Phaeobacter inhibens strain P54 plasmid pP54_d, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Phaeobacter.
Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter
Adaptation of Surface-Associated Bacteria to the Open Ocean: A Genomically Distinct Subpopulation of Phaeobacter gallaeciensis Colonizes Pacific Mesozooplankton
Submitted (21-JAN-2015) Microbial Ecology and Diversity, Leibniz Institute DSMZ, Inhoffenstr. 7 B, Braunschweig 38124, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP010654.1.\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 SMRTPortal v. 2.0.1\nAssembly Name :: p54_hgap_3sc\nGenome Coverage :: 103x\nSequencing Technology :: PacBio; Illumina HiSeq 2500\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/13/2023 09:21:06\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,021\nCDSs (total) :: 3,948\nGenes (coding) :: 3,927\nCDSs (with protein) :: 3,927\nGenes (RNA) :: 73\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 58\nncRNAs :: 3\nPseudo Genes (total) :: 21\nCDSs (without protein) :: 21\nPseudo Genes (ambiguous residues) :: 0 of 21\nPseudo Genes (frameshifted) :: 10 of 21\nPseudo Genes (incomplete) :: 11 of 21\nPseudo Genes (internal stop) :: 9 of 21\nPseudo Genes (multiple problems) :: 7 of 21\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF023228.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012187317.1
COORDINATES: similar to AA sequence:RefSeq:WP_012559875.1
COORDINATES: similar to AA sequence:RefSeq:WP_003586038.1
COORDINATES: protein motif:HMM:NF017206.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008031401.1
GO:0032784 - regulation of DNA-templated transcription elongation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012279089.1
GO:0018738 - S-formylglutathione hydrolase activity [Evidence IEA]
GO:0046292 - formaldehyde metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014420768.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0051903 - S-(hydroxymethyl)glutathione dehydrogenase activity [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]; GO:0009404 - toxin metabolic process [Evidence IEA]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_012323020.1
COORDINATES: similar to AA sequence:RefSeq:WP_015495595.1
COORDINATES: similar to AA sequence:RefSeq:WP_009817525.1
GO:0016846 - carbon-sulfur lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014110385.1
GO:0009380 - excinuclease repair complex [Evidence IEA]
GO:0009381 - excinuclease ABC activity [Evidence IEA]
GO:0006289 - nucleotide-excision repair [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012110155.1
COORDINATES: similar to AA sequence:RefSeq:WP_020469845.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460380.1
COORDINATES: similar to AA sequence:RefSeq:WP_013690418.1
COORDINATES: similar to AA sequence:RefSeq:WP_018997962.1
COORDINATES: similar to AA sequence:RefSeq:WP_018997963.1
COORDINATES: similar to AA sequence:RefSeq:WP_018997964.1
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_009503806.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187165.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327370.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009803468.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807508.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187160.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187328.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807512.1
COORDINATES: similar to AA sequence:RefSeq:WP_009803688.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327387.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820228.1
COORDINATES: similar to AA sequence:RefSeq:WP_007068964.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807937.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807938.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009803677.1
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: similar to AA sequence:RefSeq:WP_011655458.1
COORDINATES: similar to AA sequence:RefSeq:WP_011655457.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011458667.1
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: protein motif:HMM:NF012651.2
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: similar to AA sequence:RefSeq:WP_011655434.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013896367.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: protein motif:HMM:NF017736.2
COORDINATES: protein motif:HMM:NF014273.2
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120564.1
COORDINATES: similar to AA sequence:RefSeq:WP_011512321.1
COORDINATES: protein motif:HMM:NF014626.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein