08545 WP_154809802 Corrinoid protein FKV42_RS08550 WP_154809803 Corrinoid activator FKV42_RS10455 WP_154810143 CoM methyltransferase FKV42_RS10480 WP_154810148 For the organisms conducting...”
Dhaf_3310 ferredoxin from Desulfitobacterium hafniense DCB-2
39% identity, 97% coverage
- Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
Studenik, Journal of bacteriology 2012 - “...for the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank accession no. CP001336.1) as...”
- “...CCT TAT TTT TCG AAC TGC GGG TGG C 1 Dhaf_2573 Dhaf_3310 Dhaf_3879 Dhaf_4322 Dhaf_4610 Dhaf_4611 Dhaf_4612 a 2 2 2 2 2 2 2 2 For details, see Materials and...”
Dhaf_3879 ferredoxin from Desulfitobacterium hafniense DCB-2
35% identity, 95% coverage
- Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
Studenik, Journal of bacteriology 2012 - “...for the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank accession no. CP001336.1) as Strep...”
- “...TAT TTT TCG AAC TGC GGG TGG C 1 Dhaf_2573 Dhaf_3310 Dhaf_3879 Dhaf_4322 Dhaf_4610 Dhaf_4611 Dhaf_4612 a 2 2 2 2 2 2 2 2 For details, see Materials and Methods....”
Dhaf_4322 ferredoxin from Desulfitobacterium hafniense DCB-2
37% identity, 96% coverage
- Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
Studenik, Journal of bacteriology 2012 - “...the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank accession no. CP001336.1) as Strep tag...”
- “...BamHI according to the manufacturer's protocol. For Dhaf_4322, a compatible 3318 jb.asm.org Journal of Bacteriology Downloaded from http://jb.asm.org/ on March...”
AF_0010 ASKHA domain-containing protein from Archaeoglobus fulgidus DSM 4304
37% identity, 97% coverage
- A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus
Welte, Environmental microbiology 2021 - “.... Genomic and transcriptomic analysis revealed cobalamin binding protein MtoC (AF_0006) and its activator MtoD (AF_0010), Odemethylase MtoB (AF_0007) and methyl transferase MtoA (AF_0009) to be essential for growth of A. fulgidus on methoxylated aromatic compounds. CoM: coenzyme M, H 4 folate: tetrahydrofolate, CO(III): cobalamin binding...”
- “...VhtACDG (AF_137881), ATP synthase AtpAK (AF_115868), cobalamin binding protein MtoC (AF_0006) and its activator MtoD (AF_0010), Odemethylase MtoB (AF_0007) and methyl transferase MtoA (AF_0009), MFS transporters (AF_0008 & AF_0013). H 4 MPT: tetrahydromethanopterin, MQH 2 : reduced menaquinone (MQ), MFR: methanofuran, Fd: ferredoxin, F 420 H...”
Dhaf_1265 ferredoxin from Desulfitobacterium hafniense DCB-2
39% identity, 80% coverage
- Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
Studenik, Journal of bacteriology 2012 - “...components. Expression cassettes for the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank...”
- “...Desulfitobacterium hafniense DCB-2 into pET11aa Gene Primer sequence PCR step Dhaf_1265 CGC GTT CAT ATG AAT CAT TAT CGG CC CTG CGG GTG GCT CCA AGC GCT GCA GAG...”
SSCH_450007 ASKHA domain-containing protein from Syntrophaceticus schinkii
34% identity, 98% coverage
PGA1_c15200 ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) from Phaeobacter inhibens DSM 17395
PGA1_c15200 ASKHA domain-containing protein from Phaeobacter inhibens DSM 17395
32% identity, 89% coverage
- mutant phenotype: Apparently required for the reactivation of vitamin B12. Distantly related to RamA (see PMID: 19043046) (auxotroph)
- Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
Price, PLoS genetics 2018 - “...are likely to be involved in B12 reactivation: a protein with ferredoxin and DUF4445 domains (PGA1_c15200) and a DUF1638 protein (PGA1_c13340). As shown in Fig 4B , mutants in these genes are rescued by added methionine. The DUF4445 protein is distantly related to RamA, which uses...”
D9S251 Ferredoxin from Thermosediminibacter oceani (strain ATCC BAA-1034 / DSM 16646 / JW/IW-1228P)
33% identity, 99% coverage
- Analytical Validation of Loss of Heterozygosity and Mutation Detection in Pancreatic Fine-Needle Aspirates by Capillary Electrophoresis and Sanger Sequencing.
Timmaraju, Diagnostics (Basel, Switzerland) 2024 - “...150 chr5 119101810 119101960 GGTGTCAACAAAGTAATGTAAAG TGGATACATATTGTTTTCTGCTG 5q D5S615 330 chr5 125163290 125163620 GAGATAGGTAGGTAGGTAGG TCCACAGTGGTAAGAACCAG 9p D9S251 390 chr9 30819368 30819758 TGCATGTTTTATGTGCACTAAC CAATACTTTTTAAGGCTTTGTAGG 9p D9S254 120 chr9 126869098 126869218 TGGGTAATAACTGCCGGAGA GAGGATAAACCTGCTTCACTCAA 10q D10S520 180 chr10 96424526 96424706 CAGCCTATGCAACAGAACAAG GTCCTTGTGAGAAACTGGATGC 10q D10S523 150 chr10 87006333 87006483 GGTGGAGGTTGTGGTGA AACTGGGCATTTGTCTTTC...”
- Molecular Clues for Prediction of Hepatocellular Carcinoma Recurrence After Liver Transplantation.
Badwei, Journal of clinical and experimental hepatology 2023 - Role of Allelic Imbalance in Predicting Hepatocellular Carcinoma (HCC) Recurrence Risk After Liver Transplant.
Pagano, Annals of transplantation 2019 - “...Results We report that AI was associated with HCC recurrence in 3 main loci (D3S2303, D9S251, and D9S254). Tumor recurrence was associated only with 2 specific panels with 9 microsatellites previously reported to be associated with high risk for HCC recurrence. Our data show that fractional...”
- “...for D3S2303 (p=0.048) considering the presence of LOH ( Table 3A ), and D1S407 (p=0.006) D9S251 (p=0.02), D1S162 (p=0.005), D5S592 (p=0.005), D9S254 (p=0.002) and D10S520 (p=0.04) considering high-level LOH ( Table 3B ). Evaluation of specific panels and association with HCC recurrence Descriptive analysis of the...”
- The C9ORF72 expansion mutation is a common cause of ALS+/-FTD in Europe and has a single founder.
Smith, European journal of human genetics : EJHG 2013 - Clinical, neuroimaging and neuropathological features of a new chromosome 9p-linked FTD-ALS family.
Boxer, Journal of neurology, neurosurgery, and psychiatry 2011 - “...Genome-wide linkage analysis conclusively linked family VSM-20 to a 28.3 cM region between D9S1808 and D9S251 on chromosome 9p, reducing the published minimal linked region to a 3.7 Mb interval. Genomic sequencing and expression analysis failed to identify mutations in the 10 known and predicted genes...”
- “...GENESCAN and GENOTYPER software (Applied Biosystems) and normalised to the CEPH genotype database, except for D9S251 and D9S304 for which fragment sizes were not available. Mutation analyses In family VSM-20, a genomic DNA (gDNA) sequencing analysis was performed for all 10 candidate genes located within the...”
- Chromosome 9p21 in sporadic amyotrophic lateral sclerosis in the UK and seven other countries: a genome-wide association study.
Shatunov, The Lancet. Neurology 2010 - “...7 this 36 Mb locus is defined across studies by the flanking markers D9S169 and D9S251. The SNPs we have identified lie within this region, with the peak association at 1065 Kb. A GWAS that used pathological subtyping of patients with frontotemporal dementia to increase homogeneity...”
- Liver transplantation for hepatocellular carcinoma: extension of indications based on molecular markers.
Schwartz, Journal of hepatology 2008 - Use of microsatellite marker loss of heterozygosity in accurate diagnosis of pancreaticobiliary malignancy from brush cytology samples.
Khalid, Gut 2004
SMc04347 CONSERVED HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
30% identity, 92% coverage
Dhaf_2573 ferredoxin from Desulfitobacterium hafniense DCB-2
32% identity, 95% coverage
- Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
Studenik, Journal of bacteriology 2012 - “...Expression cassettes for the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank accession no....”
- “...GAT CCT TAT TTT TCG AAC TGC GGG TGG C 1 Dhaf_2573 Dhaf_3310 Dhaf_3879 Dhaf_4322 Dhaf_4610 Dhaf_4611 Dhaf_4612 a 2 2 2 2 2 2 2 2 For details, see Materials and...”
