Shewanella xiamenensis strain HD6416 plasmid pHD6416-NDM, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales; Shewanellaceae; Shewanella.
Submitted (13-JUL-2021) Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Sanxiang, Suzhou 215004, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP079717.1.\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. v0.4.9\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 09/07/2022 09:05:37\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.2\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 4,477\nCDSs (total) :: 4,339\nGenes (coding) :: 4,295\nCDSs (with protein) :: 4,295\nGenes (RNA) :: 138\nrRNAs :: 10, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 10, 9, 9 (5S, 16S, 23S)\ntRNAs :: 106\nncRNAs :: 4\nPseudo Genes (total) :: 44\nCDSs (without protein) :: 44\nPseudo Genes (ambiguous residues) :: 0 of 44\nPseudo Genes (frameshifted) :: 13 of 44\nPseudo Genes (incomplete) :: 29 of 44\nPseudo Genes (internal stop) :: 8 of 44\nPseudo Genes (multiple problems) :: 5 of 44\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF023237.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012772.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:YP_005229645.1
COORDINATES: similar to AA sequence:RefSeq:WP_001277466.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015062793.1
COORDINATES: similar to AA sequence:RefSeq:WP_013722692.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005229640.1
GO:0045340 - mercury ion binding [Evidence IEA]
mercury resistance system periplasmic binding protein MerP
COORDINATES: similar to AA sequence:RefSeq:YP_005229639.1
COORDINATES: similar to AA sequence:RefSeq:WP_000414383.1
mercury resistance transcriptional regulator MerR
COORDINATES: similar to AA sequence:RefSeq:WP_016402107.1
GO:0005575 - cellular_component [Evidence IEA]
GO:0003674 - molecular_function [Evidence IEA]
GO:0008150 - biological_process [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF022590.2
COORDINATES: similar to AA sequence:RefSeq:WP_001159683.1
anti-phage defense-associated sirtuin Dsr1
COORDINATES: similar to AA sequence:RefSeq:WP_005355955.1
COORDINATES: similar to AA sequence:RefSeq:WP_017821452.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012792.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611920.1
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_003100856.1
COORDINATES: similar to AA sequence:RefSeq:WP_007420683.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011331104.1
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_014611683.1
COORDINATES: protein motif:HMM:NF024830.2
COORDINATES: similar to AA sequence:RefSeq:WP_011918394.1
COORDINATES: similar to AA sequence:RefSeq:WP_011711692.1
COORDINATES: similar to AA sequence:RefSeq:WP_011711507.1
COORDINATES: similar to AA sequence:RefSeq:WP_011711508.1
COORDINATES: similar to AA sequence:RefSeq:WP_014620324.1
COORDINATES: protein motif:HMM:NF012339.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014620316.1
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF012321.2
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: similar to AA sequence:RefSeq:WP_012323283.1
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:NF018536.2
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: protein motif:HMM:NF021981.2
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:NF025125.2
COORDINATES: protein motif:HMM:NF020125.2
COORDINATES: similar to AA sequence:RefSeq:WP_012197033.1
COORDINATES: similar to AA sequence:RefSeq:WP_012197034.1
COORDINATES: protein motif:HMM:NF016214.2
COORDINATES: protein motif:HMM:NF024096.2
PD-(D/E)XK nuclease-like domain-containing protein
COORDINATES: protein motif:HMM:NF015776.2
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00663.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF013122.2
COORDINATES: protein motif:HMM:NF025001.2
COORDINATES: protein motif:HMM:TIGR03734.1
COORDINATES: protein motif:HMM:TIGR03737.1
COORDINATES: protein motif:HMM:NF013790.2
COORDINATES: protein motif:HMM:TIGR03736.1
COORDINATES: protein motif:HMM:NF013658.2
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_032495448.1
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: protein motif:HMM:NF024872.2
COORDINATES: protein motif:HMM:NF040179.1
COORDINATES: protein motif:HMM:NF021212.2
COORDINATES: protein motif:HMM:NF024498.2
thioredoxin fold domain-containing protein
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF018311.2
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:NF013506.2
COORDINATES: protein motif:HMM:NF025706.2
COORDINATES: protein motif:HMM:TIGR03743.1
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:NF039622.1
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:NF017300.2
DNA replication terminus site-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_001138064.1
COORDINATES: similar to AA sequence:RefSeq:WP_016236504.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221021.1
COORDINATES: similar to AA sequence:RefSeq:WP_000237816.1
NAD(+)--rifampin ADP-ribosyltransferase Arr-3
COORDINATES: similar to AA sequence:RefSeq:WP_001749985.1
trimethoprim-resistant dihydrofolate reductase DfrA27
COORDINATES: similar to AA sequence:RefSeq:WP_048608579.1
ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA16
COORDINATES: similar to AA sequence:RefSeq:WP_000679427.1
quaternary ammonium compound efflux SMR transporter QacE delta 1
COORDINATES: similar to AA sequence:RefSeq:WP_000259031.1
sulfonamide-resistant dihydropteroate synthase Sul1
COORDINATES: similar to AA sequence:RefSeq:WP_004194535.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229646.1
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_001389365.1
IS6-like element IS6100 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001137892.1
macrolide-binding transcriptional repressor MphR(A)
COORDINATES: similar to AA sequence:RefSeq:WP_000004159.1
macrolide resistance MFS transporter Mrx(A)
COORDINATES: similar to AA sequence:RefSeq:WP_000219391.1
Mph(A) family macrolide 2'-phosphotransferase
COORDINATES: similar to AA sequence:RefSeq:YP_005221000.1
IS6-like element IS26 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_013124600.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:YP_005229644.1
COORDINATES: similar to AA sequence:RefSeq:WP_016240396.1
COORDINATES: similar to AA sequence:RefSeq:WP_016239395.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229638.1
GO:0001228 - DNA-binding transcription activator activity, RNA polymerase II-specific [Evidence IEA]
Hg(II)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:YP_005229637.1
IS110-like element IS4321 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_032489893.1
broad-spectrum class A beta-lactamase TEM-1
COORDINATES: similar to AA sequence:RefSeq:WP_000971921.1
IS1182-like element ISCfr1 family transposase
COORDINATES: similar to AA sequence:RefSeq:YP_005221028.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221027.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221025.1
COORDINATES: similar to AA sequence:RefSeq:WP_000557454.1
aminoglycoside N-acetyltransferase AAC(3)-IId
COORDINATES: similar to AA sequence:RefSeq:WP_000052512.1
ABC-F type ribosomal protection protein Msr(E)
COORDINATES: similar to AA sequence:RefSeq:WP_014325835.1
Mph(E) family macrolide 2'-phosphotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_004786457.1
COORDINATES: similar to AA sequence:RefSeq:WP_004759367.1
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_002001451.1
IS4-like element ISEc29 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011334168.1
COORDINATES: similar to AA sequence:RefSeq:WP_009049036.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_002039164.1
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]; GO:0042908 - xenobiotic transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011534278.1
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_011071025.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015063357.1
quaternary ammonium compound efflux SMR transporter QacG2
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000050481.1
IS91-like element ISCR1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_000361704.1
quinolone resistance pentapeptide repeat protein QnrVC6
COORDINATES: similar to AA sequence:RefSeq:WP_017048470.1
COORDINATES: similar to AA sequence:RefSeq:WP_017045848.1
COORDINATES: similar to AA sequence:RefSeq:WP_004201169.1
protein-disulfide reductase DsbD family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004201168.1
GO:0004640 - phosphoribosylanthranilate isomerase activity [Evidence IEA]
GO:0000162 - tryptophan biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004201167.1
COORDINATES: similar to AA sequence:RefSeq:WP_032492661.1
subclass B1 metallo-beta-lactamase NDM-1
COORDINATES: similar to AA sequence:RefSeq:WP_076611607.1
COORDINATES: similar to AA sequence:RefSeq:WP_001011939.1
type A chloramphenicol O-acetyltransferase
COORDINATES: protein motif:HMM:NF019498.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]