High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India
Abstract
Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1T along with its complete genome sequence and annotation from a culture of DSM 17521T. In conclusion, the 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50 RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I project.
- Authors:
-
- DOE Joint Genome Institute, Walnut Creek, CA (United States)
- St. Petersburg State Univ., St. Petersburg (Russia); St. Petersburg Academic Univ., St. Petersburg (Russia)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
- DOE Joint Genome Institute, Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1256480
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; aerobic; gram-negative; non-motile; obligate aerobe; halotolerant; menaquinone; GEBA; KMG-I
Citation Formats
Mukherjee, Supratim, Lapidus, Alla, Shapiro, Nicole, Cheng, Jan -Fang, Han, James, Reddy, T. B. K., Huntemann, Marcel, Ivanova, Natalia, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Spring, Stefan, Goker, Markus, Markowitz, Victor, Woyke, Tanja, Tindall, Brian J., Klenk, Hans -Peter, Kyrpides, Nikos C., and Pati, Amrita. High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India. United States: N. p., 2015.
Web. doi:10.1186/1944-3277-10-8.
Mukherjee, Supratim, Lapidus, Alla, Shapiro, Nicole, Cheng, Jan -Fang, Han, James, Reddy, T. B. K., Huntemann, Marcel, Ivanova, Natalia, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Spring, Stefan, Goker, Markus, Markowitz, Victor, Woyke, Tanja, Tindall, Brian J., Klenk, Hans -Peter, Kyrpides, Nikos C., & Pati, Amrita. High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India. United States. https://doi.org/10.1186/1944-3277-10-8
Mukherjee, Supratim, Lapidus, Alla, Shapiro, Nicole, Cheng, Jan -Fang, Han, James, Reddy, T. B. K., Huntemann, Marcel, Ivanova, Natalia, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Spring, Stefan, Goker, Markus, Markowitz, Victor, Woyke, Tanja, Tindall, Brian J., Klenk, Hans -Peter, Kyrpides, Nikos C., and Pati, Amrita. 2015.
"High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India". United States. https://doi.org/10.1186/1944-3277-10-8. https://www.osti.gov/servlets/purl/1256480.
@article{osti_1256480,
title = {High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India},
author = {Mukherjee, Supratim and Lapidus, Alla and Shapiro, Nicole and Cheng, Jan -Fang and Han, James and Reddy, T. B. K. and Huntemann, Marcel and Ivanova, Natalia and Mikhailova, Natalia and Chen, Amy and Palaniappan, Krishna and Spring, Stefan and Goker, Markus and Markowitz, Victor and Woyke, Tanja and Tindall, Brian J. and Klenk, Hans -Peter and Kyrpides, Nikos C. and Pati, Amrita},
abstractNote = {Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1T along with its complete genome sequence and annotation from a culture of DSM 17521T. In conclusion, the 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50 RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I project.},
doi = {10.1186/1944-3277-10-8},
url = {https://www.osti.gov/biblio/1256480},
journal = {Standards in Genomic Sciences},
issn = {1944-3277},
number = 1,
volume = 10,
place = {United States},
year = {Mon Feb 09 00:00:00 EST 2015},
month = {Mon Feb 09 00:00:00 EST 2015}
}
Web of Science
Works referenced in this record:
Improved Prediction of Signal Peptides: SignalP 3.0
journal, July 2004
- Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009
- Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
- Standards in Genomic Sciences, Vol. 1, Issue 1
Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family 'Flexibacteraceae'
journal, July 2006
- Suresh, K.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 7
Multidrug-resistance efflux pumps ? not just for resistance
journal, August 2006
- Piddock, Laura J. V.
