Nitrobacter hamburgensis X14 plasmid 2, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Nitrobacteraceae; Nitrobacter.
Complete sequence of Plasmid2 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\nCP000321.1.\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_011505176.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007603282.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
GDCCVxC domain-containing (seleno)protein
COORDINATES: similar to AA sequence:RefSeq:WP_006023153.1
COORDINATES: similar to AA sequence:RefSeq:WP_002714858.1
COORDINATES: similar to AA sequence:RefSeq:WP_011510347.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_009337942.1
COORDINATES: similar to AA sequence:RefSeq:WP_002714861.1
COORDINATES: similar to AA sequence:RefSeq:WP_009337938.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023149.1
GO:0003677 - DNA binding [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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011930990.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930988.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011992964.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011510349.1
COORDINATES: protein motif:HMM:NF012521.2
COORDINATES: similar to AA sequence:RefSeq:WP_018508007.1
COORDINATES: similar to AA sequence:RefSeq:WP_011930989.1
COORDINATES: similar to AA sequence:RefSeq:WP_017258838.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006243373.1
beta-phosphoglucomutase family hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_002715130.1
GO:0004340 - glucokinase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020604894.1
GO:0008776 - acetate kinase activity [Evidence IEA]
GO:0006083 - acetate metabolic process [Evidence IEA]; GO:0006113 - fermentation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011474453.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008138450.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007809141.1
COORDINATES: similar to AA sequence:RefSeq:WP_014439882.1
GO:0015444 - P-type magnesium transporter activity [Evidence IEA]
GO:0015693 - magnesium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011505029.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505269.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011505174.1
metal-sensitive transcriptional regulator
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]
COORDINATES: similar to AA sequence:RefSeq:WP_013912803.1
COORDINATES: similar to AA sequence:RefSeq:WP_002714853.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011505276.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
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_076612205.1
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_052096176.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012090958.1
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_003495445.1
COORDINATES: similar to AA sequence:RefSeq:WP_011493046.1
COORDINATES: protein motif:HMM:NF015437.2
COORDINATES: similar to AA sequence:RefSeq:WP_009337940.1
COORDINATES: protein motif:HMM:NF033808.0
GO:0006825 - copper ion transport [Evidence IEA]
copper homeostasis membrane protein CopD
COORDINATES: similar to AA sequence:RefSeq:WP_008964534.1
COORDINATES: similar to AA sequence:RefSeq:WP_008964535.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913448.1
COORDINATES: protein motif:HMM:NF023036.2
COORDINATES: similar to AA sequence:RefSeq:WP_008138674.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564742.1
COORDINATES: similar to AA sequence:RefSeq:WP_013912813.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564894.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564740.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564892.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505154.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564890.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913454.1
COORDINATES: similar to AA sequence:RefSeq:WP_019677907.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913456.1
COORDINATES: similar to AA sequence:RefSeq:WP_002711889.1
COORDINATES: protein motif:HMM:NF012621.2
COORDINATES: protein motif:HMM:NF014465.2
mercuric transporter MerT family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564884.1
GO:0017004 - cytochrome complex assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011505142.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505141.1
heavy metal-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012564881.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913461.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564879.1
GO:0046872 - metal ion binding [Evidence IEA]
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007602789.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_020179933.1
GO:0050611 - arsenate reductase (azurin) activity [Evidence IEA]
arsenate reductase (azurin) small subunit
COORDINATES: similar to AA sequence:RefSeq:WP_019197311.1
arsenate reductase (azurin) large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_012564870.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564869.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
This arsenate reductase requires both glutathione and glutaredoxin to convert arsenate to arsenite, after which the efflux transporter formed by ArsA and ArsB can extrude the arsenite from the cell, providing resistance; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012557990.1
GO:0015267 - channel activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564867.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF033788.1
COORDINATES: similar to AA sequence:RefSeq:WP_007608234.1
COORDINATES: similar to AA sequence:RefSeq:WP_015687383.1
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007602810.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023727.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564827.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564826.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564825.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023723.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_012564823.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564822.1
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564821.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023719.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564818.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564817.1
VirB4 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564816.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_012564815.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564814.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013913484.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913485.1
succinoglycan biosynthesis protein exoI-like
COORDINATES: similar to AA sequence:RefSeq:WP_012564811.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564810.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564809.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913486.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023707.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023706.1
COORDINATES: similar to AA sequence:RefSeq:WP_012111257.1
bacteriophage abortive infection AbiH family protein
COORDINATES: protein motif:HMM:NF012318.2
GO:0008233 - peptidase activity [Evidence IEA]; GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013831444.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011854133.1
COORDINATES: similar to AA sequence:RefSeq:WP_004536204.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012564805.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505097.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013391794.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564801.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913489.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012554555.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822478.1
COORDINATES: similar to AA sequence:RefSeq:WP_009338100.1
COORDINATES: similar to AA sequence:RefSeq:WP_011931085.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505089.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023699.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822469.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011505086.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822467.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564792.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564791.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822464.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564790.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913491.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002719000.1
COORDINATES: similar to AA sequence:RefSeq:WP_003541094.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_002719002.1
COORDINATES: similar to AA sequence:RefSeq:WP_009339981.1
COORDINATES: similar to AA sequence:RefSeq:WP_019197732.1
COORDINATES: similar to AA sequence:RefSeq:WP_009734080.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578842.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009452555.1
COORDINATES: similar to AA sequence:RefSeq:WP_009734077.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505071.1
GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018269866.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578847.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011578848.1
COORDINATES: similar to AA sequence:RefSeq:WP_008142575.1
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_008142574.1
COORDINATES: similar to AA sequence:RefSeq:WP_008142573.1
GO:0004518 - nuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011505063.1
COORDINATES: similar to AA sequence:RefSeq:WP_008142570.1
GO:0009307 - DNA restriction-modification system [Evidence IEA]
5-methylcytosine-specific restriction endonuclease system specificity protein McrC
COORDINATES: similar to AA sequence:RefSeq:WP_009859196.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822440.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341810.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_018327596.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_011992921.1
COORDINATES: protein motif:HMM:NF018841.2
COORDINATES: similar to AA sequence:RefSeq:WP_003501678.1
COORDINATES: similar to AA sequence:RefSeq:WP_007598506.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970612.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012564774.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822436.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564771.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578802.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974971.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505047.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822431.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822429.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913429.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822427.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913431.1
COORDINATES: similar to AA sequence:RefSeq:WP_015822425.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913432.1
COORDINATES: similar to AA sequence:RefSeq:WP_019200221.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF012422.2
COORDINATES: similar to AA sequence:RefSeq:WP_012047066.1
COORDINATES: similar to AA sequence:RefSeq:WP_011087700.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564860.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564859.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023142.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_006021129.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913471.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564854.1
GO:0035438 - cyclic-di-GMP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007602784.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505177.1