Dtur_0730 ferredoxin from Dictyoglomus turgidum DSM 6724
32% identity, 97% coverage
B8R2M5 [Co(II) methylated amine-specific corrinoid protein] reductase (EC 1.16.99.1) from Acetobacterium dehalogenans (see paper)
WP_026395886 ASKHA domain-containing protein from Acetobacterium dehalogenans DSM 11527
31% identity, 97% coverage
ELI_0370 ASKHA domain-containing protein from Eubacterium callanderi
32% identity, 95% coverage
RAMQ_EUBLI / P0DX10 Corrinoid activation enzyme RamQ from Eubacterium limosum (see 2 papers)
WP_038351871 ASKHA domain-containing protein from Eubacterium limosum
31% identity, 95% coverage
- function: Involved in the degradation of the quaternary amines L- proline betaine and L-carnitine (PubMed:31341018, PubMed:32571881). Component of a corrinoid-dependent methyltransferase system that transfers a methyl group from L-proline betaine or L-carnitine to tetrahydrofolate (THF), forming methyl-THF, a key intermediate in the Wood-Ljungdahl acetogenesis pathway (PubMed:31341018, PubMed:32571881). RamQ is not required for the methyl transfer, but it stimulates reduction of reconstituted MtqC from the Co(II) state to the Co(I) state in vitro (PubMed:31341018). It also stimulates the rate of THF methylation (PubMed:32571881).
cofactor: [2Fe-2S] cluster (Binds 1 2Fe-2S cluster.) - MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation
Picking, The Journal of biological chemistry 2019 (secret)
TepiRe1_0333 ASKHA domain-containing protein from Tepidanaerobacter acetatoxydans Re1
33% identity, 78% coverage
Dred_2206 ferredoxin from Desulfotomaculum reducens MI-1
36% identity, 67% coverage
RSK20926_19267 iron-sulfur cluster-binding protein from Roseobacter sp. SK209-2-6
32% identity, 39% coverage
RSK20926_19262 iron-sulfur cluster-binding protein from Roseobacter sp. SK209-2-6
32% identity, 44% coverage
MA0849 hypothetical protein (multi-domain) from Methanosarcina acetivorans C2A
25% identity, 66% coverage
DvMF_1398 ATP-dependent reduction of co(II)balamin (RamA-like) from Desulfovibrio vulgaris Miyazaki F
DvMF_1398 iron-sulfur cluster-binding protein, putative from Desulfovibrio vulgaris str. Miyazaki F
24% identity, 86% coverage
- mutant phenotype: Cofit with the B12-dependent methionine synthase (DvMF_0476), which lacks a standard domain for the reactivation of vitamin B12.
- Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
Price, PLoS genetics 2018 - “...the standard B12 activation domain. This methionine synthase has a very similar fitness pattern as DvMF_1398, which contains two DUF4445 domains (r = 0.92 across 170 experiments; also see Fig 3 ). We infer that DUF4445 proteins perform the reactivation of vitamin B12 in diverse bacteria....”
DVU0908 ATP-dependent reduction of co(II)balamin from Desulfovibrio vulgaris Hildenborough JW710
27% identity, 65% coverage
- mutant phenotype: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM PF14574.
Mmah_1683 4Fe-4S ferredoxin iron-sulfur binding domain protein from Methanohalophilus mahii DSM 5219
24% identity, 65% coverage
Dde_2711 2Fe-2S iron-sulfur cluster binding domains protein from Desulfovibrio desulfuricans G20
25% identity, 67% coverage
ramA / B8Y445 [Co(II) methylated amines-specific corrinoid protein] reductase (EC 1.16.99.1) from Methanosarcina barkeri (see 2 papers)
RAMA_METBA / B8Y445 [Co(II) methylated amine-specific corrinoid protein] reductase; Corrinoid activation enzyme RamA; EC 1.16.99.1 from Methanosarcina barkeri (see paper)
B8Y445 [Co(II) methylated amine-specific corrinoid protein] reductase (EC 1.16.99.1) from Methanosarcina barkeri (see paper)
25% identity, 65% coverage
- function: Reductase required for the activation of corrinoid-dependent methylamine methyltransferase reactions during methanogenesis (PubMed:19043046). Mediates the ATP-dependent reduction of corrinoid proteins from the inactive cobalt(II) state to the active cobalt(I) state (PubMed:19043046). Acts on the corrinoid proteins involved in methanogenesis from monomethylamine (MMA), dimethylamine (DMA) and trimethylamine (TMA), namely MtmC, MtbC and MttC, respectively (PubMed:19043046).
catalytic activity: 2 Co(II)-[methylamine-specific corrinoid protein] + AH2 + ATP + H2O = 2 Co(I)-[methylamine-specific corrinoid protein] + A + ADP + phosphate + 3 H(+) (RHEA:65816)
catalytic activity: 2 Co(II)-[dimethylamine-specific corrinoid protein] + AH2 + ATP + H2O = 2 Co(I)-[dimethylamine-specific corrinoid protein] + A + ADP + phosphate + 3 H(+) (RHEA:65832)
catalytic activity: 2 Co(II)-[trimethylamine-specific corrinoid protein] + AH2 + ATP + H2O = 2 Co(I)-[trimethylamine-specific corrinoid protein] + A + ADP + phosphate + 3 H(+) (RHEA:65836)
cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters.)
subunit: Monomer.
MM0940 putative Flavoprotein from Methanosarcina mazei Goe1
25% identity, 65% coverage
MA0150 methylamine methyltransferase corrinoid activation protein from Methanosarcina acetivorans C2A
24% identity, 65% coverage
MM1440 conserved protein from Methanosarcina mazei Goe1
23% identity, 65% coverage
MA3972 conserved hypothetical protein from Methanosarcina acetivorans C2A
25% identity, 65% coverage
FKV42_RS10455, WP_154810143 methylamine methyltransferase corrinoid protein reductive activase from Methanolobus vulcani
24% identity, 65% coverage
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...? Methanolobus vulcani Quaternary amines MtgB methyltransferase FKV42_RS08545 WP_154809802 Corrinoid protein FKV42_RS08550 WP_154809803 Corrinoid activator FKV42_RS10455 WP_154810143 CoM methyltransferase FKV42_RS10480 WP_154810148 For the organisms conducting hydrogen-dependent methylotrophic the enzymes important for energy conversion/recycling of reducing equivalents are shown as those play an important role of the...”
- “...proteomic analysis revealed that MtgB, a corrinoid binding protein (FKV42_RS08550), a corrinoid reductive activation enzyme (FKV42_RS10455) and a methylcorrinoid:CoM methyltransferase (FKV42_RS10480) were highly abundant when M. vulcani B1d was grown on betaine relative to growth on trimethylamine. Energy conservation presumably follows what is known for methylamine...”
- “...Methanolobus vulcani Quaternary amines MtgB methyltransferase FKV42_RS08545 WP_154809802 Corrinoid protein FKV42_RS08550 WP_154809803 Corrinoid activator FKV42_RS10455 WP_154810143 CoM methyltransferase FKV42_RS10480 WP_154810148 For the organisms conducting hydrogen-dependent methylotrophic the enzymes important for energy conversion/recycling of reducing equivalents are shown as those play an important role of the special...”
MA4380 conserved hypothetical protein from Methanosarcina acetivorans C2A
22% identity, 65% coverage
Q8PXZ5 Conserved protein from Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
MM1071 conserved protein from Methanosarcina mazei Goe1
23% identity, 65% coverage
- Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1
Leon, Frontiers in microbiology 2015 - “...Rpl1P 3 62 Q8PY39 MM1025 ThiC 3 58 Q8PXZ6 MM1070 MtaA1 methylcobalamin:CoM methyltransferase 7 374 Q8PXZ5 MM1071 4Fe:4S ferredoxin, hypothetical 2 121 Q8PXZ3 MM1073 MtaC2 methyl corrinoid protein 6 230 Q8PXZ2 MM1074 MtaB2 9 250 Q8PXZ1 MM1075 Putative regulatory protein 2 92 1 Y Q8PXX0 MM1096...”
- Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1
Leon, Frontiers in microbiology 2015 - “...3 62 Q8PY39 MM1025 ThiC 3 58 Q8PXZ6 MM1070 MtaA1 methylcobalamin:CoM methyltransferase 7 374 Q8PXZ5 MM1071 4Fe:4S ferredoxin, hypothetical 2 121 Q8PXZ3 MM1073 MtaC2 methyl corrinoid protein 6 230 Q8PXZ2 MM1074 MtaB2 9 250 Q8PXZ1 MM1075 Putative regulatory protein 2 92 1 Y Q8PXX0 MM1096 Thermosome,...”
- Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
Krätzer, Journal of bacteriology 2009 - “...(C-terminal domain) MM0174 MM0175 MM0312 MM0408 MM0479 MM0924 MM1071 MM1073 MM1074 MM1075 MM1112 MM1271 MM1272 MM1273 MM1274 MM1275 MM1647 MM1648 MM1761 MM1762...”
- RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea
Ferguson, The Journal of biological chemistry 2009 - “...were found in M. acetivorans (MA4380), M. mazei (mm1071), and M. barkeri (Mbar_A1055). Additionally, other RamA homologs in Methanosarcina spp. were found, but...”
- A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life
Haas, BMC genomics 2009 - “...( M. mazei COG0523) is induced to the same extent as its neighboring ramM homolog, MM1071 , during growth in high salt conditions (2.38 and 2.21 fold, respectively) [ 104 ]. Archaeal genomes sequenced to date lack any recognizable homolog of the Fur (Fe) or Zur...”
- Characterization of a novel bifunctional dihydropteroate synthase/dihydropteroate reductase enzyme from Helicobacter pylori
Levin, Journal of bacteriology 2007 - “...MM512 MM612 MM808 MM847 MM851 MM902 MM1059 MM1060 MM1061 MM1071 Genotype or description 4064 LEVIN ET AL. and E. coli Fre. The reaction mixture was incubated...”
Q7UWS0 Na(+)-translocating NADH-quinone reductase subunit F from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
44% identity, 13% coverage
DaAHT2_0047 NADH:ubiquinone reductase (Na(+)-transporting) subunit F from Desulfurivibrio alkaliphilus AHT 2
33% identity, 17% coverage
A0A0D0J042 Na(+)-translocating NADH-quinone reductase subunit F from Prevotella pectinovora
34% identity, 16% coverage
D8DWB6 Na(+)-translocating NADH-quinone reductase subunit F from Segatella baroniae B14
38% identity, 12% coverage
- Occurrence and Function of the Na+-Translocating NADH:Quinone Oxidoreductase in Prevotella spp.
Deusch, Microorganisms 2019 - “...RnfE D8DXV3 37.36 NuoN D8DX02 19.08 NqrE D8DWB7 RnfA D8DXV2 44.50 NuoL A0A1H9A8K0 16.67 NqrF D8DWB6 RnfB D8DXV7 17.34 NuoCD D8DWN9 17.48 microorganisms-07-00117-t004_Table 4 Table 4 Subunits of the NQR, RNF, NDH-I (Nuo), and other respiratory enzymes identified from membranes solubilized with 1% or 2% (...”
