Photobacterium atrarenae strain GJH2-4 chromosome 3, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Photobacterium.
Genome sequencing of Photobacterium atrarenae GJH2-4
Submitted (12-JUL-2022) Biology, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP101510.1.\nBacteria and source DNA available from Culture collection (KCCM).\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 Method :: HGAP v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 339.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 08/02/2023 04:41:38\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) :: 4,940\nCDSs (total) :: 4,745\nGenes (coding) :: 4,695\nCDSs (with protein) :: 4,695\nGenes (RNA) :: 195\nrRNAs :: 12, 11, 11 (5S, 16S, 23S)\ncomplete rRNAs :: 12, 11, 11 (5S, 16S, 23S)\ntRNAs :: 155\nncRNAs :: 6\nPseudo Genes (total) :: 50\nCDSs (without protein) :: 50\nPseudo Genes (ambiguous residues) :: 0 of 50\nPseudo Genes (frameshifted) :: 19 of 50\nPseudo Genes (incomplete) :: 36 of 50\nPseudo Genes (internal stop) :: 10 of 50\nPseudo Genes (multiple problems) :: 13 of 50\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF013126.2
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
glycoside hydrolase family 3 N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF014026.2
glycoside hydrolase family 3 C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017447124.1
COORDINATES: similar to AA sequence:RefSeq:WP_006228497.1
COORDINATES: similar to AA sequence:RefSeq:WP_006714279.1
GO:0016832 - aldehyde-lyase activity [Evidence IEA]; GO:0016830 - carbon-carbon lyase activity [Evidence IEA]; GO:0016833 - oxo-acid-lyase activity [Evidence IEA]
bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase
COORDINATES: similar to AA sequence:RefSeq:WP_011221871.1
COORDINATES: similar to AA sequence:RefSeq:WP_009385923.1
GO:0008880 - glucuronate isomerase activity [Evidence IEA]
GO:0006064 - glucuronate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005461371.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004742882.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006228491.1
COORDINATES: similar to AA sequence:RefSeq:WP_000989019.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005595461.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004404190.1
GO:0008927 - mannonate dehydratase activity [Evidence IEA]
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_076611902.1
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_014233854.1
GO:0015558 - secondary active p-aminobenzoyl-glutamate transmembrane transporter activity [Evidence IEA]
GO:1902604 - p-aminobenzoyl-glutamate transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020334213.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020334212.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004396410.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001914753.1
COORDINATES: similar to AA sequence:RefSeq:WP_016799856.1
hydroxypyruvate isomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012551596.1
COORDINATES: similar to AA sequence:RefSeq:WP_006230484.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
four-carbon acid sugar kinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017635263.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006230482.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006879932.1
COORDINATES: protein motif:HMM:NF023210.2
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:TIGR00254.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0005525 - GTP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
GO:0009975 - cyclase activity [Evidence IEA]
GO:0009966 - regulation of signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005536335.1
COORDINATES: similar to AA sequence:RefSeq:WP_001285362.1
COORDINATES: similar to AA sequence:RefSeq:WP_005500642.1
COORDINATES: similar to AA sequence:RefSeq:WP_005329233.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF040138.1
COORDINATES: protein motif:HMM:NF014345.2
COORDINATES: similar to AA sequence:RefSeq:WP_011636340.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - DNA transposition [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: protein motif:HMM:TIGR00367.1
GO:0098662 - inorganic cation transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000853495.1
COORDINATES: similar to AA sequence:RefSeq:WP_017044119.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005458479.1
COORDINATES: similar to AA sequence:RefSeq:WP_017044122.1
COORDINATES: similar to AA sequence:RefSeq:WP_001907982.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013828.2
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016797431.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [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: protein motif:HMM:NF012245.2
COORDINATES: protein motif:HMM:NF014763.2
COORDINATES: protein motif:HMM:NF014691.2
COORDINATES: similar to AA sequence:RefSeq:WP_008072594.1
Ni(II)/Co(II)-binding transcriptional repressor RcnR
COORDINATES: similar to AA sequence:RefSeq:WP_000348318.1
GO:0015099 - nickel cation transmembrane transporter activity [Evidence IEA]
GO:0035444 - nickel cation transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017015662.1
COORDINATES: similar to AA sequence:RefSeq:WP_004741860.1
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_076611769.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:NF012301.2
GO:0000156 - phosphorelay response regulator activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000343613.1
COORDINATES: similar to AA sequence:RefSeq:WP_005524958.1
COORDINATES: similar to AA sequence:RefSeq:WP_008217370.1
COORDINATES: similar to AA sequence:RefSeq:WP_009695908.1
COORDINATES: similar to AA sequence:RefSeq:WP_005434318.1
COORDINATES: similar to AA sequence:RefSeq:WP_005429172.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005136263.1
COORDINATES: protein motif:HMM:NF019371.2
COORDINATES: similar to AA sequence:RefSeq:WP_000470624.1
COORDINATES: similar to AA sequence:RefSeq:WP_008986872.1
COORDINATES: similar to AA sequence:RefSeq:WP_020333778.1
COORDINATES: protein motif:HMM:TIGR01496.1
GO:0004156 - dihydropteroate synthase activity [Evidence IEA]
GO:0009396 - folic acid-containing compound biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007105035.1
GO:0051213 - dioxygenase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
class III extradiol ring-cleavage dioxygenase
COORDINATES: protein motif:HMM:NF015431.2
GO:0001216 - DNA-binding transcription activator activity [Evidence IEA]