Vibrio alfacsensis strain 04Ya108 plasmid pSEA1, 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\nAP024167.1.\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_014205203.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: similar to AA sequence:RefSeq:WP_014205204.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005310844.1
GO:0015926 - glucosidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012026925.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006991878.1
GO:0004803 - transposase activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005221000.1
IS6-like element IS26 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001011939.1
type A-2 chloramphenicol O-acetyltransferase CatII
COORDINATES: similar to AA sequence:RefSeq:WP_076611715.1
IS5-like element ISKpn13 family transposase
Tn3-like element ISShfr9 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001043260.1
sulfonamide-resistant dihydropteroate synthase Sul2
COORDINATES: similar to AA sequence:RefSeq:WP_014386804.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014386803.1
Mph(G) family macrolide 2'-phosphotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_001120888.1
IS91-like element ISVsa3 family transposase
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_020588360.1
COORDINATES: protein motif:HMM:NF012245.2
COORDINATES: similar to AA sequence:RefSeq:WP_001339197.1
COORDINATES: similar to AA sequence:RefSeq:WP_002319681.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
cysteine-rich KTR domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011117014.1
GO:0005525 - GTP binding [Evidence IEA]; GO:0003924 - GTPase activity [Evidence IEA]
tetracycline resistance ribosomal protection protein Tet(M)
COORDINATES: similar to AA sequence:RefSeq:WP_011058339.1
tetracycline resistance determinant leader peptide
IS4-like element ISVsa5 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_014656611.1
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_000428546.1
tetracyline resistance-associated transcriptional repressor TetC
COORDINATES: similar to AA sequence:RefSeq:WP_001089064.1
GO:0055085 - transmembrane transport [Evidence IEA]
tetracycline efflux MFS transporter Tet(B)
COORDINATES: similar to AA sequence:RefSeq:WP_000088605.1
tetracycline resistance transcriptional repressor TetR(B)
COORDINATES: similar to AA sequence:RefSeq:WP_001284954.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000460649.1
COORDINATES: similar to AA sequence:RefSeq:WP_000562370.1
COORDINATES: similar to AA sequence:RefSeq:WP_000599530.1
GO:0015501 - glutamate:sodium symporter activity [Evidence IEA]
GO:0015813 - L-glutamate transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF023254.2
COORDINATES: similar to AA sequence:RefSeq:WP_012110799.1
COORDINATES: similar to AA sequence:RefSeq:WP_011399143.1
putative urea ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF017617.2
COORDINATES: protein motif:HMM:NF012894.2
phosphate ABC transporter substrate-binding/OmpA family protein
COORDINATES: protein motif:HMM:NF012321.2
nitrate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011399149.1
COORDINATES: protein motif:HMM:NF025810.2
COORDINATES: protein motif:HMM:NF025815.2
COORDINATES: protein motif:HMM:TIGR03736.1
COORDINATES: protein motif:HMM:NF012915.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF016724.2
COORDINATES: protein motif:HMM:NF013995.2
COORDINATES: protein motif:HMM:NF025438.2
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019615501.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013087140.1
COORDINATES: similar to AA sequence:RefSeq:WP_000756239.1
COORDINATES: similar to AA sequence:RefSeq:WP_011876190.1
COORDINATES: protein motif:HMM:NF013395.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015832760.1
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: protein motif:HMM:NF013252.2
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:NF019335.2
TonB-dependent receptor plug domain-containing protein
COORDINATES: protein motif:HMM:NF024754.2
COORDINATES: protein motif:HMM:NF041281.1
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:NF024254.2
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: protein motif:HMM:NF018536.2
COORDINATES: protein motif:HMM:NF024776.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:TIGR02227.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03743.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: protein motif:HMM:NF019153.2
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024117.2
COORDINATES: protein motif:HMM:NF015688.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: protein motif:HMM:NF014786.2
COORDINATES: protein motif:HMM:TIGR00595.1
GO:0005658 - alpha DNA polymerase:primase complex [Evidence IEA]
GO:0003678 - DNA helicase activity [Evidence IEA]; GO:0003688 - DNA replication origin binding [Evidence IEA]; GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF024895.2
COORDINATES: protein motif:HMM:NF014566.2
CPBP family intramembrane metalloprotease
COORDINATES: protein motif:HMM:NF024498.2
thioredoxin fold domain-containing protein
COORDINATES: protein motif:HMM:NF024853.2
COORDINATES: protein motif:HMM:NF025706.2