- “...reductase, Fe-S pr. 1272.00 63.89 16 16 Triton 1%B D8DWC1 NqrA 1126.93 60.58 26 27 D8DWB6 NqrF 386.31 18.01 7 7 D8DWB9 NqrC 272.89 40.48 7 8 D8DWC0 NqrB 55.66 11.43 3 3 D8DWB8 NqrD 41.65 4.78 2 2 D8DWN8 NuoH 115.46 9.62 4 4 D8DWN7...”
ABO_1037 sodium-translocating NADH-ubiquinone reductase,subunit F from Alcanivorax borkumensis SK2
29% identity, 22% coverage
D5ESF6 Na(+)-translocating NADH-quinone reductase subunit F from Xylanibacter ruminicola (strain ATCC 19189 / DSM 19721 / CIP 105475 / JCM 8958 / 23)
33% identity, 16% coverage
PSPPH_4805 oxidoreductase FAD-binding domain/oxidoreductase NAD-binding domain/2Fe-2S iron-sulfur cluster binding domain protein from Pseudomonas syringae pv. phaseolicola 1448A
36% identity, 13% coverage
Psyr_4775 Ferredoxin:Oxidoreductase FAD/NAD(P)-binding:Oxidoreductase FAD-binding region from Pseudomonas syringae pv. syringae B728a
36% identity, 13% coverage
P73_2169 2Fe-2S iron-sulfur cluster-binding protein from Celeribacter indicus
32% identity, 14% coverage
- Genomic and metabolic analysis of fluoranthene degradation pathway in Celeribacter indicus P73T
Cao, Scientific reports 2015 - “...P73_2875, P73_2968, and P73_4415), ring-hydroxylating dioxygenase subunit beta (P73_0347 and P73_2150), ferredoxin (P73_0348, P73_1051, P73_2167, P73_2169, P73_2960, P73_3499, and P73_4762), and ferredoxin reductase (P73_0335, P73_0354, P73_0554, P73_1054, P73_2874, P73_4416, and P73_4758) were found in the P73 T genome. Because RHD subunit alpha plays a major role...”
gbcB / Q9HTF3 glycine betaine monooxygenase ferredoxin reductase subunit (EC 1.14.13.251) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 5 papers)
GBMOR_PSEAB / A0A0H2ZJB2 Glycine betaine monooxygenase reductase subunit; Glycine betaine catabolism B; EC 1.14.13.251 from Pseudomonas aeruginosa (strain UCBPP-PA14) (see paper)
GBMOR_PSEAE / Q9HTF3 Glycine betaine monooxygenase reductase subunit; Glycine betaine catabolism B; EC 1.14.13.251 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
PA5411 probable ferredoxin from Pseudomonas aeruginosa PAO1
PA14_71420 putative ferredoxin from Pseudomonas aeruginosa UCBPP-PA14
33% identity, 14% coverage
- function: Involved in degradation of glycine betaine (PubMed:17951379). Part of a Rieske-type oxygenase system that catalyzes the conversion of glycine betaine (GB) to dimethylglycine (DMG) (PubMed:17951379). This subunit is the ferredoxin reductase component of the system (Probable).
catalytic activity: glycine betaine + NADH + O2 + H(+) = N,N-dimethylglycine + formaldehyde + NAD(+) + H2O (RHEA:45700)
cofactor: FAD (Binds 1 FAD per subunit.)
cofactor: [2Fe-2S] cluster (Binds 1 2Fe-2S cluster per subunit.)
subunit: The system is composed of an oxygenase subunit (GbcA) and a reductase subunit (GbcB).
disruption phenotype: Mutant is unable to grow on choline or glycine betaine as a sole carbon source, but it can grow on dimethylglycine (PubMed:17951379). The gbcA-gbcB double mutant cannot grow on choline or glycine betaine as a sole carbon or nitrogen source, but it can grow in minimal medium with glucose or pyruvate as the sole carbon source (PubMed:17951379). - function: Involved in degradation of glycine betaine (PubMed:17951379). Part of a Rieske-type oxygenase system that catalyzes the conversion of glycine betaine (GB) to dimethylglycine (DMG) (Probable). This subunit is the ferredoxin reductase component of the system (Probable). Required for growth on choline and GB, but not for growth on DMG (PubMed:17951379).
catalytic activity: glycine betaine + NADH + O2 + H(+) = N,N-dimethylglycine + formaldehyde + NAD(+) + H2O (RHEA:45700)
cofactor: FAD (Binds 1 FAD per subunit.)
cofactor: [2Fe-2S] cluster (Binds 1 2Fe-2S cluster per subunit.)
subunit: The system is composed of an oxygenase subunit (GbcA) and a reductase subunit (GbcB).
disruption phenotype: Deletion of gbcA and gbcB abrogates the ability to grow on glycine betaine as a sole carbon source. - A wide-ranging Pseudomonas aeruginosa PeptideAtlas build: A useful proteomic resource for a versatile pathogen
Reales-Calderón, Journal of proteomics 2021 - “...glycine betaine catabolism [CdhR (PA5389), DgcA (PA5398), GbcB (PA5411), SoxD (PA5417), and SoxA (PA5418)] were detected only in this sample. The generation of...”
- Glycine Betaine Monooxygenase, an Unusual Rieske-Type Oxygenase System, Catalyzes the Oxidative N-Demethylation of Glycine Betaine in Chromohalobacter salexigens DSM 3043
Shao, Applied and environmental microbiology 2018 - “...mutagenesis and gene disruption, the gbcA (PA5410) and gbcB (PA5411) genes were proven to be necessary for GB catabolism in P. aeruginosa (19), and their...”
- “...the two-gene cluster identified as gbcAB (PA5410 and PA5411) from P. aeruginosa PAO1 as the query sequences (19). Csal_1004 and Csal_1005 exhibited good...”
- Characterization of the GbdR regulon in Pseudomonas aeruginosa
Hampel, Journal of bacteriology 2014 - “...PA5379 PA5396 PA5397 PA5398 PA5399 PA5401 PA5402 PA5410 PA5411 PA5415 PA5416 PA5417 PA5418 PA5419 PA5420 PA5421 plcR plcH Hypothetical Hypothetical betX pchP...”
- Homeostasis and catabolism of choline and glycine betaine: lessons from Pseudomonas aeruginosa
Wargo, Applied and environmental microbiology 2013 - “...interesting that, while Diab et al. observed abundant GbcB (PA5411) protein in response to growth on GB, they did not detect GbcA (PA5410) (80). We showed that...”
- GbdR regulates Pseudomonas aeruginosa plcH and pchP transcription in response to choline catabolites
Wargo, Infection and immunity 2009 - “...gbdR deletion at the att site In-frame PA5410 and PA5411 deletions in PAO1 (43) In-frame PA5398 deletion in PAO1 (43) In-frame plcHR deletion in PAO1 (36) PAO1...”
- Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism
Wargo, Journal of bacteriology 2008 - “...with mutations in two genes, gbcA (PA5410) and gbcB (PA5411), were capable of growth on dimethylglycine (DMG), a catabolic product of GB, but not on GB itself....”
- “...In addition, the genomic region from PA5380 to PA5411 is organized in the same manner in both genomes. Deletion constructs for PA5380, PA5410-PA5411, PA3082,...”
- Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment
Wagner, Journal of bacteriology 2003 - “...PA4911 PA4912 PA4979 PA5059 PA5097 PA5181 PA5375 PA5411 PA5543 ig 1427453-1428080 ig 4713795-4713098 ig 5820909-5820113 b VOL. 185, 2003 MICROARRAY ANALYSIS...”
- Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism
Wargo, Journal of bacteriology 2008 - “...divergently transcribed genes, PA14_71410 (corresponding to PA5410) and PA14_71420 (corresponding to PA5411). The 10 mutants in class II were unable to grow on...”
BT1155 Na+-translocating NADH-quinone reductase subunit from Bacteroides thetaiotaomicron VPI-5482
36% identity, 12% coverage
Q91_2220 2Fe-2S iron-sulfur cluster-binding protein from Cycloclasticus sp. P1
34% identity, 18% coverage
- An Intracellular Sensing and Signal Transduction System That Regulates the Metabolism of Polycyclic Aromatic Hydrocarbons in Bacteria
Wang, mSystems 2021 - “...177 Nap FERP1 fer (Q91_2219) PAH dioxygenase component ferredoxin 104 Nap, Phe, Pyr FRRP1 ferR (Q91_2220) PAH dioxygenase component ferredoxin reductase 340 Nap, Phe, Pyr PETP1-1 perT1 (Q91_2242) Permease protein 302 Nap, Phe PETP1-2 perT2 (Q91_0869) Permease protein 534 Pyr REDP1 rcd (Q91_2224) Ring cleavage dioxygenase...”
- “...with the degradation pathways of naphthalene and phenanthrene. The first operon (genes Q91_2218, Q91_2218, and Q91_2220) encoded an isomerase, PAH dioxygenase ferredoxin, and ferredoxin reductase; this electron transduction chain is shared by all PAH degradation pathways ( 19 ). The second operon (genes Q91_2224 to Q91_2227)...”
- Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1
Wang, Applied and environmental microbiology 2018 (secret)
KZ686_09965 NADH:ubiquinone reductase (Na(+)-transporting) subunit F from Cupriavidus cauae
32% identity, 24% coverage
tomA5 / Q9ANX0 toluene ortho-monooxygenase TomA5 subunit (EC 1.14.13.243) from Burkholderia cepacia (see paper)
Q9ANX0 toluene 2-monooxygenase (subunit 5/6) (EC 1.14.13.243) from Burkholderia cepacia (see 8 papers)
32% identity, 24% coverage
CTLon_0109 Na(+)-translocating NADH-quinone reductase subunit F from Chlamydia trachomatis L2b/UCH-1/proctitis
41% identity, 11% coverage
CT740 Phenolhydrolase/NADH ubiquinone oxidoreductase from Chlamydia trachomatis D/UW-3/CX
41% identity, 11% coverage
PA14_25350 Na+-translocating NADH:quinone oxidoreductase, subunit 6 from Pseudomonas aeruginosa UCBPP-PA14
35% identity, 13% coverage
NP_251684 Na(+)-translocating NADH-quinone reductase subunit F from Pseudomonas aeruginosa PAO1
Q9HZL1 Na(+)-translocating NADH-quinone reductase subunit F from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA2994 Na(+)-translocating NADH-quinone reductase subunit F from Pseudomonas aeruginosa PAO1
35% identity, 13% coverage
- Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
Hu, Frontiers in microbiology 2024 - “...Na(+)-translocating NADH-quinone reductase subunit A PA2997 NP_251687 786 nqrC Na(+)-translocating NADH-quinone reductase subunit C PA2994 NP_251684 1,224 nqrF Na(+)-translocating NADH-quinone reductase subunit F PA4538 NP_253228 1,308 ndh ndh-2 NADH dehydrogenase PA1583 NP_250274 1773 sdhA sdh Succinate dehydrogenase flavoprotein subunit PA1584 NP_250275 708 sdhB Succinate dehydrogenase ironsulfur...”
- The Novel Monooxygenase Gene dipD in the dip Gene Cluster of Alcaligenes faecalis JQ135 Is Essential for the Initial Catabolism of Dipicolinic Acid
Mu, Applied and environmental microbiology 2022 (secret) - Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
Hu, Frontiers in microbiology 2024 - “...nqr Na(+)-translocating NADH-quinone reductase subunit A PA2997 NP_251687 786 nqrC Na(+)-translocating NADH-quinone reductase subunit C PA2994 NP_251684 1,224 nqrF Na(+)-translocating NADH-quinone reductase subunit F PA4538 NP_253228 1,308 ndh ndh-2 NADH dehydrogenase PA1583 NP_250274 1773 sdhA sdh Succinate dehydrogenase flavoprotein subunit PA1584 NP_250275 708 sdhB Succinate dehydrogenase...”
- Antimicrobial Activity of, and Cellular Pathways Targeted by, p-Anisaldehyde and Epigallocatechin Gallate in the Opportunistic Human Pathogen Pseudomonas aeruginosa
Adewunmi, Applied and environmental microbiology 2020 (secret) - Antibiotic Korormicin A Kills Bacteria by Producing Reactive Oxygen Species
Maynard, Journal of bacteriology 2019 - “...aeruginosa strains PAO1 Transposon deletion of PA2994 (nqrF) Genotype and/or characteristic(s) Reference or source 80dlacZM15 (lacZYA-argF)U169 recA1 endA1...”
- The Pseudomonas aeruginosa proteome during anaerobic growth
Wu, Journal of bacteriology 2005 - “...PA1919 PA1920 PA2119 PA2127 PA2323 PA2567 PA2945 PA2991 PA2994 PA2999* PA3002 PA3150 PA3185 PA3391 PA3392 PA3394 PA3438 PA3515 PA3562* PA3694 PA3871 PA3873...”
Q84AQ0 phenol 2-monooxygenase (NADH) (subunit 1/5) (EC 1.14.13.244) from Pseudomonas stutzeri (see paper)
40% identity, 13% coverage
phlF / CAA56745.1 subunit of phenolhydroxylase from Pseudomonas putida (see 2 papers)
28% identity, 23% coverage
Rmet_1326 NADH:ubiquinone reductase (Na(+)-transporting) subunit F from Cupriavidus metallidurans CH34
Rmet_1326 Oxidoreductase FAD-binding region from Ralstonia metallidurans CH34
31% identity, 24% coverage
WP_226348815 NADH:ubiquinone reductase (Na(+)-transporting) subunit F from Alcaligenes sp. 13f
38% identity, 13% coverage
TC0116 NADH:ubiquinone oxidoreductase, beta subunit, putative from Chlamydia muridarum Nigg
30% identity, 21% coverage
Dpo_16c00350 NADH:ubiquinone reductase (Na(+)-transporting) subunit F from Desulfotignum phosphitoxidans DSM 13687
40% identity, 12% coverage
pc1533 probable Na(+)-translocating NADH-quinone reductase, chain F from Parachlamydia sp. UWE25
29% identity, 24% coverage
WP_005800144 NADH:ubiquinone reductase (Na(+)-transporting) subunit F from Bacteroides fragilis str. 2-F-2 #4
33% identity, 13% coverage
- Proteomic analysis of metronidazole resistance in the human facultative pathogen Bacteroides fragilis
Paunkov, Frontiers in microbiology 2023 - “...Na(+)-translocating NADH-quinone reductase subunit C BF638R_RS10075 WP_005787203 +5.5 BF638R_2138 NADH:ubiquinone reductase (Na(+)-transporting) subunit F BF638R_RS10090 WP_005800144 +3.6 BF638R_2141 Pyruvate, phosphate dikinase BF638R_RS12250 WP_032595946 +2.1 BF638R_2565 Thirty-five proteins involved in protein synthesis, i.e., 31 ribosomal proteins, translation initiation factor IF-3, RluA family pseudouridine synthase, elongation factor G,...”
BF638R_2141, BF638R_RS10090 NADH:ubiquinone reductase (Na(+)-transporting) subunit F from Bacteroides fragilis 638R
33% identity, 13% coverage
- Proteomic analysis of metronidazole resistance in the human facultative pathogen Bacteroides fragilis
Paunkov, Frontiers in microbiology 2023 - “...reductase subunit C BF638R_RS10075 WP_005787203 +5.5 BF638R_2138 NADH:ubiquinone reductase (Na(+)-transporting) subunit F BF638R_RS10090 WP_005800144 +3.6 BF638R_2141 Pyruvate, phosphate dikinase BF638R_RS12250 WP_032595946 +2.1 BF638R_2565 Thirty-five proteins involved in protein synthesis, i.e., 31 ribosomal proteins, translation initiation factor IF-3, RluA family pseudouridine synthase, elongation factor G, and pseudouridine...”
- “...BF638R_2137 Na(+)-translocating NADH-quinone reductase subunit C BF638R_RS10075 WP_005787203 +5.5 BF638R_2138 NADH:ubiquinone reductase (Na(+)-transporting) subunit F BF638R_RS10090 WP_005800144 +3.6 BF638R_2141 Pyruvate, phosphate dikinase BF638R_RS12250 WP_032595946 +2.1 BF638R_2565 Thirty-five proteins involved in protein synthesis, i.e., 31 ribosomal proteins, translation initiation factor IF-3, RluA family pseudouridine synthase, elongation factor...”
PP0316, PP_0316 oxidoreductase, FAD-binding, putative from Pseudomonas putida KT2440
33% identity, 13% coverage
N8H69_24105 CDP-6-deoxy-delta-3,4-glucoseen reductase from Achromobacter spanius
39% identity, 13% coverage
Npun_R0380 ferredoxin (2Fe-2S) from Nostoc punctiforme
32% identity, 15% coverage
MCA2384 Na(+)-translocating NADH-quinone reductase subunit F from Methylococcus capsulatus str. Bath
33% identity, 13% coverage
- Metal(loid) speciation and transformation by aerobic methanotrophs
Karthikeyan, Microbiome 2021 - “...that only one homologue, a putative Na + -translocating NADH-quinone reductase subunit F (locus tag MCA2384 in Mc. capsulatus (Bath)), correlates with the ability to reduce chromium (VI) and so is a candidate for the chromium (VI)-reducing activity. This homologue is not found in any currently...”
dmpP / P19734 phenol hydroxylase reductase component (EC 1.14.13.244) from Pseudomonas sp. (strain CF600) (see 9 papers)
DMPP_PSEUF / P19734 Phenol 2-monooxygenase, reductase component DmpP; Phenol 2-monooxygenase P5 component; Phenol hydroxylase P5 protein; EC 1.14.13.244 from Pseudomonas sp. (strain CF600) (see 2 papers)
P19734 phenol 2-monooxygenase (NADH) (subunit 5/6) (EC 1.14.13.244) from Pseudomonas sp. CF600 (see paper)
dmpP phenol hydroxylase P5 protein; EC 1.14.13.7 from Pseudomonas sp. CF600 (see 2 papers)
dmpP / AAA25944.1 phenol hydroxylase from Pseudomonas putida (see paper)
36% identity, 13% coverage
- function: Part of a multicomponent enzyme which catalyzes the degradation of phenol and some of its methylated derivatives (PubMed:2254259). DmpP probably transfers electrons from NADH, via FAD and the iron-sulfur center, to the oxygenase component of the complex (PubMed:2254259). Required for growth on phenol and for in vitro phenol hydroxylase activity (PubMed:2254258, PubMed:2254259).
catalytic activity: phenol + NADH + O2 + H(+) = catechol + NAD(+) + H2O (RHEA:57952)
cofactor: FAD (Binds 1 FAD per subunit.)
cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit.)
subunit: The multicomponent enzyme phenol hydroxylase is formed by DmpL (P1 component), DmpM (P2 component), DmpN (P3 component), DmpO (P4 component) and DmpP (P5 component).
disruption phenotype: Cells lacking this gene cannot grow on phenol. - Purification and identification of trichloroethylene induced proteins from Stenotrophomonas maltophilia PM102 by immuno-affinity-chromatography and MALDI-TOF Mass spectrometry
Mukherjee, SpringerPlus 2013 - “...6.77 Propane monooxygenase from Rhodococcus sp . Q0SJK9 63222.42 5.56 Phenol hydroxylase from Pseudomonas sp. P19734 38477.58 4.79 Competing interests The authors declare that they have no competing interests regarding any of the research work reported in this paper. Authors contribution PM carried out the biochemical...”
