Xylanimonas cellulosilytica DSM 15894 plasmid pXCEL01, complete sequence.
Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Promicromonosporaceae; Xylanimonas.
Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07)
The complete plasmid of Xylanimonas cellulosilytica DSM 15894
Submitted (12-NOV-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001822.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4082373\nSource DNA and organism available from Hans-Peter Klenk at the\nGerman Collection of Microorganisms and Cell Cultures (DSMZ)\n(hans-peter.klenk@dsmz.de)\nContacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-PGF\nAnnotation by JGI-ORNL and JGI-PGF\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Metadata-START##\nOrganism Display Name :: Xylanimonas cellulosilytica XIL07, DSM\n 15894\nCulture Collection ID :: DSM 15894, CECT 5975, LMG 20990\nGOLD Stamp ID :: Gi02069\nGreengenes ID :: 62747\nFunding Program :: DOE-GEBA 2007\nGene Calling Method :: Prodigal\nIsolation Site :: Decaying tree in Salamanca Spain\nIsolation Country :: Spain\nLatitude :: 40.964972\nLongitude :: -5.663047\nOxygen Requirement :: Aerobe\nCell Shape :: Coccus-shaped\nMotility :: Nonmotile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nTemperature Optimum :: 28C\nGram Staining :: gram+\nBiotic Relationship :: Free living\nDiseases :: None\nHabitat :: Soil\nPhenotypes :: Cellulose degrader, Lacks Mycolic acids,\n Xylan degrader\nEnergy Source :: Chemoorganotroph\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/02/2023 01:37:30\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,516\nCDSs (total) :: 3,453\nGenes (coding) :: 3,424\nCDSs (with protein) :: 3,424\nGenes (RNA) :: 63\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 3\nPseudo Genes (total) :: 29\nCDSs (without protein) :: 29\nPseudo Genes (ambiguous residues) :: 0 of 29\nPseudo Genes (frameshifted) :: 6 of 29\nPseudo Genes (incomplete) :: 26 of 29\nPseudo Genes (internal stop) :: 3 of 29\nPseudo Genes (multiple problems) :: 6 of 29\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Xylanimonas cellulosilytica
COORDINATES: protein motif:HMM:NF025200.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF014442.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016665868.1
COORDINATES: similar to AA sequence:RefSeq:WP_012687022.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007299944.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720547.1
COORDINATES: similar to AA sequence:RefSeq:WP_006244148.1
COORDINATES: similar to AA sequence:RefSeq:WP_018791988.1
COORDINATES: similar to AA sequence:RefSeq:WP_010143871.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013632.2
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF020250.2
COORDINATES: similar to AA sequence:RefSeq:WP_009774468.1
COORDINATES: similar to AA sequence:RefSeq:WP_009774469.1
COORDINATES: similar to AA sequence:RefSeq:WP_020487626.1
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009774471.1
COORDINATES: similar to AA sequence:RefSeq:WP_014375310.1
COORDINATES: similar to AA sequence:RefSeq:WP_008357418.1
COORDINATES: similar to AA sequence:RefSeq:WP_020489839.1
TadE/TadG family type IV pilus assembly protein
COORDINATES: protein motif:HMM:NF024792.2
COORDINATES: protein motif:HMM:NF015649.2
LysM peptidoglycan-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012880168.1
COORDINATES: similar to AA sequence:RefSeq:WP_005050621.1
GO:0016407 - acetyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024056.2
COORDINATES: protein motif:HMM:NF024254.2
COORDINATES: protein motif:HMM:NF013073.2
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003941261.1
PDDEXK nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF021378.2
COORDINATES: similar to AA sequence:RefSeq:WP_010523895.1
GO:0097573 - glutathione oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024359.2
COORDINATES: similar to AA sequence:RefSeq:WP_018762934.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005148585.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF038083.1
COORDINATES: protein motif:HMM:TIGR02937.1
GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]
COORDINATES: protein motif:HMM:NF018154.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016432.2
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_013883705.1
COORDINATES: similar to AA sequence:RefSeq:WP_010839086.1
GO:0008233 - peptidase activity [Evidence IEA]; GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012686791.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011599951.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720535.1
COORDINATES: similar to AA sequence:RefSeq:WP_011599953.1