COORDINATES: protein motif:HMM:NF024642.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:TIGR02762.1
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF018148.2
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013324.2
COORDINATES: protein motif:HMM:NF013122.2
GO:0004527 - exonuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024996.2
GO:0015288 - porin activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019282658.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_076612302.1
COORDINATES: similar to AA sequence:RefSeq:WP_011494503.1
COORDINATES: similar to AA sequence:RefSeq:WP_005463131.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017189290.1
GO:0016209 - antioxidant activity [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005484390.1
COORDINATES: similar to AA sequence:RefSeq:WP_017817790.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005484637.1
COORDINATES: similar to AA sequence:RefSeq:WP_017632496.1
COORDINATES: protein motif:HMM:NF014668.2
GO:0006282 - regulation of DNA repair [Evidence IEA]
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF017300.2
GO:0006274 - DNA replication termination [Evidence IEA]
DNA replication terminus site-binding protein
COORDINATES: protein motif:HMM:NF024206.2
ankyrin repeat domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016790685.1
COORDINATES: similar to AA sequence:RefSeq:WP_016790684.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612097.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017074772.1
COORDINATES: similar to AA sequence:RefSeq:WP_006880978.1
COORDINATES: similar to AA sequence:RefSeq:WP_004735232.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017088853.1
COORDINATES: similar to AA sequence:RefSeq:WP_017088854.1
COORDINATES: similar to AA sequence:RefSeq:WP_017088855.1
COORDINATES: similar to AA sequence:RefSeq:WP_017074769.1
COORDINATES: similar to AA sequence:RefSeq:WP_004741153.1
This protein contains a GlyGly-CTERM protein-sorting domain, as detected by TIGR03501. These domains are found at the C-terminus of secreted proteins in organisms that possess both rhombosortase, which is an intramembrane serine proteinase (see TIGR03902), and a type II secretion system (T2SS). In at least some cases, such as VesB from Vibrio cholerae, cleavage by rhombosortase is followed first by attachment of a glycerophosphoethanolamine-containing moiety, then by transport by the T2SS across the outer membrane and release into the medium in soluble form; Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
GlyGly-CTERM sorting domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019023005.1
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: protein motif:HMM:NF014752.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004518 - nuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025642.2
COORDINATES: protein motif:HMM:NF013704.2
COORDINATES: similar to AA sequence:RefSeq:WP_005505285.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015313689.1
arabinose operon transcriptional regulator AraC
COORDINATES: similar to AA sequence:RefSeq:WP_017058040.1
COORDINATES: similar to AA sequence:RefSeq:WP_005477429.1
GO:0008733 - L-arabinose isomerase activity [Evidence IEA]
GO:0005996 - monosaccharide metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017447150.1
COORDINATES: similar to AA sequence:RefSeq:WP_017447151.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0008741 - ribulokinase activity [Evidence IEA]
GO:0019569 - L-arabinose catabolic process to xylulose 5-phosphate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020331889.1
arabinose ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014235070.1
GO:0015612 - ABC-type L-arabinose transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
GO:0042882 - L-arabinose transmembrane transport [Evidence IEA]
L-arabinose ABC transporter ATP-binding protein AraG
COORDINATES: similar to AA sequence:RefSeq:WP_013855627.1
Part of the ABC transporter complex AraFGH involved in the high affinity transport of arabinose; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
L-arabinose ABC transporter permease AraH
COORDINATES: similar to AA sequence:RefSeq:WP_076612134.1
COORDINATES: protein motif:HMM:NF033632.1
COORDINATES: similar to AA sequence:RefSeq:WP_004734423.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004335 - galactokinase activity [Evidence IEA]
GO:0046835 - carbohydrate phosphorylation [Evidence IEA]; GO:0006012 - galactose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020335215.1
GO:0008108 - UDP-glucose:hexose-1-phosphate uridylyltransferase activity [Evidence IEA]
GO:0006012 - galactose metabolic process [Evidence IEA]
UDP-glucose--hexose-1-phosphate uridylyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_015297204.1
GO:0003978 - UDP-glucose 4-epimerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_064624027.1
COORDINATES: similar to AA sequence:RefSeq:WP_001898375.1
COORDINATES: similar to AA sequence:RefSeq:WP_014205198.1
COORDINATES: similar to AA sequence:RefSeq:WP_004726158.1
COORDINATES: similar to AA sequence:RefSeq:WP_014205200.1
COORDINATES: similar to AA sequence:RefSeq:WP_004726160.1
COORDINATES: similar to AA sequence:RefSeq:WP_014205201.1
COORDINATES: similar to AA sequence:RefSeq:WP_014205202.1