- Proteogenomic elucidation of the initial steps in the benzene degradation pathway of a novel halophile, Arhodomonas sp. strain Rozel, isolated from a hypersaline environment
Dalvi, Applied and environmental microbiology 2012 - “...P19730 66 2e25 Q9RAF7 77 0 Q5KT19 56 4e35 O84962 64 3e161 P19734 44 3e15 A1K6K5 69 e129 Q1LNR9 50 8e139 Q2W7L9 48 4e49 A1K899 59 2e27 Q49KG4 70 0 G6YS35 a Shown...”
- “...component (P19732), and phenol 2-monooxygenase P5 component (P19734). October 2012 Volume 78 Number 20 aem.asm.org 7313 Downloaded from http://aem.asm.org/ on...”
- Epoxyalkane: coenzyme M transferase in the ethene and vinyl chloride biodegradation pathways of mycobacterium strain JS60
Coleman, Journal of bacteriology 2003 - “...41.8 P27353 BAA07115 DmpP Pseudomonas strain CF600 40.4 P19734 GctB CatJ CAA10043 Organism Incomplete ORF. (amoABCD) of Rhodococcus strain B-276. The sequence...”
- Duplicate copies of genes encoding methanesulfonate monooxygenase in Marinosulfonomonas methylotropha strain TR3 and detection of methanesulfonate utilizers in the environment
Baxter, Applied and environmental microbiology 2002 - “...42 42 Pseudomonas sp. strain CF600 P. putida P. putida P19734 Q52126 P23101 OrfX Cyc6 Cyc6 Cytochrome c6 Cytochrome c6 33 32 44 47 E. gracilis M. aeruginosa...”
D7KW69 Ferredoxin from Arabidopsis lyrata subsp. lyrata
34% identity, 15% coverage
YPK_3192 oxidoreductase FAD/NAD(P)-binding subunit from Yersinia pseudotuberculosis YPIII
YPO3116 cdp-6-deoxy-delta-3,4-glucoseen reductase from Yersinia pestis CO92
33% identity, 14% coverage
- Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
Mahmud, mSystems 2020 - “...GTGGCGCGTTATTTGCGT 10.5 28,24 YPK_3152 NA 80, 152 IrGS33 3491164 5.6 4.1 3.5 GTGGAACAGGTTTTGCAC 9.94 28,32,54,70 YPK_3192 YPK_3191 5, 10, 181 IrGS34 3558532 6.5 5.8 4.2 TTGGTACGTTACTTGCTC + 10.7 28,54,32,38,24 YPK_3253 NA 44, 73, 89, 95 IrGS35 3621908 4.7 5.0 4.4 CTGGCAAATTTTCTGAAA 9.43 54,32,28 YPK_3308 YPK_3307 2,...”
- Identification of MrtAB, an ABC transporter specifically required for Yersinia pseudotuberculosis to colonize the mesenteric lymph nodes
Crimmins, PLoS pathogens 2012 - “...( Table 1 ). Interpreting the phenotypes of mutations in the main O-Ag synthesis operon, YPK_3192 YPK_3177, is difficult based solely on our screen, because any of these transposon insertions could disrupt expression of neighboring genes in the operon. This operon encodes proteins that produce the...”
- Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis
Hinchliffe, Genome research 2003 - “...YPO3111 YPO3112 YPO3113 YPO3114 YPO3115 YPO3116 O-antigen chain length determinant (wzz) Phosphomannomutase (manB) Glycosyltransferase (wbyL)...”
- Application of high-density array-based signature-tagged mutagenesis to discover novel Yersinia virulence-associated genes
Karlyshev, Infection and immunity 2001 - “...sugar dehydratase YPO3114 (1D9), and ascarylose biosynthesis protein YPO3116 (3F3). These genes are also present in Y. pestis. Other genes related to...”
- “...pestis (%) YPO3657/8 (intergenic) YPO3834 YPO3965 YPO3572 YPO3116 YPO3144 YPO3100 YPO3104 YPO3114 YPO3099 YPO3004 YPO3099 YPO2532 YPO2712 YPO2440 YPO2287a...”
ascD / Q66DP5 CDP-6-deoxy-L-threo-D-glycero-4-hexulose-3-dehydrase reductase (EC 1.17.1.1) from Yersinia pseudotuberculosis serotype I (strain IP32953) (see paper)
TC 5.B.1.3.1 / Q66DP5 CDP-6-deoxy-delta-3,4-glucoseen reductase from Yersinia pseudotuberculosis serotype I (strain IP32953)
CH_006376 CDP-6-deoxy-L-threo-D-glycero-4-hexulose-3-dehydrase reductase from Yersinia pseudotuberculosis (see paper)
YPTB0998 cdp-6-deoxy-delta-3,4-glucoseen reductase from Yersinia pseudotuberculosis IP 32953
YPTB_RS05510 CDP-6-deoxy-delta-3,4-glucoseen reductase from Yersinia pseudotuberculosis IP 32953
33% identity, 14% coverage
- substrates: Electrons
- Genome-wide assessment of antimicrobial tolerance in Yersinia pseudotuberculosis under ciprofloxacin stress
Willcocks, Microbial genomics 2019 - “...livG ABC type branched-chain amino acid transport YPTB0263 rfaH Transcription antitermination protein YPTB0775 nlpD Lipoprotein YPTB0998 ddhD CDP-6-deoxy- l -threo- d -glycero-4-hexulose-3-dehydrase reductase YPTB1001 ddhC Putative CDP-4-keto-6-deoxy- d -glucose-3-dehydratase YPTB1002 prt Paratose synthase YPTB1003 wbyH Putative exported protein YPTB1004 wzx Putative O-unit flippase YPTB1005 YPTB1005 Uncharacterized...”
- Lipopolysaccharide Biosynthesis Genes of Yersinia pseudotuberculosis Promote Resistance to Antimicrobial Chemokines
Erickson, PloS one 2016 - “...YPTB0055 hldD ADP-L-glycero-D-manno-heptose-6-epimerase 67.6 1097 3 YPTB0263 rfaH transcriptional regulation of capsule/LPS 68.7 430 3 YPTB0998 ddhD CDP-6-deoxy-delta-3,4-glucoseen reductase 50.2 226 2 YPTB0999 ddhA glucose-1-phosphate cytidylyltransferase 43.5 327 1 YPTB1000 ddhB CDP-glucose 4,6-dehydratase 53.8 228 2 YPTB1001 ddhC putative CDP-4-keto-6-deoxy-D-glucose-3-dehydratase 45.5 700 1 YPTB1003 wbyH glycosyl...”
- “...predicted to be involved in O-polysaccharide synthesis ( Table 1 ), which are clustered between YPTB0998 and YPTB1014 in strain IP32953. This suggests that the absence of O-antigen in Y . pseudotuberculosis IP32953 (serotype O:1b) has a strong effect on its interaction with AMCs. Y ....”
- The Novel Monooxygenase Gene dipD in the dip Gene Cluster of Alcaligenes faecalis JQ135 Is Essential for the Initial Catabolism of Dipicolinic Acid.
Mu, Applied and environmental microbiology 2022 (no snippet) - Genomic Epidemiology and Phenotyping Reveal on-Farm Persistence and Cold Adaptation of Raw Milk Outbreak-Associated Yersinia pseudotuberculosis
Castro, Frontiers in microbiology 2019 - “...locus tag Functional role NS sites a References Virulence Stress response Biofilm/motility ST42 ST43 ascD YPTB_RS05510 0 1 Joshua et al., 2015 cckA YPTB_RS20595 1 0 Joshua et al., 2015 cheA YPTB_RS13085 0 5 Palonen et al., 2011 clsA YPTB_RS11560 0 2 Revel and Miller, 2001...”
Pden_4896 oxidoreductase FAD/NAD(P)-binding domain protein from Paracoccus denitrificans PD1222
32% identity, 12% coverage
APPSER1_RS05140 ISC system 2Fe-2S type ferredoxin from Actinobacillus pleuropneumoniae serovar 1 str. 4074
33% identity, 15% coverage
- Effects of OxyR regulator on oxidative stress, Apx toxin secretion and virulence of Actinobacillus pleuropneumoniae
Guo, Frontiers in cellular and infection microbiology 2023 - “...APPSER1_RS05915 -1.20739 thioredoxin-disulfide reductase APPSER1_RS00445 -1.15478 aspartate-semialdehyde dehydrogenase APPSER1_RS00025 -1.14156 ISC system 2Fe-2S type ferredoxin APPSER1_RS05140 -1.04767 deferrochelatase/peroxidase EfeB APPSER1_RS03575 -0.99253 Apx toxin activity RTX family hemolysin ApxIA APPSER1_RS07655 1.244011 RTX family hemolysin APPSER1_RS05270 1.035245 RTX-II toxin-activating lysine-acyltransferase ApxIIC APPSER1_RS05275 0.893181 Urea metabolic process urease accessory...”
A2SI47 Phenol hydrolase reductase from Methylibium petroleiphilum (strain ATCC BAA-1232 / LMG 22953 / PM1)
29% identity, 17% coverage
C6KUI9 Ferredoxin oxidoreductase from bacterium
29% identity, 25% coverage
PFLU4951 putative iron/sulphur-binding oxidoreductase from Pseudomonas fluorescens SBW25
38% identity, 16% coverage
N6YI82 Phenol 2-monooxygenase from Thauera sp. 63
33% identity, 13% coverage
FER2_ARATH / P16972 Ferredoxin-2, chloroplastic; AtFd2 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_176291 2Fe-2S ferredoxin-like superfamily protein from Arabidopsis thaliana
AT1G60950 FED A; 2 iron, 2 sulfur cluster binding / electron carrier/ iron-sulfur cluster binding from Arabidopsis thaliana
34% identity, 14% coverage
- function: Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions
cofactor: [2Fe-2S] cluster Note=Binds 1 [2Fe-2S] cluster
subunit: Interacts with PGRL1A and PGRL1B. - New In Vivo Approach to Broaden the Thioredoxin Family Interactome in Chloroplasts
Ancín, Antioxidants (Basel, Switzerland) 2022 - “...4 thylakoid m A0A140G1S8 Cytochrome f P56771 Cytochrome f 90 2 thylakoid m A0A1S3YVN4 Ferredoxin P16972 Ferredoxin-2 (Fd2) 65.7 4 stroma A0A1S4B5N2 Ferredoxin-thioredoxin reductase A0A1P8BDN6 Ferredoxin-thioredoxin reductase subunit A (Variable subunit) 2 46.5 stroma Q84QE8 Oxygen evolving complex 33 kDa photosystem II protein Q9S841 Oxygen-evolving enhancer...”