- Nature Reviews Microbiology, Vol. 4, Issue 8
Pseudomonas indica sp. nov., a novel butane-utilizing species
journal, September 2002
- Pandey, K. K.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 52, Issue 5
Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation: Context-Guided Identification of Novel Cellulases
journal, May 2014
- Piao, Hailan; Froula, Jeff; Du, Changbin
- Biotechnology and Bioengineering, Vol. 111, Issue 8
The DNA Bank Network: The Start from a German Initiative
journal, March 2011
- Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger
- Biopreservation and Biobanking, Vol. 9, Issue 1
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006
- DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
- Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
A new isochorismate synthase specifically involved in menaquinone (vitamin K2) biosynthesis encoded by the menF gene
journal, July 1996
- Daruwala, R.; Kwon, O.; Meganathan, R.
- FEMS Microbiology Letters, Vol. 140, Issue 2-3
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
journal, April 2007
- Lagesen, Karin; Hallin, Peter; Rødland, Einar Andreas
- Nucleic Acids Research, Vol. 35, Issue 9
Recruitment of a Foreign Quinone into the A 1 Site of Photosystem I : I. GENETIC AND PHYSIOLOGICAL CHARACTERIZATION OF PHYLLOQUINONE BIOSYNTHETIC PATHWAY MUTANTS IN
journal, March 2000
- Johnson, T. Wade; Shen, Gaozhong; Zybailov, Boris
- Journal of Biological Chemistry, Vol. 275, Issue 12
Pontibacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil
journal, September 2013
- Singh, A. K.; Garg, N.; Lata, P.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 1
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010
- Gnerre, S.; MacCallum, I.; Przybylski, D.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea
journal, December 2005
- Mongodin, E. F.; Nelson, K. E.; Daugherty, S.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 50
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
Pontibacter akesuensis sp. nov., isolated from a desert soil in China
journal, February 2007
- Zhou, Y.; Wang, X.; Liu, H.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 2
Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum 'Bacteroidetes', and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003
journal, November 2005
- Nedashkovskaya, O. I.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 6
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990
- Woese, C. R.; Kandler, O.; Wheelis, M. L.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997
- Lowe, Todd M.; Eddy, Sean R.
- Nucleic Acids Research, Vol. 25, Issue 5
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
journal, December 2013
- Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A.
- Standards in Genomic Sciences, Vol. 9, Issue 3
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
Menaquinone (vitamin K2) biosynthesis: nucleotide sequence and expression of the menB gene from Escherichia coli.
journal, January 1992
- Sharma, V.; Suvarna, K.; Meganathan, R.
- Journal of Bacteriology, Vol. 174, Issue 15
Rfam: an RNA family database
journal, January 2003
- Griffiths-Jones, S.
- Nucleic Acids Research, Vol. 31, Issue 1
Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export
journal, June 2000
- Koronakis, Vassilis; Sharff, Andrew; Koronakis, Eva
- Nature, Vol. 405, Issue 6789
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
journal, June 2007
- Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah
- BMC Bioinformatics, Vol. 8, Issue 1
Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects
journal, May 2013
- Göker, Markus; Klenk, Hans-Peter
- Standards in Genomic Sciences, Vol. 8, Issue 2
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
journal, June 2007
- Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah
- BMC Bioinformatics, Vol. 8, Issue 1
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
journal, May 2011
- Tamura, K.; Peterson, D.; Peterson, N.
- Molecular Biology and Evolution, Vol. 28, Issue 10
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
journal, January 2001
- Krogh, Anders; Larsson, Björn; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 305, Issue 3
Menaquinone (vitamin K2) biosynthesis: cloning, nucleotide sequence, and expression of the menC gene from Escherichia coli
journal, August 1993
- Sharma, V.; Meganathan, R.; Hudspeth, M. E.
- Journal of Bacteriology, Vol. 175, Issue 15
Structural organization of a Bacillus subtilis operon encoding menaquinone biosynthetic enzymes
journal, December 1995
- Rowland, Belinda; Hill, Kevin; Miller, Paul
- Gene, Vol. 167, Issue 1-2
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997
- Lowe, Todd M.; Eddy, Sean R.
- Nucleic Acids Research, Vol. 25, Issue 5
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
journal, December 2011
- Pagani, I.; Liolios, K.; Jansson, J.
- Nucleic Acids Research, Vol. 40, Issue D1
Roseococcus pinisoli sp. nov., lacking pufL and pufM bacteriochlorophyll a: synthesizing genes
journal, May 2022
- Shen, Lei; An, Miao-miao; Liang, Rui-na
- Archives of Microbiology, Vol. 204, Issue 6
Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menE gene from Escherichia coli
journal, January 1996
- Sharma, V.; Hudspeth, M. E. S.; Meganathan, R.
- Gene, Vol. 168, Issue 1
IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013
- Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 42, Issue D1
Antibiotic Stress, Genetic Response and Altered Permeability of E. coli
journal, April 2007
- Viveiros, Miguel; Dupont, Myrielle; Rodrigues, Liliana
- PLoS ONE, Vol. 2, Issue 4
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
journal, July 1987
- Saitou, N.; Nei, M.
- Molecular Biology and Evolution, Vol. 4, Issue 4, p. 406-425
Genomic Standards Consortium Projects
journal, February 2014
- Field, Dawn; Sterk, Peter; Kottmann, Renzo
- Standards in Genomic Sciences, Vol. 9, Issue 3
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012
- Mavromatis, Konstantinos; Land, Miriam L.; Brettin, Thomas S.
- PLoS ONE, Vol. 7, Issue 12
Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum 'Bacteroidetes', and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003
journal, November 2005
- Nedashkovskaya, O. I.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 55, Issue 6
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010
- Gnerre, S.; MacCallum, I.; Przybylski, D.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009
- Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
- Nature, Vol. 462, Issue 7276
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010
- Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
- Nature Methods, Vol. 7, Issue 6
Improved Prediction of Signal Peptides: SignalP 3.0
journal, July 2004
- Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009
- Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
- Standards in Genomic Sciences, Vol. 1, Issue 1
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009
- Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
- Nature, Vol. 462, Issue 7276
Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass
journal, February 2020
- Xu, Xiaoheng; Feng, Guangyan; Huang, Linkai
- Molecular Biology Reports, Vol. 47, Issue 3
Pseudomonas indica sp. nov., a novel butane-utilizing species
journal, September 2002
- Pandey, K. K.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 52, Issue 5
The DNA Bank Network: The Start from a German Initiative
journal, March 2011
- Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger
- Biopreservation and Biobanking, Vol. 9, Issue 1
An Alternative Menaquinone Biosynthetic Pathway Operating in Microorganisms
journal, September 2008
- Hiratsuka, T.; Furihata, K.; Ishikawa, J.
- Science, Vol. 321, Issue 5896
Evolution of Enzymatic Activity in the Enolase Superfamily: Structure of o -Succinylbenzoate Synthase from Escherichia coli in Complex with Mg 2+ and o -Succinylbenzoate ,
journal, August 2000
- Thompson, Thomas B.; Garrett, James B.; Taylor, Erika A.
- Biochemistry, Vol. 39, Issue 35
Pontibacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil
journal, September 2013
- Singh, A. K.; Garg, N.; Lata, P.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 1
Menaquinone (Vitamin K 2 ) Biosynthesis: Localization and Characterization of the menA Gene from Escherichia coli
journal, May 1998
- Suvarna, K.; Stevenson, D.; Meganathan, R.
- Journal of Bacteriology, Vol. 180, Issue 10
The Futalosine Pathway Played an Important Role in Menaquinone Biosynthesis during Early Prokaryote Evolution
journal, January 2014
- Zhi, Xiao-Yang; Yao, Ji-Cheng; Tang, Shu-Kun
- Genome Biology and Evolution, Vol. 6, Issue 1
Cloning and complete nucleotide sequence determination of the catB gene encoding m,m-muconate lactonizing enzyme
journal, January 1987
- Aldrich, Teri L.; Frantz, Betsy; Gill, John F.
