Roseomonas gilardii strain U14-5 plasmid 1, 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\nCP015585.1.\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:0030983 - mismatched DNA binding [Evidence IEA]
GO:0006298 - mismatch repair [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019460434.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
type IV secretion system DNA-binding domain-containing protein
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010517045.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460427.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460426.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF028126.2
Members of this family include DotD of type IVB secretion systems and TraH of plasmid conjugative plasmid systems, both lipoproteins; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004129311.1
COORDINATES: protein motif:HMM:NF013970.2
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019460424.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460422.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460421.1
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: similar to AA sequence:RefSeq:WP_019460418.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_012383004.1
COORDINATES: protein motif:HMM:NF013540.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019460412.1
COORDINATES: protein motif:HMM:TIGR04346.1
COORDINATES: similar to AA sequence:RefSeq:WP_019460407.1
COORDINATES: similar to AA sequence:RefSeq:WP_003945970.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004274505.1
GO:0030976 - thiamine pyrophosphate binding [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: similar to AA sequence:RefSeq:WP_013203797.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019462106.1
aspartate/glutamate racemase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007437279.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012329542.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009490381.1
COORDINATES: similar to AA sequence:RefSeq:WP_007614368.1
COORDINATES: similar to AA sequence:RefSeq:WP_007004657.1
COORDINATES: protein motif:HMM:NF012707.2
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007437272.1
amino acid ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007437271.1
COORDINATES: protein motif:HMM:NF012993.2
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_019462104.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611390.1
COORDINATES: protein motif:HMM:NF012464.2
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_003631061.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: similar to AA sequence:RefSeq:WP_012553902.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [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: protein motif:HMM:NF014505.2
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019460386.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819915.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF014654.2
COORDINATES: protein motif:HMM:NF020859.2
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008873507.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_003523017.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_020308032.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012779116.1
COORDINATES: similar to AA sequence:RefSeq:WP_043766079.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_014501008.1
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: protein motif:HMM:NF027681.2
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: protein motif:HMM:NF021616.2
COORDINATES: protein motif:HMM:NF016903.2
COORDINATES: protein motif:HMM:NF025072.2
COORDINATES: similar to AA sequence:RefSeq:WP_005793466.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_011440462.1
GO:0008831 - dTDP-4-dehydrorhamnose reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007005655.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007005656.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012453218.1
COORDINATES: similar to AA sequence:RefSeq:WP_011087945.1
COORDINATES: similar to AA sequence:RefSeq:WP_009490015.1
COORDINATES: protein motif:HMM:NF024880.2
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611905.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612007.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611908.1
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_076611297.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: protein motif:HMM:NF012354.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007676181.1
COORDINATES: protein motif:HMM:NF016670.2
COORDINATES: similar to AA sequence:RefSeq:WP_019462881.1
amino acid ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012039795.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008604015.1
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: similar to AA sequence:RefSeq:WP_004664983.1
metal ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012590346.1
COORDINATES: similar to AA sequence:RefSeq:WP_013396269.1
COORDINATES: similar to AA sequence:RefSeq:WP_009858215.1
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor [Evidence IEA]
cytochrome d ubiquinol oxidase subunit II
COORDINATES: similar to AA sequence:RefSeq:WP_015447583.1
COORDINATES: similar to AA sequence:RefSeq:WP_002723451.1
PLP-dependent aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002723455.1
GO:0003870 - 5-aminolevulinate synthase activity [Evidence IEA]
GO:0006783 - heme biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006560294.1
COORDINATES: similar to AA sequence:RefSeq:WP_007436229.1
COORDINATES: similar to AA sequence:RefSeq:WP_019463375.1
COORDINATES: protein motif:HMM:NF025126.2
COORDINATES: similar to AA sequence:RefSeq:WP_007406260.1
COORDINATES: similar to AA sequence:RefSeq:WP_020091604.1
COORDINATES: protein motif:HMM:NF017206.2
COORDINATES: similar to AA sequence:RefSeq:WP_013844050.1
COORDINATES: protein motif:HMM:NF027824.2
COORDINATES: similar to AA sequence:RefSeq:WP_012049861.1
