HMMER web server: 2018 update

Potter, Simon; Luciani, Aurélien; Eddy, Sean R.; Park, Young Mi; López, Rodrigo; Finn, Robert D.

doi:10.1093/nar/gky448

Cited by 1,643 publications

(1,387 citation statements)

References 20 publications

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“…YSD1 was a useful model to identify and determine the candidate structural proteins that comprise the architectural features in the tail tube, tail spike and curling tail fibre for the Chi‐like family. Table documents outcomes from analyses with BLASTp (https://blast.ncbi.nlm.nih.gov/Blast.cgi), HMMer [(Finn et al , ; Potter et al , ); https://www.ebi.ac.uk/Tools/hmmer/], HHpred [(Zimmermann et al , ); https://toolkit.tuebingen.mpg.de/#/tools/hhpred] and Phyre2 [(Kelley et al , ); http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index] searching for domains generally characteristic of phage tail proteins, with candidates: YSD1_22, YSD1_25 and YSD1_29, and also putative tail assembly chaperones (YSD1_21, YSD1_23, YSD1_26, YSD1_27 and YSD1_28), as well as a tape measure protein (YSD1_24). When assessed by SDS‐PAGE, the protein profile for the virions of YSD1 showed two highly‐abundant proteins (the putative major capsid and tail proteins) present in hundreds of copies per virion, in addition to other proteins present at reduced stoichiometry (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…YSD1 was a useful model to identify and determine the candidate structural proteins that comprise the architectural features in the tail tube, tail spike and curling tail fibre for the Chi-like family. (Finn et al, 2011;Potter et al, 2018); https :// www.ebi.ac.uk/Tools/ hmmer/ ], HHpred [(Zimmermann et al, 2018); https ://toolk it.tuebi ngen.mpg.de/#/tools/ hhpred] and Phyre2 [(Kelley et al, 2015); http://www.sbg. bio.ic.ac.uk/phyre 2/html/page.cgi?id=index ] searching for domains generally characteristic of phage tail proteins, with candidates: YSD1_22, YSD1_25 and YSD1_29, and also putative tail assembly chaperones (YSD1_21, YSD1_23, YSD1_26, YSD1_27 and YSD1_28), as well as a tape measure protein (YSD1_24).…”

Section: Architecture Of Proteins In the Tail Structure Of Ysd1mentioning

confidence: 99%

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The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi‐like protein tail fibre

Dunstan

Pickard

Dougan

et al. 2019

Molecular Microbiology

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Summary The discovery of a Salmonella‐targeting phage from the waterways of the United Kingdom provided an opportunity to address the mechanism by which Chi‐like bacteriophage (phage) engages with bacterial flagellae. The long tail fibre seen on Chi‐like phages has been proposed to assist the phage particle in docking to a host cell flagellum, but the identity of the protein that generates this fibre was unknown. We present the results from genome sequencing of this phage, YSD1, confirming its close relationship to the original Chi phage and suggesting candidate proteins to form the tail structure. Immunogold labelling in electron micrographs revealed that YSD1_22 forms the main shaft of the tail tube, while YSD1_25 forms the distal part contributing to the tail spike complex. The long curling tail fibre is formed by the protein YSD1_29, and treatment of phage with the antibodies that bind YSD1_29 inhibits phage infection of Salmonella. The host range for YSD1 across Salmonella serovars is broad, but not comprehensive, being limited by antigenic features of the flagellin subunits that make up the Salmonella flagellum, with which YSD1_29 engages to initiate infection.

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Section: Resultsmentioning

confidence: 99%

“…YSD1 was a useful model to identify and determine the candidate structural proteins that comprise the architectural features in the tail tube, tail spike and curling tail fibre for the Chi-like family. (Finn et al, 2011;Potter et al, 2018); https :// www.ebi.ac.uk/Tools/ hmmer/ ], HHpred [(Zimmermann et al, 2018); https ://toolk it.tuebi ngen.mpg.de/#/tools/ hhpred] and Phyre2 [(Kelley et al, 2015); http://www.sbg. bio.ic.ac.uk/phyre 2/html/page.cgi?id=index ] searching for domains generally characteristic of phage tail proteins, with candidates: YSD1_22, YSD1_25 and YSD1_29, and also putative tail assembly chaperones (YSD1_21, YSD1_23, YSD1_26, YSD1_27 and YSD1_28), as well as a tape measure protein (YSD1_24).…”

Section: Architecture Of Proteins In the Tail Structure Of Ysd1mentioning

confidence: 99%

The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi‐like protein tail fibre

Dunstan

Pickard

Dougan

et al. 2019

Molecular Microbiology

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“…Based on microbial rhodopsin sequences (Supporting Information Table S1) previously reported (Pushkarev et al, 2018) we created a graftM (Boyd et al, 2018) gene classification package to identify and classify proteins into rhodopsins or heliorhodopsins. GraftM is a tool for fast and accurate phylogenetically informed classification of genes, which employs hidden Markov Models (HMM) (Boyd et al, 2018;Potter et al, 2018). Using the graftM, we scanned a nonredundant collection of all the ORFs from the Tara Oceans microbiome and virome as well as ORFs from freshwater metagenomic datasets (Supporting Information Table S6) to identify putative rhodopsins.…”

