Roseibium alexandrii DFL-11 plasmid pLADFL_2, whole genome shotgun sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales; Stappiaceae; Roseibium.
Submitted (10-APR-2013) Microbiology, DSMZ German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7b, Braunschweig, Lower Saxony 38124, Germany
Submitted (23-JAN-2008) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCM011004.1.\nBacteria available from DSM 17067.\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 :: consed v. 20.0\nGenome Coverage :: 9.1x\nSequencing Technology :: Sanger dideoxy sequencing\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/22/2022 02:55:10\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\nGenes (total) :: 5,069\nCDSs (total) :: 5,004\nGenes (coding) :: 4,973\nCDSs (with protein) :: 4,973\nGenes (RNA) :: 65\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 4\nPseudo Genes (total) :: 31\nCDSs (without protein) :: 31\nPseudo Genes (ambiguous residues) :: 0 of 31\nPseudo Genes (frameshifted) :: 9 of 31\nPseudo Genes (incomplete) :: 16 of 31\nPseudo Genes (internal stop) :: 9 of 31\nPseudo Genes (multiple problems) :: 3 of 31\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007120947.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR01843.1
GO:0030253 - protein secretion by the type I secretion system [Evidence IEA]
HlyD family type I secretion periplasmic adaptor subunit
COORDINATES: protein motif:HMM:NF013592.2
GO:0008237 - metallopeptidase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF016103.2
COORDINATES: protein motif:HMM:NF020137.2
GO:0005615 - extracellular space [Evidence IEA]
GO:0005509 - calcium ion binding [Evidence IEA]
M10 family metallopeptidase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019895282.1
COORDINATES: similar to AA sequence:RefSeq:WP_013080350.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018244892.1
COORDINATES: similar to AA sequence:RefSeq:WP_006414625.1
COORDINATES: similar to AA sequence:RefSeq:WP_008563383.1
COORDINATES: similar to AA sequence:RefSeq:WP_009602377.1
Lrp/AsnC family transcriptional regulator
COORDINATES: protein motif:HMM:NF024966.2
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011454443.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012187449.1
COORDINATES: protein motif:HMM:NF012437.2
adenylate/guanylate cyclase domain-containing protein
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: similar to AA sequence:RefSeq:WP_010443224.1
GO:0008168 - methyltransferase activity [Evidence IEA]
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011567950.1
COORDINATES: similar to AA sequence:RefSeq:WP_019296476.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]
GO:0006276 - plasmid maintenance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004356840.1
type II toxin-antitoxin system CcdA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018688776.1
GO:0004151 - dihydroorotase activity [Evidence IEA]
GO:0009220 - pyrimidine ribonucleotide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018387846.1
COORDINATES: similar to AA sequence:RefSeq:WP_000466893.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
Vi polysaccharide biosynthesis UDP-N-acetylglucosamine C-6 dehydrogenase TviB
COORDINATES: similar to AA sequence:RefSeq:WP_013442146.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF012707.2
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF013884.2
COORDINATES: similar to AA sequence:RefSeq:WP_009465882.1
COORDINATES: similar to AA sequence:RefSeq:WP_006940530.1
GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
nucleotidyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013844964.1
COORDINATES: similar to AA sequence:RefSeq:WP_009465877.1
COORDINATES: similar to AA sequence:RefSeq:WP_007007332.1
COORDINATES: similar to AA sequence:RefSeq:WP_009756421.1
COORDINATES: similar to AA sequence:RefSeq:WP_009465888.1
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: similar to AA sequence:RefSeq:WP_009465872.1
nucleoside-diphosphate sugar epimerase/dehydratase
COORDINATES: protein motif:HMM:NF040132.1
type I secretion target GGXGXDXXX repeat protein
COORDINATES: similar to AA sequence:RefSeq:WP_014490841.1
COORDINATES: similar to AA sequence:RefSeq:WP_002622597.1
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: similar to AA sequence:RefSeq:WP_011387739.1
COORDINATES: protein motif:HMM:NF013245.2
COORDINATES: similar to AA sequence:RefSeq:WP_003578449.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019517861.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_012050204.1
GO:0008831 - dTDP-4-dehydrorhamnose reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012050202.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]