Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family (Q24649588)

2

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Shmuel Pietrokovski

object named as

Shmuel Pietrokovski

5

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author name string

Bareket Dassa

1

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Barry L Stoddard

I-TASSER server for protein 3D structure prediction

3

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language of work or name

English

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publication date

May 2009

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published in

Nucleic Acids Research

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volume

37

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issue

8

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page(s)

2560-73

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cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

MEME: discovering and analyzing DNA and protein sequence motifs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

A self-splicing group I intron in DNA polymerase genes of T7-like bacteriophages

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

The Phage Proteomic Tree: a genome-based taxonomy for phage

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Structure-based Protocol for Identifying Mutations that Enhance Protein–Protein Binding Affinities

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

CAP3: A DNA sequence assembly program

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

The natural history of group I introns

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

DNA binding and cleavage by the HNH homing endonuclease I-HmuI

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Gene families: the taxonomy of protein paralogs and chimeras

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Detecting protein function and protein-protein interactions from genome sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Macromolecular modeling with rosetta

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Cis- and trans-splicing of group II introns in plant mitochondria

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Comparative genomics of Bacillus thuringiensis phage 0305phi8-36: defining patterns of descent in a novel ancient phage lineage.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Insertion of a homing endonuclease creates a genes-in-pieces ribonucleotide reductase that retains function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Occurrence of protein structure elements in conserved sequence regions.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Plasticity of the gene functions for DNA replication in the T4-like phages

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Genetic diversity among five T4-like bacteriophages

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Homing endonuclease structure and function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Selecton: a server for detecting evolutionary forces at a single amino-acid site

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

DIALIGN: multiple DNA and protein sequence alignment at BiBiServ

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Protein splicing and auto-cleavage of bacterial intein-like domains lacking a C'-flanking nucleophilic residue

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Group I self-splicing intron in the recA gene of Bacillus anthracis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Intein spread and extinction in evolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Protein-splicing intein: Genetic mobility, origin, and evolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Protein splicing and related forms of protein autoprocessing

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Coupling of open reading frames by translational bypassing

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Isolation and characterization of a split B-type DNA polymerase from the archaeon Methanobacterium thermoautotrophicum deltaH.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Protein trans-splicing by a split intein encoded in a split DnaE gene of Synechocystis sp. PCC6803

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Protein splicing in trans by purified N- and C-terminal fragments of the Mycobacterium tuberculosis RecA intein

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

28 September 2017

Non-canonical inteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Group I and group II introns

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Protein splicing elements: inteins and exteins--a definition of terms and recommended nomenclature

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Evolution of mobile group I introns: recognition of intron sequences by an intron-encoded endonuclease

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Regulation of a bacteriophage T4 late gene, soc, which maps in an early region

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Translational regulation of expression of the bacteriophage T4 lysozyme gene

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

DNA polymerase III gene of Bacillus subtilis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Construction of a small-molecule-integrated semisynthetic split intein for in vivo protein ligation.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Multiple controls regulate the expression of mobE, an HNH homing endonuclease gene embedded within a ribonucleotide reductase gene of phage Aeh1

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Control of protein splicing by intein fragment reassembly.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

Automated construction and graphical presentation of protein blocks from unaligned sequences.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866

New type of polyubiquitin-like genes with intein-like autoprocessing domains.

30 May 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP095

Distribution of split DnaE inteins in cyanobacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP095

Synthetic two-piece and three-piece split inteins for protein trans-splicing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP095

Trans protein splicing of cyanobacterial split inteins in endogenous and exogenous combinations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP095

Protein trans-splicing and characterization of a split family B-type DNA polymerase from the hyperthermophilic archaeal parasite Nanoarchaeum equitans.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP095

Modular organization of inteins and C-terminal autocatalytic domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP095

Genes within genes: independent expression of phage T4 intron open reading frames and the genes in which they reside

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP095

A novel group I intron-encoded endonuclease specific for the anticodon region of tRNA(fMet) genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP095

Dual recognition–incision enzymes might be involved in mismatch repair and meiosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP095

Diversity of structure and function of DNA polymerase (gp43) of T4-related bacteriophages

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2677866