Rhizobium pseudoryzae strain DSM 19479 plasmid unnamed4, 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\nCP049245.1.\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: similar to AA sequence:RefSeq:WP_003592416.1
GO:0055085 - transmembrane transport [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
dicarboxylate transporter/tellurite-resistance protein TehA
COORDINATES: similar to AA sequence:RefSeq:WP_003590941.1
GSU2403 family nucleotidyltransferase fold protein
COORDINATES: similar to AA sequence:RefSeq:WP_007741292.1
COORDINATES: similar to AA sequence:RefSeq:WP_018901444.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013338331.1
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003517453.1
COORDINATES: similar to AA sequence:RefSeq:WP_019565667.1
COORDINATES: similar to AA sequence:RefSeq:WP_019565668.1
COORDINATES: similar to AA sequence:RefSeq:WP_052096176.1
GO:0004803 - transposase activity [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003495445.1
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_020174520.1
PAS domain-containing methyl-accepting chemotaxis protein
COORDINATES: similar to AA sequence:RefSeq:WP_010236891.1
COORDINATES: similar to AA sequence:RefSeq:WP_019566848.1
COORDINATES: protein motif:HMM:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007762012.1
COORDINATES: similar to AA sequence:RefSeq:WP_007762011.1
COORDINATES: similar to AA sequence:RefSeq:WP_007762008.1
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: protein motif:HMM:NF016107.2
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007599714.1
COORDINATES: similar to AA sequence:RefSeq:WP_006728265.1
COORDINATES: similar to AA sequence:RefSeq:WP_006728264.1
COORDINATES: similar to AA sequence:RefSeq:WP_006728263.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008827617.1
COORDINATES: similar to AA sequence:RefSeq:WP_003538823.1
COORDINATES: similar to AA sequence:RefSeq:WP_006728261.1
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_013845913.1
COORDINATES: similar to AA sequence:RefSeq:WP_018325506.1
COORDINATES: similar to AA sequence:RefSeq:WP_014331632.1
COORDINATES: similar to AA sequence:RefSeq:WP_008230235.1
COORDINATES: similar to AA sequence:RefSeq:WP_006728257.1
COORDINATES: protein motif:HMM:NF024809.2
glutathione S-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011931084.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018326272.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326271.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017184819.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654728.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326269.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018326268.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326267.1
COORDINATES: similar to AA sequence:RefSeq:WP_018482054.1
COORDINATES: similar to AA sequence:RefSeq:WP_018516741.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017273099.1
COORDINATES: similar to AA sequence:RefSeq:WP_012477327.1
COORDINATES: similar to AA sequence:RefSeq:WP_004676096.1
COORDINATES: similar to AA sequence:RefSeq:WP_007636151.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013760951.1
COORDINATES: similar to AA sequence:RefSeq:WP_006724079.1
COORDINATES: similar to AA sequence:RefSeq:WP_006958134.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982890.1
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_018482051.1
COORDINATES: similar to AA sequence:RefSeq:WP_008684588.1
COORDINATES: similar to AA sequence:RefSeq:WP_012559843.1
COORDINATES: similar to AA sequence:RefSeq:WP_003576950.1
COORDINATES: similar to AA sequence:RefSeq:WP_004119812.1
COORDINATES: similar to AA sequence:RefSeq:WP_007538552.1
COORDINATES: similar to AA sequence:RefSeq:WP_004119814.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_018516734.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_015341946.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048127.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_020048128.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0008233 - peptidase activity [Evidence IEA]
conjugative transfer signal peptidase TraF
COORDINATES: similar to AA sequence:RefSeq:WP_010875412.1
COORDINATES: similar to AA sequence:RefSeq:WP_016558649.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011427447.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427448.1
COORDINATES: similar to AA sequence:RefSeq:WP_013637380.1
COORDINATES: similar to AA sequence:RefSeq:WP_017968929.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: protein motif:HMM:NF039962.1
COORDINATES: protein motif:HMM:NF015338.2
endonuclease/exonuclease/phosphatase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018115834.1
COORDINATES: similar to AA sequence:RefSeq:WP_007823311.1
transglutaminase-like cysteine peptidase
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: similar to AA sequence:RefSeq:WP_007823301.1
polysaccharide biosynthesis/export family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019564828.1
GO:0045226 - extracellular polysaccharide biosynthetic process [Evidence IEA]
polysaccharide biosynthesis tyrosine autokinase
COORDINATES: protein motif:HMM:NF012376.2
COORDINATES: similar to AA sequence:RefSeq:WP_007816016.1
COORDINATES: similar to AA sequence:RefSeq:WP_020051287.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974358.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007823282.1
UDP-glucose/GDP-mannose dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611884.1
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_012778812.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012275096.1
COORDINATES: similar to AA sequence:RefSeq:WP_010337103.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611472.1
