Duncaniella dubosii strain H5 plasmid pH5-3.
Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Muribaculaceae; Duncaniella.
Cultivation and description of Duncaniella dubosii sp. nov., Duncaniella freteri sp. nov. and emended description of the species Duncaniella muris
Submitted (28-FEB-2019) Henning Seedorf Group, Temasek Life Sciences Laboratory Limited, 1 Research Link National University of Singapore Singapore, Singapore 117604, Singapore
REFSEQ INFORMATION: The reference sequence is identical to\nCP039399.1.\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/\n\n##Genome-Assembly-Data-START##\nAssembly Method :: Canu v. 1.8\nAssembly Name :: MuDubo_H5_1.1\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 317.98x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/06/2022 04:05:55\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 3,339\nCDSs (total) :: 3,271\nGenes (coding) :: 3,086\nCDSs (with protein) :: 3,086\nGenes (RNA) :: 68\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 53\nncRNAs :: 3\nPseudo Genes (total) :: 185\nCDSs (without protein) :: 185\nPseudo Genes (ambiguous residues) :: 0 of 185\nPseudo Genes (frameshifted) :: 142 of 185\nPseudo Genes (incomplete) :: 55 of 185\nPseudo Genes (internal stop) :: 5 of 185\nPseudo Genes (multiple problems) :: 17 of 185\n##Genome-Annotation-Data-END##
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF024811.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013887.2
COORDINATES: protein motif:HMM:NF024957.2
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005935374.1
GO:0045203 - integral component of cell outer membrane [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0071702 - organic substance transport [Evidence IEA]
SusC/RagA family TonB-linked outer membrane protein
COORDINATES: protein motif:HMM:NF025680.2
RagB/SusD family nutrient uptake outer membrane protein
COORDINATES: protein motif:HMM:NF016232.2
COORDINATES: similar to AA sequence:RefSeq:WP_005846071.1
GO:0005506 - iron ion binding [Evidence IEA]; GO:0043768 - S-ribosylhomocysteine lyase activity [Evidence IEA]
GO:0009372 - quorum sensing [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF004079.0
GO:0008782 - adenosylhomocysteine nucleosidase activity [Evidence IEA]; GO:0008930 - methylthioadenosine nucleosidase activity [Evidence IEA]
GO:0019509 - L-methionine salvage from methylthioadenosine [Evidence IEA]; GO:0009164 - nucleoside catabolic process [Evidence IEA]; GO:0009116 - nucleoside metabolic process [Evidence IEA]
5'-methylthioadenosine/adenosylhomocysteine nucleosidase
COORDINATES: similar to AA sequence:RefSeq:WP_008140199.1
GO:0005887 - integral component of plasma membrane [Evidence IEA]
GO:0015628 - protein secretion by the type II secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008760985.1
twin-arginine translocase TatA/TatE family subunit
COORDINATES: similar to AA sequence:RefSeq:WP_010799941.1
GO:0004314 - [acyl-carrier-protein] S-malonyltransferase activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF021445.2
phosphatidylglycerol lysyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019246457.1
GO:0004414 - homoserine O-acetyltransferase activity [Evidence IEA]
GO:0009086 - methionine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013088.2
incomplete; too short partial abutting assembly gap; missing N-terminus; Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.