Pukyongiella litopenaei strain SH-1 plasmid p2, 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\nCP043620.1.\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_009820070.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012187387.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574206.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_009827215.1
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_005859736.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_009827208.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065906.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138202.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803272.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574197.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574196.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820093.1
COORDINATES: similar to AA sequence:RefSeq:WP_009450564.1
antitoxin of toxin-antitoxin stability system
COORDINATES: similar to AA sequence:RefSeq:WP_020038226.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803282.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803284.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018065917.1
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009820102.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065919.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187105.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012187106.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187107.1
COORDINATES: similar to AA sequence:RefSeq:WP_007424858.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009574191.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
strawberry notch C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008336055.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803302.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574187.1
COORDINATES: similar to AA sequence:RefSeq:WP_011388540.1
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_008227318.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819739.1
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005859685.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002718002.1
Qat anti-phage system QueC-like protein QatC
COORDINATES: similar to AA sequence:RefSeq:WP_015599826.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
Qat anti-phage system TatD family nuclease QatD
COORDINATES: similar to AA sequence:RefSeq:WP_008336079.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001740.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574167.1
COORDINATES: similar to AA sequence:RefSeq:WP_008336084.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574160.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_010139194.1
COORDINATES: similar to AA sequence:RefSeq:WP_010139195.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859624.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005859623.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859622.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_005859619.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859617.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138156.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859613.1
COORDINATES: similar to AA sequence:RefSeq:WP_008336095.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018001728.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010398642.1
COORDINATES: similar to AA sequence:RefSeq:WP_008336115.1
COORDINATES: protein motif:HMM:NF023390.2
COORDINATES: similar to AA sequence:RefSeq:WP_010138164.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_009815479.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573601.1
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018303599.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009827282.1
GO:0031966 - mitochondrial membrane [Evidence IEA]
GO:0033617 - mitochondrial cytochrome c oxidase assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009815483.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001721.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503840.1
GO:0016531 - copper chaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008889345.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807977.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013959872.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803463.1
GO:0046873 - metal ion transmembrane transporter activity [Evidence IEA]
GO:0030001 - metal ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009573591.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009573590.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008889351.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009807971.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815498.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503854.1
GO:0016746 - acyltransferase activity [Evidence IEA]; GO:0071972 - peptidoglycan L,D-transpeptidase activity [Evidence IEA]
GO:0018104 - peptidoglycan-protein cross-linking [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011102826.1
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_012187391.1
COORDINATES: similar to AA sequence:RefSeq:WP_010138187.1
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_009827042.1