Beijerinckia indica subsp. indica ATCC 9039 plasmid pBIND02, complete sequence.
Beijerinckia indica subsp. indica ATCC 9039
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Beijerinckiaceae; Beijerinckia.
Complete sequence of plasmid2 of Beijerinckia indica subsp. indica ATCC 9039
Submitted (26-MAR-2008) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001018.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4082525\nSource DNA available from Peter Dunfield (pfdunfie@ucalgary.ca)\nBacteria available from ATCC: ATCC 9039\nContacts: Peter Dunfield (pfdunfie@ucalgary.ca)\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-PGF\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).\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 :: 04/24/2023 01:27:59\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) :: 3,958\nCDSs (total) :: 3,895\nGenes (coding) :: 3,788\nCDSs (with protein) :: 3,788\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) :: 107\nCDSs (without protein) :: 107\nPseudo Genes (ambiguous residues) :: 0 of 107\nPseudo Genes (frameshifted) :: 57 of 107\nPseudo Genes (incomplete) :: 68 of 107\nPseudo Genes (internal stop) :: 18 of 107\nPseudo Genes (multiple problems) :: 32 of 107\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Beijerinckia indica subsp. indica
COORDINATES: similar to AA sequence:RefSeq:WP_012590653.1
GO:0008198 - ferrous iron binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013257.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014051.2
COORDINATES: similar to AA sequence:RefSeq:WP_011778937.1
COORDINATES: protein motif:HMM:NF013884.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01007.1
GO:0045226 - extracellular polysaccharide biosynthetic process [Evidence IEA]
polysaccharide biosynthesis tyrosine autokinase
COORDINATES: protein motif:HMM:NF019552.2
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016918948.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]; GO:0003979 - UDP-glucose 6-dehydrogenase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007005544.1
COORDINATES: similar to AA sequence:RefSeq:WP_007005545.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012338189.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501130.1
COORDINATES: similar to AA sequence:RefSeq:WP_012252763.1
GO:0009317 - acetyl-CoA carboxylase complex [Evidence IEA]
GO:0003989 - acetyl-CoA carboxylase activity [Evidence IEA]; GO:0004075 - biotin carboxylase activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
acetyl-CoA carboxylase biotin carboxylase subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018408226.1
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018408225.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018408224.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018268365.1
COORDINATES: similar to AA sequence:RefSeq:WP_018408220.1
polyketide synthase dehydratase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012382815.1
3-oxoacyl-[acyl-carrier-protein] synthase III C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF014815.2
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012701508.1
COORDINATES: similar to AA sequence:RefSeq:WP_018408218.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012382988.1
COORDINATES: similar to AA sequence:RefSeq:WP_007601818.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007601813.1
GO:0016787 - hydrolase activity [Evidence IEA]
serine hydrolase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015436766.1
sigma-54-dependent Fis family transcriptional regulator
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF012334.2
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF024950.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611413.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024765.2
COORDINATES: similar to AA sequence:RefSeq:WP_012384749.1
COORDINATES: protein motif:HMM:TIGR04370.1
GO:0008755 - O antigen polymerase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012744.2