Vibrio alfacsensis strain 04Ya108 plasmid pYa108, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio.
Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis
DOI:10.1371/journal.pone.0271627 Publication Status: Online-Only
Submitted (19-NOV-2020) Contact:Hirokazu Yano Tohoku University, Graduate School of Life Sciences; 2-1-1 Katahira, Aobaku, Sendai 9808577, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP024168.1.\nAnnotated at DFAST https://dfast.nig.ac.jp/\n\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 :: HGAP v. 3.0\nGenome Coverage :: 218x\nSequencing Technology :: Pacbio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/20/2023 06:06:41\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) :: 4,823\nCDSs (total) :: 4,644\nGenes (coding) :: 4,584\nCDSs (with protein) :: 4,584\nGenes (RNA) :: 179\nrRNAs :: 14, 13, 13 (5S, 16S, 23S)\ncomplete rRNAs :: 14, 13, 13 (5S, 16S, 23S)\ntRNAs :: 135\nncRNAs :: 4\nPseudo Genes (total) :: 60\nCDSs (without protein) :: 60\nPseudo Genes (ambiguous residues) :: 0 of 60\nPseudo Genes (frameshifted) :: 31 of 60\nPseudo Genes (incomplete) :: 36 of 60\nPseudo Genes (internal stop) :: 9 of 60\nPseudo Genes (multiple problems) :: 11 of 60\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011151850.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0033225 - ATPase-coupled 2-aminoethylphosphonate transporter activity [Evidence IEA]
GO:0033223 - 2-aminoethylphosphonate transport [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
putative 2-aminoethylphosphonate ABC transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_017819754.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0033225 - ATPase-coupled 2-aminoethylphosphonate transporter activity [Evidence IEA]
putative 2-aminoethylphosphonate ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017075813.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0033226 - 2-aminoethylphosphonate binding [Evidence IEA]; GO:0033225 - ATPase-coupled 2-aminoethylphosphonate transporter activity [Evidence IEA]
putative 2-aminoethylphosphonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_004749659.1
GO:0047304 - 2-aminoethylphosphonate-pyruvate transaminase activity [Evidence IEA]
GO:0019700 - organic phosphonate catabolic process [Evidence IEA]
2-aminoethylphosphonate--pyruvate transaminase
COORDINATES: similar to AA sequence:RefSeq:WP_005374071.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]; GO:0008483 - transaminase activity [Evidence IEA]
aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011999177.1
GO:0050194 - phosphonoacetaldehyde hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015728484.1
nuclear transport factor 2 family protein
COORDINATES: protein motif:HMM:NF019474.2
COORDINATES: similar to AA sequence:RefSeq:WP_009696401.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014234397.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009696403.1
COORDINATES: similar to AA sequence:RefSeq:WP_017011673.1
GO:0047689 - aspartate racemase activity [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020196330.1
COORDINATES: protein motif:HMM:NF014081.2
COORDINATES: protein motif:HMM:NF024242.2
helix-turn-helix transcriptional regulator
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF016830.2
GO:0015288 - porin activity [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017082542.1
COORDINATES: similar to AA sequence:RefSeq:WP_012277212.1
COORDINATES: similar to AA sequence:RefSeq:WP_010656624.1
COORDINATES: similar to AA sequence:RefSeq:WP_018991378.1
COORDINATES: similar to AA sequence:RefSeq:WP_019826404.1
COORDINATES: similar to AA sequence:RefSeq:WP_008843782.1
COORDINATES: similar to AA sequence:RefSeq:WP_012277181.1
COORDINATES: similar to AA sequence:RefSeq:WP_005536335.1
COORDINATES: similar to AA sequence:RefSeq:WP_010324647.1
COORDINATES: similar to AA sequence:RefSeq:WP_010324648.1
COORDINATES: similar to AA sequence:RefSeq:WP_012277226.1
COORDINATES: similar to AA sequence:RefSeq:WP_010324631.1
COORDINATES: similar to AA sequence:RefSeq:WP_010324627.1
COORDINATES: similar to AA sequence:RefSeq:WP_010324625.1
GO:0003824 - catalytic activity [Evidence IEA]
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011765706.1
GO:0008774 - acetaldehyde dehydrogenase (acetylating) activity [Evidence IEA]
acetaldehyde dehydrogenase (acetylating)
COORDINATES: similar to AA sequence:RefSeq:WP_012277177.1