- Arabidopsis Iron Superoxide Dismutase FSD1 Protects Against Methyl Viologen-Induced Oxidative Stress in a Copper-Dependent Manner
Melicher, Frontiers in plant science 2022 - “...chloroplastic 0.557 0.493 0.483 O04090 Ferredoxin-1, chloroplastic 0.363 0.342 Q39161 Ferredoxinnitrite reductase, chloroplastic 0.542 0.541 P16972 Ferredoxin-2, chloroplastic 0.309 0.344 Q9C7Y4 Ferredoxin C 2, chloroplastic 0.38 PSII protein turnover O80860 ATP-dependent zinc metalloprotease FtsH 2, chloroplastic 0.568 Q39102 ATP-dependent zinc metalloprotease FtsH 1, chloroplastic 0.477 Note...”
- “...0.482 0.01 Q9STG9 Amidophosphoribosyltransferase 2, chloroplastic 0.392 0.423 0.478 Q39161 Ferredoxinnitrite reductase, chloroplastic 0.542 0.541 P16972 Ferredoxin-2, chloroplastic 0.309 0.344 Q84JT6 Peptide methionine sulfoxide reductase B9 0.348 P92980 5-adenylylsulfate reductase 3, chloroplastic 0.01 Q9FLI7 CDGSH iron-sulfur domain-containing protein NEET 1.728 1.694 O04090 Ferredoxin-1, chloroplastic 0.363 0.342...”
- Insights into the function of NADPH thioredoxin reductase C (NTRC) based on identification of NTRC-interacting proteins in vivo
González, Journal of experimental botany 2019 - “...0 P56767 AtCg00340 D1, PSI P700 chlorophyll a apoprotein PsaB C 2 12.89 2 (2) P16972 At1g60950 Ferredoxin-2 C 2 2.7 5 (5) x Q8L3U4 At5g36700 PGLP-1, Phosphoglycolate phosphatase 1, PGLP-1 C, Cyt 2 6.97 8 (5) Carbon metabolism: Calvin cycle, starch, glycolysis, OPP, and TCA...”
- Establishment of a pure culture of the hitherto uncultured unicellular cyanobacterium Aphanothece sacrum, and phylogenetic position of the organism
Fujishiro, Applied and environmental microbiology 2004 - “...(P11051); (M) Arabidopsis thaliana plastid (higher plant) (P16972) (the numbers in parentheses are amino acid sequence accession numbers). The underlined areas...”
- Structure of the bacterial plant-ferredoxin receptor FusA
Grinter, Nature communications 2016 - “...ferredoxin domain from pectocin M1 (PM1 fer ), and ferredoxin isoform 2 from Arabidopsis thaliana (NP_176291) (Fer ara ). Titration of purified FusA into 15 N-labelled Fer ara resulted in a decrease in the intensity of the 15 N heteronuclear single quantum correlation (HSQC) spectral peaks...”
- A deficiency in chloroplastic ferredoxin 2 facilitates effective photosynthetic capacity during long-term high light acclimation in Arabidopsis thaliana.
Liu, The Plant journal : for cell and molecular biology 2013 (PubMed)- GeneRIF: Fd2 deficiency enhances the recovery of photosynthetic efficiency following long-term high light treatment
- Electrostatic interaction of phytochromobilin synthase and ferredoxin for biosynthesis of phytochrome chromophore.
Chiu, The Journal of biological chemistry 2010 - GeneRIF: Study found that one of the six Arabidopsis Fds, AtFd2, was the preferred electron donor for HY2.
- LcMPK3 and LcMPK6 positively regulate fruitlet abscission in litchi
Wang, Molecular horticulture 2024 - “...Hypersensitive-induced response protein-like protein 1 AT5G62740 LITCHI022202 Hypersensitive-induced response protein-like protein 1 AT5G62740 LITCHI000429 Ferredoxin-1 AT1G60950 LITCHI000431 Multiple organellar RNA editing factor 1 AT4G20020 LITCHI001279 Glycine-rich RNA-binding protein GRP1A AT2G21660 LITCHI001819 Glycine-rich RNA-binding protein GRP1A AT2G21660 LITCHI001928 Fructose-bisphosphate aldolase 2 AT4G38970 LITCHI002792 Osmotin-like protein OSM34 AT4G11650...”
- Altering cold-regulated gene expression decouples the salicylic acid-growth trade-off in Arabidopsis
Ortega, The Plant cell 2024 - “...genes used in this study are: ACT2 (AT3G18780), COR6.6 (AT5G15970), COR15a (AT2G42540), COR15b (AT2G42530), FD (At1g60950), and Irp9 (CAB46570). RNA-seq data are available from the National Center for Biotechnology Information Sequence Read Archive under accession numbers PRJNA939115 and PRJNA942941. Supplementary Material koae210_Supplementary_Data Acknowledgments We thank Kate...”
- Ferredoxin C2 is required for chlorophyll biosynthesis and accumulation of photosynthetic antennae in Arabidopsis
Tournaire, Plant, cell & environment 2023 - “...In the model plant Arabidopsis thaliana (Arabidopsis), this function is mainly carried out by Fd2 (AT1G60950), which is the most abundant of the two typical photosynthetictype Fd isoforms in the leaves (around 90%95%) (Hanke et al., 2004 ; Voss et al., 2011 ). It has been...”
- A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress
Karami, PloS one 2023 - “...except for the light-harvesting complex photosystem II subunit 6 ( LHCB6 ; AT1G15820) and petF (AT1G60950) genes. These genes were up-regulated in C4 and down-regulated in C3 plants, as shown in Fig 5 . 10.1371/journal.pone.0287761.g005 Fig 5 Meta-DEGs related to the photosynthesis pathway and antenna proteins...”
- Large-scale top-down proteomics of the Arabidopsis thaliana leaf and chloroplast proteomes
Wang, Proteomics 2023 - “...[ 7 ]. Proteoform patterns of the two chloroplast ferredoxin isoforms (Ferredoxin-1; at1g10960, and Ferrredoxin-2; at1g60950) represent unusual cases ( Figure 4 , Table S3 ). Both proteins hold a predicted cTP cleavage site at residue 52 M-53A (the same residue and position in both isoforms)....”
- The Cluster Transfer Function of AtNEET Supports the Ferredoxin-Thioredoxin Network of Plant Cells
Zandalinas, Antioxidants (Basel, Switzerland) 2022 - “...on these electrons [ 53 ]. In Arabidopsis, four nuclear-encoded ferredoxins, namely, AtFd1 (AT1G10960), AtFd2 (AT1G60950), AtFd3 (AT2G27510), and AtFd4 (AT5G10000) exist. AtFd1 and AtFd2 are thought to be chloroplastic ferredoxins. AtFd1 may preferentially function in cyclic electron flow, while AtFd2 may participate in linear electron...”
- Transcriptome analysis provides new insights into plants responses under phosphate starvation in association with chilling stress
Gao, BMC plant biology 2022 - “...(At5g54470), BBX31 (At3g21890), RBCS (At5g38430), AGT1 (At2g13360), GOX1 (At3g14420), PSAH2 (At1g52230), HY2 (AT3G09150), FED A (At1g60950). Supplementary Information Additional file 1: Figure S1. Relative phosphate starvation and chilling stressinduced gene expression (as determined by qPCR) in 7-day-old seedlings of WTgrown on +P and -P media under...”
- The photosynthesis apparatus of European mistletoe (Viscum album)
Schröder, Plant physiology 2022 - “...2 ferredoxin AT1G32550 X VaGs24838; VaGs37132 ferredoxin 1 ferredoxin AT1G10960 VaGs33762 X ferredoxin 2 ferredoxin At1g60950 VaGs33666; VaGs34701; VaGs35670; VaGs36681 ferredoxin 3 ferredoxin AT2G27510 VaGs36222 ferredoxin 4 ferredoxin AT5G10000 ferredoxin-NADP+ OR FNR1 ferredoxin-NADP+ OR AT5G66190 X VaGs38832; VaGs38833 FNR2 ferredoxin-NADP+ OR AT1G20020 X VaGs36566 ; VaGs38836...”
- More
BMF77_01935 2Fe-2S iron-sulfur cluster-binding protein from Dolichospermum sp. UHCC 0315A
31% identity, 15% coverage
- Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
Teikari, Scientific reports 2019 - “...CpcG4 1,13 BMF77_00909 Cytochrome c oxidase subunit 2 1,05 BMF77_02997 Ferredoxin 1,89 BMF77_01997 Ferredoxin 1,38 BMF77_01935 Ferredoxin, heterocyst 1,57 BMF77_02996 Ferredoxin-3 1,79 BMF77_03623 Plastocyanin 1,25 Nitrogen cycle BMF77_04749 2-isopropylmalate synthase 1,21 BMF77_01994 Nitrogenase iron protein 2,00 BMF77_01967 Nitrogenase iron protein 1 1,98 BMF77_01966 Nitrogenase molybdenum-iron protein...”