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 N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011504961.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
right-handed parallel beta-helix repeat-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007754634.1
COORDINATES: protein motif:HMM:NF013077.2
COORDINATES: similar to AA sequence:RefSeq:WP_009515991.1
putative colanic acid biosynthesis acetyltransferase
COORDINATES: protein motif:HMM:NF016145.2
polysaccharide pyruvyl transferase family protein
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF014051.2
COORDINATES: similar to AA sequence:RefSeq:WP_007754615.1
COORDINATES: similar to AA sequence:RefSeq:WP_007754613.1
COORDINATES: similar to AA sequence:RefSeq:WP_007754611.1
COORDINATES: similar to AA sequence:RefSeq:WP_011509784.1
COORDINATES: similar to AA sequence:RefSeq:WP_014531097.1
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_076612018.1
COORDINATES: similar to AA sequence:RefSeq:WP_028714619.1
COORDINATES: similar to AA sequence:RefSeq:WP_012973766.1
COORDINATES: similar to AA sequence:RefSeq:WP_003526174.1
COORDINATES: similar to AA sequence:RefSeq:WP_020811857.1
COORDINATES: similar to AA sequence:RefSeq:WP_018856628.1
COORDINATES: similar to AA sequence:RefSeq:WP_004688994.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970376.1
COORDINATES: similar to AA sequence:RefSeq:WP_018856624.1
COORDINATES: similar to AA sequence:RefSeq:WP_010336579.1
COORDINATES: similar to AA sequence:RefSeq:WP_012707166.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611752.1
COORDINATES: similar to AA sequence:RefSeq:WP_004128939.1
COORDINATES: similar to AA sequence:RefSeq:WP_003584341.1
nucleotidyltransferase and HEPN domain-containing protein
COORDINATES: protein motif:HMM:NF012698.2
COORDINATES: similar to AA sequence:RefSeq:WP_006468233.1
COORDINATES: similar to AA sequence:RefSeq:WP_015887160.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015887159.1
aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018328194.1
COORDINATES: similar to AA sequence:RefSeq:WP_007538975.1
COORDINATES: similar to AA sequence:RefSeq:WP_018237564.1
COORDINATES: similar to AA sequence:RefSeq:WP_018097202.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328190.1
ABC transporter substrate-binding protein
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_018237552.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
COORDINATES: protein motif:HMM:NF015437.2
COORDINATES: protein motif:HMM:NF024871.2
COORDINATES: similar to AA sequence:RefSeq:WP_013984777.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_020048152.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427455.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_018482029.1
COORDINATES: similar to AA sequence:RefSeq:WP_018516719.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_018482027.1
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020048157.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_015341956.1
COORDINATES: similar to AA sequence:RefSeq:WP_018010282.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970255.1
COORDINATES: similar to AA sequence:RefSeq:WP_018329034.1
COORDINATES: similar to AA sequence:RefSeq:WP_015934295.1
COORDINATES: similar to AA sequence:RefSeq:WP_004674049.1
COORDINATES: similar to AA sequence:RefSeq:WP_012648911.1
COORDINATES: similar to AA sequence:RefSeq:WP_010682313.1
COORDINATES: similar to AA sequence:RefSeq:WP_012591321.1
COORDINATES: protein motif:HMM:NF018527.2
COORDINATES: similar to AA sequence:RefSeq:WP_015242672.1
COORDINATES: similar to AA sequence:RefSeq:WP_007761334.1
COORDINATES: similar to AA sequence:RefSeq:WP_014763931.1
histidine kinase dimerization/phosphoacceptor domain -containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006015699.1
COORDINATES: similar to AA sequence:RefSeq:WP_007797695.1
COORDINATES: similar to AA sequence:RefSeq:WP_007826392.1
COORDINATES: similar to AA sequence:RefSeq:WP_018242080.1
COORDINATES: similar to AA sequence:RefSeq:WP_019566737.1
COORDINATES: similar to AA sequence:RefSeq:WP_003511482.1
COORDINATES: similar to AA sequence:RefSeq:WP_017269417.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611153.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654075.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970612.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_006015924.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518564.1
COORDINATES: similar to AA sequence:RefSeq:WP_004493738.1
COORDINATES: similar to AA sequence:RefSeq:WP_002713068.1
COORDINATES: similar to AA sequence:RefSeq:WP_008066907.1
GO:0051920 - peroxiredoxin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008066910.1
COORDINATES: similar to AA sequence:RefSeq:WP_018075966.1
COORDINATES: similar to AA sequence:RefSeq:WP_020163984.1
COORDINATES: similar to AA sequence:RefSeq:WP_017965623.1
COORDINATES: similar to AA sequence:RefSeq:WP_018901600.1
COORDINATES: similar to AA sequence:RefSeq:WP_017965579.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:1902600 - proton transmembrane transport [Evidence IEA]
monovalent cation:proton antiporter-2 (CPA2) family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020808351.1
COORDINATES: protein motif:HMM:NF024242.2
COORDINATES: similar to AA sequence:RefSeq:WP_011546983.1
COORDINATES: similar to AA sequence:RefSeq:WP_017339561.1
COORDINATES: similar to AA sequence:RefSeq:WP_018241297.1
COORDINATES: similar to AA sequence:RefSeq:WP_003519249.1
COORDINATES: similar to AA sequence:RefSeq:WP_003539817.1
COORDINATES: similar to AA sequence:RefSeq:WP_013946796.1
COORDINATES: similar to AA sequence:RefSeq:WP_020808334.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020808336.1
COORDINATES: similar to AA sequence:RefSeq:WP_019585182.1