Photobacterium ganghwense strain C2.2 plasmid pPGC22, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Photobacterium.
The complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate
Submitted (03-MAR-2021) Genetics, University of Bucharest, Splaiul Independentei, 91-95, Bucharest 050095, Romania
REFSEQ INFORMATION: The reference sequence is identical to\nCP071327.1.\nBacteria and source DNA available from Ana-Maria Tanase.\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 :: 10-JAN-2020\nAssembly Method :: wtdbg2 v. 2.5; Flye v. 2.6\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 113.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/09/2023 04:34:31\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) :: 5,231\nCDSs (total) :: 4,984\nGenes (coding) :: 4,926\nCDSs (with protein) :: 4,926\nGenes (RNA) :: 247\nrRNAs :: 19, 18, 18 (5S, 16S, 23S)\ncomplete rRNAs :: 19, 18, 18 (5S, 16S, 23S)\ntRNAs :: 188\nncRNAs :: 4\nPseudo Genes (total) :: 58\nCDSs (without protein) :: 58\nPseudo Genes (ambiguous residues) :: 0 of 58\nPseudo Genes (frameshifted) :: 29 of 58\nPseudo Genes (incomplete) :: 31 of 58\nPseudo Genes (internal stop) :: 11 of 58\nPseudo Genes (multiple problems) :: 12 of 58\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF041494.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017085218.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_000743450.1
COORDINATES: protein motif:HMM:NF018836.2
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_001049717.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_017085224.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_000595749.1
COORDINATES: similar to AA sequence:RefSeq:WP_011899401.1
COORDINATES: protein motif:HMM:NF025125.2
COORDINATES: protein motif:HMM:NF024498.2
thioredoxin fold domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013141552.1
COORDINATES: protein motif:HMM:NF021981.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_000911304.1
COORDINATES: protein motif:HMM:NF014036.2
COORDINATES: protein motif:HMM:NF012570.2
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: similar to AA sequence:RefSeq:WP_017085243.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00621.2
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_001282585.1
GO:0006259 - DNA metabolic process [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: protein motif:HMM:TIGR03033.1
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: similar to AA sequence:RefSeq:WP_000039317.1
COORDINATES: similar to AA sequence:RefSeq:WP_011899383.1
COORDINATES: similar to AA sequence:RefSeq:WP_011148230.1
GO:0097163 - sulfur carrier activity [Evidence IEA]
GO:0002143 - tRNA wobble position uridine thiolation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611500.1
GO:0004803 - transposase activity [Evidence IEA]
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: protein motif:HMM:NF012339.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: protein motif:HMM:NF013658.2
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF015140.2
COORDINATES: protein motif:HMM:NF019237.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: similar to AA sequence:RefSeq:WP_017849606.1
COORDINATES: similar to AA sequence:RefSeq:WP_007471236.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611474.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006646957.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612081.1
COORDINATES: similar to AA sequence:RefSeq:WP_015835222.1
phage antirepressor KilAC domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017634036.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018699035.1
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_017188768.1
COORDINATES: similar to AA sequence:RefSeq:WP_000993344.1
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:NF041281.1
COORDINATES: similar to AA sequence:RefSeq:WP_017065033.1
COORDINATES: similar to AA sequence:RefSeq:WP_005452728.1
COORDINATES: similar to AA sequence:RefSeq:WP_005452730.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004748968.1
COORDINATES: similar to AA sequence:RefSeq:WP_006961877.1
COORDINATES: protein motif:HMM:NF012955.2
COORDINATES: protein motif:HMM:NF024609.2
COORDINATES: similar to AA sequence:RefSeq:WP_006229026.1
COORDINATES: similar to AA sequence:RefSeq:WP_017790831.1
COORDINATES: similar to AA sequence:RefSeq:WP_014232169.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017071594.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017033942.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017062689.1
GO:0016020 - membrane [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005450194.1
COORDINATES: protein motif:HMM:NF016362.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: protein motif:HMM:NF014626.2
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: protein motif:HMM:NF017300.2
GO:0006274 - DNA replication termination [Evidence IEA]
DNA replication terminus site-binding protein
COORDINATES: protein motif:HMM:TIGR02740.1
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017086043.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF017124.2
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF037161.2
GO:0000166 - nucleotide binding [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: similar to AA sequence:RefSeq:WP_016800228.1
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF025815.2
COORDINATES: protein motif:HMM:TIGR03736.1
COORDINATES: similar to AA sequence:RefSeq:WP_000201432.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_041205051.1
COORDINATES: similar to AA sequence:RefSeq:WP_011152773.1
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_011152772.1
COORDINATES: similar to AA sequence:RefSeq:WP_005483224.1
COORDINATES: similar to AA sequence:RefSeq:WP_005380669.1
COORDINATES: similar to AA sequence:RefSeq:WP_017008012.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]; GO:0001072 - transcription antitermination factor activity, RNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014234825.1
GO:0003994 - aconitate hydratase activity [Evidence IEA]
GO:0006099 - tricarboxylic acid cycle [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005379001.1
GO:0006885 - regulation of pH [Evidence IEA]; GO:0006814 - sodium ion transport [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_012543393.1
COORDINATES: similar to AA sequence:RefSeq:WP_011081612.1
GO:0015385 - sodium:proton antiporter activity [Evidence IEA]
GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0006814 - sodium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005379003.1
GO:0045861 - negative regulation of proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014234828.1
COORDINATES: protein motif:HMM:NF018070.2
COORDINATES: protein motif:HMM:NF039792.1
COORDINATES: similar to AA sequence:RefSeq:WP_000829618.1
GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF024853.2
COORDINATES: similar to AA sequence:RefSeq:WP_069212063.1
COORDINATES: protein motif:HMM:NF017528.2
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_017052232.1
COORDINATES: similar to AA sequence:RefSeq:WP_016788405.1
lecithin retinol acyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_069211897.1
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: similar to AA sequence:RefSeq:WP_014620989.1
GO:0004519 - endonuclease activity [Evidence IEA]
HNH endonuclease signature motif containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000366822.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]