Protein Family Classification Based on Searching a Database of Blocks

Henikoff, Steven

doi:10.1006/geno.1994.1018

Cited by 351 publications

(209 citation statements)

References 41 publications

(56 reference statements)

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“…The Blocks search engine (http://blocks.fhcrc.org/blocks/blocks_search.html) [7] predicted that the new protein bears a single kringle domain (Supp. Figure 1: red box-signature NYCRNPD AA underlined in red) and a sequence towards the C-terminus with homology to the iSH2 domain of the regulatory subunit (p85 beta) of bovine PI3K (Supp.…”

Section: Resultsmentioning

confidence: 99%

PI3K is negatively regulated by PIK3IP1, a novel p110 interacting protein

Zhu¹,

He²,

Johnson³

et al. 2007

Biochemical and Biophysical Research Communications

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Signaling initiated by Class Ia phosphatidylinositol-3-kinases (PI3Ks) is essential for cell proliferation and survival. We discovered a novel protein we call PI3K Interacting Protein 1 (PIK3IP1) that shares homology with the p85 regulatory PI3K subunit. Using a variety of in vitro and cell based assays, we demonstrate that PIK3IP1 directly binds to the p110 catalytic subunit and modulates PI3K activity. Our studies suggest that PIK3IP1 is a new type of PI3K regulator.

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Section: Resultsmentioning

confidence: 99%

PI3K is negatively regulated by PIK3IP1, a novel p110 interacting protein

Zhu¹,

He²,

Johnson³

et al. 2007

Biochemical and Biophysical Research Communications

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“…In some instances, additional synthetic custom primers were necessary to obtain at least threefold coverage for each base. After proofreading with the XBAP program, the sequence analysis was performed on either a Sun workstation or Dec VAX computer with the programs contained within the GCG package (Genetics Computer Group, 1994), and the BLAST (Altshul et al, 1990), BEAUTY ᮊ 1998 Blackwell Science Ltd, Molecular Microbiology, 28, 37-53 (Worley et al, 1995) and BLOCKS (Henikoff and Henikoff, 1994) programs. The complete sequence of cosmid 36 from H. pylori strain NCTC11638 has been deposited in GenBank under accession no.…”

Section: Dna Sequencingmentioning

confidence: 99%

Analyses of the cag pathogenicity island of Helicobacter pylori

Akopyants¹,

Clifton²,

Kersulyte³

et al. 1998

Molecular Microbiology

674

331

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SummaryMost strains of Helicobacter pylori from patients with peptic ulcer disease or intestinal-type gastric cancer carry cagA, a gene that encodes an immunodominant protein of unknown function, whereas many of the strains from asymptomatically infected persons lack this gene. Recent studies showed that the cagA gene lies near the right end of a Ϸ37 kb DNA segment (a pathogenicity island, or PAI) that is unique to cagA þ strains and that the cag PAI was split in half by a transposable element insertion in the reference strain NCTC11638. In complementary experiments reported here, we also found the same cag PAI, and sequenced a 39 kb cosmid clone containing the left 'cagII' half of this PAI. Encoded in cagII were four proteins each with homology to four components of multiprotein complexes of Bordetella pertussis ('Ptl'), Agrobacterium tumefaciens ('Vir'), and conjugative plasmids ('Tra') that help deliver pertussis toxin and T (tumour inducing) and plasmid DNA, respectively, to target eukaryotic or prokaryotic cells, and also homologues of eukaryotic proteins that are involved in cytoskeletal structure. To the left of cagII in this cosmid were genes for homologues of HslU (heat-shock protein) and Era (essential GTPase); to the right of cagII were homologues of genes for a type I restriction endonuclease and ion transport functions. Deletion of the cag PAI had no effect on synthesis of the vacuolating cytotoxin, but this deletion and several cag insertion mutations blocked induction of synthesis of proinflammatory cytokine IL-8 in gastric epithelial cells. Comparisons among H. pylori strains indicated that cag PAI gene content and arrangement are rather well conserved. We also identified two genome rearrangements with end-points in the cag PAI. One, in reference strain NCTC11638, involved IS605, a recently described transposable element (as also found by others). Another rearrangement, in 3 of 10 strains tested (including type strain NCTC11637), separated the normally adjacent cagA and picA genes and did not involve IS605. Our results are discussed in terms of how cagencoded proteins might help trigger the damaging inflammatory responses in the gastric epithelium and possible contributions of DNA rearrangements to genome evolution.

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“…All sequences were analyzed for openreading frame (ORF) by computer analysis using GeneWorks version 2.4 (IntelliGenetics, Mountain View, CA) and were compared at the NCBI server to known sequences with the BLAST and FASTA algorithms [18,19]. Protein motif analysis and prediction of protein features were performed via the EMBL-Heidelberg world-wide web service by different computer analysis programs [20][21][22][23][24][25][26].…”

Section: Sequence Analysismentioning

confidence: 99%