Croceicoccus naphthovorans strain PQ-2 plasmid p2, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Erythrobacteraceae; Croceicoccus.
Submitted (05-JUN-2015) Environmental Science, Zhejiang University, 688 Yu Hang Tang Road, Hangzhou, Zhejiang 310058, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP011772.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP v. 2.2.0\nGenome Coverage :: 100\nSequencing Technology :: PacBio RS II\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/03/2023 03:27:14\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) :: 3,899\nCDSs (total) :: 3,848\nGenes (coding) :: 3,764\nCDSs (with protein) :: 3,764\nGenes (RNA) :: 51\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 3\nPseudo Genes (total) :: 84\nCDSs (without protein) :: 84\nPseudo Genes (ambiguous residues) :: 0 of 84\nPseudo Genes (frameshifted) :: 29 of 84\nPseudo Genes (incomplete) :: 55 of 84\nPseudo Genes (internal stop) :: 13 of 84\nPseudo Genes (multiple problems) :: 12 of 84\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Croceicoccus naphthovorans
COORDINATES: protein motif:HMM:NF024867.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019054215.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007015908.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015910.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949361.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054830.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054492.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_013301526.1
COORDINATES: protein motif:HMM:NF016167.2
COORDINATES: similar to AA sequence:RefSeq:WP_006949344.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890898.1
COORDINATES: similar to AA sequence:RefSeq:WP_007684500.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054123.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015706.1
COORDINATES: similar to AA sequence:RefSeq:WP_020820505.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503291.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012554517.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019195708.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019195707.1
COORDINATES: similar to AA sequence:RefSeq:WP_010659169.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010343091.1
GO:0042597 - periplasmic space [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015457576.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_002516206.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0003955 - NAD(P)H dehydrogenase (quinone) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008832397.1
COORDINATES: similar to AA sequence:RefSeq:WP_008928624.1
zinc-binding alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007119835.1
COORDINATES: similar to AA sequence:RefSeq:WP_015457575.1
COORDINATES: similar to AA sequence:RefSeq:WP_020419314.1
alpha/beta hydrolase fold domain-containing protein
COORDINATES: protein motif:HMM:NF014173.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611527.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: similar to AA sequence:RefSeq:WP_003042804.1
GO:0008800 - beta-lactamase activity [Evidence IEA]
GO:0030655 - beta-lactam antibiotic catabolic process [Evidence IEA]; GO:0046677 - response to antibiotic [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007689240.1
COORDINATES: similar to AA sequence:RefSeq:WP_011616989.1
GO:0008253 - 5'-nucleotidase activity [Evidence IEA]; GO:0004309 - exopolyphosphatase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]; GO:0106411 - XMP 5'-nucleosidase activity [Evidence IEA]
GO:0006950 - response to stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007704915.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007704917.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0042908 - xenobiotic transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006961738.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007016037.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007016038.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054105.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890987.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054103.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_017184780.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_006949488.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_006949487.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054099.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053916.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949478.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053918.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906603.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_006952528.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406336.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_006949469.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828785.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_007015857.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_010890973.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460508.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949458.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015861.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054084.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO:0001558 - regulation of cell growth [Evidence IEA]
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_016956558.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006949450.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949446.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949444.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054377.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054077.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054076.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006949427.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890951.1
COORDINATES: similar to AA sequence:RefSeq:WP_013837200.1
COORDINATES: similar to AA sequence:RefSeq:WP_011443932.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949422.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949418.1
COORDINATES: similar to AA sequence:RefSeq:WP_010512657.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015449402.1
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_006949406.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054469.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906610.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949392.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906614.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054461.1
COORDINATES: similar to AA sequence:RefSeq:WP_019087166.1
COORDINATES: similar to AA sequence:RefSeq:WP_009867220.1
COORDINATES: protein motif:HMM:NF024977.2
COORDINATES: similar to AA sequence:RefSeq:WP_013419523.1
COORDINATES: similar to AA sequence:RefSeq:WP_008996382.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015907.1
COORDINATES: similar to AA sequence:RefSeq:WP_017501043.1
COORDINATES: similar to AA sequence:RefSeq:WP_006953701.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019054499.1
COORDINATES: protein motif:HMM:TIGR00180.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819636.1
incomplete; too short partial abutting assembly gap; missing N-terminus; Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.