GO:0008701 - 4-hydroxy-2-oxovalerate aldolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003446472.1
COORDINATES: similar to AA sequence:RefSeq:WP_017061984.1
COORDINATES: similar to AA sequence:RefSeq:WP_006958798.1
COORDINATES: similar to AA sequence:RefSeq:WP_008843814.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008843815.1
COORDINATES: protein motif:HMM:NF012955.2
COORDINATES: similar to AA sequence:RefSeq:WP_012155360.1
class I adenylate-forming enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019821808.1
COORDINATES: similar to AA sequence:RefSeq:WP_002937700.1
COORDINATES: similar to AA sequence:RefSeq:WP_010324651.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_002925067.1
COORDINATES: similar to AA sequence:RefSeq:WP_003445112.1
COORDINATES: similar to AA sequence:RefSeq:WP_011327588.1
COORDINATES: protein motif:HMM:NF019225.2
PEP-CTERM sorting domain-containing protein
COORDINATES: protein motif:HMM:NF038322.1
COORDINATES: similar to AA sequence:RefSeq:WP_008020850.1
COORDINATES: similar to AA sequence:RefSeq:WP_012277229.1
COORDINATES: similar to AA sequence:RefSeq:WP_010322477.1
COORDINATES: protein motif:HMM:NF012596.2
COORDINATES: similar to AA sequence:RefSeq:WP_010322648.1
electron transfer flavoprotein-ubiquinone oxidoreductase
COORDINATES: protein motif:HMM:TIGR00254.1
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_012584881.1
COORDINATES: similar to AA sequence:RefSeq:WP_016403878.1
COORDINATES: protein motif:HMM:TIGR02917.1
GO:0005515 - protein binding [Evidence IEA]
PEP-CTERM system TPR-repeat protein PrsT
COORDINATES: protein motif:HMM:NF024871.2
COORDINATES: protein motif:HMM:NF024832.2
COORDINATES: protein motif:HMM:NF013607.2
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: protein motif:HMM:NF016145.2
polysaccharide pyruvyl transferase family protein
COORDINATES: protein motif:HMM:NF025082.2
COORDINATES: protein motif:HMM:TIGR02916.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011576031.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]
PEP-CTERM-box response regulator transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_012988794.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03097.1
putative O-glycosylation ligase, exosortase A system-associated
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: similar to AA sequence:RefSeq:WP_002782161.1
COORDINATES: similar to AA sequence:RefSeq:WP_013136716.1
COORDINATES: protein motif:HMM:NF012695.2
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF006088.0
GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014706626.1
COORDINATES: similar to AA sequence:RefSeq:WP_011045746.1
COORDINATES: protein motif:HMM:TIGR03007.1
COORDINATES: similar to AA sequence:RefSeq:WP_007618463.1
COORDINATES: similar to AA sequence:RefSeq:WP_016404019.1
TIGR03013 family PEP-CTERM/XrtA system glycosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_006991432.1
COORDINATES: similar to AA sequence:RefSeq:WP_008843138.1
GO:0005575 - cellular_component [Evidence IEA]
GO:0003674 - molecular_function [Evidence IEA]
GO:0008150 - biological_process [Evidence IEA]
FemAB family PEP-CTERM system-associated protein
COORDINATES: protein motif:HMM:TIGR03087.1
TIGR03087 family PEP-CTERM/XrtA system glycosyltransferase
COORDINATES: protein motif:HMM:TIGR03109.1
GO:0004197 - cysteine-type endopeptidase activity [Evidence IEA]
GO:0043687 - post-translational protein modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018993304.1
GO:0004066 - asparagine synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0006529 - asparagine biosynthetic process [Evidence IEA]
amidotransferase 1, exosortase A system-associated
COORDINATES: similar to AA sequence:RefSeq:WP_007618477.1
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: similar to AA sequence:RefSeq:WP_017791282.1
COORDINATES: protein motif:HMM:NF016357.2
GO:0047355 - CDP-glycerol glycerophosphotransferase activity [Evidence IEA]
CDP-glycerol glycerophosphotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016857361.1
phosphocholine cytidylyltransferase family protein
COORDINATES: protein motif:HMM:NF019342.2
GO:0016787 - hydrolase activity [Evidence IEA]
Members of this family of hydrolases with an active site Cys residue belong to MEROPS family C26; Derived by automated computational analysis using gene prediction method: Protein Homology.
