Sulfitobacter indolifex strain DSM 14862 plasmid pDSM14862_f, 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\nCP084957.1.\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: similar to AA sequence:RefSeq:WP_007120631.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009820211.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820212.1
helix-turn-helix 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_009819701.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009819700.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820102.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120639.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807542.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120641.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187358.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807539.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_009820261.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187076.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012187077.1
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_007120648.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019956866.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819682.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503768.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327427.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187348.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819680.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187346.1
COORDINATES: similar to AA sequence:RefSeq:WP_015459160.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282936.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282937.1
COORDINATES: similar to AA sequence:RefSeq:WP_012563552.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913042.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820257.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536569.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120663.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807938.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807937.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF012257.2
GO:0030551 - cyclic nucleotide binding [Evidence IEA]
cyclic nucleotide-binding domain-containing protein
COORDINATES: protein motif:HMM:NF024676.2
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020398669.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808070.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120671.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187154.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820228.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327387.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808065.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807512.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820232.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120678.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009815545.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807508.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808058.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327370.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282965.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120686.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009808043.1
COORDINATES: similar to AA sequence:RefSeq:WP_006204614.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009503854.1
GO:0016746 - acyltransferase activity [Evidence IEA]; GO:0071972 - peptidoglycan L,D-transpeptidase activity [Evidence IEA]
GO:0018104 - peptidoglycan-protein cross-linking [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013963890.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820137.1
GO:0042834 - peptidoglycan binding [Evidence IEA]; GO:0071972 - peptidoglycan L,D-transpeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009820243.1
GO:0008168 - methyltransferase activity [Evidence IEA]
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009820244.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_008282972.1
COORDINATES: similar to AA sequence:RefSeq:WP_005645239.1
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017927563.1
COORDINATES: similar to AA sequence:RefSeq:WP_018303599.1
COORDINATES: similar to AA sequence:RefSeq:WP_018303600.1
GO:0031966 - mitochondrial membrane [Evidence IEA]
GO:0033617 - mitochondrial cytochrome c oxidase assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009452625.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001721.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803470.1
GO:0016531 - copper chaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008946249.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803467.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803465.1
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_007803461.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008282831.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007425974.1
COORDINATES: similar to AA sequence:RefSeq:WP_008889351.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120876.1
COORDINATES: similar to AA sequence:RefSeq:WP_018324544.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014527051.1
COORDINATES: similar to AA sequence:RefSeq:WP_011316285.1
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_006200950.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_009820141.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820142.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009820143.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
ABC transporter transmembrane domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120884.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0009055 - electron transfer activity [Evidence IEA]
plastocyanin/azurin family copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120885.1
COORDINATES: similar to AA sequence:RefSeq:WP_010968681.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820147.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009824197.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282876.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503816.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187038.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018065824.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Cu(I)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009503819.1
COORDINATES: similar to AA sequence:RefSeq:WP_007796189.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121398.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503821.1
GO:0017004 - cytochrome complex assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009503822.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820200.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121402.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503826.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005613368.1
DsbE family thiol:disulfide interchange protein
COORDINATES: similar to AA sequence:RefSeq:WP_009820202.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007121580.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820203.1
COORDINATES: similar to AA sequence:RefSeq:WP_014332191.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120831.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820205.1
COORDINATES: similar to AA sequence:RefSeq:WP_007117802.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009820206.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120629.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820208.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]