Nitrosomonas eutropha C91 plasmid p1, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Nitrosomonadales; Nitrosomonadaceae; Nitrosomonas.
Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation
Complete sequence of Plasmid1 of Nitrosomonas eutropha C91
Submitted (25-AUG-2006) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000451.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 3634486\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 :: 04/09/2023 01:24:15\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) :: 2,741\nCDSs (total) :: 2,693\nGenes (coding) :: 2,581\nCDSs (with protein) :: 2,581\nGenes (RNA) :: 48\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 41\nncRNAs :: 4\nPseudo Genes (total) :: 112\nCDSs (without protein) :: 112\nPseudo Genes (ambiguous residues) :: 0 of 112\nPseudo Genes (frameshifted) :: 58 of 112\nPseudo Genes (incomplete) :: 79 of 112\nPseudo Genes (internal stop) :: 38 of 112\nPseudo Genes (multiple problems) :: 51 of 112\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_020651377.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003118422.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006661905.1
GO:0004518 - nuclease activity [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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_014607315.1
COORDINATES: similar to AA sequence:RefSeq:WP_011630679.1
COORDINATES: similar to AA sequence:RefSeq:WP_010103397.1
COORDINATES: similar to AA sequence:RefSeq:WP_010103398.1
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_019331447.1
COORDINATES: similar to AA sequence:RefSeq:NP_490534.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_001262004.1
COORDINATES: similar to AA sequence:RefSeq:WP_018079573.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011871604.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018079575.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010103400.1
COORDINATES: protein motif:HMM:TIGR02783.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_001472379.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_020309002.1
COORDINATES: similar to AA sequence:RefSeq:WP_003829110.1
COORDINATES: similar to AA sequence:RefSeq:WP_004167241.1
COORDINATES: similar to AA sequence:RefSeq:WP_003829113.1
COORDINATES: similar to AA sequence:RefSeq:WP_010895198.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004359424.1
COORDINATES: similar to AA sequence:RefSeq:WP_014106734.1
COORDINATES: similar to AA sequence:RefSeq:WP_011111848.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_005204747.1
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_001138064.1
COORDINATES: similar to AA sequence:RefSeq:WP_016236504.1
COORDINATES: similar to AA sequence:RefSeq:WP_000993245.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229645.1
COORDINATES: similar to AA sequence:RefSeq:WP_001277466.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000281123.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017901292.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229640.1
GO:0045340 - mercury ion binding [Evidence IEA]
mercury resistance system periplasmic binding protein MerP
COORDINATES: similar to AA sequence:RefSeq:YP_005229639.1
COORDINATES: similar to AA sequence:RefSeq:WP_001166627.1
GO:0001228 - DNA-binding transcription activator activity, RNA polymerase II-specific [Evidence IEA]
Hg(II)-responsive transcriptional regulator
COORDINATES: protein motif:HMM:NF024555.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017739318.1
GO:0008233 - peptidase activity [Evidence IEA]; GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011630691.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011485838.1
COORDINATES: similar to AA sequence:RefSeq:WP_003829133.1
COORDINATES: similar to AA sequence:RefSeq:WP_015397453.1
COORDINATES: protein motif:HMM:NF036299.2
COORDINATES: similar to AA sequence:RefSeq:WP_006199029.1
COORDINATES: protein motif:HMM:NF015397.2
TraI/MobA(P) family conjugative relaxase
COORDINATES: similar to AA sequence:RefSeq:WP_004167199.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: similar to AA sequence:RefSeq:WP_004167197.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004167196.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012806100.1
COORDINATES: similar to AA sequence:RefSeq:WP_002706502.1
COORDINATES: protein motif:HMM:NF016146.2
COORDINATES: similar to AA sequence:RefSeq:WP_013801113.1