gamma-glutamyl-gamma-aminobutyrate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012154656.1
GO:0016772 - transferase activity, transferring phosphorus-containing groups [Evidence IEA]
GO:0016310 - phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004738750.1
GO:0004781 - sulfate adenylyltransferase (ATP) activity [Evidence IEA]
GO:0019419 - sulfate reduction [Evidence IEA]
sulfate adenylyltransferase subunit CysD
COORDINATES: similar to AA sequence:RefSeq:WP_005528550.1
GO:0005525 - GTP binding [Evidence IEA]; GO:0003924 - GTPase activity [Evidence IEA]
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
sulfate adenylyltransferase subunit CysN
COORDINATES: similar to AA sequence:RefSeq:WP_004410374.1
COORDINATES: similar to AA sequence:RefSeq:WP_008020991.1
COORDINATES: similar to AA sequence:RefSeq:WP_008844340.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004256669.1
COORDINATES: similar to AA sequence:RefSeq:WP_011327580.1
COORDINATES: similar to AA sequence:RefSeq:WP_002925295.1
COORDINATES: similar to AA sequence:RefSeq:WP_008062503.1
COORDINATES: similar to AA sequence:RefSeq:WP_007946123.1
COORDINATES: similar to AA sequence:RefSeq:WP_012277198.1
COORDINATES: similar to AA sequence:RefSeq:WP_008844333.1
COORDINATES: similar to AA sequence:RefSeq:WP_011327574.1
COORDINATES: similar to AA sequence:RefSeq:WP_004257046.1
COORDINATES: similar to AA sequence:RefSeq:WP_012277194.1
electron transfer flavoprotein subunit beta/FixA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004733823.1
COORDINATES: similar to AA sequence:RefSeq:WP_009832954.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012068888.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010324650.1
COORDINATES: similar to AA sequence:RefSeq:WP_012155365.1
COORDINATES: similar to AA sequence:RefSeq:WP_012600212.1
COORDINATES: similar to AA sequence:RefSeq:WP_017085380.1
COORDINATES: protein motif:HMM:NF018561.2
COORDINATES: similar to AA sequence:RefSeq:WP_012600224.1
COORDINATES: similar to AA sequence:RefSeq:WP_017108001.1
COORDINATES: similar to AA sequence:RefSeq:WP_012600222.1
GO:0031522 - cell envelope Sec protein transport complex [Evidence IEA]
GO:0015450 - protein-transporting ATPase activity [Evidence IEA]
GO:0043952 - protein transport by the Sec complex [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017041954.1
COORDINATES: similar to AA sequence:RefSeq:WP_012600220.1
COORDINATES: similar to AA sequence:RefSeq:WP_012600218.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017091757.1
COORDINATES: similar to AA sequence:RefSeq:WP_012600214.1
COORDINATES: similar to AA sequence:RefSeq:WP_017091761.1
mechanosensitive ion channel family protein
COORDINATES: protein motif:HMM:NF027890.2
COORDINATES: similar to AA sequence:RefSeq:WP_011081628.1
COORDINATES: protein motif:HMM:NF024039.2
COORDINATES: similar to AA sequence:RefSeq:WP_004733856.1
GO:0046872 - metal ion binding [Evidence IEA]
SEC-C metal-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005464459.1
COORDINATES: similar to AA sequence:RefSeq:WP_010371061.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_003057430.1
COORDINATES: similar to AA sequence:RefSeq:WP_016780483.1
COORDINATES: similar to AA sequence:RefSeq:WP_008056564.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008568681.1
COORDINATES: similar to AA sequence:RefSeq:WP_010324691.1
COORDINATES: similar to AA sequence:RefSeq:WP_002925183.1
COORDINATES: similar to AA sequence:RefSeq:WP_003445134.1
COORDINATES: similar to AA sequence:RefSeq:WP_008843792.1
COORDINATES: similar to AA sequence:RefSeq:WP_012155391.1
COORDINATES: similar to AA sequence:RefSeq:WP_012277214.1
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002939152.1
COORDINATES: protein motif:HMM:TIGR04352.1
COORDINATES: protein motif:HMM:NF026257.2
COORDINATES: protein motif:HMM:NF013757.2
IclR family transcriptional regulator C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF012334.2
COORDINATES: similar to AA sequence:RefSeq:WP_009704074.1
COORDINATES: similar to AA sequence:RefSeq:WP_010429562.1
COORDINATES: protein motif:HMM:NF040521.1
COORDINATES: similar to AA sequence:RefSeq:WP_005435676.1
COORDINATES: similar to AA sequence:RefSeq:WP_013110145.1
COORDINATES: similar to AA sequence:RefSeq:WP_016401827.1
GO:0019867 - outer membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005435642.1
COORDINATES: similar to AA sequence:RefSeq:WP_017037868.1
GO:0006629 - lipid metabolic process [Evidence IEA]
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015728271.1
COORDINATES: protein motif:HMM:NF013283.2
autotransporter assembly complex family protein
COORDINATES: protein motif:HMM:NF006560.0
COORDINATES: similar to AA sequence:RefSeq:WP_017035934.1
COORDINATES: similar to AA sequence:RefSeq:WP_010429930.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016799688.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010647375.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_017018434.1
COORDINATES: similar to AA sequence:RefSeq:WP_012548923.1
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.
transposase zinc-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010450779.1
COORDINATES: similar to AA sequence:RefSeq:WP_005374048.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
phosphonate utilization transcriptional regulator PhnR