Shewanella oneidensis MR-1 megaplasmid, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella.
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
Submitted (22-MAR-2013) Biological Sciences Division, Department of Microbiology, Pascific Northwest National Laboratory, 902 Battelle, Blvd, Richland, WA 99352, USA
Submitted (02-AUG-2006) The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
Submitted (12-SEP-2002) The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA
REFSEQ INFORMATION: The reference sequence is identical to\nAE014300.1.\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 :: 03/12/2023 12:52:49\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,607\nCDSs (total) :: 4,469\nGenes (coding) :: 4,339\nCDSs (with protein) :: 4,339\nGenes (RNA) :: 138\nrRNAs :: 10, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 10, 9, 9 (5S, 16S, 23S)\ntRNAs :: 104\nncRNAs :: 6\nPseudo Genes (total) :: 130\nCDSs (without protein) :: 130\nPseudo Genes (ambiguous residues) :: 0 of 130\nPseudo Genes (frameshifted) :: 46 of 130\nPseudo Genes (incomplete) :: 89 of 130\nPseudo Genes (internal stop) :: 32 of 130\nPseudo Genes (multiple problems) :: 32 of 130\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_008989869.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001000833.1
COORDINATES: similar to AA sequence:RefSeq:WP_011938062.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017474988.1
COORDINATES: similar to AA sequence:RefSeq:WP_020194944.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017413076.1
COORDINATES: similar to AA sequence:RefSeq:WP_005502877.1
COORDINATES: similar to AA sequence:RefSeq:WP_017061976.1
COORDINATES: similar to AA sequence:RefSeq:WP_016797436.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_017097178.1
COORDINATES: similar to AA sequence:RefSeq:WP_001565356.1
COORDINATES: similar to AA sequence:RefSeq:WP_012197034.1
COORDINATES: similar to AA sequence:RefSeq:WP_011637424.1
COORDINATES: similar to AA sequence:RefSeq:WP_011074356.1
GO:0004803 - transposase activity [Evidence IEA]
Tn3-like element ISSod9 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001247892.1
COORDINATES: similar to AA sequence:RefSeq:WP_001293886.1
COORDINATES: similar to AA sequence:RefSeq:WP_019897068.1
COORDINATES: similar to AA sequence:RefSeq:WP_015060658.1
GO:0006313 - transposition, DNA-mediated [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_011070736.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011074360.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011074361.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS3-like element ISSod1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_012197921.1
COORDINATES: similar to AA sequence:RefSeq:WP_012589049.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_011979508.1
type II toxin-antitoxin system HicB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_014615255.1
COORDINATES: similar to AA sequence:RefSeq:WP_014615254.1
COORDINATES: similar to AA sequence:RefSeq:WP_005054087.1
IS256-like element ISSod4 family transposase
COORDINATES: protein motif:HMM:NF025054.2
COORDINATES: similar to AA sequence:RefSeq:WP_011979515.1
COORDINATES: similar to AA sequence:RefSeq:WP_014620404.1
COORDINATES: protein motif:HMM:NF014505.2
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011074377.1
COORDINATES: similar to AA sequence:RefSeq:WP_011847860.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012153860.1
COORDINATES: similar to AA sequence:RefSeq:WP_011074382.1
peptidase domain-containing ABC transporter
COORDINATES: similar to AA sequence:RefSeq:WP_014611436.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_006087379.1
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: similar to AA sequence:RefSeq:WP_012197906.1
COORDINATES: similar to AA sequence:RefSeq:WP_012197907.1
COORDINATES: protein motif:HMM:NF020265.2
COORDINATES: similar to AA sequence:RefSeq:WP_012198006.1
COORDINATES: similar to AA sequence:RefSeq:WP_012198005.1
COORDINATES: similar to AA sequence:RefSeq:WP_011074415.1
IS6-like element ISSod8 family transposase
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_014609707.1
COORDINATES: similar to AA sequence:RefSeq:WP_018877550.1
COORDINATES: similar to AA sequence:RefSeq:WP_011918370.1
COORDINATES: similar to AA sequence:RefSeq:WP_006081628.1
COORDINATES: similar to AA sequence:RefSeq:WP_014620400.1
COORDINATES: similar to AA sequence:RefSeq:WP_011074398.1
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]
type II toxin-antitoxin system HigB family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006080318.1
COORDINATES: similar to AA sequence:RefSeq:WP_011071076.1
IS5-like element ISSod6 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_014610919.1
COORDINATES: similar to AA sequence:RefSeq:WP_014610908.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_014610907.1
COORDINATES: similar to AA sequence:RefSeq:NP_414793.2
COORDINATES: protein motif:HMM:NF026766.2
immunity 26/phosphotriesterase HocA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014609912.1
COORDINATES: similar to AA sequence:RefSeq:WP_011979499.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_005306617.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011638902.1
COORDINATES: similar to AA sequence:RefSeq:WP_011638898.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011918375.1
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: similar to AA sequence:RefSeq:WP_011638896.1
COORDINATES: similar to AA sequence:RefSeq:WP_011071469.1
IS4-like element ISSod3 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_006958798.1
COORDINATES: similar to AA sequence:RefSeq:WP_006087336.1
COORDINATES: similar to AA sequence:RefSeq:WP_017035244.1
COORDINATES: protein motif:HMM:NF019581.2
COORDINATES: similar to AA sequence:RefSeq:WP_000669954.1
COORDINATES: protein motif:HMM:NF033543.1
COORDINATES: similar to AA sequence:RefSeq:WP_017409207.1
COORDINATES: similar to AA sequence:RefSeq:WP_012768904.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_011074420.1
COORDINATES: similar to AA sequence:RefSeq:WP_011074419.1
COORDINATES: similar to AA sequence:RefSeq:WP_014615268.1
COORDINATES: protein motif:HMM:NF024895.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612157.1
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_015904381.1
COORDINATES: similar to AA sequence:RefSeq:WP_011073373.1
IS481-like element ISSod13 family transposase
COORDINATES: protein motif:HMM:NF016876.2
COORDINATES: similar to AA sequence:RefSeq:WP_011073174.1
IS5-like element ISSod12 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011074233.1
NirD/YgiW/YdeI family stress tolerance protein
COORDINATES: similar to AA sequence:RefSeq:WP_000627495.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014610914.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011791210.1
COORDINATES: similar to AA sequence:RefSeq:WP_017420759.1
IS110-like element ISSod21 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_076611921.1
IS3-like element ISSod17 family transposase
COORDINATES: protein motif:HMM:NF012698.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612164.1
IS3-like element ISSod24 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_014611343.1
COORDINATES: similar to AA sequence:RefSeq:WP_011790522.1
COORDINATES: similar to AA sequence:RefSeq:WP_011847619.1
COORDINATES: protein motif:HMM:NF028295.2
COORDINATES: similar to AA sequence:RefSeq:WP_006081627.1
frameshifted; internal stop; 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_011074394.1
COORDINATES: similar to AA sequence:RefSeq:WP_018403379.1
COORDINATES: similar to AA sequence:RefSeq:WP_011074195.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_012588829.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_006084607.1
heavy metal-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006084606.1
COORDINATES: similar to AA sequence:RefSeq:WP_012090543.1
COORDINATES: similar to AA sequence:RefSeq:WP_014620549.1
COORDINATES: similar to AA sequence:RefSeq:WP_017103493.1
COORDINATES: similar to AA sequence:RefSeq:WP_011638859.1
GO:0018738 - S-formylglutathione hydrolase activity [Evidence IEA]
GO:0046292 - formaldehyde metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005499962.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0051903 - S-(hydroxymethyl)glutathione dehydrogenase activity [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]; GO:0009404 - toxin metabolic process [Evidence IEA]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_009314320.1
TraR/DksA family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007424023.1
GO:0051907 - S-(hydroxymethyl)glutathione synthase activity [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003450106.1
COORDINATES: similar to AA sequence:RefSeq:WP_011638871.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_086558334.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019442213.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011620836.1