Sphingomonas paucimobilis strain FDAARGOS_908 plasmid unnamed2, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas.
FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS): Supporting development and validation of Infectious Disease Dx tests
Submitted (02-DEC-2020) Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993-0002, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP065671.1.\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. 1.7\nGenome Coverage :: 849.08x\nSequencing Technology :: Pacbio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/19/2022 15:15:39\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,081\nCDSs (total) :: 4,014\nGenes (coding) :: 3,967\nCDSs (with protein) :: 3,967\nGenes (RNA) :: 67\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 3\nPseudo Genes (total) :: 47\nCDSs (without protein) :: 47\nPseudo Genes (ambiguous residues) :: 0 of 47\nPseudo Genes (frameshifted) :: 23 of 47\nPseudo Genes (incomplete) :: 31 of 47\nPseudo Genes (internal stop) :: 5 of 47\nPseudo Genes (multiple problems) :: 11 of 47\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Sphingomonas paucimobilis
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_010402266.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611592.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014732.2
exopolysaccharide transport family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011415592.1
polysaccharide biosynthesis/export family protein
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: protein motif:HMM:TIGR03025.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0032508 - DNA duplex unwinding [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]
exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF013884.2
COORDINATES: similar to AA sequence:RefSeq:WP_019370336.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611376.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611473.1
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_011906605.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611975.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611908.1
COORDINATES: similar to AA sequence:RefSeq:WP_007404579.1
GO:0003983 - UTP:glucose-1-phosphate uridylyltransferase activity [Evidence IEA]
GO:0009225 - nucleotide-sugar metabolic process [Evidence IEA]
UTP--glucose-1-phosphate uridylyltransferase GalU
COORDINATES: similar to AA sequence:RefSeq:WP_013041578.1
COORDINATES: similar to AA sequence:RefSeq:WP_019517859.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251339.1
COORDINATES: similar to AA sequence:RefSeq:WP_019517853.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212934.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017482513.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007404386.1
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_014075654.1
COORDINATES: similar to AA sequence:RefSeq:WP_007403430.1
GO:0009116 - nucleoside metabolic process [Evidence IEA]
phosphoribosyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010545563.1
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF014376.2
COORDINATES: similar to AA sequence:RefSeq:WP_015449221.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010183454.1
autotransporter outer membrane beta-barrel domain-containing protein
COORDINATES: protein motif:HMM:NF020366.2
COORDINATES: protein motif:HMM:NF040127.1
RHS repeat-associated core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003167461.1
GO:0019867 - outer membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017668111.1
GO:0016158 - 3-phytase activity [Evidence IEA]
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: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:TIGR02686.1
COORDINATES: similar to AA sequence:RefSeq:WP_016508770.1
COORDINATES: protein motif:HMM:NF017315.2
ankyrin repeat domain-containing protein