Pantoea deleyi strain LMG24200 plasmid Plas1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Erwiniaceae; Pantoea.
Genome sequence of soft rot disease pathogen
Submitted (02-MAR-2021) Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, shuguanghuayuan road, beijing 100097, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP071406.1.\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-Assembly-Data-START##\nAssembly Date :: 20-FEB-2021\nAssembly Method :: Unicycler v. v0.4.8\nAssembly Name :: LMG24200\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 290x\nSequencing Technology :: Oxford Nanopore PromethION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/07/2023 05:38:31\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) :: 4,362\nCDSs (total) :: 4,252\nGenes (coding) :: 4,205\nCDSs (with protein) :: 4,205\nGenes (RNA) :: 110\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 77\nncRNAs :: 11\nPseudo Genes (total) :: 47\nCDSs (without protein) :: 47\nPseudo Genes (ambiguous residues) :: 0 of 47\nPseudo Genes (frameshifted) :: 21 of 47\nPseudo Genes (incomplete) :: 30 of 47\nPseudo Genes (internal stop) :: 14 of 47\nPseudo Genes (multiple problems) :: 15 of 47\nPseudo Genes (short protein) :: 1 of 47\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_008926788.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_009093254.1
COORDINATES: similar to AA sequence:RefSeq:WP_006118233.1
GGDEF domain-containing phosphodiesterase
COORDINATES: similar to AA sequence:RefSeq:WP_013356498.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926786.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671953.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356501.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005224569.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093262.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671950.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926782.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671949.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010671948.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671947.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850677.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671945.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014604593.1
COORDINATES: similar to AA sequence:RefSeq:NP_308490.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093121.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926773.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008926772.1
GO:0016020 - membrane [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010257019.1
GO:0001216 - DNA-binding transcription activator activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014605940.1
GO:0006950 - response to stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012815421.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356518.1
COORDINATES: similar to AA sequence:RefSeq:WP_017799524.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257048.1
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_013356523.1
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_003850529.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013356527.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257059.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850534.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257065.1
GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013356531.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926832.1
GO:0046914 - transition metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010257075.1
GO:0015093 - ferrous iron transmembrane transporter activity [Evidence IEA]; GO:0005525 - GTP binding [Evidence IEA]
GO:0006826 - iron ion transport [Evidence IEA]
Fe(2+) transporter permease subunit FeoB
COORDINATES: similar to AA sequence:RefSeq:WP_013356528.1
membrane lipoprotein lipid attachment site-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006177040.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671927.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017132327.1
COORDINATES: similar to AA sequence:RefSeq:WP_008109372.1
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
SfnB family sulfur acquisition oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013356541.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093145.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_006325453.1
MetQ/NlpA family ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008109368.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013511463.1
GO:0033232 - ABC-type D-methionine transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0048473 - D-methionine transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009093149.1
COORDINATES: similar to AA sequence:RefSeq:WP_014593915.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356548.1
COORDINATES: similar to AA sequence:RefSeq:WP_019105005.1
COORDINATES: similar to AA sequence:RefSeq:WP_015378420.1
GO:0008726 - alkanesulfonate monooxygenase activity [Evidence IEA]; GO:0010181 - FMN binding [Evidence IEA]
FMNH2-dependent alkanesulfonate monooxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_010257098.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]; GO:0005488 - binding [Evidence IEA]
GO:0042918 - alkanesulfonate transport [Evidence IEA]
aliphatic sulfonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_015700094.1
sulfonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009093197.1
COORDINATES: similar to AA sequence:RefSeq:WP_006119677.1
GO:0018784 - (S)-2-haloacid dehalogenase activity [Evidence IEA]
GO:0006805 - xenobiotic metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010671913.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356558.1
4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF
COORDINATES: similar to AA sequence:RefSeq:WP_010671911.1
4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE
COORDINATES: similar to AA sequence:RefSeq:WP_003850558.1
GO:0000030 - mannosyltransferase activity [Evidence IEA]; GO:0016763 - pentosyltransferase activity [Evidence IEA]
