Sphingomonas taxi strain ATCC 55669 plasmid STP2, 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\nCP009573.1.\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: similar to AA sequence:RefSeq:WP_008971017.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007406239.1
GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007406255.1
COORDINATES: similar to AA sequence:RefSeq:WP_011299921.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01734
Fluoride riboswitches increase expression of downstream genes that help mitigate the toxic effects of very high levels of fluoride; They are found in a wide variety of bacteria and archaea; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_007686136.1
voltage-gated chloride channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007406288.1
COORDINATES: similar to AA sequence:RefSeq:WP_011638900.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010542917.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_013832728.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
This arsenate reductase requires both glutathione and glutaredoxin to convert arsenate to arsenite, after which the efflux transporter formed by ArsA and ArsB can extrude the arsenite from the cell, providing resistance; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010217637.1
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_018251258.1
arsenic resistance N-acetyltransferase ArsN2
COORDINATES: similar to AA sequence:RefSeq:WP_007187125.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_008901296.1
COORDINATES: similar to AA sequence:RefSeq:WP_016509812.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832610.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_016509651.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165403.1
COORDINATES: similar to AA sequence:RefSeq:WP_018251318.1
COORDINATES: similar to AA sequence:RefSeq:WP_008830766.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213377.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010189082.1
COORDINATES: similar to AA sequence:RefSeq:WP_010189084.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339747.1
COORDINATES: similar to AA sequence:RefSeq:WP_007565538.1
COORDINATES: similar to AA sequence:RefSeq:WP_006699327.1
COORDINATES: similar to AA sequence:RefSeq:WP_007565534.1
COORDINATES: similar to AA sequence:RefSeq:WP_006725883.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0009036 - type II site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
DpnII family type II restriction endonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_012383036.1
GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0032775 - DNA methylation on adenine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014414412.1
COORDINATES: similar to AA sequence:RefSeq:WP_019368240.1
COORDINATES: similar to AA sequence:RefSeq:WP_003046458.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011413839.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]; GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_010123226.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016744762.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_012048818.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_007406258.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008830651.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406242.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406272.1
COORDINATES: similar to AA sequence:RefSeq:WP_007406227.1
COORDINATES: protein motif:HMM:NF014373.2