Rhizobium pseudoryzae strain DSM 19479 plasmid unnamed1, complete sequence.
Rhizobium pseudoryzae (Allorhizobium pseudoryzae)
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
Complete genome of Allorhizobium pseudoryzae DSM19479
Submitted (23-FEB-2020) College of Agriculture and Life Sciences, Kyungpook National University, Daehak-ro, Daegu 41566, Korea, Republic of
REFSEQ INFORMATION: The reference sequence is identical to\nCP049242.1.\nBacteria and source DNA available from Shin's Lab.\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 :: 07-FEB-2020\nAssembly Method :: HGAP v. 4\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 815.0x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/13/2023 10:51:52\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) :: 5,154\nCDSs (total) :: 5,082\nGenes (coding) :: 5,002\nCDSs (with protein) :: 5,002\nGenes (RNA) :: 72\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 56\nncRNAs :: 4\nPseudo Genes (total) :: 80\nCDSs (without protein) :: 80\nPseudo Genes (ambiguous residues) :: 0 of 80\nPseudo Genes (frameshifted) :: 29 of 80\nPseudo Genes (incomplete) :: 60 of 80\nPseudo Genes (internal stop) :: 13 of 80\nPseudo Genes (multiple problems) :: 19 of 80\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0008146 - sulfotransferase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
sulfotransferase family 2 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012336521.1
frameshifted; 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_011053350.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
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]
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_076611472.1
GO:0015074 - DNA integration [Evidence IEA]
frameshifted; internal stop; 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_011544395.1
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_011508718.1
COORDINATES: similar to AA sequence:RefSeq:WP_018240490.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213243.1
COORDINATES: protein motif:HMM:NF025079.2
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611153.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013849885.1
internal stop; 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_014242209.1
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_013067973.1
COORDINATES: similar to AA sequence:RefSeq:WP_011910724.1
COORDINATES: similar to AA sequence:RefSeq:WP_013067971.1
COORDINATES: protein motif:HMM:NF036807.2
COORDINATES: protein motif:HMM:NF025217.2
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013067968.1
COORDINATES: protein motif:HMM:NF012360.2
COORDINATES: similar to AA sequence:RefSeq:WP_013067966.1
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_006954973.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845260.1
COORDINATES: protein motif:HMM:NF017528.2
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_014989244.1
COORDINATES: similar to AA sequence:RefSeq:WP_012506293.1
COORDINATES: similar to AA sequence:RefSeq:WP_012288924.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: protein motif:HMM:NF018877.2
COORDINATES: protein motif:HMM:NF016850.2
GO:0008168 - methyltransferase activity [Evidence IEA]
GO:0008610 - lipid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018064506.1
GO:0005525 - GTP binding [Evidence IEA]; GO:0003924 - GTPase activity [Evidence IEA]
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
sulfate adenylyltransferase subunit CysN
COORDINATES: similar to AA sequence:RefSeq:WP_010914955.1
GO:0004781 - sulfate adenylyltransferase (ATP) activity [Evidence IEA]
GO:0019419 - sulfate reduction [Evidence IEA]
sulfate adenylyltransferase subunit CysD
COORDINATES: similar to AA sequence:RefSeq:WP_007009319.1
COORDINATES: similar to AA sequence:RefSeq:WP_007009318.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341688.1
COORDINATES: protein motif:HMM:NF013245.2
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF027681.2
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: protein motif:HMM:NF024880.2
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: similar to AA sequence:RefSeq:WP_007009311.1
COORDINATES: similar to AA sequence:RefSeq:WP_008832119.1
GO:0008446 - GDP-mannose 4,6-dehydratase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012652937.1
COORDINATES: protein motif:HMM:NF013884.2
COORDINATES: similar to AA sequence:RefSeq:WP_012029919.1
COORDINATES: similar to AA sequence:RefSeq:WP_012457145.1
COORDINATES: similar to AA sequence:RefSeq:WP_004435236.1
COORDINATES: similar to AA sequence:RefSeq:WP_015343181.1
COORDINATES: similar to AA sequence:RefSeq:WP_007683474.1
COORDINATES: similar to AA sequence:RefSeq:WP_006746220.1
COORDINATES: similar to AA sequence:RefSeq:WP_003584777.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017502925.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013845952.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003563307.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845945.1
COORDINATES: similar to AA sequence:RefSeq:WP_010399291.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: protein motif:HMM:NF039997.1
COORDINATES: similar to AA sequence:RefSeq:WP_008532882.1
nucleotidyltransferase and HEPN domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018328203.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase 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_019054745.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007598791.1
GO:0008831 - dTDP-4-dehydrorhamnose reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_002516572.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
frameshifted; 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_011391057.1
sulfotransferase domain-containing protein
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012606126.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017980723.1
COORDINATES: similar to AA sequence:RefSeq:WP_009996985.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427378.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611416.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558212.1
COORDINATES: protein motif:HMM:NF017026.2