Sphingopyxis alaskensis RB2256 F plasmid, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingopyxis.
The genomic basis of trophic strategy in marine bacteria
Complete sequence of F plasmid of Sphingopyxis alaskensis RB2256
Submitted (20-APR-2006) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000357.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 3634495\nSource DNA and bacteria available from Rick Cavicchioli\n(rcavicchioli@unsw.edu.au)\nContacts: Rick Cavicchioli (rcavicchioli@unsw.edu.au)\n Paul Richardson (microbes@cuba.jgi-psf.org)\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LLNL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\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)\nAdditional Notes:\nSphingopyxis alaskensis RB2256 appears to have about a 28.5kb\nextrachromosomal piece of DNA with significantly lower coverage\nthan the chromosome. It appears to be of F plasmid origin because\nof the presence of traA gene, a conjugal transfer protein. It can\nbe integrated into the genome between 856688 and 859197, excising a\npiece of chromosomal DNA 2517 bp long. Perhaps a fraction of the\npopulation has this 28.5 kb fragment integrated. Within 2 kb of\nthe excision point is an IS21 element with ORF1 and ORF2 of\ntransposase and perfect inverted repeats. However, we have been\nunsuccessful in circularizing the 28.5 kb fragment with pcr,\nperhaps because of the low representation in the genome.\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##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/12/2023 16:35:48\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,299\nCDSs (total) :: 3,248\nGenes (coding) :: 3,212\nCDSs (with protein) :: 3,212\nGenes (RNA) :: 51\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 3\nPseudo Genes (total) :: 36\nCDSs (without protein) :: 36\nPseudo Genes (ambiguous residues) :: 0 of 36\nPseudo Genes (frameshifted) :: 14 of 36\nPseudo Genes (incomplete) :: 24 of 36\nPseudo Genes (internal stop) :: 9 of 36\nPseudo Genes (multiple problems) :: 10 of 36\n##Genome-Annotation-Data-END##
COORDINATES: similar to AA sequence:RefSeq:WP_014492790.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
phytanoyl-CoA dioxygenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009802117.1
COORDINATES: similar to AA sequence:RefSeq:WP_009802116.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_009802115.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023181.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015740.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015741.1
sigma-54 dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015126474.1
COORDINATES: similar to AA sequence:RefSeq:WP_020176873.1
nickel-dependent hydrogenase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013896579.1
COORDINATES: similar to AA sequence:RefSeq:WP_012040800.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015747.1
GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015748.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015749.1
COORDINATES: similar to AA sequence:RefSeq:WP_020176868.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007015752.1
GO:0005506 - iron ion binding [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
GO:0016226 - iron-sulfur cluster assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015753.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015754.1
GO:0003998 - acylphosphatase activity [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011910301.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0051082 - unfolded protein binding [Evidence IEA]
GO:0065003 - protein-containing complex assembly [Evidence IEA]
HypC/HybG/HupF family hydrogenase formation chaperone
COORDINATES: similar to AA sequence:RefSeq:WP_007015756.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015757.1
GO:0016530 - metallochaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015758.1
hydrogenase expression/formation protein HypE
COORDINATES: similar to AA sequence:RefSeq:WP_011536539.1
high frequency lysogenization protein HflD
COORDINATES: protein motif:HMM:NF013334.2
hydrogenase maturation nickel metallochaperone HypA
COORDINATES: similar to AA sequence:RefSeq:WP_007015761.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
hydrogenase nickel incorporation protein HypB
COORDINATES: similar to AA sequence:RefSeq:WP_009802104.1
COORDINATES: similar to AA sequence:RefSeq:WP_009802103.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012711.2
class I adenylate-forming enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004618811.1
MaoC family dehydratase N-terminal domain-containing protein