Dongshaea marina strain DM2 plasmid unnamed, complete sequence.
Bacteria; Proteobacteria; Gammaproteobacteria; Aeromonadales; Aeromonadaceae; Dongshaea.
A facutatively anaerobic marine bacterium
Submitted (14-APR-2018) Institute of Oceanography, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 106, Taiwan
REFSEQ INFORMATION: The reference sequence is identical to\nCP028898.1.\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-Assembly-Data-START##\nAssembly Date :: 2018\nAssembly Method :: HGAP v. 2013\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 90.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/08/2022 02:24:36\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,909\nCDSs (total) :: 4,761\nGenes (coding) :: 4,517\nCDSs (with protein) :: 4,517\nGenes (RNA) :: 148\nrRNAs :: 12, 10, 10 (5S, 16S, 23S)\ncomplete rRNAs :: 12, 10, 10 (5S, 16S, 23S)\ntRNAs :: 112\nncRNAs :: 4\nPseudo Genes (total) :: 244\nCDSs (without protein) :: 244\nPseudo Genes (ambiguous residues) :: 0 of 244\nPseudo Genes (frameshifted) :: 206 of 244\nPseudo Genes (incomplete) :: 47 of 244\nPseudo Genes (internal stop) :: 8 of 244\nPseudo Genes (multiple problems) :: 17 of 244\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011264006.1
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: protein motif:HMM:NF012485.2
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF012318.2
COORDINATES: similar to AA sequence:RefSeq:WP_005460020.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
H-NS family nucleoid-associated regulatory protein
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_017043047.1
GO:0004518 - nuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006085285.1
COORDINATES: similar to AA sequence:RefSeq:WP_041207141.1
GO:0004803 - transposase activity [Evidence IEA]
plasmid mobilization relaxosome protein MobC
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: similar to AA sequence:RefSeq:WP_011264012.1
COORDINATES: similar to AA sequence:RefSeq:WP_011264014.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: similar to AA sequence:RefSeq:WP_005970980.1
COORDINATES: similar to AA sequence:RefSeq:WP_010301495.1
COORDINATES: similar to AA sequence:RefSeq:WP_012278406.1
GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity [Evidence IEA]
GO:0006400 - tRNA modification [Evidence IEA]
tRNA (N6-threonylcarbamoyladenosine(37)-N6)-methyltransferase TrmO
COORDINATES: protein motif:HMM:NF014035.2
sulfite exporter TauE/SafE family protein
COORDINATES: protein motif:HMM:NF015949.2
COORDINATES: protein motif:HMM:NF015048.2
COORDINATES: protein motif:HMM:NF014620.2
COORDINATES: similar to AA sequence:RefSeq:WP_001137910.1
COORDINATES: protein motif:HMM:NF033538.1
COORDINATES: similar to AA sequence:RefSeq:WP_012301821.1
frameshifted; 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_041412878.1
COORDINATES: similar to AA sequence:RefSeq:WP_043851824.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024583.2
COORDINATES: similar to AA sequence:RefSeq:WP_001389365.1
internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
DDE-type integrase/transposase/recombinase
COORDINATES: protein motif:HMM:TIGR02532.1
prepilin-type N-terminal cleavage/methylation domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011839967.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: similar to AA sequence:RefSeq:WP_006707381.1
COORDINATES: similar to AA sequence:RefSeq:WP_015724380.1
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: similar to AA sequence:RefSeq:WP_014611693.1
COORDINATES: similar to AA sequence:RefSeq:WP_011148005.1
COORDINATES: similar to AA sequence:RefSeq:WP_005348531.1
COORDINATES: similar to AA sequence:RefSeq:WP_013784644.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF013231.2
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_020485770.1
COORDINATES: similar to AA sequence:RefSeq:WP_003660025.1
GO:0003729 - mRNA binding [Evidence IEA]
type II toxin-antitoxin system HicA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_016914543.1
type II toxin-antitoxin system HicB family antitoxin
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024675.2
COORDINATES: similar to AA sequence:RefSeq:WP_006714551.1
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_011263998.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_007968805.1
COORDINATES: protein motif:HMM:TIGR02781.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_011264002.1
COORDINATES: similar to AA sequence:RefSeq:WP_006714544.1
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006706362.1
COORDINATES: similar to AA sequence:RefSeq:WP_015282495.1
zincin-like metallopeptidase domain-containing protein