GO:0006493 - protein O-linked glycosylation [Evidence IEA]
lipid IV(A) 4-amino-4-deoxy-L-arabinosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_010671909.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
4-deoxy-4-formamido-L-arabinose- phosphoundecaprenol deformylase
COORDINATES: similar to AA sequence:RefSeq:WP_009093173.1
GO:0016742 - hydroxymethyl-, formyl- and related transferase activity [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
bifunctional UDP-4-amino-4-deoxy-L-arabinose formyltransferase/UDP-glucuronic acid oxidase ArnA
COORDINATES: similar to AA sequence:RefSeq:WP_010257142.1
GO:0016780 - phosphotransferase activity, for other substituted phosphate groups [Evidence IEA]
undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
COORDINATES: similar to AA sequence:RefSeq:WP_013356564.1
GO:0008483 - transaminase activity [Evidence IEA]
UDP-4-amino-4-deoxy-L-arabinose aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_011093576.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850564.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671904.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_010671903.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356572.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257166.1
Hha/YmoA family nucleoid-associated regulatory protein
COORDINATES: protein motif:HMM:NF014452.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003850570.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093183.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013356578.1
COORDINATES: similar to AA sequence:RefSeq:WP_001707549.1
GO:0007155 - cell adhesion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009093187.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0071555 - cell wall organization [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004952375.1
COORDINATES: protein motif:HMM:NF012635.2
COORDINATES: similar to AA sequence:RefSeq:WP_009093190.1
COORDINATES: protein motif:HMM:NF012422.2
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009093192.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009093193.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_009093194.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
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]; GO:0008233 - peptidase activity [Evidence IEA]
peptidase domain-containing ABC transporter
COORDINATES: similar to AA sequence:RefSeq:WP_009093195.1
COORDINATES: similar to AA sequence:RefSeq:WP_017383642.1
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_009093200.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926812.1
COORDINATES: similar to AA sequence:RefSeq:WP_015963455.1
COORDINATES: similar to AA sequence:RefSeq:NP_490541.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_003850580.1
COORDINATES: similar to AA sequence:RefSeq:WP_013096847.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009093206.1
COORDINATES: similar to AA sequence:RefSeq:WP_014333093.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003850585.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356609.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356610.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926804.1
GO:0047605 - acetolactate decarboxylase activity [Evidence IEA]
GO:0045151 - acetoin biosynthetic process [Evidence IEA]; GO:0006113 - fermentation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003850593.1
GO:0003984 - acetolactate synthase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
GO:0034077 - butanediol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013356613.1
GO:0019152 - acetoin dehydrogenase activity [Evidence IEA]
GO:0045150 - acetoin catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013356614.1
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0071973 - bacterial-type flagellum-dependent cell motility [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013025938.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256859.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850604.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213072.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_001261287.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010671973.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003850617.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010256889.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256895.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671968.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671967.1
COORDINATES: similar to AA sequence:RefSeq:WP_013027309.1
GO:0052621 - diguanylate cyclase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014594380.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
sigma 54-interacting transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017145285.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093231.1
GO:0008509 - monoatomic anion transmembrane transporter activity [Evidence IEA]
GO:0006820 - monoatomic anion transport [Evidence IEA]
DASS family sodium-coupled anion symporter
COORDINATES: similar to AA sequence:RefSeq:WP_009061574.1
COORDINATES: similar to AA sequence:RefSeq:WP_004106636.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850629.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671964.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256917.1
GO:0046417 - chorismate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010256922.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010256926.1
GO:0004564 - beta-fructofuranosidase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005225625.1
GO:0008982 - protein-N(PI)-phosphohistidine-sugar phosphotransferase activity [Evidence IEA]
GO:0009401 - phosphoenolpyruvate-dependent sugar phosphotransferase system [Evidence IEA]
sucrose-specific PTS transporter subunit IIBC
COORDINATES: similar to AA sequence:RefSeq:WP_013024233.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926789.1
GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010256937.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093252.1