COORDINATES: similar to AA sequence:RefSeq:WP_012638432.1
COORDINATES: similar to AA sequence:RefSeq:WP_010336794.1
COORDINATES: similar to AA sequence:RefSeq:WP_003537135.1
COORDINATES: protein motif:HMM:NF023228.2
COORDINATES: protein motif:HMM:NF024935.2
COORDINATES: similar to AA sequence:RefSeq:WP_012168287.1
COORDINATES: similar to AA sequence:RefSeq:WP_009210560.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612078.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611527.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611857.1
COORDINATES: similar to AA sequence:RefSeq:WP_003508779.1
COORDINATES: similar to AA sequence:RefSeq:WP_003575317.1
COORDINATES: similar to AA sequence:RefSeq:WP_008969541.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007079691.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612037.1
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008918880.1
COORDINATES: similar to AA sequence:RefSeq:WP_007536947.1
COORDINATES: protein motif:HMM:NF037406.2
COORDINATES: similar to AA sequence:RefSeq:WP_012330183.1
COORDINATES: similar to AA sequence:RefSeq:WP_012452124.1
COORDINATES: similar to AA sequence:RefSeq:WP_017484310.1
internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012972787.1
COORDINATES: protein motif:HMM:NF024883.2
COORDINATES: similar to AA sequence:RefSeq:WP_007006481.1
COORDINATES: protein motif:HMM:NF013594.2
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011315345.1
COORDINATES: similar to AA sequence:RefSeq:WP_011077905.1
COORDINATES: similar to AA sequence:RefSeq:WP_003044989.1
zinc-binding alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003613735.1
COORDINATES: similar to AA sequence:RefSeq:WP_013169102.1
type 1 glutamine amidotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007684618.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503035.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503034.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578756.1
COORDINATES: similar to AA sequence:RefSeq:WP_004573923.1
glutathione-independent formaldehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_014132971.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611833.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823887.1
COORDINATES: similar to AA sequence:RefSeq:NP_308438.1
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_012783831.1
metal/formaldehyde-sensitive transcriptional repressor
COORDINATES: similar to AA sequence:RefSeq:WP_007406876.1
zinc-dependent alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017503026.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183090.1
COORDINATES: similar to AA sequence:RefSeq:WP_059669267.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982932.1
phosphate-starvation-inducible PsiE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003603272.1
COORDINATES: similar to AA sequence:RefSeq:WP_003603273.1
COORDINATES: similar to AA sequence:RefSeq:WP_020084956.1
COORDINATES: similar to AA sequence:RefSeq:WP_003167682.1
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003603276.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO:0051301 - cell division [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013651411.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020084960.1
COORDINATES: similar to AA sequence:RefSeq:WP_004637113.1
GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
GO:0022900 - electron transport chain [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010339452.1
COORDINATES: protein motif:HMM:NF023398.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF021778.2
beta-propeller fold lactonase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018259971.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012385496.1
COORDINATES: similar to AA sequence:RefSeq:WP_058167704.1
COORDINATES: similar to AA sequence:RefSeq:WP_013480126.1
COORDINATES: protein motif:HMM:NF033517.1
COORDINATES: similar to AA sequence:RefSeq:WP_011997478.1
COORDINATES: similar to AA sequence:RefSeq:WP_017482500.1
COORDINATES: similar to AA sequence:RefSeq:WP_009488330.1
COORDINATES: similar to AA sequence:RefSeq:WP_019015579.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010505062.1
DUF3991 and TOPRIM domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011798055.1
COORDINATES: similar to AA sequence:RefSeq:WP_019462446.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019462445.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006953712.1
COORDINATES: similar to AA sequence:RefSeq:WP_019462441.1
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_012606182.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_016733503.1
GO:0015109 - chromate transmembrane transporter activity [Evidence IEA]
GO:0015703 - chromate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019462439.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019462437.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019462436.1
COORDINATES: similar to AA sequence:RefSeq:WP_004211483.1
COORDINATES: similar to AA sequence:RefSeq:WP_017882792.1
COORDINATES: similar to AA sequence:RefSeq:WP_008029020.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019463272.1
COORDINATES: similar to AA sequence:RefSeq:WP_019463271.1
COORDINATES: similar to AA sequence:RefSeq:WP_019463270.1
COORDINATES: similar to AA sequence:RefSeq:WP_019463268.1
COORDINATES: protein motif:HMM:NF012596.2
COORDINATES: similar to AA sequence:RefSeq:WP_013338285.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF016876.2
COORDINATES: similar to AA sequence:RefSeq:WP_007985296.1
COORDINATES: protein motif:HMM:NF013098.2
COORDINATES: similar to AA sequence:RefSeq:WP_013419417.1
COORDINATES: similar to AA sequence:RefSeq:WP_002727480.1
GO:0016740 - transferase activity [Evidence IEA]
type B chloramphenicol O-acetyltransferase
COORDINATES: protein motif:HMM:NF024809.2
glutathione S-transferase family protein
COORDINATES: protein motif:HMM:NF012662.2
COORDINATES: similar to AA sequence:RefSeq:WP_019460438.1