Riemerella anatipestifer strain 20190403E1-1 plasmid unnamed1, complete sequence.
Bacteria; Bacteroidota; Flavobacteriia; Flavobacteriales; Weeksellaceae; Riemerella.
Chromosome-mediated tet(X) variants that confer different levels of tigecycline resistence in Riemerella anatipestifer
Submitted (23-MAR-2021) Veterinary College, Yangzhou University, Shuangqiao, Yangzhou 225000, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP072187.1.\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 :: Unicycler v. v0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 50.0x\nSequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/06/2022 23:25:42\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 2,064\nCDSs (total) :: 2,012\nGenes (coding) :: 1,995\nCDSs (with protein) :: 1,995\nGenes (RNA) :: 52\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 40\nncRNAs :: 3\nPseudo Genes (total) :: 17\nCDSs (without protein) :: 17\nPseudo Genes (ambiguous residues) :: 0 of 17\nPseudo Genes (frameshifted) :: 8 of 17\nPseudo Genes (incomplete) :: 9 of 17\nPseudo Genes (internal stop) :: 5 of 17\nPseudo Genes (multiple problems) :: 3 of 17\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_014937764.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013446996.1
GO:0016226 - iron-sulfur cluster assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014937763.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004920528.1
COORDINATES: similar to AA sequence:RefSeq:WP_013446999.1
COORDINATES: similar to AA sequence:RefSeq:WP_013447000.1
GO:0019628 - urate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920540.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920541.1
COORDINATES: similar to AA sequence:RefSeq:WP_014937759.1
GO:0005198 - structural molecule activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013447003.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004920552.1
GO:0004594 - pantothenate kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920554.1
COORDINATES: similar to AA sequence:RefSeq:WP_017686191.1
COORDINATES: similar to AA sequence:RefSeq:WP_014615084.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_014937753.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920566.1
COORDINATES: similar to AA sequence:RefSeq:WP_018675005.1
GO:0008760 - UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity [Evidence IEA]
GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
UDP-N-acetylglucosamine 1-carboxyvinyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_004920572.1
GO:0052381 - tRNA dimethylallyltransferase activity [Evidence IEA]
GO:0006400 - tRNA modification [Evidence IEA]
tRNA (adenosine(37)-N6)-dimethylallyltransferase MiaA
COORDINATES: similar to AA sequence:RefSeq:WP_014937749.1
COORDINATES: similar to AA sequence:RefSeq:WP_013447007.1
COORDINATES: similar to AA sequence:RefSeq:WP_015807161.1
GO:0022625 - cytosolic large ribosomal subunit [Evidence IEA]; GO:0000315 - organellar large ribosomal subunit [Evidence IEA]
GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920582.1
GO:0022625 - cytosolic large ribosomal subunit [Evidence IEA]; GO:0000311 - plastid large ribosomal subunit [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920587.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920589.1
GO:0071949 - FAD binding [Evidence IEA]; GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920592.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920595.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920599.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_004920602.1
COORDINATES: similar to AA sequence:RefSeq:WP_014937731.1
GO:0008784 - alanine racemase activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016874 - ligase activity [Evidence IEA]
GO:0006522 - alanine metabolic process [Evidence IEA]; GO:0009058 - biosynthetic process [Evidence IEA]
bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase
COORDINATES: similar to AA sequence:RefSeq:WP_004920607.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004797 - thymidine kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920609.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920612.1
GO:0008649 - rRNA methyltransferase activity [Evidence IEA]; GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity [Evidence IEA]
GO:0000451 - rRNA 2'-O-methylation [Evidence IEA]
16S rRNA (cytidine(1402)-2'-O)-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_015782609.1
GO:0004316 - 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
3-oxoacyl-[acyl-carrier-protein] reductase
COORDINATES: similar to AA sequence:RefSeq:WP_004920618.1
COORDINATES: similar to AA sequence:RefSeq:WP_014937726.1
COORDINATES: similar to AA sequence:RefSeq:WP_014937703.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014615080.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920628.1
GO:0008997 - ribonuclease R activity [Evidence IEA]
GO:0006401 - RNA catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920632.1
GO:0004751 - ribose-5-phosphate isomerase activity [Evidence IEA]
GO:0009052 - pentose-phosphate shunt, non-oxidative branch [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920635.1
COORDINATES: similar to AA sequence:RefSeq:WP_018674713.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920641.1
ATP-dependent Clp protease ATP-binding subunit
COORDINATES: protein motif:HMM:NF014893.2
COORDINATES: similar to AA sequence:RefSeq:WP_002982105.1
COORDINATES: similar to AA sequence:RefSeq:WP_013447015.1
COORDINATES: similar to AA sequence:RefSeq:WP_017686188.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920655.1
GO:0008252 - nucleotidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920656.1
COORDINATES: similar to AA sequence:RefSeq:WP_014937712.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920662.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920665.1
DCC1-like thiol-disulfide oxidoreductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004920668.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920670.1
GO:0003855 - 3-dehydroquinate dehydratase activity [Evidence IEA]
GO:0009423 - chorismate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014937707.1
regulatory iron-sulfur-containing complex subunit RicT
COORDINATES: similar to AA sequence:RefSeq:WP_004920675.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920678.1
transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004920681.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920687.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004920695.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891297.1
IS982-like element ISRa1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_013446985.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920430.1
COORDINATES: similar to AA sequence:RefSeq:WP_014937795.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]
GO:0008033 - tRNA processing [Evidence IEA]; GO:0002098 - tRNA wobble uridine modification [Evidence IEA]
tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG
COORDINATES: similar to AA sequence:RefSeq:WP_002661759.1
COORDINATES: protein motif:HMM:NF040365.1
COORDINATES: similar to AA sequence:RefSeq:WP_009090065.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0004540 - ribonuclease activity [Evidence IEA]
GO:0042254 - ribosome biogenesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013446986.1
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013446987.1
COORDINATES: similar to AA sequence:RefSeq:WP_014937789.1
GO:0004612 - phosphoenolpyruvate carboxykinase (ATP) activity [Evidence IEA]
GO:0006094 - gluconeogenesis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920445.1
COORDINATES: similar to AA sequence:RefSeq:WP_014937787.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013446988.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920456.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_014937784.1
GO:0008966 - phosphoglucosamine mutase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]; GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013446991.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920464.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920469.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920472.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920475.1
GO:0009058 - biosynthetic process [Evidence IEA]
aminodeoxychorismate synthase component I
COORDINATES: similar to AA sequence:RefSeq:WP_004920479.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014937777.1
COORDINATES: similar to AA sequence:RefSeq:WP_004920483.1
heavy metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004920485.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_004920486.1
Fic/DOC family N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014937773.1
COORDINATES: similar to AA sequence:RefSeq:WP_013446993.1
COORDINATES: similar to AA sequence:RefSeq:WP_013446994.1
outer membrane beta-barrel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004920496.1
pyridoxal phosphate-dependent aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_013446995.1
GO:0004822 - isoleucine-tRNA ligase activity [Evidence IEA]
GO:0006428 - isoleucyl-tRNA aminoacylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920503.1
GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920506.1
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920509.1
COORDINATES: similar to AA sequence:RefSeq:WP_002686394.1
COORDINATES: similar to AA sequence:RefSeq:WP_018278301.1
GO:0005525 - GTP binding [Evidence IEA]; GO:0003924 - GTPase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004920516.1
iron-sulfur cluster assembly accessory protein