Pukyongiella litopenaei strain SH-1 plasmid p5, 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\nCP043623.1.\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_011144108.1
with OppABCD is involved in the transport of oligopeptides; OppF and OppD are ATP-binding proteins; incomplete; too short partial abutting assembly gap; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
oligopeptide ABC transporter ATP-binding protein OppF
COORDINATES: similar to AA sequence:RefSeq:WP_011655527.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009503752.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_010505209.1
COORDINATES: similar to AA sequence:RefSeq:WP_011655537.1
COORDINATES: similar to AA sequence:RefSeq:WP_012556062.1
GO:0003729 - mRNA binding [Evidence IEA]
type II toxin-antitoxin system HicA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007427348.1
type II toxin-antitoxin system HicB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009381671.1
COORDINATES: similar to AA sequence:RefSeq:WP_006871427.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF019498.2
COORDINATES: similar to AA sequence:RefSeq:WP_013177445.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF012738.2
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016817.2
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]
succinylglutamate desuccinylase/aspartoacylase family protein
COORDINATES: protein motif:HMM:NF012706.2
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF014081.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012870874.1
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_014432391.1