BV82_0258 ISC system 2Fe-2S type ferredoxin from Pseudomonas donghuensis
34% identity, 13% coverage
P73_4416 hybrid-cluster NAD(P)-dependent oxidoreductase from Celeribacter indicus
31% identity, 14% coverage
- Genomic and metabolic analysis of fluoranthene degradation pathway in Celeribacter indicus P73T
Cao, Scientific reports 2015 - “...P73_1051, P73_2167, P73_2169, P73_2960, P73_3499, and P73_4762), and ferredoxin reductase (P73_0335, P73_0354, P73_0554, P73_1054, P73_2874, P73_4416, and P73_4758) were found in the P73 T genome. Because RHD subunit alpha plays a major role in determining substrate specificity, RHD alpha subunit has been used in phylogenetic analysis...”
4zhoA / P16972 The crystal structure of arabidopsis ferredoxin 2 with 2fe-2s cluster (see paper)
33% identity, 14% coverage
- Ligand: fe2/s2 (inorganic) cluster (4zhoA)
K8XRS6 Phenol hydrolase from Rhodococcus opacus M213
38% identity, 11% coverage
Bcep1808_3415 oxidoreductase FAD-binding subunit from Burkholderia vietnamiensis G4
29% identity, 14% coverage
FXO12_24280 ISC system 2Fe-2S type ferredoxin from Pseudomonas sp. J380
35% identity, 13% coverage
- A Novel Marine Pathogen Isolated from Wild Cunners (Tautogolabrus adspersus): Comparative Genomics and Transcriptome Profiling of Pseudomonas sp. Strain J380
Umasuthan, Microorganisms 2021 - “...of several genes encoding proteins related to iron-sulfur cluster (ISC), including hscA (FXO12_24275) and fdx (FXO12_24280), two other putative fdx -like genes (FXO12_11905, FXO12_19935) and cyaY (FXO12_19255) decreased under iron-limited conditions ( Figure 8 C and Table 4 ). Interactive analysis of GO terms and genes...”
- “...* 5301261..5301782 hscB Co-chaperone HscB 0.98 5.49 10 3 HscB maturation of iron-sulfur cluster-containing proteins FXO12_24280 5303700..5304041 fdx ISC system 2Fe-2S type ferredoxin 1.59 2.33 10 7 Fdx_isc Electron transfer agent FXO12_11905 2627651..2627974 Ferredoxin family protein 1.97 2.54 10 12 DUF3470 Electron transfer agent FXO12_19935 Complement...”
CRC_02876 2Fe-2S iron-sulfur cluster-binding protein from Cylindrospermopsis raciborskii CS-505
29% identity, 15% coverage
Slit_1671 ferredoxin from Sideroxydans lithotrophicus ES-1
32% identity, 14% coverage
B9Z02_RS19315 2Fe-2S iron-sulfur cluster-binding protein from Rhodococcus rhodochrous J3
31% identity, 14% coverage
BCAM2318 putative ferredoxin oxidoreductase protein from Burkholderia cenocepacia J2315
29% identity, 14% coverage
- Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species
Van, PloS one 2013 - “...CGCGGCCGTTTGCGTATTCA BCAM0970 Succinate dehydrogenase iron-sulfur subunit CCTCCAGTCGCCGGAAGAGC CACCAGAAGCTCGGGCACGA BCAM0965 Malate dehydrogenase CCGGTCGCGTCGATCGAGAA GCGAAGCGGAAGTCCGGGTA Other genes BCAM2318 Putative ferredoxin oxidoreductase TGAAGCTGATCGCGCCGGAT GCGCACCGCCTTCATGTACG Reference genes BCAL0036 ATP synthase beta chain CAAGACCGTCAACATGATGGA TCGAGTCCTTCATTTCGTGGTA BCAL0289 Glutamate synthase ATCATCCAGCAGGGTCTGAAGA GCCATTTCCTCGCGATAGAA BCAL0421 DNA gyrase B subunit GTTCCACTGCATCGCGACTT GGGCTTCGTCGAATTCATCA BCAL1459 Calcineurin-like phosphoesterase ATCCCTTGAAATCGAGCATCA...”
- “...S-transferase 3.4* BCAL0463 Putative thioredoxin 1.6* BCAL2013 AhpC/TSA family protein 1.9* BCAL2106 Glutathion peroxidase 1.6* BCAM2318 Putative ferredoxin oxidoreductase 10.0* 33.3* Fe-storage BCAM2627 Putative hemin ABC transporter protein 5.2* BCAM2630 Hemin importer ATP binding subunit 2.8* BCAM2224 Putative pyochelin receptor protein FptA 2.7* BCAL1790 Putative iron-transport...”
LOC103868066 ferredoxin-1, chloroplastic from Brassica rapa
33% identity, 14% coverage
LOC4344439 ferredoxin-1, chloroplastic from Oryza sativa Japonica Group
A2YQD9 Ferredoxin-1, chloroplastic from Oryza sativa subsp. indica
Q0J8M2 Ferredoxin-1, chloroplastic from Oryza sativa subsp. japonica
32% identity, 14% coverage
- Integrated transcriptome and metabolome analysis of salinity tolerance in response to foliar application of choline chloride in rice (Oryza sativa L.)
Huo, Frontiers in plant science 2024 - “...Os01g0938100), photosystem I subunit O ( OsPsaO , LOC4335799, Os04g0414700), ferredoxin 1 ( OsFd1 , LOC4344439, Os08g0104600), photosystem I reaction center subunit V ( OsPSAG , LOC4347395, Os09g0481200), photosystem I reaction center subunit N ( OspsaN , LOC4351694, Os12g0189400) and ferredoxin ( OsFd5 , LOC9270637, Os01g0860601)...”
- Identification of hub genes and key pathways in arsenic-treated rice (Oryza sativa L.) based on 9 topological analysis methods of CytoHubba
Yu, Environmental health and preventive medicine 2024 - “...2.68 1.01E-04 4350344 Os11g0306400 7.02 3.42E-05 Os.12296.1.S1_at LOC4333359 2.67 2.25E-05 4338119 Os05g0217800 6.85 9.85E-06 Os.1314.1.S1_at LOC4344439 2.53 1.85E-05 4349245 Os10g0537800 6.83 3.01E-06 Os.10959.1.S1_at LOC4352021 2.41 1.18E-06 4350388 Os11g0428800 6.77 1.60E-06 Up-regulated Up-regulated Os.9013.1.S1_at LOC4349181 5.09 1.95E-05 4345814 Os08g0473900 12.78 2.84E-07 Os.8178.1.S1_at LOC4350823 4.88 7.67E-05 4338883 Os05g0432200...”
- Physiological and proteomic characterization of manganese sensitivity and tolerance in rice (Oryza sativa) in comparison with barley (Hordeum vulgare)
Führs, Annals of botany 2010 - “...14.20 NP_001058899 40S ribosomal protein S12 33.10 A2YQD9 Ferredoxin-1, chloroplast precursor (Ferredoxin I) (anti-disease protein 1) 19.30 P56724 60S acidic...”
- Rice plants treated with biochar derived from Spirulina (Arthrospira platensis) optimize resource allocation towards seed production
Minello, Frontiers in plant science 2024 - “...1.29 Peptidylprolyl isomerase Q5Z4M6 9 0.04375 1.16 Photosynthesis/Carbon assimilation Carbonic anhydrase A0A0P0V5S4 2 Ferredoxin-1, chloroplastic Q0J8M2 3 0.04140 1.46 Photosynthesis Photosystem I iron-sulfur center P0C361 5 0.03461 1.22 Oxygen-evolving complex protein PsbP Q2QNI4 2 0.01038 0.64 Amino acid degradation Glycine cleavage system H protein, mitochondrial A3C6G9...”
- ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress
Qing, Breeding science 2022 - “...aspartyl protease family protein, expressed 10 25.34 0.44 Q2R8Z8 LOC_Os11g10470 Expressed protein 1 13.86 5.01 Q0J8M2 LOC_Os08g01380 Ferredoxin-1, chloroplastic 4 40.29 0.30 P41344 LOC_Os06g01850 FerredoxinNADP reductase, leaf isozyme 1, chloroplastic 30 56.08 1.58 Q6ZFJ3 LOC_Os02g01340 FerredoxinNADP reductase, leaf isozyme 2, chloroplastic 29 54.37 1.71 Q40677 LOC_Os11g07020...”
BPSS0555 putative ferredoxin oxidoreductase protein from Burkholderia pseudomallei K96243
28% identity, 14% coverage
P00228 Ferredoxin, chloroplastic from Triticum aestivum
31% identity, 15% coverage
- Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV
Ragupathy, Scientific reports 2016 - “...HP68 A7J2I2 Cluster: Plasma membrane intrinsic protein Q41539 Cluster: Endochitinase precursor Q9LKM4 Cluster: Cold-responsive protein P00228 Cluster: Ferredoxin; chloroplast precursor Q9S7U0 Cluster: Inositol-3-phosphate synthase miR156 8 7 Q9ATQ5 Cluster: LRK33 (ATP binding) Q0JGI1 Cluster: Squamosa promoter-binding-like protein 2 Q49I55 Cluster: Teosinte glume architecture 1 A6MD03 Cluster:...”
- Exploiting a wheat EST database to assess genetic diversity
Karakas, Genetics and molecular biology 2010 - “...protein, chloroplast precursor (LHCII type I CAB) (LHCP) P04784 Contig 17 100 ferredoxin, chloroplast precursor P00228 Contig 19 100 triosephosphate-isomerase CAC14917 Contig 21 196 putative glycine decarboxylase subunit AAM92707 Contig 22 281 eukaryotic translation initiation factor 5A1 AAZ95171 Contig 24 100 single-stranded nucleic acid binding protein...”
- “...CA598557 79 type 2 non-specific lipid transfer protein precursor CAH69201 CA598577 252 ferredoxin, chloroplast precursor P00228 CA598584 258 putative fructose 1-,6-biphosphate aldolase CAD12665 CA598630 101 translationally-controlled tumor protein homolog (TCTP) Q8LRM8 CA598637 100 histone H2A AAB00193 CA598672 100 lipid transfer protein ABB90546 CA598674 100 glutathione transferase...”
