Nitrobacter hamburgensis X14 plasmid 3, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Nitrobacteraceae; Nitrobacter.
Complete sequence of Plasmid3 of Nitrobacter hamburgensis X14
Submitted (28-MAR-2006) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000322.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 3634489\nSource DNA and bacteria available from Dan Arp (arpd@bcc.orst.edu)\nContacts: Dan Arp (arpd@bcc.orst.edu)\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).\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 :: 05/27/2023 01:34:17\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) :: 4,899\nCDSs (total) :: 4,840\nGenes (coding) :: 4,488\nCDSs (with protein) :: 4,488\nGenes (RNA) :: 59\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 4\nPseudo Genes (total) :: 352\nCDSs (without protein) :: 352\nPseudo Genes (ambiguous residues) :: 0 of 352\nPseudo Genes (frameshifted) :: 168 of 352\nPseudo Genes (incomplete) :: 274 of 352\nPseudo Genes (internal stop) :: 34 of 352\nPseudo Genes (multiple problems) :: 109 of 352\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_020048127.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_003508820.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0008233 - peptidase activity [Evidence IEA]
conjugative transfer signal peptidase TraF
COORDINATES: similar to AA sequence:RefSeq:WP_003501346.1
COORDINATES: similar to AA sequence:RefSeq:WP_011504836.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF013970.2
COORDINATES: similar to AA sequence:RefSeq:WP_012640573.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - DNA transposition [Evidence IEA]
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_011505255.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505257.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011087990.1
COORDINATES: similar to AA sequence:RefSeq:WP_007613480.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_003606573.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF033542.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015437.2
autoinducer binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003523583.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_012649093.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650736.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_018482029.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913815.1
P-type conjugative transfer protein TrbL
COORDINATES: protein motif:HMM:NF022361.2
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003523577.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_012654968.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650639.1
COORDINATES: similar to AA sequence:RefSeq:WP_008120555.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913822.1
GO:0061579 - N-acyl homoserine lactone synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006205756.1
COORDINATES: similar to AA sequence:RefSeq:WP_014989225.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578657.1
COORDINATES: similar to AA sequence:RefSeq:WP_010023905.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018444840.1
COORDINATES: similar to AA sequence:RefSeq:WP_018097622.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003533691.1
COORDINATES: similar to AA sequence:RefSeq:WP_017270337.1
COORDINATES: similar to AA sequence:RefSeq:WP_008873506.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009804176.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341783.1
COORDINATES: similar to AA sequence:RefSeq:WP_019200236.1
COORDINATES: protein motif:HMM:NF023398.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001110447.1
COORDINATES: similar to AA sequence:RefSeq:WP_017423245.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004211994.1
GO:0009975 - cyclase activity [Evidence IEA]
GO:0009966 - regulation of signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011510130.1
IS1380-like element ISNha3 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011512263.1
COORDINATES: similar to AA sequence:RefSeq:WP_011090936.1
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: similar to AA sequence:RefSeq:WP_014762198.1
COORDINATES: similar to AA sequence:RefSeq:WP_010960204.1
COORDINATES: similar to AA sequence:RefSeq:WP_013554209.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505246.1
GO:0015385 - sodium:proton antiporter activity [Evidence IEA]
GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0006814 - sodium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611419.1
COORDINATES: similar to AA sequence:RefSeq:WP_011504889.1
COORDINATES: similar to AA sequence:RefSeq:WP_011510990.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016717 - oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008888406.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611416.1
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_011744672.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012496700.1
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_076612206.1
COORDINATES: protein motif:HMM:NF012464.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF026092.2
glycogen debranching N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010909820.1
COORDINATES: similar to AA sequence:RefSeq:WP_008872444.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505254.1
GO:0015103 - inorganic anion transmembrane transporter activity [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF03058
sul1 is cis-regulatory element that is thought to sense ions involved in sulfur or methionine metabolism; They are found in Alphaproteobacteria; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_086558360.1
COORDINATES: similar to AA sequence:RefSeq:WP_016845155.1
COORDINATES: protein motif:HMM:NF024983.2
COORDINATES: similar to AA sequence:RefSeq:WP_007674248.1
COORDINATES: similar to AA sequence:RefSeq:WP_003597873.1
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012779149.1
COORDINATES: similar to AA sequence:RefSeq:WP_012114880.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012752928.1
COORDINATES: similar to AA sequence:RefSeq:WP_012330134.1
COORDINATES: similar to AA sequence:RefSeq:WP_009800218.1
COORDINATES: similar to AA sequence:RefSeq:WP_015821561.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505029.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505176.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011505175.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009337975.1
COORDINATES: similar to AA sequence:RefSeq:WP_013912802.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564755.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013912803.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564751.1
COORDINATES: similar to AA sequence:RefSeq:WP_002714853.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505169.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011084500.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015822454.1
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010414738.1
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009338166.1
Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate; 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_002718067.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002718066.1
COORDINATES: similar to AA sequence:RefSeq:WP_002718065.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_013742194.1
COORDINATES: similar to AA sequence:RefSeq:WP_010451298.1
COORDINATES: similar to AA sequence:RefSeq:WP_002718062.1
putative DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002718061.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993073.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993002.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564798.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564796.1
COORDINATES: similar to AA sequence:RefSeq:WP_015242556.1
type II toxin-antitoxin system MqsA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_015242555.1
type II toxin-antitoxin system MqsR family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012564795.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010974883.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564793.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427430.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993085.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993086.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341881.1
COORDINATES: similar to AA sequence:RefSeq:WP_018494937.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013845238.1
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: protein motif:HMM:NF014430.2
COORDINATES: similar to AA sequence:RefSeq:WP_005859736.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930898.1
COORDINATES: similar to AA sequence:RefSeq:WP_004119813.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501747.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_020046837.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_018458955.1