Roseomonas gilardii strain U14-5 plasmid 2, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodospirillales; Acetobacteraceae; Roseomonas.
Complete Genome and Methylome Analysis of Psychrotrophic Bacterial Isolates from Antarctic Lake Untersee
Submitted (10-MAY-2016) Research, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP015586.1.\nSource DNA and Bacteria are available from Dr.Vladimir N. Akimov,\nInstitute of Biochemistry and Physiology of Microorganisms,#Moscow\nregion, Pushino, 5 Science Ave, 142290 Russia.\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 Method :: HGAP.3/Quiver v. v2.3.0\nGenome Coverage :: 287x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 03:51:24\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) :: 4,961\nCDSs (total) :: 4,881\nGenes (coding) :: 4,824\nCDSs (with protein) :: 4,824\nGenes (RNA) :: 80\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 61\nncRNAs :: 4\nPseudo Genes (total) :: 57\nCDSs (without protein) :: 57\nPseudo Genes (ambiguous residues) :: 0 of 57\nPseudo Genes (frameshifted) :: 20 of 57\nPseudo Genes (incomplete) :: 41 of 57\nPseudo Genes (internal stop) :: 7 of 57\nPseudo Genes (multiple problems) :: 11 of 57\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Vladimir Akimov, Institute of Biochemistry and Physiology of Microorganisms
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012453218.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076612078.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF019349.2
COORDINATES: protein motif:HMM:NF012607.2
COORDINATES: similar to AA sequence:RefSeq:WP_012427589.1
COORDINATES: similar to AA sequence:RefSeq:WP_007436342.1
COORDINATES: protein motif:HMM:NF017893.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611126.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_008918880.1
COORDINATES: similar to AA sequence:RefSeq:WP_007536947.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183759.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612037.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: protein motif:HMM:NF014763.2
COORDINATES: similar to AA sequence:RefSeq:WP_015314688.1
COORDINATES: protein motif:HMM:NF024583.2
COORDINATES: similar to AA sequence:RefSeq:WP_015950036.1
COORDINATES: protein motif:HMM:NF022603.2
COORDINATES: similar to AA sequence:RefSeq:WP_018968659.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019015539.1
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF024139.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF013540.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_014853817.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010364340.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612064.1
COORDINATES: protein motif:HMM:NF012524.2
COORDINATES: protein motif:HMM:NF037408.2
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: protein motif:HMM:NF025495.2
GO:0004518 - nuclease activity [Evidence IEA]
dsDNA nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007740824.1
COORDINATES: similar to AA sequence:RefSeq:WP_014439470.1
COORDINATES: similar to AA sequence:RefSeq:WP_016974520.1
GO:0015293 - symporter activity [Evidence IEA]
cation:dicarboxylase symporter family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_009452800.1
dihydrodipicolinate synthase family protein
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_015668515.1
COORDINATES: similar to AA sequence:RefSeq:WP_019463225.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019463390.1
COORDINATES: similar to AA sequence:RefSeq:WP_012812344.1
COORDINATES: similar to AA sequence:RefSeq:WP_011907535.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.