Pantoea vagans strain LMG 24199 plasmid pVag2, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Erwiniaceae; Pantoea.
Pantoea vagans LMG 24199 Whole Genome Sequencing
Submitted (03-APR-2019) School of Forest Protection, Nanjing Forestry University, Longpan Road 159, Nanjing, Jiangsu 210037, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP038855.1.\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 Method :: canu v. 1.7.11; circlator v. 1.5.5\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 263.86x\nSequencing Technology :: Oxford Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/13/2023 02:10:46\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) :: 4,435\nCDSs (total) :: 4,324\nGenes (coding) :: 4,296\nCDSs (with protein) :: 4,296\nGenes (RNA) :: 111\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 79\nncRNAs :: 10\nPseudo Genes (total) :: 28\nCDSs (without protein) :: 28\nPseudo Genes (ambiguous residues) :: 0 of 28\nPseudo Genes (frameshifted) :: 7 of 28\nPseudo Genes (incomplete) :: 16 of 28\nPseudo Genes (internal stop) :: 9 of 28\nPseudo Genes (multiple problems) :: 4 of 28\nPseudo Genes (short protein) :: 1 of 28\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_010835630.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
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_010256926.1
GO:0004564 - beta-fructofuranosidase activity [Evidence IEA]
GO:0005975 - carbohydrate 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_010256919.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256917.1
GO:0046417 - chorismate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011347320.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093237.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256916.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671964.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850629.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356632.1
GO:0009975 - cyclase activity [Evidence IEA]
GO:0009966 - regulation of signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006118233.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926796.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010256895.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356625.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356624.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671973.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010256878.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256874.1
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]
type II toxin-antitoxin system HigB family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013356620.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356619.1
COORDINATES: similar to AA sequence:RefSeq:NP_707909.1
COORDINATES: similar to AA sequence:RefSeq:NP_416521.2
YoeB-YefM toxin-antitoxin system antitoxin YefM
COORDINATES: similar to AA sequence:RefSeq:WP_010256859.1
COORDINATES: similar to AA sequence:RefSeq:WP_003110367.1
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_013356613.1
GO:0019152 - acetoin dehydrogenase activity [Evidence IEA]
GO:0045150 - acetoin catabolic process [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_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_013356610.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356609.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356608.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356607.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013356606.1
COORDINATES: similar to AA sequence:RefSeq:WP_013096847.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003850580.1
COORDINATES: similar to AA sequence:RefSeq:NP_490541.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_013356600.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356599.1
GO:0004315 - 3-oxoacyl-[acyl-carrier-protein] synthase activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010671991.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010671992.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma 54-interacting transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010256810.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013812884.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256805.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926812.1
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_017374486.1
peptidase domain-containing ABC transporter
COORDINATES: similar to AA sequence:RefSeq:WP_010256789.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013356586.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: similar to AA sequence:RefSeq:WP_013356578.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010256756.1
COORDINATES: similar to AA sequence:RefSeq:WP_004099291.1
COORDINATES: protein motif:HMM:NF012565.2
COORDINATES: protein motif:HMM:NF012786.2
fimbria/pilus outer membrane usher protein
COORDINATES: similar to AA sequence:RefSeq:WP_004941020.1
GO:0007155 - cell adhesion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013356577.1
NirD/YgiW/YdeI family stress tolerance protein
COORDINATES: protein motif:HMM:NF015827.2
COORDINATES: protein motif:HMM:NF014452.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010257166.1
Hha/YmoA family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_013356572.1
COORDINATES: similar to AA sequence:RefSeq:WP_013202185.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008926818.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850564.1
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_013356565.1
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_003850561.1
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_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_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_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_010671911.1
4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE
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_010671913.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850554.1
GO:0018784 - (S)-2-haloacid dehalogenase activity [Evidence IEA]
GO:0006805 - xenobiotic metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:NP_462552.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004213599.1
COORDINATES: similar to AA sequence:RefSeq:WP_010277983.1
COORDINATES: similar to AA sequence:RefSeq:WP_003178827.1
COORDINATES: similar to AA sequence:RefSeq:WP_008359507.1
COORDINATES: similar to AA sequence:RefSeq:WP_010277996.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008118771.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008118773.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010278006.1
GO:0016805 - dipeptidase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
Sapep family Mn(2+)-dependent dipeptidase
COORDINATES: similar to AA sequence:RefSeq:WP_020317119.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_001585135.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010671918.1
glutathione-independent formaldehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_015700094.1
sulfonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010257098.1
sigma-54-dependent Fis family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003850550.1
GO:0008726 - alkanesulfonate monooxygenase activity [Evidence IEA]; GO:0010181 - FMN binding [Evidence IEA]
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
FMNH2-dependent alkanesulfonate monooxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_008926826.1
COORDINATES: similar to AA sequence:RefSeq:WP_007372543.1
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_008806264.1
methionine ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017490567.1
COORDINATES: similar to AA sequence:RefSeq:WP_002915265.1
MetQ/NlpA family ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013356547.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850546.1
COORDINATES: similar to AA sequence:RefSeq:WP_013185435.1
GO:0030253 - protein secretion by the type I secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013096399.1
HlyD family type I secretion periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013096400.1
COORDINATES: similar to AA sequence:RefSeq:WP_013096401.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671926.1
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_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_008926832.1
GO:0046914 - transition metal ion binding [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_010257071.1
YgiW/YdeI family stress tolerance OB fold protein
COORDINATES: similar to AA sequence:RefSeq:WP_013356531.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257065.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850534.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257059.1
COORDINATES: protein motif:HMM:NF021526.2
COORDINATES: similar to AA sequence:RefSeq:WP_003850529.1
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_010671933.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013356523.1
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_010257048.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356521.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010257042.1
COORDINATES: similar to AA sequence:RefSeq:WP_017799524.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356518.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356516.1
COORDINATES: similar to AA sequence:RefSeq:WP_014605940.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257007.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093121.1
COORDINATES: similar to AA sequence:RefSeq:WP_006122144.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:NP_308490.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356512.1
GO:0050532 - 2-phosphosulfolactate phosphatase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014604593.1
COORDINATES: similar to AA sequence:RefSeq:WP_004388541.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356508.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671947.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671948.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671949.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926782.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926783.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356502.1
COORDINATES: similar to AA sequence:RefSeq:WP_001030595.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256962.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671953.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926786.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356498.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850652.1
GGDEF domain-containing phosphodiesterase
COORDINATES: similar to AA sequence:RefSeq:WP_009093254.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093253.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_009093252.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256937.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926789.1
GO:0016301 - kinase activity [Evidence IEA]