Sulfitobacter indolifex strain DSM 14862 plasmid pDSM14862_e, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Sulfitobacter.
Beyond the ABCs#Discovery of Three New Plasmid Types in Rhodobacterales (RepQ, RepY, RepW)
Submitted (08-OCT-2021) Microbial Ecology and Diversity, Leibniz Institute DSMZ, Inhoffenstr. 7 B, Braunschweig 38124, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP084956.1.\nAnnotated using Prokka 1.13 from\nhttps://github.com/tseemann/prokka.\nBacteria and source DNA available from Leibniz Institute DSMZ.\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 :: HGAP3 SMRTPortal v. 2.3.0\nGenome Coverage :: 378x\nSequencing Technology :: PacBio RSII; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/15/2023 03:39:47\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) :: 4,368\nCDSs (total) :: 4,303\nGenes (coding) :: 4,228\nCDSs (with protein) :: 4,228\nGenes (RNA) :: 65\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 4\nPseudo Genes (total) :: 75\nCDSs (without protein) :: 75\nPseudo Genes (ambiguous residues) :: 0 of 75\nPseudo Genes (frameshifted) :: 38 of 75\nPseudo Genes (incomplete) :: 46 of 75\nPseudo Genes (internal stop) :: 27 of 75\nPseudo Genes (multiple problems) :: 29 of 75\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Seawater from the North Sea by Helgoland
pDSM14862_e occurs in a longer and a shorter version with a comparable coverage. This file contains the sequence of the longer version. All genes only occurring in the longer plasmid version are indicated with the note 'gene missing in shorter plasmid version'
COORDINATES: similar to AA sequence:RefSeq:WP_009827317.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007120936.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827315.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009827314.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827313.1
COORDINATES: protein motif:HMM:NF024206.2
ankyrin repeat domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010660167.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009827310.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009827309.1
COORDINATES: similar to AA sequence:RefSeq:WP_015497422.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_009179468.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807881.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807882.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009574084.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009816243.1
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_010969406.1
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_008226258.1
COORDINATES: similar to AA sequence:RefSeq:WP_008229132.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010969401.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019963868.1
COORDINATES: similar to AA sequence:RefSeq:WP_019963867.1
COORDINATES: similar to AA sequence:RefSeq:WP_008758869.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009827298.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009819650.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827296.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_009827295.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121044.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827293.1
COORDINATES: similar to AA sequence:RefSeq:WP_009804200.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827380.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007121040.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335580.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_009819927.1
COORDINATES: protein motif:HMM:NF013618.2
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120603.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120602.1
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: similar to AA sequence:RefSeq:WP_012556062.1
GO:0003729 - mRNA binding [Evidence IEA]
type II toxin-antitoxin system HicA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009827370.1
type II toxin-antitoxin system HicB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_007121030.1
COORDINATES: similar to AA sequence:RefSeq:WP_011569683.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011569682.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0015803 - branched-chain amino acid transport [Evidence IEA]
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_011569681.1
COORDINATES: similar to AA sequence:RefSeq:WP_011569680.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011569679.1
COORDINATES: similar to AA sequence:RefSeq:WP_011569677.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120579.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011569675.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013962061.1
aspartate aminotransferase family protein
COORDINATES: protein motif:HMM:NF018915.2
contact-dependent growth inhibition system immunity protein
COORDINATES: similar to AA sequence:RefSeq:WP_007008337.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120656.1
COORDINATES: similar to AA sequence:RefSeq:WP_008336057.1
COORDINATES: similar to AA sequence:RefSeq:WP_011388268.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048026.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019361332.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574117.1
COORDINATES: similar to AA sequence:RefSeq:WP_009804195.1
COORDINATES: similar to AA sequence:RefSeq:WP_009179475.1
COORDINATES: similar to AA sequence:RefSeq:WP_009179414.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120612.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574112.1
COORDINATES: similar to AA sequence:RefSeq:WP_009804201.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335582.1
COORDINATES: similar to AA sequence:RefSeq:WP_009179425.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120605.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574105.1
COORDINATES: similar to AA sequence:RefSeq:WP_009804208.1
COORDINATES: protein motif:HMM:NF024252.2
COORDINATES: similar to AA sequence:RefSeq:WP_007120599.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
GO:0019619 - 3,4-dihydroxybenzoate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014878829.1
COORDINATES: similar to AA sequence:RefSeq:WP_014878828.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_028710025.1
frameshifted; internal stop; 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_011746548.1
COORDINATES: similar to AA sequence:RefSeq:WP_012415749.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_009804224.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120593.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120592.1
GO:0030554 - adenyl nucleotide binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120591.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120590.1
GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120589.1
GO:0016790 - thiolester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612067.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009574128.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120578.1
COORDINATES: similar to AA sequence:RefSeq:WP_008599021.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606169.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009827364.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612218.1
COORDINATES: protein motif:HMM:TIGR03233.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827323.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120564.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827321.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827320.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827040.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120938.1