- Gene, Vol. 52, Issue 2-3
Multidrug-resistance efflux pumps ? not just for resistance
journal, August 2006
- Piddock, Laura J. V.
- Nature Reviews Microbiology, Vol. 4, Issue 8
AcrB Multidrug Efflux Pump of Escherichia coli : Composite Substrate-Binding Cavity of Exceptional Flexibility Generates Its Extremely Wide Substrate Specificity
journal, September 2003
- Yu, Edward W.; Aires, Julio R.; Nikaido, Hiroshi
- Journal of Bacteriology, Vol. 185, Issue 19
Structural organization of a Bacillus subtilis operon encoding menaquinone biosynthetic enzymes
journal, December 1995
- Rowland, Belinda; Hill, Kevin; Miller, Paul
- Gene, Vol. 167, Issue 1-2
Gene Ontology: tool for the unification of biology
journal, May 2000
- Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
- Nature Genetics, Vol. 25, Issue 1
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012
- Mavromatis, Konstantinos; Land, Miriam L.; Brettin, Thomas S.
- PLoS ONE, Vol. 7, Issue 12
The Genomic Standards Consortium
journal, June 2011
- Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy
- PLoS Biology, Vol. 9, Issue 6
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990
- Woese, C. R.; Kandler, O.; Wheelis, M. L.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menE gene from Escherichia coli
journal, January 1996
- Sharma, V.; Hudspeth, M. E. S.; Meganathan, R.
- Gene, Vol. 168, Issue 1
IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009
- Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.
- Bioinformatics, Vol. 25, Issue 17
En route to a genome-based classification of Archaea and Bacteria?
journal, June 2010
- Klenk, H. -P.; Göker, M.
- Systematic and Applied Microbiology, Vol. 33, Issue 4
Draft Genome Sequence of Pontibacter sp. nov. BAB1700, a Halotolerant, Industrially Important Bacterium
journal, October 2012
- Joshi, M. N.; Sharma, A. C.; Pandya, R. V.
- Journal of Bacteriology, Vol. 194, Issue 22
IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013
- Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 42, Issue D1
Approved Lists of Bacterial Names
journal, January 1980
- Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1
The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea
journal, December 2005
- Mongodin, E. F.; Nelson, K. E.; Daugherty, S.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 50
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008
- Zerbino, D. R.; Birney, E.
- Genome Research, Vol. 18, Issue 5
Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family 'Flexibacteraceae'
journal, July 2006
- Suresh, K.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 7
Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes
journal, March 1999
- Itoh, T.; Takemoto, K.; Mori, H.
- Molecular Biology and Evolution, Vol. 16, Issue 3
Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export
journal, June 2000
- Koronakis, Vassilis; Sharff, Andrew; Koronakis, Eva
- Nature, Vol. 405, Issue 6789
Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes
journal, March 1999
- Itoh, T.; Takemoto, K.; Mori, H.
- Molecular Biology and Evolution, Vol. 16, Issue 3
Antibiotic Stress, Genetic Response and Altered Permeability of E. coli
journal, April 2007
- Viveiros, Miguel; Dupont, Myrielle; Rodrigues, Liliana
- PLoS ONE, Vol. 2, Issue 4
Genomic Standards Consortium Projects
journal, February 2014
- Field, Dawn; Sterk, Peter; Kottmann, Renzo
- Standards in Genomic Sciences, Vol. 9, Issue 3
Rfam: an RNA family database
journal, January 2003
- Griffiths-Jones, S.
- Nucleic Acids Research, Vol. 31, Issue 1
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication
journal, June 1981
- Collins, M. D.; Jones, D.
- Microbiological Reviews, Vol. 45, Issue 2
Dietary palmitic acid promotes a prometastatic memory via Schwann cells
journal, November 2021
- Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc
- Nature, Vol. 599, Issue 7885
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
journal, December 2011
- Pagani, I.; Liolios, K.; Jansson, J.
