Pantoea agglomerans strain FDAARGOS 1447 plasmid unnamed1, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Erwiniaceae; Pantoea; Pantoea agglomerans group.
FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS): Supporting development and validation of Infectious Disease Dx tests
Submitted (17-JUN-2021) Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Avenue, White Oak, MD 20903, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP077367.1.\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 :: SMRT v. 9.0.0, HGAP v. 4.0\nGenome Coverage :: 1370.74x\nSequencing Technology :: Pacbio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/29/2023 04:40:20\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) :: 4,248\nGenes (coding) :: 4,209\nCDSs (with protein) :: 4,209\nGenes (RNA) :: 114\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 77\nncRNAs :: 15\nPseudo Genes (total) :: 39\nCDSs (without protein) :: 39\nPseudo Genes (ambiguous residues) :: 0 of 39\nPseudo Genes (frameshifted) :: 13 of 39\nPseudo Genes (incomplete) :: 31 of 39\nPseudo Genes (internal stop) :: 13 of 39\nPseudo Genes (multiple problems) :: 16 of 39\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
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]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010256858.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256859.1
COORDINATES: similar to AA sequence:RefSeq:NP_416521.2
YoeB-YefM toxin-antitoxin system antitoxin YefM
COORDINATES: similar to AA sequence:RefSeq:NP_707909.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256865.1
COORDINATES: similar to AA sequence:RefSeq:WP_006685024.1
COORDINATES: similar to AA sequence:RefSeq:WP_010260482.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611473.1
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_010256878.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671973.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010671972.1
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
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006118233.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671966.1
GO:0052621 - diguanylate cyclase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_010671965.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671964.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256916.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256917.1
GO:0046417 - chorismate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010256919.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256922.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LacI family DNA-binding transcriptional regulator
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
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_009093254.1
COORDINATES: similar to AA sequence:RefSeq:WP_020885163.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850652.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256955.1
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_010256962.1
COORDINATES: similar to AA sequence:RefSeq:WP_001030595.1
COORDINATES: similar to AA sequence:RefSeq:WP_008926784.1
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
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_004710385.1
COORDINATES: similar to AA sequence:RefSeq:NP_308490.1
COORDINATES: similar to AA sequence:RefSeq:WP_006122144.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010257007.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0042908 - xenobiotic transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010671942.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010257016.1
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
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_010257030.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:NP_416082.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
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_007676525.1
predicted Zn-dependent protease with a strongly conserved HExxH motif; Derived by automated computational analysis using gene prediction method: Protein Homology.
DUF2268 domain-containing putative Zn-dependent protease
COORDINATES: similar to AA sequence:RefSeq:WP_010257042.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257045.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010257048.1
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_010257050.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257053.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850529.1
COORDINATES: protein motif:HMM:NF021526.2
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_000756598.1
YgiW/YdeI family stress tolerance OB fold protein
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_010671927.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010671926.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257085.1
COORDINATES: similar to AA sequence:RefSeq:WP_014593915.1
COORDINATES: similar to AA sequence:RefSeq:YP_005228524.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_010257091.1
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_010257098.1
sigma-54-dependent Fis family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004124383.1
sulfonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007888991.1
COORDINATES: similar to AA sequence:RefSeq:NP_312500.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257107.1
COORDINATES: similar to AA sequence:RefSeq:WP_012441826.1
COORDINATES: similar to AA sequence:RefSeq:WP_001595120.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
GO:0003677 - DNA binding [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO:0045927 - positive regulation of growth [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_020317119.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512916.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512915.1
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_076612015.1
COORDINATES: protein motif:HMM:NF012955.2
COORDINATES: similar to AA sequence:RefSeq:WP_017802622.1
COORDINATES: similar to AA sequence:RefSeq:WP_010904489.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_010257118.1
COORDINATES: similar to AA sequence:RefSeq:WP_009113699.1
COORDINATES: similar to AA sequence:RefSeq:WP_008455371.1
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_003850554.1
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_009093176.1
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]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_010671903.1
COORDINATES: similar to AA sequence:RefSeq:WP_017801976.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257161.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356572.1
COORDINATES: protein motif:HMM:NF017162.2
Hha/YmoA family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_003850570.1
COORDINATES: similar to AA sequence:RefSeq:WP_010257171.1
autotransporter outer membrane beta-barrel domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010257173.1
NirD/YgiW/YdeI family stress tolerance protein
COORDINATES: protein motif:HMM:NF027890.2
GO:0030253 - protein secretion by the type I secretion system [Evidence IEA]
HlyD family type I secretion periplasmic adaptor subunit
COORDINATES: protein motif:HMM:TIGR03375.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF014385.2
COORDINATES: protein motif:HMM:NF039533.1
COORDINATES: similar to AA sequence:RefSeq:WP_009093183.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356578.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356579.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356580.1
COORDINATES: similar to AA sequence:RefSeq:WP_013356581.1
GO:0007155 - cell adhesion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013356582.1
GO:0061077 - chaperone-mediated protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013356583.1
GO:0015473 - fimbrial usher porin activity [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]
fimbria/pilus outer membrane usher protein
COORDINATES: similar to AA sequence:RefSeq:WP_010256778.1
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013356586.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010256789.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013356588.1
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_013356589.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256798.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256802.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010256805.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013812884.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256810.1
COORDINATES: similar to AA sequence:RefSeq:WP_010256816.1
GO:0051119 - sugar transmembrane transporter activity [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010671992.1
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_010671991.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019362816.1
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_010256830.1
COORDINATES: similar to AA sequence:RefSeq:WP_011147726.1
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_010671984.1
COORDINATES: similar to AA sequence:RefSeq:WP_003850584.1
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]