Rhizobium pseudoryzae strain DSM 19479 plasmid unnamed2, 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\nCP049243.1.\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_006724939.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_006724937.1
COORDINATES: similar to AA sequence:RefSeq:WP_006724936.1
COORDINATES: protein motif:HMM:NF024934.2
COORDINATES: similar to AA sequence:RefSeq:WP_008888128.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_015918659.1
COORDINATES: similar to AA sequence:RefSeq:WP_006986362.1
COORDINATES: similar to AA sequence:RefSeq:WP_009287916.1
COORDINATES: similar to AA sequence:RefSeq:WP_009572662.1
COORDINATES: similar to AA sequence:RefSeq:WP_009564086.1
GO:0050304 - nitrous-oxide reductase activity [Evidence IEA]
GO:0019333 - denitrification pathway [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011750447.1
nitrous oxide reductase family maturation protein NosD
COORDINATES: similar to AA sequence:RefSeq:WP_011750446.1
COORDINATES: similar to AA sequence:RefSeq:WP_012643415.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012179858.1
nitrous oxide reductase accessory protein NosL
COORDINATES: similar to AA sequence:RefSeq:WP_011750443.1
GO:0017013 - protein flavinylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018900701.1
COORDINATES: similar to AA sequence:RefSeq:WP_018426593.1
COORDINATES: similar to AA sequence:RefSeq:WP_017275279.1
COORDINATES: protein motif:HMM:NF018154.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003586920.1
COORDINATES: similar to AA sequence:RefSeq:WP_007637631.1
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012653067.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241491.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653070.1
COORDINATES: similar to AA sequence:RefSeq:WP_003537746.1
COORDINATES: similar to AA sequence:RefSeq:WP_017958563.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_006697887.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558208.1
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_012881324.1
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_003534459.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653083.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653084.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012559808.1
COORDINATES: similar to AA sequence:RefSeq:WP_012559809.1
COORDINATES: similar to AA sequence:RefSeq:WP_012648911.1
COORDINATES: similar to AA sequence:RefSeq:WP_007602596.1
COORDINATES: similar to AA sequence:RefSeq:WP_014330854.1
COORDINATES: similar to AA sequence:RefSeq:WP_007601950.1
COORDINATES: similar to AA sequence:RefSeq:WP_007601952.1
COORDINATES: similar to AA sequence:RefSeq:WP_014531058.1
COORDINATES: similar to AA sequence:RefSeq:WP_017265125.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015241453.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017268591.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653016.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_013845309.1
COORDINATES: similar to AA sequence:RefSeq:WP_009469549.1
COORDINATES: similar to AA sequence:RefSeq:WP_009469550.1
COORDINATES: similar to AA sequence:RefSeq:WP_009469551.1
COORDINATES: similar to AA sequence:RefSeq:WP_014531075.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011971088.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_014531077.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_009469555.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653024.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845318.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653026.1
COORDINATES: similar to AA sequence:RefSeq:WP_009469559.1
COORDINATES: similar to AA sequence:RefSeq:WP_011971081.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653029.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653030.1
COORDINATES: similar to AA sequence:RefSeq:WP_013040822.1
COORDINATES: similar to AA sequence:RefSeq:WP_013040823.1
COORDINATES: similar to AA sequence:RefSeq:WP_018698109.1
COORDINATES: similar to AA sequence:RefSeq:WP_010298730.1
COORDINATES: similar to AA sequence:RefSeq:WP_019565673.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501499.1
COORDINATES: similar to AA sequence:RefSeq:WP_007605109.1
PAS domain-containing methyl-accepting chemotaxis protein
COORDINATES: similar to AA sequence:RefSeq:WP_006699148.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:NF018894.2
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: similar to AA sequence:RefSeq:WP_003554634.1
COORDINATES: similar to AA sequence:RefSeq:WP_020039302.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974357.1
COORDINATES: similar to AA sequence:RefSeq:WP_018239549.1
COORDINATES: similar to AA sequence:RefSeq:WP_003551661.1
COORDINATES: similar to AA sequence:RefSeq:WP_020479427.1
COORDINATES: similar to AA sequence:RefSeq:WP_017269639.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011654078.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_003518564.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974257.1
