Aeromonas media strain TR3_1 plasmid p1, complete sequence.
type: Entry
definition: Aeromonas media strain TR3_1 plasmid p1, complete sequence.
sequence version: NZ_CP075565.1
sequence date: 2022-10-27
sequence: sequence
division: CON
label: NZ_CP075565.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN19237318
keyword: RefSeq
source: Aeromonas media
organism: Aeromonas media
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Aeromonadales; Aeromonadaceae; Aeromonas.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP075565.1.\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. v0.4.7\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 400.0x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/27/2022 04:07:57\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) :: 4,198\nCDSs (total) :: 4,034\nGenes (coding) :: 3,967\nCDSs (with protein) :: 3,967\nGenes (RNA) :: 164\nrRNAs :: 11, 10, 10 (5S, 16S, 23S)\ncomplete rRNAs :: 11, 10, 10 (5S, 16S, 23S)\ntRNAs :: 127\nncRNAs :: 6\nPseudo Genes (total) :: 68\nCDSs (without protein) :: 67\nPseudo Genes (ambiguous residues) :: 0 of 68\nPseudo Genes (frameshifted) :: 22 of 68\nPseudo Genes (incomplete) :: 46 of 68\nPseudo Genes (internal stop) :: 13 of 68\nPseudo Genes (multiple problems) :: 11 of 68\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 9182
topology: circular
so has quality: SO_0000988
location: 1..9182
location: region:1-9182:1
RO_0002162: 651

NZ_CP075565
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN19237318
type: BioSample
SIO_000068: biosample

1
title: The superbug in activated sludge of wastewater treatment plant increases the risk of antibiotic resistance genes spread in the water cycle
author: Wan, C.
author: Tang, R.
author: Fu, L.
author: Wang, L.
author: Wang, P.
author: Liu, X.
author: Yu, Y.
author: Wu, C.
journal: Unpublished

2
title: Direct Submission
author: Wan, C.
author: Tang, R.
author: Fu, L.
author: Wang, L.
author: Wang, P.
author: Liu, X.
author: Yu, Y.
author: Wu, C.
journal: Submitted (17-MAY-2021) Department of Environmental Science and Engineering; Research Center of Environmental Pollution Control Technology; Center of Analysis and Measurement, Fudan University and Chinese Research Academy of Environmental Sciences, 220 Handan Road, Shanghai 200438, China

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9182:1
position: 9182
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9182:1:source
so part of: sequence
organism: Aeromonas media
mol type: genomic DNA
strain: TR3_1
isolation source: sludge of the aeration tanks of urban wastewater treatment plants
plasmid: p1
country: China
collection date: 2020-10-03

651
type: Taxonomy
SIO_000068: taxonomy

KI797_RS20920
type: Gene
subclass of: SO_0000704
RO_0002162: 651
locus tag: KI797_RS20920
old locus tag: KI797_20860
so part of: sequence
location: complement(join(8782..9182,1..1150))
location: region:1-9182:-1
so has part: feature:1-1150:-1:exon
so has part: feature:8782-9182:-1:exon
subclass of: SO_0000010

69410300
type: Gene
SIO_000068: ncbigene

position:1:-1
position: 1
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9182:-1
position: 9182
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-1150:-1:exon

position:1150:-1
position: 1150
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:8782-9182:-1:exon

position:8782:-1
position: 8782
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

KI797_RS20920
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 651
locus tag: KI797_RS20920
old locus tag: KI797_20860
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: MobQ family relaxase
translation: MAIYHCSVKTFSRRNGQSSTAAAAYRSGEKLLDENTGELHDYRRKGGVISATIILPSHAPAWASDRARLWNEAERAETRINSTVAREFEIALPHELSPNDRERLAHEFARELVEKHGFAADVAIHAPPEFQKGGTGKVIDNQNHHAHILLSTRRLGPNGFTEKTREFDARSNERDDDSYLFGPALIEHWRERFALLQNLYLARAGVAAQVDHRSNKARGLDAVPTRHLGPAVVGFERRMGIDSEKRQREALAVRAVDERVQELDAEVRGELAELDAQEAVIAAELAENLRYVAMDDAELTEVISKTQPADIDAQVASSWEVSKAKSDVTELEGERDSVARRITSWEEGHGFRTWLNSKGIGGAELDELRTELEQLGNRITKAIRRVRKATEAASARLWPEYNRRITLFDELIELRKAKRQRKILQVQKAQSLDFTTIALQRSLGAFGWADGGREWNACPKPLQRLIEDYLSTSGGERETMSAEIGRSRDVRDWLAQQKRGIDPAPAPKRNHGPRLG
SIO_010081: KI797_RS20920
subclass of: SO_0000673
so part of: KI797_RS20920
location: complement(join(8782..9182,1..1150))
location: region:1-9182:-1
so has part: feature:1-1150:-1:exon
so has part: feature:8782-9182:-1:exon

