Roseobacter litoralis Och 149 plasmid pRLO149_63, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Roseobacter.
Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis
Submitted (23-MAR-2011) Goettingen Genomics Laboratory, Georg-August University Goettingen, Grisebachstr. 8, Goettingen, Lower Saxony D-37077, Germany
Submitted (19-NOV-2007) J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002626.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/02/2023 02:19:05\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) :: 4,549\nCDSs (total) :: 4,505\nGenes (coding) :: 4,405\nCDSs (with protein) :: 4,405\nGenes (RNA) :: 44\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 38\nncRNAs :: 3\nPseudo Genes (total) :: 100\nCDSs (without protein) :: 100\nPseudo Genes (ambiguous residues) :: 0 of 100\nPseudo Genes (frameshifted) :: 49 of 100\nPseudo Genes (incomplete) :: 63 of 100\nPseudo Genes (internal stop) :: 31 of 100\nPseudo Genes (multiple problems) :: 36 of 100\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_013959933.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011836179.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011655500.1
VPLPA-CTERM sorting domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011655499.1
COORDINATES: similar to AA sequence:RefSeq:WP_011655501.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_011655502.1
GO:0004197 - cysteine-type endopeptidase activity [Evidence IEA]
GO:0043687 - post-translational protein modification [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF014430.2
COORDINATES: similar to AA sequence:RefSeq:WP_010915363.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; 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_076611960.1
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_076611339.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; internal stop; 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_007257267.1
COORDINATES: similar to AA sequence:RefSeq:WP_011655482.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_011655483.1
GO:0008831 - dTDP-4-dehydrorhamnose reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002724808.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020041597.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011453091.1
GO:0003978 - UDP-glucose 4-epimerase activity [Evidence IEA]
GO:0006012 - galactose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019965822.1
GO:0003824 - catalytic activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009825185.1
bifunctional sulfate adenylyltransferase/adenylylsulfate kinase
COORDINATES: similar to AA sequence:RefSeq:WP_011569549.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008229928.1
COORDINATES: protein motif:HMM:NF024997.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076612405.1
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.; internal stop; 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_011053446.1
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_076611519.1
GO:0015074 - DNA integration [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008994567.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]; GO:0003979 - UDP-glucose 6-dehydrogenase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012187422.1
COORDINATES: protein motif:HMM:NF039218.1
SGNH hydrolase domain-containing protein
COORDINATES: protein motif:HMM:NF024627.2
right-handed parallel beta-helix repeat-containing protein
COORDINATES: protein motif:HMM:TIGR04099.1
COORDINATES: protein motif:HMM:NF012744.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: protein motif:HMM:NF036807.2
COORDINATES: similar to AA sequence:RefSeq:WP_017942192.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF021616.2
COORDINATES: protein motif:HMM:NF013884.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611156.1
COORDINATES: protein motif:HMM:NF033573.1
COORDINATES: protein motif:HMM:NF014453.2
COORDINATES: similar to AA sequence:RefSeq:WP_013959971.1
COORDINATES: similar to AA sequence:RefSeq:WP_013959972.1
COORDINATES: similar to AA sequence:RefSeq:WP_011655486.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004715 - non-membrane spanning protein tyrosine kinase activity [Evidence IEA]; GO:0004713 - protein tyrosine kinase activity [Evidence IEA]
CpsD/CapB family tyrosine-protein kinase
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_011655490.1
COORDINATES: similar to AA sequence:RefSeq:WP_011655491.1
GO:0016020 - membrane [Evidence IEA]; GO:0042597 - periplasmic space [Evidence IEA]
GO:0015159 - polysaccharide transmembrane transporter activity [Evidence IEA]
polysaccharide biosynthesis/export family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011655492.1
COORDINATES: similar to AA sequence:RefSeq:WP_012180042.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
rhomboid family intramembrane serine protease
COORDINATES: similar to AA sequence:RefSeq:WP_011655513.1