Rhizobium rhizoryzae strain DSM 29514 plasmid unnamed2, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
Complete genome of Rhizobium rhizoryzae DSM29514
Submitted (24-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\nCP049248.1.\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 :: 524.0x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/06/2023 02:33:55\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) :: 4,664\nCDSs (total) :: 4,586\nGenes (coding) :: 4,530\nCDSs (with protein) :: 4,530\nGenes (RNA) :: 78\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 59\nncRNAs :: 4\nPseudo Genes (total) :: 56\nCDSs (without protein) :: 56\nPseudo Genes (ambiguous residues) :: 0 of 56\nPseudo Genes (frameshifted) :: 21 of 56\nPseudo Genes (incomplete) :: 46 of 56\nPseudo Genes (internal stop) :: 6 of 56\nPseudo Genes (multiple problems) :: 15 of 56\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_018115834.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_006467461.1
COORDINATES: similar to AA sequence:RefSeq:WP_004126925.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341606.1
amino acid--[acyl-carrier-protein] ligase
COORDINATES: similar to AA sequence:RefSeq:WP_010972410.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003504852.1
COORDINATES: similar to AA sequence:RefSeq:WP_013900068.1
COORDINATES: similar to AA sequence:RefSeq:WP_007597395.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0015803 - branched-chain amino acid transport [Evidence IEA]
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_006728268.1
COORDINATES: similar to AA sequence:RefSeq:WP_006728269.1
COORDINATES: similar to AA sequence:RefSeq:WP_008596523.1
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: similar to AA sequence:RefSeq:WP_006728271.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019172298.1
COORDINATES: similar to AA sequence:RefSeq:WP_018896741.1
COORDINATES: similar to AA sequence:RefSeq:WP_008833981.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF013884.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: protein motif:HMM:NF025314.2
COORDINATES: similar to AA sequence:RefSeq:WP_010687177.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF012514.2
COORDINATES: protein motif:HMM:NF012630.2
COORDINATES: similar to AA sequence:RefSeq:WP_015341696.1
COORDINATES: protein motif:HMM:NF020137.2
bluetail domain-containing putative surface protein
COORDINATES: similar to AA sequence:RefSeq:WP_006786183.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024880.2
methyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF012744.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020051287.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_016733867.1
COORDINATES: similar to AA sequence:RefSeq:WP_004435236.1
COORDINATES: similar to AA sequence:RefSeq:WP_014341989.1
COORDINATES: similar to AA sequence:RefSeq:WP_014341988.1
COORDINATES: similar to AA sequence:RefSeq:WP_017969049.1
COORDINATES: protein motif:HMM:NF027681.2
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: similar to AA sequence:RefSeq:WP_018988031.1
COORDINATES: similar to AA sequence:RefSeq:WP_020158929.1
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_020192384.1
COORDINATES: similar to AA sequence:RefSeq:WP_006335148.1
COORDINATES: protein motif:HMM:NF014732.2
COORDINATES: protein motif:HMM:NF038256.1
VpsF, distantly related to oligosaccharide ligases, is encoded next to the probable flippase VpsE; Derived by automated computational analysis using gene prediction method: Protein Homology.
VpsF family polysaccharide biosynthesis protein
COORDINATES: similar to AA sequence:RefSeq:WP_008209680.1
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]
COORDINATES: similar to AA sequence:RefSeq:WP_008209681.1
COORDINATES: similar to AA sequence:RefSeq:WP_020085367.1
COORDINATES: similar to AA sequence:RefSeq:WP_008876237.1
COORDINATES: similar to AA sequence:RefSeq:WP_008876236.1
COORDINATES: similar to AA sequence:RefSeq:WP_006335135.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0071704 - organic substance metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006335130.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024871.2
COORDINATES: similar to AA sequence:RefSeq:WP_016918686.1
GO:0008767 - UDP-galactopyranose mutase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012631198.1
COORDINATES: similar to AA sequence:RefSeq:WP_008523924.1
GO:0031522 - cell envelope Sec protein transport complex [Evidence IEA]
GO:0015450 - protein-transporting ATPase activity [Evidence IEA]
GO:0043952 - protein transport by the Sec complex [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004127253.1
COORDINATES: protein motif:HMM:NF040115.1
COORDINATES: similar to AA sequence:RefSeq:WP_007536803.1
COORDINATES: similar to AA sequence:RefSeq:WP_006778728.1
COORDINATES: similar to AA sequence:RefSeq:WP_015916283.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015916284.1
COORDINATES: similar to AA sequence:RefSeq:WP_015459207.1
COORDINATES: similar to AA sequence:RefSeq:WP_006726462.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
GO:0016310 - phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014615782.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003504218.1
COORDINATES: similar to AA sequence:RefSeq:WP_018066164.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]; GO:0001072 - transcription antitermination factor activity, RNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017957701.1
COORDINATES: similar to AA sequence:RefSeq:WP_007662817.1
COORDINATES: protein motif:HMM:NF014897.2
GO:0004517 - nitric-oxide synthase activity [Evidence IEA]
GO:0006809 - nitric oxide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004230607.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF024910.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017995535.1
COORDINATES: similar to AA sequence:RefSeq:WP_011313608.1
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:NF012422.2
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: protein motif:HMM:NF017815.2
transglutaminase-like cysteine peptidase
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: similar to AA sequence:RefSeq:WP_018114625.1
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: similar to AA sequence:RefSeq:WP_003520878.1
GO:0045226 - extracellular polysaccharide biosynthetic process [Evidence IEA]
polysaccharide biosynthesis tyrosine autokinase
COORDINATES: protein motif:HMM:NF012376.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03025.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0032508 - DNA duplex unwinding [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]
exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_076611153.1
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_004587716.1