Pukyongiella litopenaei strain SH-1 plasmid p1, 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\nCP043619.1.\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: protein motif:HMM:NF019322.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024808.2
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF012738.2
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014763021.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: similar to AA sequence:RefSeq:WP_003535705.1
GO:0097367 - carbohydrate derivative binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013434.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015888254.1
COORDINATES: similar to AA sequence:RefSeq:WP_002602235.1
COORDINATES: protein motif:HMM:NF012515.2
COORDINATES: similar to AA sequence:RefSeq:WP_007121009.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_014492132.1
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020043201.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019051906.1
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012227095.1
COORDINATES: similar to AA sequence:RefSeq:WP_012227094.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_007803215.1
COORDINATES: protein motif:HMM:NF012870.2
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187038.1
GO:0005507 - copper ion 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_007803412.1
GO:0046872 - metal ion binding [Evidence IEA]
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807488.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327301.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803406.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803405.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803403.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803401.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807486.1
GO:0042834 - peptidoglycan binding [Evidence IEA]; GO:0071972 - peptidoglycan L,D-transpeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008327290.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803395.1
protein-disulfide reductase DsbD family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808008.1
GO:0051082 - unfolded protein binding [Evidence IEA]
GO:0017004 - cytochrome complex assembly [Evidence IEA]
c-type cytochrome biogenesis protein CcmI
COORDINATES: similar to AA sequence:RefSeq:WP_007803391.1
cytochrome c-type biogenesis protein CcmH
COORDINATES: similar to AA sequence:RefSeq:WP_009808006.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0015036 - disulfide oxidoreductase activity [Evidence IEA]
DsbE family thiol:disulfide interchange protein
COORDINATES: similar to AA sequence:RefSeq:WP_007803387.1
COORDINATES: similar to AA sequence:RefSeq:WP_020042978.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327277.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803380.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611865.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009573528.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859475.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819736.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859468.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015497448.1
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_013844596.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010138187.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574209.1
COORDINATES: similar to AA sequence:RefSeq:WP_005617061.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335985.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574206.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_009827215.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009451523.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335990.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859736.1
COORDINATES: protein motif:HMM:NF024242.2
GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008198436.1
COORDINATES: similar to AA sequence:RefSeq:WP_015007619.1
COORDINATES: similar to AA sequence:RefSeq:WP_013742928.1
COORDINATES: similar to AA sequence:RefSeq:WP_010443108.1
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_009820087.1
COORDINATES: similar to AA sequence:RefSeq:WP_009179395.1
COORDINATES: similar to AA sequence:RefSeq:WP_006018700.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820090.1
COORDINATES: similar to AA sequence:RefSeq:WP_009338093.1
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_009574196.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820093.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803278.1
antitoxin of toxin-antitoxin stability system
COORDINATES: similar to AA sequence:RefSeq:WP_008759285.1
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_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_012187107.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187106.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187105.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574191.1
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: protein motif:HMM:NF015437.2
autoinducer binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002723354.1
COORDINATES: similar to AA sequence:RefSeq:WP_009502502.1
COORDINATES: protein motif:HMM:TIGR02686.1
COORDINATES: similar to AA sequence:RefSeq:WP_009175352.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF013488.2
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: similar to AA sequence:RefSeq:WP_017140544.1
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:TIGR02742.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_011331482.1
conjugal transfer pilus assembly protein TraU
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: similar to AA sequence:RefSeq:WP_011331481.1
type-F conjugative transfer system protein TraW
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: protein motif:HMM:NF021213.2
COORDINATES: protein motif:HMM:NF024254.2
COORDINATES: similar to AA sequence:RefSeq:WP_011331476.1
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: protein motif:HMM:TIGR02762.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_011331471.1
COORDINATES: protein motif:HMM:NF012967.2
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014780344.1
COORDINATES: similar to AA sequence:RefSeq:WP_015498238.1
COORDINATES: similar to AA sequence:RefSeq:WP_011581885.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004592 - pantoate-beta-alanine ligase activity [Evidence IEA]
GO:0015940 - pantothenate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011746664.1
frameshifted; 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_036744399.1
COORDINATES: similar to AA sequence:RefSeq:WP_011540540.1
COORDINATES: similar to AA sequence:RefSeq:WP_010142243.1
type I restriction-modification system subunit M N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611978.1
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_020723269.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016646 - oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010659193.1
indolepyruvate oxidoreductase subunit beta family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018064725.1
indolepyruvate ferredoxin oxidoreductase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_007762424.1
GO:0005324 - long-chain fatty acid transporter activity [Evidence IEA]; GO:0004467 - long-chain fatty acid-CoA ligase activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013722.2
MaoC/PaaZ C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF024212.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019965606.1
COORDINATES: similar to AA sequence:RefSeq:WP_008968197.1
aspartate/glutamate racemase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006226416.1
GO:0016812 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007755720.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_019996156.1
COORDINATES: similar to AA sequence:RefSeq:WP_011086212.1
organic hydroperoxide resistance protein
COORDINATES: similar to AA sequence:RefSeq:WP_008597749.1
COORDINATES: similar to AA sequence:RefSeq:WP_008597748.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0015556 - C4-dicarboxylate transmembrane transporter activity [Evidence IEA]
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008597747.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008597746.1
C4-dicarboxylate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005605943.1
GO:0000334 - 3-hydroxyanthranilate 3,4-dioxygenase activity [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009812765.1
GO:0005215 - transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009178491.1
GO:0009436 - glyoxylate catabolic process [Evidence IEA]; GO:0071704 - organic substance metabolic process [Evidence IEA]
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011454575.1
GO:0033735 - aspartate dehydrogenase activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009178401.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010441131.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_005639568.1
GO:0004425 - indole-3-glycerol-phosphate synthase activity [Evidence IEA]
GO:0006568 - tryptophan metabolic process [Evidence IEA]
indole-3-glycerol phosphate synthase TrpC
COORDINATES: similar to AA sequence:RefSeq:WP_004119906.1
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]
internal stop; 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_006174787.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611724.1
COORDINATES: similar to AA sequence:RefSeq:WP_020593968.1
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_007426053.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121183.1