- Gene identification and expression analysis of 86,136 Expressed Sequence Tags (EST) from the rice genome
Zhou, Genomics, proteomics & bioinformatics 2003 - “...chloroplast rRNA-operon Unkown 0.10 6.34E-15 Contig13718 Contig13638 Contig12674 Oryza sativa mRNA for ferredoxin, complete cds (P00228) Ferredoxin, chloroplast precursor 9.24 3.57E-13 Contig13727 Contig12420 rsiced_10341.y1.abd rsiced_4570.y1.abd Hordeum vulgare chloroplast photosystem I PSK-I subunit mRNA, complete cds (P36886) Photosystem I reaction center subunit X, chloropla 8.56 1.00E-10 Contig27...”
Q76CS9 2Fe-2S ferredoxin from Pseudomonas putida
PP0847, PP_0847 ferredoxin, 2Fe-2S from Pseudomonas putida KT2440
34% identity, 14% coverage
3ah7A / Q76CS9 Crystal structure of the isc-like [2fe-2s] ferredoxin (fdxb) from pseudomonas putida jcm 20004
34% identity, 14% coverage
- Ligand: fe2/s2 (inorganic) cluster (3ah7A)
AFA2_03347 2Fe-2S iron-sulfur cluster-binding protein from Alcaligenes faecalis subsp. faecalis NBRC 13111
34% identity, 13% coverage
- Gene expression analysis of Alcaligenes faecalis during induction of heterotrophic nitrification
Tsujino, Scientific reports 2021 - “...AFA2_02843 Flagellin 3.67 9.34E05 639.6 8159.2 AFA2_03346 Aminobenzoate oxygenase/hydroxylamine oxidase DnfA 2.48 0.01329 3688.9 664.2 AFA2_03347 Ferredoxin DnfB 2.57 0.00909 2007.2 339.3 AFA2_03348 Glutamine amidotransferase DnfC 2.44 0.01566 2472.4 456.5 AFA2_03446 Phosphoadenosine phosphosulfate reductase 2.29 0.02805 240.3 1184.5 AFA2_03447 Sulfate adenylyltransferase subunit 2 2.69 0.00647 159.0...”
ndoR / Q52126 naphthalene 1,2-dioxygenase complex ferredoxin reductase component (EC 1.14.12.12) from Pseudomonas putida (see paper)
NDOR_PSEPU / Q52126 Naphthalene 1,2-dioxygenase system ferredoxin--NAD(P)(+), reductase component; Ferredoxin--NAD(P)(+) reductase (naphthalene dioxygenase ferredoxin-specific); EC 1.18.1.7 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see 3 papers)
Q52126 ferredoxin-NAD(P)+ reductase (naphthalene dioxygenase ferredoxin-specific) (EC 1.18.1.7) from Pseudomonas putida (see 2 papers)
nahAa / AAA25904.1 naphthalene 1,2-dioxygenase reductase component from Pseudomonas putida (see 3 papers)
23% identity, 22% coverage
- function: Component of the naphthalene dioxygenase (NDO) multicomponent enzyme system which catalyzes the incorporation of both atoms of molecular oxygen into naphthalene to form cis-(1R,2S)-dihydroxy-1,2- dihydronaphthalene (PubMed:10692370, PubMed:2294092, PubMed:7037744). Ferredoxin reductase catalyzes the transfer of electrons from NADH to ferredoxin (NdoA) (PubMed:2294092). NADPH is also effective but yields only 39% of the activity obtained with NADH (PubMed:2294092, PubMed:7037744). Also able to catalyze the cis-dihydroxylation of biphenyl and phenanthrene (PubMed:10692370).
catalytic activity: 2 reduced [2Fe-2S]-[ferredoxin] + NAD(+) + H(+) = 2 oxidized [2Fe-2S]-[ferredoxin] + NADH (RHEA:16521)
catalytic activity: 2 reduced [2Fe-2S]-[ferredoxin] + NADP(+) + H(+) = 2 oxidized [2Fe-2S]-[ferredoxin] + NADPH (RHEA:20125)
cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster.)
cofactor: FAD (Binds 1 mole of FAD per mole of enzyme. Also able to use FMN, but the activity is less than that obtained with FAD.)
subunit: The naphthalene dioxygenase (NDO) multicomponent enzyme system is composed of an electron transfer component and a dioxygenase component (iron sulfur protein (ISP)). The electron transfer component is composed of a ferredoxin reductase (NdoR) and a ferredoxin (NdoA), and the dioxygenase component is formed of a heterohexamer (trimer of heterodimers) of three large alpha subunits (NdoB) and three small beta subunits (NdoC). - Crystal structure of the ferredoxin reductase component of carbazole 1,9a-dioxygenase from Janthinobacterium sp. J3
Ashikawa, Acta crystallographica. Section D, Structural biology 2021 - “...cepacia (PDO-R; PDB entry 2pia ), naphthalene dioxygenase reductase from P. putida (NDO-R; UniProt entry Q52126) and the FNRferredoxin complex from maize leaf (FdxRed; PDB entry 1gaq ) was performed using PROMALS 3 D (Pei et al. , 2008 ). Secondary-structure assignments and the colour scheme...”
- Duplicate copies of genes encoding methanesulfonate monooxygenase in Marinosulfonomonas methylotropha strain TR3 and detection of methanesulfonate utilizers in the environment
Baxter, Applied and environmental microbiology 2002 - “...42 Pseudomonas sp. strain CF600 P. putida P. putida P19734 Q52126 P23101 OrfX Cyc6 Cyc6 Cytochrome c6 Cytochrome c6 33 32 44 47 E. gracilis M. aeruginosa P00119...”
SYNW1768 possible ferredoxin [2Fe-2S] from Synechococcus sp. WH 8102
35% identity, 13% coverage
dsoF / O32433 DMSO monooxygenase reductase component (EC 1.14.13.245) from Acinetobacter sp. (see 4 papers)
O32433 assimilatory dimethylsulfide S-monooxygenase (subunit 1/6) (EC 1.14.13.245) from Acinetobacter sp. (see 2 papers)
36% identity, 13% coverage
YPO1359 putative oxidoreductase from Yersinia pestis CO92
35% identity, 11% coverage
GBMOR_CHRSD / Q1QYU6 Glycine betaine monooxygenase reductase subunit; BMO reductase subunit; GB monooxygenase reductase subunit; BMO NADH-dependent flavine reductase component; EC 1.14.13.251 from Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11) (see paper)
Csal_1005 Oxidoreductase FAD-binding protein from Chromohalobacter salexigens DSM 3043
31% identity, 13% coverage
- function: Involved in degradation of glycine betaine (PubMed:29703733). Part of a Rieske-type oxygenase system that catalyzes the conversion of glycine betaine (GB) to dimethylglycine (DMG) (PubMed:29703733). This subunit is the ferredoxin reductase component of the system (PubMed:29703733). NADH is the preferred electron donor (PubMed:29703733).
catalytic activity: glycine betaine + NADH + O2 + H(+) = N,N-dimethylglycine + formaldehyde + NAD(+) + H2O (RHEA:45700)
cofactor: FAD (Binds 1 FAD per subunit (PubMed:29703733). FAD is the native cofactor, but activity is slightly higher with FMN (PubMed:29703733).)
cofactor: [2Fe-2S] cluster (Binds 1 2Fe-2S cluster per subunit.)
subunit: Monomer (PubMed:29703733). The system is composed of an oxygenase subunit (BmoA) and a reductase subunit (BmoB) (PubMed:29703733). Maximal specific activity is obtained when the ratio of BmoA to BmoB is 5:1 (PubMed:29703733).
disruption phenotype: Can use glucose or dimethylglycine as the sole carbon source, but is incapable of growth on glycine betaine as the sole source of carbon. - Role of N,N-Dimethylglycine and Its Catabolism to Sarcosine in Chromohalobacter salexigens DSM 3043
Yang, Applied and environmental microbiology 2020 (secret) - Glycine Betaine Monooxygenase, an Unusual Rieske-Type Oxygenase System, Catalyzes the Oxidative N-Demethylation of Glycine Betaine in Chromohalobacter salexigens DSM 3043
Shao, Applied and environmental microbiology 2018 - “...suggested that the open reading frames Csal_1004 and Csal_1005, designated bmoA and bmoB, respectively, may act as the terminal oxygenase and the ferredoxin...”
- “...as the query sequences (19). Csal_1004 and Csal_1005 exhibited good homology with PA5410 (66% identity/81% similarity) and PA5411 (76% identity/84% similarity),...”
Q938R2 Ferredoxin reductase from Pseudomonas fluorescens
21% identity, 22% coverage
Q52574 toluene 2-monooxygenase (subunit 1/6) (EC 1.14.13.243) from Pseudomonas sp. (see paper)
tbmF / AAA88461.1 oxidoreductase from Pseudomonas sp (see paper)
33% identity, 13% coverage
O04683 Ferredoxin-1, chloroplastic from Mesembryanthemum crystallinum
32% identity, 15% coverage
- Electron transport in acetate-grown Methanosarcina acetivorans.
Wang, BMC microbiology 2011 - “...sequence of the 2Fe-2S Spinacia oleracea ferredoxin was obtained from the NCBI database (accession number O04683). Panel A, Phylogenetic analysis of ferredoxins. The tree was constructed by the neighbor-joining method with the MEGA4 program [ 45 ]. Bootstrap values are shown at the nodes. Bar, evolutionary...”
1pfdA / Q7M1S1 The solution structure of high plant parsley [2fe-2s] ferredoxin, nmr, 18 structures (see paper)
31% identity, 14% coverage
- Ligand: fe2/s2 (inorganic) cluster (1pfdA)
VCA0924 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
36% identity, 11% coverage
BTH_II1860 iron-sulfur cluster-binding protein from Burkholderia thailandensis E264
29% identity, 14% 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