Beijerinckia indica subsp. indica ATCC 9039 plasmid pBIND01, complete sequence.
Beijerinckia indica subsp. indica ATCC 9039
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Beijerinckiaceae; Beijerinckia.
Complete sequence of plasmid1 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\nCP001017.1.\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: protein motif:HMM:NF028126.2
Members of this family include DotD of type IVB secretion systems and TraH of plasmid conjugative plasmid systems, both lipoproteins; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012813305.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
type IV secretion system DotC family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019460427.1
COORDINATES: similar to AA sequence:RefSeq:WP_010517045.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019460434.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003182829.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_015917135.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012385897.1
COORDINATES: protein motif:HMM:NF015431.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019460438.1
COORDINATES: protein motif:HMM:NF013636.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
proprotein convertase P-domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007630885.1
GO:0030253 - protein secretion by the type I secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008523529.1
HlyD family type I secretion periplasmic adaptor subunit
COORDINATES: protein motif:HMM:NF014548.2
COORDINATES: similar to AA sequence:RefSeq:WP_012382865.1
COORDINATES: protein motif:HMM:NF033857.1
COORDINATES: similar to AA sequence:RefSeq:WP_012382868.1
COORDINATES: protein motif:HMM:NF019324.2
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012318852.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006023671.1
COORDINATES: similar to AA sequence:RefSeq:WP_008121576.1
COORDINATES: protein motif:HMM:NF017496.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008495721.1
COORDINATES: similar to AA sequence:RefSeq:WP_012047441.1
COORDINATES: similar to AA sequence:RefSeq:WP_019463270.1
COORDINATES: protein motif:HMM:NF010406.0
ParB N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF019903.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]; GO:0006275 - regulation of DNA replication [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019462441.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611663.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018268666.1
COORDINATES: similar to AA sequence:RefSeq:WP_018268668.1
DUF3991 and toprim domain-containing protein
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_010316831.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_015933349.1
COORDINATES: similar to AA sequence:RefSeq:WP_007437421.1
COORDINATES: similar to AA sequence:RefSeq:WP_007005301.1
COORDINATES: similar to AA sequence:RefSeq:WP_006767167.1
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_076612137.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009618210.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_002805372.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611908.1
COORDINATES: similar to AA sequence:RefSeq:WP_012382921.1
COORDINATES: similar to AA sequence:RefSeq:WP_008510818.1
COORDINATES: similar to AA sequence:RefSeq:WP_012382923.1
COORDINATES: similar to AA sequence:RefSeq:WP_009340078.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007645483.1
COORDINATES: similar to AA sequence:RefSeq:WP_014132745.1
nucleoside triphosphate pyrophosphohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013698483.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819956.1
COORDINATES: protein motif:HMM:NF025056.2
GO:0003953 - NAD+ nucleosidase activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010434897.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564771.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003615618.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845224.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564775.1
COORDINATES: protein motif:HMM:NF025724.2
COORDINATES: similar to AA sequence:RefSeq:WP_003612899.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007753352.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012043345.1
COORDINATES: similar to AA sequence:RefSeq:WP_002710902.1
COORDINATES: protein motif:HMM:NF018841.2
COORDINATES: similar to AA sequence:RefSeq:WP_012385760.1
COORDINATES: similar to AA sequence:RefSeq:WP_017967989.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018497491.1
COORDINATES: similar to AA sequence:RefSeq:WP_014329271.1
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003566720.1
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_008533428.1
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011253610.1
COORDINATES: similar to AA sequence:RefSeq:WP_006117327.1
COORDINATES: similar to AA sequence:RefSeq:WP_008850953.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611413.1
COORDINATES: similar to AA sequence:RefSeq:WP_011084340.1
GO:0004802 - transketolase activity [Evidence IEA]
GO:0006098 - pentose-phosphate shunt [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018388564.1
GO:0004801 - transaldolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015664653.1
GO:0005515 - protein binding [Evidence IEA]; GO:0004856 - xylulokinase activity [Evidence IEA]
GO:0042732 - D-xylose metabolic process [Evidence IEA]; GO:0005997 - xylulose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008126486.1
COORDINATES: similar to AA sequence:RefSeq:WP_010912802.1
COORDINATES: similar to AA sequence:RefSeq:WP_014006930.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_015931503.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612399.1
COORDINATES: similar to AA sequence:RefSeq:WP_006469957.1
COORDINATES: similar to AA sequence:RefSeq:WP_008874645.1
COORDINATES: similar to AA sequence:RefSeq:WP_012331773.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611229.1
COORDINATES: protein motif:HMM:NF013936.2
COORDINATES: similar to AA sequence:RefSeq:WP_012383893.1
COORDINATES: protein motif:HMM:NF012922.2
COORDINATES: similar to AA sequence:RefSeq:WP_012385900.1
GO:0016787 - hydrolase activity [Evidence IEA]
isochorismatase family cysteine hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_012385899.1
COORDINATES: similar to AA sequence:RefSeq:WP_012385898.1
COORDINATES: protein motif:HMM:NF033580.1
COORDINATES: protein motif:HMM:NF017758.2
COORDINATES: similar to AA sequence:RefSeq:WP_004272258.1
COORDINATES: similar to AA sequence:RefSeq:WP_012385917.1
COORDINATES: similar to AA sequence:RefSeq:WP_003554634.1
COORDINATES: similar to AA sequence:RefSeq:WP_011509706.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]; GO:0048038 - quinone binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015243309.1
GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0008984 - protein-glutamate methylesterase activity [Evidence IEA]
GO:0006935 - chemotaxis [Evidence IEA]; GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018327563.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611187.1
frameshifted; internal stop; 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_010409169.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; 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_012340188.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018240468.1
COORDINATES: similar to AA sequence:RefSeq:WP_007626712.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016877537.1
iron-containing redox enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012384395.1
COORDINATES: similar to AA sequence:RefSeq:WP_012385242.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012382819.1
COORDINATES: protein motif:HMM:NF040974.1
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: similar to AA sequence:RefSeq:WP_019460407.1
COORDINATES: protein motif:HMM:TIGR04346.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460412.1
COORDINATES: protein motif:HMM:NF013540.2
COORDINATES: similar to AA sequence:RefSeq:WP_019460417.1
DotI/IcmL family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_019460418.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_003615684.1
COORDINATES: similar to AA sequence:RefSeq:WP_007396679.1
COORDINATES: similar to AA sequence:RefSeq:WP_016738530.1
COORDINATES: protein motif:HMM:NF022337.2
COORDINATES: similar to AA sequence:RefSeq:WP_020085921.1
GO:0030261 - chromosome condensation [Evidence IEA]