Sphingomonas morindae strain NBD5 plasmid p1, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas.
Genomic Analysis of Sphingopyxis sp. USTB-05 for Biodegrading Cyanobacterial Hepatotoxins
Submitted (12-OCT-2021) University of Science and Technology Beijing, School of Chemistry and Biological Engineering, 30 Xueyuan Road, Beijing 100083, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP084932.1.\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 :: SPAdes v. v3.6.2\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 360.0x\nSequencing Technology :: Illumina; PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 07/26/2023 04:20:09\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) :: 3,996\nCDSs (total) :: 3,933\nGenes (coding) :: 3,896\nCDSs (with protein) :: 3,896\nGenes (RNA) :: 63\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 3\nPseudo Genes (total) :: 37\nCDSs (without protein) :: 37\nPseudo Genes (ambiguous residues) :: 0 of 37\nPseudo Genes (frameshifted) :: 7 of 37\nPseudo Genes (incomplete) :: 30 of 37\nPseudo Genes (internal stop) :: 3 of 37\nPseudo Genes (multiple problems) :: 3 of 37\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011387953.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011842162.1
COORDINATES: similar to AA sequence:RefSeq:WP_004713999.1
COORDINATES: similar to AA sequence:RefSeq:WP_011473969.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019644338.1
COORDINATES: similar to AA sequence:RefSeq:WP_015343357.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012332229.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014198671.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007404401.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006498421.1
COORDINATES: protein motif:HMM:NF012655.2
COORDINATES: similar to AA sequence:RefSeq:WP_006391147.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018046056.1
COORDINATES: similar to AA sequence:RefSeq:WP_013949364.1
GO:0008661 - 1-deoxy-D-xylulose-5-phosphate synthase activity [Evidence IEA]
GO:0009240 - isopentenyl diphosphate biosynthetic process [Evidence IEA]; GO:0008615 - pyridoxine biosynthetic process [Evidence IEA]; GO:0009228 - thiamine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010236663.1
COORDINATES: similar to AA sequence:RefSeq:WP_019860992.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013793399.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013393138.1
COORDINATES: similar to AA sequence:RefSeq:WP_006480109.1
COORDINATES: similar to AA sequence:RefSeq:WP_004941032.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013953674.1
COORDINATES: protein motif:HMM:NF014573.2
COORDINATES: similar to AA sequence:RefSeq:WP_006408482.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
PLP-dependent aminotransferase family protein
COORDINATES: protein motif:HMM:NF018984.2
CGNR zinc finger domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012521629.1
COORDINATES: similar to AA sequence:RefSeq:WP_007629306.1
GO:0008837 - diaminopimelate epimerase activity [Evidence IEA]
GO:0009089 - lysine biosynthetic process via diaminopimelate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011353347.1
COORDINATES: similar to AA sequence:RefSeq:WP_004547623.1
GO:0008902 - hydroxymethylpyrimidine kinase activity [Evidence IEA]; GO:0008972 - phosphomethylpyrimidine kinase activity [Evidence IEA]
GO:0009228 - thiamine biosynthetic process [Evidence IEA]
bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase
COORDINATES: protein motif:HMM:TIGR00654.1
GO:0016853 - isomerase activity [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
PhzF family phenazine biosynthesis protein
COORDINATES: similar to AA sequence:RefSeq:WP_012978423.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012652305.1
COORDINATES: similar to AA sequence:RefSeq:WP_008992981.1
COORDINATES: similar to AA sequence:RefSeq:WP_009876097.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015636448.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008992978.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009635041.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_015603651.1
COORDINATES: similar to AA sequence:RefSeq:WP_012075274.1
COORDINATES: similar to AA sequence:RefSeq:WP_013592443.1
COORDINATES: similar to AA sequence:RefSeq:WP_016348546.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: protein motif:HMM:NF012791.2
COORDINATES: protein motif:HMM:NF013088.2
GO:0005215 - transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008459105.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_014593516.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824046.1
COORDINATES: similar to AA sequence:RefSeq:WP_013849039.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212859.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_007688084.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406711.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010124626.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054339.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124624.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124622.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010124621.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124620.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124619.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124618.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124617.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124616.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124614.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339722.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124611.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124610.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405792.1
COORDINATES: similar to AA sequence:RefSeq:WP_010124607.1
COORDINATES: protein motif:HMM:NF024491.2
COORDINATES: similar to AA sequence:RefSeq:WP_008829869.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950494.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339733.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460600.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405780.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015563.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950430.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054787.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409146.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405773.1
COORDINATES: similar to AA sequence:RefSeq:WP_014076970.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - DNA damage response [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010405769.1
GO:0008233 - peptidase activity [Evidence IEA]; GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
COORDINATES: protein motif:HMM:NF025388.2
COORDINATES: similar to AA sequence:RefSeq:WP_012553005.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010405766.1
COORDINATES: protein motif:HMM:NF039631.1
COORDINATES: protein motif:HMM:NF024676.2
COORDINATES: similar to AA sequence:RefSeq:WP_013419523.1
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: similar to AA sequence:RefSeq:WP_004212815.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010161916.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405760.1
COORDINATES: similar to AA sequence:RefSeq:WP_010406934.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339754.1
Stk19 family serine/threonine-protein kinase
COORDINATES: similar to AA sequence:RefSeq:WP_010124788.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019054648.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015600.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015601.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054280.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405706.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818495.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_015460511.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_011950635.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405697.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_010124755.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405693.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_019054288.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818502.1
COORDINATES: similar to AA sequence:RefSeq:WP_020818503.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405687.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406582.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405683.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_011950625.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_015460523.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_010339789.1
COORDINATES: similar to AA sequence:RefSeq:WP_010405676.1
COORDINATES: similar to AA sequence:RefSeq:WP_011950621.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007406700.1
COORDINATES: protein motif:HMM:NF033542.1
COORDINATES: protein motif:HMM:NF019310.2
COORDINATES: similar to AA sequence:RefSeq:WP_015672200.1
COORDINATES: protein motif:HMM:TIGR01262.1
GO:0016034 - maleylacetoacetate isomerase activity [Evidence IEA]
GO:0006559 - L-phenylalanine catabolic process [Evidence IEA]; GO:0006572 - tyrosine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012699062.1
COORDINATES: similar to AA sequence:RefSeq:WP_003821135.1
COORDINATES: similar to AA sequence:RefSeq:WP_011349542.1
COORDINATES: similar to AA sequence:RefSeq:WP_017331011.1
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_004274266.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004938785.1
GO:0016020 - membrane [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008971475.1
COORDINATES: similar to AA sequence:RefSeq:WP_018080191.1
GO:0045250 - cytosolic pyruvate dehydrogenase complex [Evidence IEA]
GO:0004739 - pyruvate dehydrogenase (acetyl-transferring) activity [Evidence IEA]
GO:0006086 - acetyl-CoA biosynthetic process from pyruvate [Evidence IEA]
pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
COORDINATES: protein motif:HMM:NF014035.2
COORDINATES: similar to AA sequence:RefSeq:WP_014229972.1
COORDINATES: similar to AA sequence:RefSeq:WP_017452679.1
COORDINATES: similar to AA sequence:RefSeq:WP_012288045.1
COORDINATES: similar to AA sequence:RefSeq:WP_007880184.1
lipocalin-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007878814.1
COORDINATES: similar to AA sequence:RefSeq:WP_016554476.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003163922.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020817929.1
COORDINATES: similar to AA sequence:RefSeq:WP_007407192.1
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.; 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; 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_009823855.1