Pukyongiella litopenaei strain SH-1 plasmid p4, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Pukyongiella.
Submitted (11-SEP-2019) Microbiology, Pukyong National University, Yongso-Ro, Busan KS012, South Korea
Annotation update by database at the request of the submitter due to the addition of plasmids to the assembly
Submitted (29-AUG-2019) Microbiology, Pukyong National University, Yongso-Ro, Busan KS012, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP043622.1.\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 :: 06-MAR-2018\nAssembly Method :: HGAP v. 3.0\nAssembly Name :: SH-1 chromosome and plasmids\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 218.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/26/2023 06:03:00\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) :: 4,189\nCDSs (total) :: 4,141\nGenes (coding) :: 4,049\nCDSs (with protein) :: 4,049\nGenes (RNA) :: 48\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 42\nncRNAs :: 3\nPseudo Genes (total) :: 92\nCDSs (without protein) :: 92\nPseudo Genes (ambiguous residues) :: 0 of 92\nPseudo Genes (frameshifted) :: 22 of 92\nPseudo Genes (incomplete) :: 75 of 92\nPseudo Genes (internal stop) :: 14 of 92\nPseudo Genes (multiple problems) :: 17 of 92\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_014236596.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014881795.1
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_009804242.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010687710.1
COORDINATES: similar to AA sequence:RefSeq:WP_007427784.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803874.1
helix-turn-helix domain-containing protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_015224431.1
COORDINATES: similar to AA sequence:RefSeq:WP_002708894.1
GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
putative toxin-antitoxin system toxin component, PIN family
COORDINATES: similar to AA sequence:RefSeq:WP_011749544.1
COORDINATES: protein motif:HMM:NF033542.1
COORDINATES: similar to AA sequence:RefSeq:WP_001549957.1
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_009807927.1
COORDINATES: similar to AA sequence:RefSeq:WP_012554517.1
COORDINATES: protein motif:HMM:NF015431.2
GO:0001216 - DNA-binding transcription activator activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019402432.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013209791.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017454718.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011537208.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF012706.2
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF019474.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012517.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
LLM class flavin-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: similar to AA sequence:RefSeq:WP_015934130.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003813978.1
hydantoinase/oxoprolinase family protein
COORDINATES: protein motif:HMM:NF013756.2
COORDINATES: similar to AA sequence:RefSeq:WP_028714619.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611865.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_010141882.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611527.1