Sphingomonas taxi strain ATCC 55669 plasmid STP1, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas.
Using Illumina technology Improving SMRT sequencing Genome Assembly by RASTools
Submitted (30-SEP-2014) Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan, Hubei 430072, P.R. China
REFSEQ INFORMATION: The reference sequence is identical to\nCP009572.1.\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 Date :: SEP-2014\nAssembly Method :: Celera Assembler v. 7.0\nGenome Coverage :: 300x\nSequencing Technology :: PacBio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/03/2023 03:24:33\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) :: 3,801\nCDSs (total) :: 3,737\nGenes (coding) :: 3,709\nCDSs (with protein) :: 3,709\nGenes (RNA) :: 64\nrRNAs :: 3, 2, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 2, 3 (5S, 16S, 23S)\ntRNAs :: 53\nncRNAs :: 3\nPseudo Genes (total) :: 28\nCDSs (without protein) :: 28\nPseudo Genes (ambiguous residues) :: 0 of 28\nPseudo Genes (frameshifted) :: 6 of 28\nPseudo Genes (incomplete) :: 20 of 28\nPseudo Genes (internal stop) :: 7 of 28\nPseudo Genes (multiple problems) :: 4 of 28\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_012382806.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR02937.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF016648.2
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: protein motif:HMM:NF015506.2
GO:0015291 - secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020820384.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011415591.1
polysaccharide biosynthesis tyrosine autokinase
COORDINATES: similar to AA sequence:RefSeq:WP_011415592.1
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: protein motif:HMM:NF016800.2
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF015013.2
COORDINATES: similar to AA sequence:RefSeq:WP_018387846.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019833865.1
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_018858132.1
GO:0016740 - transferase activity [Evidence IEA]
GO:0006486 - protein glycosylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF013530.2
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF012745.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: protein motif:HMM:NF026247.2
COORDINATES: similar to AA sequence:RefSeq:WP_013046832.1
GO:0004066 - asparagine synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0006529 - asparagine biosynthetic process [Evidence IEA]
asparagine synthase (glutamine-hydrolyzing)
COORDINATES: similar to AA sequence:RefSeq:WP_012418447.1
COORDINATES: similar to AA sequence:RefSeq:WP_011464961.1
nucleoside-diphosphate sugar epimerase/dehydratase
COORDINATES: similar to AA sequence:RefSeq:WP_010406322.1
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]
UDP-glucose/GDP-mannose dehydrogenase family protein
COORDINATES: protein motif:HMM:NF027681.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612266.1
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_019517860.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251340.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251339.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018251338.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00504
glycine riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_018251335.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0003941 - L-serine ammonia-lyase activity [Evidence IEA]
GO:0009063 - amino acid catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008264279.1
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_018251333.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
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: protein motif:HMM:NF013652.2
COORDINATES: protein motif:HMM:NF012925.2
COORDINATES: similar to AA sequence:RefSeq:WP_010214877.1
COORDINATES: similar to AA sequence:RefSeq:WP_019370335.1
COORDINATES: similar to AA sequence:RefSeq:WP_012041344.1
COORDINATES: similar to AA sequence:RefSeq:WP_010218110.1
COORDINATES: protein motif:HMM:NF013250.2
GO:0005886 - plasma membrane [Evidence IEA]
GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0016780 - phosphotransferase activity, for other substituted phosphate groups [Evidence IEA]
GO:0008654 - phospholipid biosynthetic process [Evidence IEA]
CDP-alcohol phosphatidyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012469591.1
COORDINATES: similar to AA sequence:RefSeq:WP_019463138.1
COORDINATES: similar to AA sequence:RefSeq:WP_004194035.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
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_011444408.1
COORDINATES: similar to AA sequence:RefSeq:WP_011444407.1
COORDINATES: protein motif:HMM:NF025072.2
COORDINATES: similar to AA sequence:RefSeq:WP_007014492.1
COORDINATES: similar to AA sequence:RefSeq:WP_010123145.1
GO:0016987 - sigma factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017980828.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024832.2
COORDINATES: similar to AA sequence:RefSeq:WP_018270720.1
GO:0003978 - UDP-glucose 4-epimerase activity [Evidence IEA]
GO:0006012 - galactose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009182348.1
COORDINATES: similar to AA sequence:RefSeq:WP_010214641.1
COORDINATES: protein motif:HMM:NF013884.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: protein motif:HMM:NF018894.2
GO:0035438 - cyclic-di-GMP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010402297.1
COORDINATES: similar to AA sequence:RefSeq:WP_015927587.1
COORDINATES: similar to AA sequence:RefSeq:WP_010411239.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010215476.1
GO:0045226 - extracellular polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF021589.2
COORDINATES: similar to AA sequence:RefSeq:WP_008065671.1
COORDINATES: protein motif:HMM:NF017815.2
transglutaminase-like cysteine peptidase
COORDINATES: similar to AA sequence:RefSeq:WP_010164687.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406138.1
COORDINATES: protein motif:HMM:NF012376.2
GO:0046872 - metal ion binding [Evidence IEA]; GO:0042578 - phosphoric ester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014075412.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0015343 - siderophore-iron transmembrane transporter activity [Evidence IEA]
GO:0015891 - siderophore transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007403672.1
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: similar to AA sequence:RefSeq:WP_015823988.1
COORDINATES: similar to AA sequence:RefSeq:WP_008994793.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010163014.1
COORDINATES: similar to AA sequence:RefSeq:WP_010163015.1
COORDINATES: similar to AA sequence:RefSeq:WP_009365753.1
COORDINATES: protein motif:HMM:NF024260.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF025013.2
COORDINATES: similar to AA sequence:RefSeq:WP_019516244.1
COORDINATES: similar to AA sequence:RefSeq:WP_010216071.1
COORDINATES: similar to AA sequence:RefSeq:WP_010218197.1
COORDINATES: similar to AA sequence:RefSeq:WP_010218196.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007806145.1
COORDINATES: similar to AA sequence:RefSeq:WP_017979310.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212437.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017979312.1
COORDINATES: similar to AA sequence:RefSeq:WP_007404629.1
COORDINATES: similar to AA sequence:RefSeq:WP_011240762.1
COORDINATES: protein motif:HMM:NF025341.2
retroviral-like aspartic protease family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020486625.1
COORDINATES: protein motif:HMM:NF013166.2
GO:0009058 - biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020185120.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008068749.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017669964.1
COORDINATES: similar to AA sequence:RefSeq:WP_008995120.1
GO:0005247 - voltage-gated chloride channel activity [Evidence IEA]
GO:0006821 - chloride transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007714301.1
GO:0052621 - diguanylate cyclase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_017669994.1
GO:0030552 - cAMP binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_020095762.1
COORDINATES: similar to AA sequence:RefSeq:WP_010163639.1
L-dopachrome tautomerase-related protein
COORDINATES: similar to AA sequence:RefSeq:WP_014266664.1
COORDINATES: similar to AA sequence:RefSeq:WP_019369563.1
COORDINATES: similar to AA sequence:RefSeq:WP_015074565.1
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014594231.1
COORDINATES: protein motif:HMM:NF013180.2
COORDINATES: similar to AA sequence:RefSeq:WP_018251330.1
GO:0016901 - oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor [Evidence IEA]; GO:0070968 - pyrroloquinoline quinone binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015449221.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824069.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823472.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219187.1
polysaccharide pyruvyl transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007562603.1
COORDINATES: similar to AA sequence:RefSeq:WP_010161698.1
COORDINATES: similar to AA sequence:RefSeq:WP_018250713.1
GO:0016758 - hexosyltransferase activity [Evidence IEA]