Pseudorhizobium flavum strain YW14 plasmid 4, 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\nLR723673.1.\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_009737315.1
GO:0008643 - carbohydrate transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002713042.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GMC family oxidoreductase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019197764.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0004362 - glutathione-disulfide reductase (NADPH) activity [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
GO:0045454 - cell redox homeostasis [Evidence IEA]; GO:0006749 - glutathione metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611875.1
GO:0015074 - DNA integration [Evidence IEA]
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.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014497719.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [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.
COORDINATES: similar to AA sequence:RefSeq:WP_003575527.1
COORDINATES: similar to AA sequence:RefSeq:WP_003810964.1
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_076611552.1
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_013500414.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006018763.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
glutathione S-transferase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611376.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS630-like element ISRm10-1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_002716815.1
class I adenylate-forming enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008834688.1
COORDINATES: similar to AA sequence:RefSeq:WP_014528793.1
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_003537129.1
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_014531052.1
helix-turn-helix transcriptional regulator
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_017268596.1
COORDINATES: similar to AA sequence:RefSeq:WP_018210763.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845298.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_014330857.1
COORDINATES: similar to AA sequence:RefSeq:WP_014330858.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982997.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006386121.1
Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; 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_018271138.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558312.1
COORDINATES: similar to AA sequence:RefSeq:WP_009467802.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003501082.1
COORDINATES: similar to AA sequence:RefSeq:WP_004672573.1
IS21-like element ISRel5 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_007015319.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611755.1
COORDINATES: protein motif:HMM:TIGR00254.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0005525 - GTP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003296514.1
CerR family C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012275073.1
COORDINATES: protein motif:HMM:NF012241.2
COORDINATES: similar to AA sequence:RefSeq:WP_020011295.1
COORDINATES: similar to AA sequence:RefSeq:WP_014161214.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007354063.1
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Evidence IEA]
COORDINATES: protein motif:HMM:NF022603.2
COORDINATES: similar to AA sequence:RefSeq:WP_003572833.1
COORDINATES: protein motif:HMM:NF020965.2
COORDINATES: similar to AA sequence:RefSeq:WP_018860470.1
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_076612399.1
frameshifted; internal stop; 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_076611431.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501391.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003501388.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018431454.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_016558251.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_003501379.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654900.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523830.1
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010915775.1
COORDINATES: similar to AA sequence:RefSeq:WP_012648972.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_016558654.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_003523837.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523838.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_010892384.1
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_003501346.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501345.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003501343.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654946.1
COORDINATES: similar to AA sequence:RefSeq:WP_007827581.1
COORDINATES: similar to AA sequence:RefSeq:WP_041684032.1
COORDINATES: similar to AA sequence:RefSeq:WP_002711908.1
GO:0010124 - phenylacetate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006466356.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0004174 - electron-transferring-flavoprotein dehydrogenase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0022900 - electron transport chain [Evidence IEA]
electron transfer flavoprotein-ubiquinone oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_002965036.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]
electron transfer flavoprotein subunit alpha/FixB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017966359.1
GO:0009055 - electron transfer activity [Evidence IEA]
electron transfer flavoprotein subunit beta/FixA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011237751.1
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_009803833.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0016020 - membrane [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0015658 - branched-chain amino acid transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012333050.1
COORDINATES: similar to AA sequence:RefSeq:WP_014189497.1
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_006967014.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020747959.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
GO:0019619 - 3,4-dihydroxybenzoate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014189505.1
GO:0008691 - 3-hydroxybutyryl-CoA dehydrogenase activity [Evidence IEA]; GO:0070403 - NAD+ binding [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]; GO:0010124 - phenylacetate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019198736.1
GO:0070402 - NADPH binding [Evidence IEA]; GO:0003960 - NADPH:quinone reductase activity [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0048038 - quinone binding [Evidence IEA]
NADPH:quinone oxidoreductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003501317.1
CaiB/BaiF CoA-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003501310.1
COORDINATES: similar to AA sequence:RefSeq:WP_010931399.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003501305.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501303.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003501299.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501298.1
COORDINATES: similar to AA sequence:RefSeq:WP_003815607.1
COORDINATES: similar to AA sequence:RefSeq:WP_012112931.1
COORDINATES: protein motif:HMM:NF024109.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024212.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014593.2
GO:0003864 - 3-methyl-2-oxobutanoate hydroxymethyltransferase activity [Evidence IEA]
GO:0015940 - pantothenate biosynthetic process [Evidence IEA]
3-methyl-2-oxobutanoate hydroxymethyltransferase
internal stop; 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_003501291.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_012654962.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650736.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_003523580.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974835.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_012649097.1
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003523577.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_012649099.1
COORDINATES: similar to AA sequence:RefSeq:WP_010892446.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650743.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649103.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018009855.1
COORDINATES: similar to AA sequence:RefSeq:WP_006312309.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129924.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341778.1
COORDINATES: similar to AA sequence:RefSeq:WP_012760230.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003518564.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524386.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020810313.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007876242.1
COORDINATES: similar to AA sequence:RefSeq:WP_018115395.1
COORDINATES: similar to AA sequence:RefSeq:WP_010973441.1
GO:0016153 - urocanate hydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018209755.1
GO:0050129 - N-formylglutamate deformylase activity [Evidence IEA]
GO:0019557 - histidine catabolic process to glutamate and formate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010973443.1
GO:0004397 - histidine ammonia-lyase activity [Evidence IEA]
GO:0006548 - histidine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015341566.1
GO:0050480 - imidazolonepropionase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006315467.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012652806.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006724010.1
GO:0004056 - argininosuccinate lyase activity [Evidence IEA]
GO:0042450 - arginine biosynthetic process via ornithine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006759530.1
GO:0006865 - amino acid transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006724012.1
amino acid ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006724013.1
COORDINATES: similar to AA sequence:RefSeq:WP_006724014.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003345999.1
COORDINATES: similar to AA sequence:RefSeq:WP_010660353.1
GO:0004540 - ribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018010711.1
ISL3-like element ISRsp8 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_019197706.1
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006936646.1
COORDINATES: similar to AA sequence:RefSeq:WP_009449322.1
catalyzes the formation of malate from glyoxylate and acetyl-CoA; 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.
COORDINATES: similar to AA sequence:RefSeq:WP_014989409.1
GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014989408.1
COORDINATES: similar to AA sequence:RefSeq:WP_009337719.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]
FAD-linked oxidase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019143082.1
COORDINATES: similar to AA sequence:RefSeq:WP_002713040.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: similar to AA sequence:RefSeq:WP_006018746.1
COORDINATES: similar to AA sequence:RefSeq:WP_002713038.1