Sulfitobacter indolifex strain DSM 14862 plasmid pDSM14862_d, 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\nCP084955.1.\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
COORDINATES: protein motif:HMM:NF023069.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
DnaA N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013385643.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824260.1
ParB N-terminal domain-containing protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_018516653.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF023228.2
COORDINATES: similar to AA sequence:RefSeq:WP_009820068.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009820067.1
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_005859468.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007121138.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007121139.1
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_086558106.1
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF017437.2
COORDINATES: similar to AA sequence:RefSeq:WP_005859473.1
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_028710025.1
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:NF021616.2
COORDINATES: protein motif:HMM:NF025025.2
trifunctional glycosyltransferase/class I SAM-dependent methyltransferase/polysaccharide deacetylase
COORDINATES: protein motif:HMM:NF012869.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013962035.1
GO:0008146 - sulfotransferase activity [Evidence IEA]
sulfotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011569913.1
polysaccharide biosynthesis C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013960570.1
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019956495.1
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: similar to AA sequence:RefSeq:WP_011569925.1
COORDINATES: similar to AA sequence:RefSeq:WP_011569924.1
COORDINATES: protein motif:HMM:NF033537.1
COORDINATES: protein motif:HMM:NF012936.2
GO:0004066 - asparagine synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0006529 - asparagine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011569921.1
COORDINATES: protein motif:HMM:NF015527.2
sulfotransferase family 2 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015497729.1
COORDINATES: similar to AA sequence:RefSeq:WP_007635327.1
COORDINATES: protein motif:HMM:NF014453.2
COORDINATES: protein motif:HMM:NF024627.2
right-handed parallel beta-helix repeat-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003168745.1
COORDINATES: protein motif:HMM:NF014732.2
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
Wzz/FepE/Etk N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF026257.2
COORDINATES: protein motif:HMM:NF014606.2
GO:0015159 - polysaccharide transmembrane transporter activity [Evidence IEA]
GO:0015774 - polysaccharide transport [Evidence IEA]
polysaccharide biosynthesis/export family protein
COORDINATES: protein motif:HMM:NF024120.2
glycosyl hydrolase family 28-related protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612253.1
COORDINATES: similar to AA sequence:RefSeq:WP_011746418.1
COORDINATES: similar to AA sequence:RefSeq:WP_007668202.1
COORDINATES: protein motif:HMM:NF018513.2
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: protein motif:HMM:NF015445.2
TRAP dicarboxylate transporter- DctP subunit
COORDINATES: protein motif:HMM:NF037995.1
GO:0055085 - transmembrane transport [Evidence IEA]
TRAP transporter substrate-binding protein DctP
COORDINATES: protein motif:HMM:NF019349.2
COORDINATES: protein motif:HMM:NF014071.2
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019460083.1
hydantoinase B/oxoprolinase family protein
TRAP transporter substrate-binding protein
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003811597.1
GO:0015556 - C4-dicarboxylate transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019322.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_006204614.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121027.1
COORDINATES: similar to AA sequence:RefSeq:WP_007117831.1
COORDINATES: similar to AA sequence:RefSeq:WP_007117832.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120977.1
COORDINATES: similar to AA sequence:RefSeq:WP_007117834.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007121168.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121166.1
COORDINATES: protein motif:HMM:TIGR00229.1
PAS domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_007121548.1
COORDINATES: protein motif:HMM:NF013561.2
COORDINATES: similar to AA sequence:RefSeq:WP_007121443.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827115.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_007121490.1
COORDINATES: similar to AA sequence:RefSeq:WP_007816903.1
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_007121144.1
COORDINATES: protein motif:HMM:NF014021.2
COORDINATES: similar to AA sequence:RefSeq:WP_016392562.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
MurR/RpiR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008553655.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018390055.1
COORDINATES: similar to AA sequence:RefSeq:WP_008555232.1
COORDINATES: similar to AA sequence:RefSeq:WP_016958492.1
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]
amino acid ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008557397.1
GO:0016836 - hydro-lyase activity [Evidence IEA]
GO:0009234 - menaquinone biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013066373.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016103.2
COORDINATES: similar to AA sequence:RefSeq:WP_032490240.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013690338.1
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_076612067.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010972061.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187132.1
COORDINATES: similar to AA sequence:RefSeq:WP_013963365.1
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009573044.1
GO:0015079 - potassium ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020043192.1
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_008230163.1
COORDINATES: similar to AA sequence:RefSeq:WP_018302362.1
GO:0070004 - cysteine-type exopeptidase activity [Evidence IEA]; GO:0016805 - dipeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007117443.1
COORDINATES: similar to AA sequence:RefSeq:WP_009489493.1
COORDINATES: similar to AA sequence:RefSeq:WP_012490094.1
GO:0042314 - bacteriochlorophyll binding [Evidence IEA]
GO:0019684 - photosynthesis, light reaction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012330183.1
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: protein motif:HMM:NF016228.2
COORDINATES: similar to AA sequence:RefSeq:WP_008834263.1
GO:0030552 - cAMP binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
Crp/Fnr family transcriptional regulator
COORDINATES: protein motif:HMM:NF017088.2
COORDINATES: similar to AA sequence:RefSeq:WP_007255764.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009805313.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_010142328.1
COORDINATES: protein motif:HMM:NF024408.2
COORDINATES: protein motif:HMM:NF015038.2
COORDINATES: similar to AA sequence:RefSeq:WP_012178777.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121476.1
COORDINATES: protein motif:HMM:NF024583.2
GAF domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_007813144.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970376.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_005848479.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807491.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_017927554.1
COORDINATES: similar to AA sequence:RefSeq:WP_009805271.1
COORDINATES: similar to AA sequence:RefSeq:WP_009805272.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803463.1
GO:0046873 - metal ion transmembrane transporter activity [Evidence IEA]
GO:0030001 - metal ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007117797.1
COORDINATES: similar to AA sequence:RefSeq:WP_005848437.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120831.1
COORDINATES: similar to AA sequence:RefSeq:WP_007117800.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120830.1
COORDINATES: similar to AA sequence:RefSeq:WP_007117802.1
COORDINATES: similar to AA sequence:RefSeq:WP_007117803.1
COORDINATES: protein motif:HMM:NF014430.2
COORDINATES: protein motif:HMM:NF013695.2
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF012707.2
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009178594.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF014425.2
COORDINATES: similar to AA sequence:RefSeq:WP_006871971.1
COORDINATES: protein motif:HMM:NF016060.2
COORDINATES: protein motif:HMM:NF015378.2
COORDINATES: protein motif:HMM:NF012376.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011870613.1
COORDINATES: protein motif:HMM:NF021425.2
COORDINATES: similar to AA sequence:RefSeq:WP_008226613.1
COORDINATES: similar to AA sequence:RefSeq:WP_015496948.1
GO:0004671 - protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity [Evidence IEA]
GO:0006481 - C-terminal protein methylation [Evidence IEA]
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008233197.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187055.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820065.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558248.1
COORDINATES: similar to AA sequence:RefSeq:WP_015502016.1