Section: Resultsmentioning

confidence: 99%

Heliorhodopsins are absent in diderm (Gram‐negative) bacteria: Some thoughts and possible implications for activity

Flores‐Uribe

Hevroni

Ghai

et al. 2019

Environ Microbiol Rep

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Summary Microbial heliorhodopsins are a new type of rhodopsins, currently believed to engage in light sensing, with an opposite membrane topology compared to type‐1 and type‐2 rhodopsins. We determined heliorhodopsins presence/absence is monoderms and diderms representatives from the Tara Oceans and freshwater metagenomes as well as metagenome assembled genome collections. Heliorhodopsins are absent in diderms, confirming our previous observations in cultured Proteobacteria. We do not rule out the possibility that heliorhodopsins serve as light sensors. However, this does not easily explain their absence from diderms. Based on these observations, we speculate on the putative role of heliorhodopsins in light‐driven transport of amphiphilic molecules.

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“…[132] using jackhammer [133] until convergence with an e-value cut-off of 0.01 for sequence and 0.03 for hits. Full length protein sequences from representative species were chosen and aligned using hmmalign [133] and alignancer, trimmed using trimAL [134] with the automated1 flag, and a phylogenetic tree was made using raxml [135] (options -f a -x 12345 -p 12345 -N autoMRE -m PROTGAMMAJTTF). Matching sequences were found exclusively in species within the Kinetoplastida class.…”

Section: Cell Cycle Analysismentioning

confidence: 99%

Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes

et al. 2020

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Base J, β-D-glucosyl-hydroxymethyluracil, is a modification of thymine DNA base involved in RNA Polymerase (Pol) II transcription termination in kinetoplastid protozoa. Little is understood regarding how specific thymine residues are targeted for J-modification or the mechanism of J regulated transcription termination. To identify proteins involved in J-synthesis, we expressed a tagged version of the J-glucosyltransferase (JGT) in Leishmania tarentolae, and identified four co-purified proteins by mass spectrometry: protein phosphatase (PP1), a homolog of Wdr82, a potential PP1 regulatory protein (PNUTS) and a protein containing a J-DNA binding domain (named JBP3). Gel shift studies indicate JBP3 is a J-DNA binding protein. Reciprocal tagging, co-IP and sucrose gradient analyses indicate PP1, JGT, JBP3, Wdr82 and PNUTS form a multimeric complex in kinetoplastids, similar to the mammalian PTW/PP1 complex involved in transcription termination via PP1 mediated dephosphorylation of Pol II. Using RNAi and analysis of Pol II termination by RNA-seq and RT-PCR, we demonstrate that ablation of PNUTS, JBP3 and Wdr82 lead to defects in Pol II termination at the 3'-end of polycistronic gene arrays in Trypanosoma brucei. Mutants also contain increased antisense RNA levels upstream of transcription start sites, suggesting an additional role of the complex in regulating termination of bi-directional transcription. In addition, PNUTS loss causes derepression of silent Variant Surface Glycoprotein genes involved in host immune evasion. Our results suggest a novel mechanistic link between base J and Pol II polycistronic transcription termination in kinetoplastids. Author summaryTrypanosoma brucei is a parasitic protozoan that causes African sleeping sickness in humans. The genome of T. brucei is organized into polycistronic gene clusters that contain multiple genes that are co-transcribed from a single promoter. We have recently described the presence of a modified DNA base J and variant of histone H3 (H3.V) at transcription termination sites within gene clusters where the loss of base J and H3.V leads to read-through transcription and the expression of downstream genes. We now PLOS Genetics | https://doi.identify a novel stable multimeric complex containing a J binding protein (JBP3), base J glucosyltransferase (JGT), PP1 phosphatase, PP1 interactive-regulatory protein (PNUTS) and Wdr82, which we refer to as PJW/PP1. A similar complex (PTW/PP1) has been shown to be involved in Pol II termination in humans and yeast. We demonstrate that PNUTS, JBP3 and Wdr82 mutants lead to read-through transcription in T. brucei. Our data suggest the PJW/PP1 complex regulates termination by recruitment to termination sites via JBP3-base J interactions and dephosphorylation of specific proteins (including Pol II and termination factors) by PP1. These findings significantly expand our understanding of mechanisms underlying transcription termination in eukaryotes, including organisms that utilize polycistronic transcription and novel epigenetic marks...

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HMMER web server: 2018 update

Cited by 1,643 publications

References 20 publications

The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi‐like protein tail fibre

The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi‐like protein tail fibre

Heliorhodopsins are absent in diderm (Gram‐negative) bacteria: Some thoughts and possible implications for activity

Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes

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