WP_167557709.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-1150:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:8782-9182:-1:exon

KI797_RS20925
type: Gene
subclass of: SO_0000704
RO_0002162: 651
locus tag: KI797_RS20925
old locus tag: KI797_20865
so part of: sequence
location: 1308..1637
location: region:1308-1637:1
so has part: feature:1308-1637:1:exon
subclass of: SO_0000010

69410301
type: Gene
SIO_000068: ncbigene

position:1308:1
position: 1308
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1637:1
position: 1637
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1308-1637:1:exon

KI797_RS20925
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 651
locus tag: KI797_RS20925
old locus tag: KI797_20865
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005671594.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: mobilization protein
translation: MTVIEQRIENLEKKLKQAKAEKQRKEARIRAQERKRTREQDTRRKILVGAVYLAIADSDDAALKALTDRMDKALTRDDDRALFDLPPRPEPKAEAEAEAEAEAPEPSAN
SIO_010081: KI797_RS20925
subclass of: SO_0000673
so part of: KI797_RS20925
location: 1308..1637
location: region:1308-1637:1
so has part: feature:1308-1637:1:exon

WP_226173250.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1308-1637:1:exon

KI797_RS20930
type: Gene
subclass of: SO_0000704
RO_0002162: 651
locus tag: KI797_RS20930
old locus tag: KI797_20870
so part of: sequence
location: complement(1624..1866)
location: region:1624-1866:-1
so has part: feature:1624-1866:-1:exon
subclass of: SO_0000010

69410299
type: Gene
SIO_000068: ncbigene

position:1624:-1
position: 1624
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1866:-1
position: 1866
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1624-1866:-1:exon

KI797_RS20930
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 651
locus tag: KI797_RS20930
old locus tag: KI797_20870
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005321398.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid replication protein RepB
translation: MEELQAKWVFDQGGFSKVLVVPTPMGAGYHLHLVKFGRQSETVVLERQRGGWRVFKSIDAAANTAHGIGFRRIEIDLSSR
SIO_010081: KI797_RS20930
subclass of: SO_0000673
so part of: KI797_RS20930
location: complement(1624..1866)
location: region:1624-1866:-1
so has part: feature:1624-1866:-1:exon

WP_167557714.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1624-1866:-1:exon

KI797_RS20935
type: Gene
subclass of: SO_0000704
RO_0002162: 651
locus tag: KI797_RS20935
old locus tag: KI797_20875
so part of: sequence
location: complement(2095..3060)
location: region:2095-3060:-1
so has part: feature:2095-3060:-1:exon
subclass of: SO_0000010

69410297
type: Gene
SIO_000068: ncbigene

position:2095:-1
position: 2095
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3060:-1
position: 3060
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2095-3060:-1:exon

KI797_RS20935
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 651
locus tag: KI797_RS20935
old locus tag: KI797_20875
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005321767.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MVKPALLAAAFIERLPRRPYCTDDKSSGLLIRPQATALGYLHIQYNPPPHVSSLVFDLDKPDSYHAWKDAGLPAPHWVSVNRTNGHAHIGYMLAAPVARTCAARQKPLRYLAAIEHVLAKRLGADMGYSGLITKNPTHSDWLTVWHQIEPYSLDYLAEFCPDADLAAYSRRSRKEVGGLGRNVTVFDNVREWAYSAVRAYWRPNGYEAWADAVRAACESANAFGREQGGPLPVSEIKATAKSISRWVWNRFTPAGFSQVQAHRGAKGGRISKRPTKNGKARADLLPEVIKLKAQGYSNRDIAEDLQISAGSVSNYLRRDRE
SIO_010081: KI797_RS20935
subclass of: SO_0000673
so part of: KI797_RS20935
location: complement(2095..3060)
location: region:2095-3060:-1
so has part: feature:2095-3060:-1:exon