COORDINATES: similar to AA sequence:RefSeq:WP_014077354.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014077353.1
COORDINATES: similar to AA sequence:RefSeq:WP_017957255.1
COORDINATES: similar to AA sequence:RefSeq:WP_017957254.1
COORDINATES: protein motif:HMM:NF024835.2
COORDINATES: similar to AA sequence:RefSeq:WP_017957252.1
COORDINATES: similar to AA sequence:RefSeq:WP_009797621.1
COORDINATES: similar to AA sequence:RefSeq:WP_012222369.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564778.1
COORDINATES: protein motif:HMM:NF025840.2
DarT ssDNA thymidine ADP-ribosyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008878434.1
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: similar to AA sequence:RefSeq:WP_005628339.1
COORDINATES: protein motif:HMM:NF024700.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012556002.1
COORDINATES: similar to AA sequence:RefSeq:WP_012590993.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018115052.1
COORDINATES: similar to AA sequence:RefSeq:WP_018115051.1
COORDINATES: similar to AA sequence:RefSeq:WP_018859713.1
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_006726485.1
COORDINATES: similar to AA sequence:RefSeq:WP_006726486.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
GO:0098662 - inorganic cation transmembrane transport [Evidence IEA]
monovalent cation/H+ antiporter subunit A
COORDINATES: similar to AA sequence:RefSeq:WP_006726487.1
COORDINATES: similar to AA sequence:RefSeq:WP_006726488.1
monovalent cation/H+ antiporter subunit D
COORDINATES: similar to AA sequence:RefSeq:WP_006726489.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002966126.1
GO:0015075 - monoatomic ion transmembrane transporter activity [Evidence IEA]
GO:0034220 - monoatomic ion transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006726491.1
GO:0098662 - inorganic cation transmembrane transport [Evidence IEA]; GO:1902600 - proton transmembrane transport [Evidence IEA]
monovalent cation/H(+) antiporter subunit G
COORDINATES: similar to AA sequence:RefSeq:WP_019565581.1
COORDINATES: similar to AA sequence:RefSeq:WP_003519380.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009803648.1
COORDINATES: similar to AA sequence:RefSeq:WP_006728354.1
COORDINATES: similar to AA sequence:RefSeq:WP_018237695.1
GO:0005506 - iron ion binding [Evidence IEA]
GO:0030091 - protein repair [Evidence IEA]
iron-sulfur cluster repair di-iron protein
COORDINATES: similar to AA sequence:RefSeq:WP_010661747.1
GO:0006744 - ubiquinone biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007877599.1
COORDINATES: similar to AA sequence:RefSeq:WP_010967678.1
SCP2 sterol-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011090356.1
COORDINATES: similar to AA sequence:RefSeq:WP_010973807.1
COORDINATES: protein motif:HMM:NF017727.2
COORDINATES: similar to AA sequence:RefSeq:WP_011750395.1
COORDINATES: similar to AA sequence:RefSeq:WP_012178123.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020084335.1
COORDINATES: similar to AA sequence:RefSeq:WP_014198841.1
COORDINATES: similar to AA sequence:RefSeq:WP_018238760.1
COORDINATES: protein motif:HMM:NF013936.2
COORDINATES: similar to AA sequence:RefSeq:WP_006466567.1
COORDINATES: similar to AA sequence:RefSeq:WP_012460496.1
COORDINATES: similar to AA sequence:RefSeq:WP_011288919.1
COORDINATES: similar to AA sequence:RefSeq:WP_002966338.1
COORDINATES: similar to AA sequence:RefSeq:WP_006466560.1
COORDINATES: similar to AA sequence:RefSeq:WP_008936443.1
COORDINATES: similar to AA sequence:RefSeq:WP_012707562.1
COORDINATES: similar to AA sequence:RefSeq:WP_012707563.1
GO:0051989 - coproporphyrinogen dehydrogenase activity [Evidence IEA]
GO:0006779 - porphyrin-containing compound biosynthetic process [Evidence IEA]
oxygen-independent coproporphyrinogen III oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_014990078.1
COORDINATES: similar to AA sequence:RefSeq:WP_012561421.1
COORDINATES: similar to AA sequence:RefSeq:WP_034790564.1
GO:0050421 - nitrite reductase (NO-forming) activity [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014327933.1
SUMF1/EgtB/PvdO family nonheme iron enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_011970955.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018009713.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0009055 - electron transfer activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014764550.1
COORDINATES: similar to AA sequence:RefSeq:WP_018327464.1
nitrate reductase cytochrome c-type subunit
COORDINATES: similar to AA sequence:RefSeq:WP_010967653.1
GO:0009325 - nitrate reductase complex [Evidence IEA]
GO:0008940 - nitrate reductase activity [Evidence IEA]
GO:0042126 - nitrate metabolic process [Evidence IEA]
periplasmic nitrate reductase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_012707575.1
COORDINATES: protein motif:HMM:NF024247.2
COORDINATES: similar to AA sequence:RefSeq:WP_018302964.1
periplasmic nitrate reductase, NapE protein