Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T )

Cliff Han, Stefan Spring, Alla Lapidus, Tijana Glavina Del Rio, Hope Tice, Alex Copeland, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia C. Jeffries, Elizabeth Saunders, Olga Chertkov, Thomas Brettin, Markus Göker, Manfred Rohde, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and John C. Detter

[1]  E. Korn,et al.  The degradation of heparin by bacterial enzymes. I. Adaptation and lyophilized cells. , 1956, The Journal of biological chemistry.

[2]  R. Langer,et al.  Heparinase production by Flavobacterium heparinum , 1981, Applied and environmental microbiology.

[3]  W. de Boer,et al.  In vitro suppression of fungi caused by combinations of apparently non-antagonistic soil bacteria. , 2007, FEMS microbiology ecology.

[4]  Christopher J. Lee,et al.  Multiple sequence alignment using partial order graphs , 2002, Bioinform..

[5]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[6]  L. Ten,et al.  Pedobacter panaciterrae sp. nov., isolated from soil in South Korea. , 2007, International journal of systematic and evolutionary microbiology.

[7]  A. Tocilj,et al.  Crystal Structure of Heparinase II from Pedobacter heparinus and Its Complex with a Disaccharide Product* , 2006, Journal of Biological Chemistry.

[8]  A. Matte,et al.  Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 A resolution. , 1999, Journal of molecular biology.

[9]  P. Christensen Description and Taxonomic Status of Cytophaga heparina (Payza and Korn) comb. nov. (Basionym: Flavobacterium heparinum Payza and Korn 1956) , 1980 .

[10]  Patrick Chain,et al.  Finishing Repetitive Regions Automatically with Dupfinisher , 2006, BIOCOMP.

[11]  C. Dietrich,et al.  Sequential degradation of heparin in Flavobacterium heparinum. Purification and properties of five enzymes involved in heparin degradation. , 1973, The Journal of biological chemistry.

[12]  A. Konopka,et al.  Effect of Nutrient Periodicity on Microbial Community Dynamics , 2006, Applied and Environmental Microbiology.

[13]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[14]  Nikos Kyrpides,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[15]  K. Kersters,et al.  Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. , 1998, International journal of systematic bacteriology.

[16]  A. Yokota,et al.  Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., sphingobacterium thalpophilum comb. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum. , 1992 .

[17]  James R. Cole,et al.  Taxonomic Outline of the Bacteria and Archaea: Formerly the Taxonomic Outline of the Prokaryotes , 2007 .

[18]  H. Su,et al.  Expression System for High Levels of GAG Lyase Gene Expression and Study of the hepA Upstream Region in Flavobacterium heparinum , 2002, Journal of bacteriology.

[19]  Chris F. Taylor,et al.  The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.

[20]  J. Rougemont,et al.  A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.