WP_167557711.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2095-3060:-1:exon

KI797_RS20940
type: Gene
subclass of: SO_0000704
RO_0002162: 651
locus tag: KI797_RS20940
old locus tag: KI797_20880
so part of: sequence
location: 3283..4752
location: region:3283-4752:1
so has part: feature:3283-4752:1:exon
subclass of: SO_0000010

69410292
type: Gene
SIO_000068: ncbigene

position:3283:1
position: 3283
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4752:1
position: 4752
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3283-4752:1:exon

KI797_RS20940
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 651
locus tag: KI797_RS20940
old locus tag: KI797_20880
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001686642.1
GO function: GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0006304 - DNA modification [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Eco57I restriction-modification methylase domain-containing protein
translation: MLQRLEIADNVRRTIAPQTTQKHKSEFGQFMTPSSVARFMASLFPHSPLKTCHLLDAGAGVGALSCAFLDRWVTGGFGFESVEATAYEIDEQLRGHLAQHLAGYNRVTPRILAGDYIELATGEGLLDRGYTHVILNPPYKKINSQSAHRLALRTVGIETVNLYSAFVALAVGETAPGGQIVAIIPRSFCNGPYYRPFRDFILERAAIRHMHLFESRNKAFRDDEVLQENIIIRLERGGQQGPVTVTTSTDDSFSDLTTHEHPFDRIVFPDDQERFIHVPTTTDKSAIELSPAVRCSLADIGVKVSTGPVVDFRLKAHLRDMPEPGTVPLIYPGHLSMTGTVWPVAGLKKPNAIMRNDETEKWLYPNGFYCLVRRFSSKEEKRRVVASLVEPTAFGDHSVLGFENHMNLFHEGKHGLPEALARGLVVFLNTTAVDEHFRRFNGHTQVNATDLKQMKYPSRDTLIDLGKWAMQQGVLTQEEIDGKLGTLTA
SIO_010081: KI797_RS20940
subclass of: SO_0000673
so part of: KI797_RS20940
location: 3283..4752
location: region:3283-4752:1
so has part: feature:3283-4752:1:exon

WP_167557712.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3283-4752:1:exon

KI797_RS20945
type: Gene
subclass of: SO_0000704
RO_0002162: 651
locus tag: KI797_RS20945
old locus tag: KI797_20885
so part of: sequence
location: 4749..5702
location: region:4749-5702:1
so has part: feature:4749-5702:1:exon
subclass of: SO_0000010

69410295
type: Gene
SIO_000068: ncbigene

position:4749:1
position: 4749
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5702:1
position: 5702
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4749-5702:1:exon

KI797_RS20945
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 651
locus tag: KI797_RS20945
old locus tag: KI797_20885
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001064713.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: BsuBI/PstI family type II restriction endonuclease
translation: MNNQNDYIEAAQQIIISLGLPRAQQNERSALCLLALLNLTPGKAWADAENPLVGITPIMDWAREHYGKEYAPNTRETFRRQSMHQFCDAGVALYNPDKPDRPVNSPKAVYQIEPAALALLRTFGTPAWHDSLTTYLAERETLVARYAKEREQNRIPVEIAPGQQITLSPGEHSELIRAIIEDFAPRFAPGSVLVYAGDTGDKWGYFDAALLTGLGVDVDSHGKMPDVVLHFTAKNWLLLVESVTSHGPVDGKRHAELAKLFAGSTAGLVYVTAFPNRAIMGRYLGEIAWETEVWVADAPSHLIHFNGVRFLGPYPTE
SIO_010081: KI797_RS20945
subclass of: SO_0000673
so part of: KI797_RS20945
location: 4749..5702
location: region:4749-5702:1
so has part: feature:4749-5702:1:exon

WP_167557713.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4749-5702:1:exon

KI797_RS20950
type: Gene
subclass of: SO_0000704
RO_0002162: 651
locus tag: KI797_RS20950
old locus tag: KI797_20890
so part of: sequence
location: 5720..5968
location: region:5720-5968:1
so has part: feature:5720-5968:1:exon
subclass of: SO_0000010

69410296
type: Gene
SIO_000068: ncbigene

position:5720:1
position: 5720
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5968:1
position: 5968
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5720-5968:1:exon

KI797_RS20950
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 651
locus tag: KI797_RS20950
old locus tag: KI797_20890
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004356308.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MITPTTETAKEVLRGYGRANEAALASLMDVQDWQRIARQELERRATSIVQALDDATLKAIAAGELDMRAMCLQVTNEIHQTA
SIO_010081: KI797_RS20950
subclass of: SO_0000673
so part of: KI797_RS20950
location: 5720..5968
location: region:5720-5968:1
so has part: feature:5720-5968:1:exon

WP_182939827.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5720-5968:1:exon

KI797_RS20955
type: Gene
subclass of: SO_0000704
RO_0002162: 651
locus tag: KI797_RS20955
old locus tag: KI797_20895
so part of: sequence
location: 6321..6704
location: region:6321-6704:1
so has part: feature:6321-6704:1:exon
subclass of: SO_0000010

69410293
type: Gene
SIO_000068: ncbigene

position:6321:1
position: 6321
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6704:1
position: 6704
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6321-6704:1:exon

KI797_RS20955
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 651
locus tag: KI797_RS20955
old locus tag: KI797_20895
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MGGRSVEAFFISCDDHYLAKNLSSIRDEVMAEGEALTNYVRGHIIQRRKWGEFDKERARELWGDAEGIEITNSYCSNPGLMTAVVGDEWWYDLPMVDNPDYTYLCRIIQAVRDGLREYTKSTPAAAA
SIO_010081: KI797_RS20955
subclass of: SO_0000673
so part of: KI797_RS20955
location: 6321..6704
location: region:6321-6704:1
so has part: feature:6321-6704:1:exon

WP_139743097.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6321-6704:1:exon

KI797_RS20960
type: Gene
subclass of: SO_0000704
RO_0002162: 651
locus tag: KI797_RS20960
old locus tag: KI797_20900
so part of: sequence
location: 6725..6997
location: region:6725-6997:1
so has part: feature:6725-6997:1:exon
subclass of: SO_0000010

69410294
type: Gene
SIO_000068: ncbigene

position:6725:1
position: 6725
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6997:1
position: 6997
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6725-6997:1:exon

KI797_RS20960
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 651
locus tag: KI797_RS20960
old locus tag: KI797_20900
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSNENHQLFTTEQIRQRLEEGGESARWLAQAVVSYYRPAAPAPSLFSFSTKLDEEAQGMFFQMLLIRSKPDWSDDQLAALVRECEQYLAN
SIO_010081: KI797_RS20960
subclass of: SO_0000673
so part of: KI797_RS20960
location: 6725..6997
location: region:6725-6997:1
so has part: feature:6725-6997:1:exon

WP_139743096.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6725-6997:1:exon

KI797_RS20965
type: Gene
subclass of: SO_0000704
RO_0002162: 651
locus tag: KI797_RS20965
old locus tag: KI797_20905
so part of: sequence
location: 7496..8152
location: region:7496-8152:1
so has part: feature:7496-8152:1:exon
subclass of: SO_0000010

69410298
type: Gene
SIO_000068: ncbigene

position:7496:1
position: 7496
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8152:1
position: 8152
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7496-8152:1:exon

KI797_RS20965
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 651
locus tag: KI797_RS20965
old locus tag: KI797_20905
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001516695.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: quinolone resistance pentapeptide repeat protein QnrS2
translation: METYRHTYRHHSFSHQDLSDITFTACTFIRCDFRRANLRDATFINCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIELRECDLKGANFSRANFANQVSNRMYFCSAFITGCNLSYANMERVCLEKCELFENRWIGTHLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIASWQQEQLLEALGIVVFPD
SIO_010081: KI797_RS20965
subclass of: SO_0000673
so part of: KI797_RS20965
location: 7496..8152
location: region:7496-8152:1
so has part: feature:7496-8152:1:exon

WP_012537714.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7496-8152:1:exon