- Nucleic Acids Research, Vol. 40, Issue D1
Four Novel Genes Required for Optimal Photoautotrophic Growth of the Cyanobacterium Synechocystis sp. Strain PCC 6803 Identified by In Vitro Transposon Mutagenesis
journal, January 2004
- Zhang, S.; Laborde, S. M.; Frankel, L. K.
- Journal of Bacteriology, Vol. 186, Issue 3
Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects
journal, May 2013
- Göker, Markus; Klenk, Hans-Peter
- Standards in Genomic Sciences, Vol. 8, Issue 2
Recruitment of a Foreign Quinone into the A 1 Site of Photosystem I : I. GENETIC AND PHYSIOLOGICAL CHARACTERIZATION OF PHYLLOQUINONE BIOSYNTHETIC PATHWAY MUTANTS IN
journal, March 2000
- Johnson, T. Wade; Shen, Gaozhong; Zybailov, Boris
- Journal of Biological Chemistry, Vol. 275, Issue 12
Pontibacter xinjiangensis sp. nov., in the phylum 'Bacteroidetes', and reclassification of [Effluviibacter] roseus as Pontibacter roseus comb. nov.
journal, July 2009
- Wang, Y.; Zhang, K.; Cai, F.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 1
En route to a genome-based classification of Archaea and Bacteria?
journal, June 2010
- Klenk, H. -P.; Göker, M.
- Systematic and Applied Microbiology, Vol. 33, Issue 4
Approved Lists of Bacterial Names
journal, January 1980
- Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
journal, December 2013
- Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A.
- Standards in Genomic Sciences, Vol. 9, Issue 3
IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009
- Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.
- Bioinformatics, Vol. 25, Issue 17
Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication
journal, June 1981
- Collins, M. D.; Jones, D.
- Microbiological Reviews, Vol. 45, Issue 2
Menaquinone (vitamin K2) biosynthesis: nucleotide sequence and expression of the menB gene from Escherichia coli.
journal, January 1992
- Sharma, V.; Suvarna, K.; Meganathan, R.
- Journal of Bacteriology, Vol. 174, Issue 15
Unexpected Divergence of Enzyme Function and Sequence: “ N -Acylamino Acid Racemase” Is o -Succinylbenzoate Synthase
journal, March 1999
- Palmer, David R. J.; Garrett, James B.; Sharma, V.
- Biochemistry, Vol. 38, Issue 14
Evolution of Enzymatic Activity in the Enolase Superfamily: Structure of o -Succinylbenzoate Synthase from Escherichia coli in Complex with Mg 2+ and o -Succinylbenzoate ,
journal, August 2000
- Thompson, Thomas B.; Garrett, James B.; Taylor, Erika A.
- Biochemistry, Vol. 39, Issue 35
Can sequence determine function?
journal, November 2000
- Gerlt, John A.; Babbitt, Patricia C.
- Genome Biology, Vol. 1, Issue 5, p. reviews0005.1
Menaquinone (vitamin K2) biosynthesis: cloning, nucleotide sequence, and expression of the menC gene from Escherichia coli
journal, August 1993
- Sharma, V.; Meganathan, R.; Hudspeth, M. E.
- Journal of Bacteriology, Vol. 175, Issue 15
Barbiturate-mediated regulation of expression of the cytochrome P450BM-3 gene of Bacillus megaterium by Bm3R1 protein.
journal, March 1992
- Shaw, G. C.; Fulco, A. J.
- Journal of Biological Chemistry, Vol. 267, Issue 8
Works referencing / citing this record:
Pontibacter oryzae sp. nov., a carotenoid-producing species isolated from a rice paddy field
journal, July 2019
- Chhetri, Geeta; Kim, Jiyoun; Kim, Hyungdong
- Antonie van Leeuwenhoek, Vol. 112, Issue 11