Pseudorhizobium flavum strain YW14 plasmid 5, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Pseudorhizobium.
Submitted (20-OCT-2020) UNIVERSITY COLLEGE LONDON, UCL Genetics Institute, Gower Street, London WC1E 6BT, United Kingdom
Submitted (07-OCT-2019) UNIVERSITY COLLEGE LONDON, UCL Genetics Institute, Gower Street, London WC1E 6BT, United Kingdom
REFSEQ INFORMATION: The reference sequence is identical to\nLR723674.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 04:57:52\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) :: 4,621\nCDSs (total) :: 4,558\nGenes (coding) :: 4,447\nCDSs (with protein) :: 4,447\nGenes (RNA) :: 63\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 4\nPseudo Genes (total) :: 111\nCDSs (without protein) :: 111\nPseudo Genes (ambiguous residues) :: 0 of 111\nPseudo Genes (frameshifted) :: 53 of 111\nPseudo Genes (incomplete) :: 79 of 111\nPseudo Genes (internal stop) :: 19 of 111\nPseudo Genes (multiple problems) :: 33 of 111\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Paddy soil under the long-term application of triazophos insecticide
COORDINATES: similar to AA sequence:RefSeq:WP_015916284.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003163966.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014189897.1
COORDINATES: similar to AA sequence:RefSeq:WP_020811333.1
GO:0008767 - UDP-galactopyranose mutase activity [Evidence IEA]
GO:0009273 - peptidoglycan-based cell wall biogenesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014327299.1
COORDINATES: similar to AA sequence:RefSeq:WP_015916637.1
COORDINATES: protein motif:HMM:NF040115.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_004432490.1
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0071973 - bacterial-type flagellum-dependent cell motility [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012556612.1
COORDINATES: protein motif:HMM:NF018458.2
COORDINATES: protein motif:HMM:NF013884.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008530272.1
COORDINATES: similar to AA sequence:RefSeq:WP_007598477.1
COORDINATES: similar to AA sequence:RefSeq:WP_018096619.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_006724018.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF024784.2
COORDINATES: similar to AA sequence:RefSeq:WP_014330936.1
COORDINATES: similar to AA sequence:RefSeq:WP_014330937.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011749831.1
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; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF015513.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012606012.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013080.2
GO:0008484 - sulfuric ester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013066393.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004143 - diacylglycerol kinase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0006654 - phosphatidic acid biosynthetic process [Evidence IEA]; GO:0008654 - phospholipid biosynthetic process [Evidence IEA]; GO:0016310 - phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012497740.1
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024871.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611421.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007801588.1
GO:0043163 - cell envelope organization [Evidence IEA]
WecB/TagA/CpsF family glycosyltransferase
COORDINATES: protein motif:HMM:NF014732.2
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: protein motif:HMM:NF014051.2
COORDINATES: protein motif:HMM:NF025292.2
lipocalin-like domain-containing protein
COORDINATES: protein motif:HMM:NF012698.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003574557.1
GO:0016779 - nucleotidyltransferase 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.
nucleotidyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611865.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007773203.1
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_011424107.1
COORDINATES: protein motif:HMM:NF025314.2
COORDINATES: similar to AA sequence:RefSeq:WP_015318710.1
COORDINATES: similar to AA sequence:RefSeq:WP_009210110.1
GO:0008446 - GDP-mannose 4,6-dehydratase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120947.1
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:NF015437.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01965.1
COORDINATES: similar to AA sequence:RefSeq:WP_011387743.1
COORDINATES: protein motif:HMM:NF020137.2
COORDINATES: similar to AA sequence:RefSeq:WP_018988031.1
COORDINATES: similar to AA sequence:RefSeq:WP_014818909.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016485365.1
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]
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF024880.2
methyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF037144.2
COORDINATES: similar to AA sequence:RefSeq:WP_008188390.1
COORDINATES: protein motif:HMM:NF012630.2
COORDINATES: similar to AA sequence:RefSeq:WP_004121588.1
COORDINATES: similar to AA sequence:RefSeq:WP_012029919.1
COORDINATES: protein motif:HMM:NF012514.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_086558312.1
COORDINATES: similar to AA sequence:RefSeq:WP_015914926.1
COORDINATES: similar to AA sequence:RefSeq:WP_012881262.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012881263.1
COORDINATES: similar to AA sequence:RefSeq:WP_012760581.1
COORDINATES: similar to AA sequence:RefSeq:WP_018068214.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_012760350.1
COORDINATES: similar to AA sequence:RefSeq:WP_011439477.1
COORDINATES: similar to AA sequence:RefSeq:WP_011439476.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin