Hafnia paralvei strain AVS0177 plasmid pAVS0177-b, complete sequence.
type: Entry
definition: Hafnia paralvei strain AVS0177 plasmid pAVS0177-b, complete sequence.
sequence version: NZ_CP083739.1
sequence date: 2023-03-26
sequence: sequence
division: CON
label: NZ_CP083739.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN21366585
keyword: RefSeq
source: Hafnia paralvei
organism: Hafnia paralvei
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Hafniaceae; Hafnia.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP083739.1.\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 :: 100.0x\nSequencing Technology :: Illumina MiniSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/26/2023 07:08:51\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) :: 4,545\nCDSs (total) :: 4,434\nGenes (coding) :: 4,376\nCDSs (with protein) :: 4,376\nGenes (RNA) :: 111\nrRNAs :: 8, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 8, 8 (5S, 16S, 23S)\ntRNAs :: 81\nncRNAs :: 6\nPseudo Genes (total) :: 58\nCDSs (without protein) :: 58\nPseudo Genes (ambiguous residues) :: 0 of 58\nPseudo Genes (frameshifted) :: 23 of 58\nPseudo Genes (incomplete) :: 41 of 58\nPseudo Genes (internal stop) :: 12 of 58\nPseudo Genes (multiple problems) :: 14 of 58\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5733
topology: circular
so has quality: SO_0000988
location: 1..5733
location: region:1-5733:1
RO_0002162: 546367

NZ_CP083739
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN21366585
type: BioSample
SIO_000068: biosample

1
title: Complete Genome Sequence of Hafnia paralvei Isolate AVS0177 harboring mcr-9 on a Plasmid
author: Biggel, M.
journal: Unpublished

2
title: Direct Submission
author: Biggel, M.
journal: Submitted (09-SEP-2021) Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, Zurich 8057, Switzerland

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

position:5733:1
position: 5733
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5733:1:source
so part of: sequence
organism: Hafnia paralvei
mol type: genomic DNA
strain: AVS0177
isolation source: lake water
plasmid: pAVS0177-b
country: Switzerland: Lake Zug
collection date: 2020-09

546367
type: Taxonomy
SIO_000068: taxonomy

K9N75_RS22695
type: Gene
subclass of: SO_0000704
RO_0002162: 546367
locus tag: K9N75_RS22695
old locus tag: K9N75_22695
so part of: sequence
location: complement(278..763)
location: region:278-763:-1
so has part: feature:278-763:-1:exon
subclass of: SO_0000010

69640912
type: Gene
SIO_000068: ncbigene

position:278:-1
position: 278
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:763:-1
position: 763
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:278-763:-1:exon

K9N75_RS22695
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 546367
locus tag: K9N75_RS22695
old locus tag: K9N75_22695
inference: COORDINATES: protein motif:HMM:NF016710.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MbeB family mobilization protein
translation: MSEILNLAKGFEEKSKQQAQDTEQSVKREFERLETSISEDLKSSSQSISNAIHEQNGRLTGMIRATATTALIWIVVCSALLIGILSGIIWLQGQIISSRLSDIDGYSQQLASLKAKSGAGVTIYSDDSQKNGYLVVLPVKAHGVESYTSTAGNTVVKYTAK
SIO_010081: K9N75_RS22695
subclass of: SO_0000673
so part of: K9N75_RS22695
location: complement(278..763)
location: region:278-763:-1
so has part: feature:278-763:-1:exon

WP_224452648.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:278-763:-1:exon

K9N75_RS22700
type: Gene
subclass of: SO_0000704
RO_0002162: 546367
locus tag: K9N75_RS22700
old locus tag: K9N75_22700
pseudo: true
so part of: sequence
location: complement(<813..1232)
location: region:813-1232:-1
so has part: feature:813-1232:-1:exon
subclass of: SO_0000010

69640913
type: Gene
SIO_000068: ncbigene

position:813:-1
position: 813
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:1232:-1
position: 1232
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:813-1232:-1:exon

K9N75_RS22700
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 546367
locus tag: K9N75_RS22700
old locus tag: K9N75_22700
inference: COORDINATES: protein motif:HMM:NF015397.2
note: incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: relaxase/mobilization nuclease domain-containing protein
SIO_010081: K9N75_RS22700
subclass of: SO_0000673
so part of: K9N75_RS22700
location: complement(<813..1232)
location: region:813-1232:-1
so has part: feature:813-1232:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:813-1232:-1:exon

K9N75_RS22705
type: Gene
subclass of: SO_0000704
RO_0002162: 546367
gene: mobC
locus tag: K9N75_RS22705
old locus tag: K9N75_22705
so part of: sequence
location: complement(1441..1767)
location: region:1441-1767:-1
so has part: feature:1441-1767:-1:exon
subclass of: SO_0000010

69640914
type: Gene
SIO_000068: ncbigene

position:1441:-1
position: 1441
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1767:-1
position: 1767
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1441-1767:-1:exon

K9N75_RS22705
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 546367
gene: mobC
locus tag: K9N75_RS22705
old locus tag: K9N75_22705
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006674374.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid mobilization relaxosome protein MobC
translation: MEKRTREIKIRLTDSEHQRLIDRCDRTHLAEWLRQLGLGEHTARKRRLPDVAPELLRQVSGIGNNLNQIARRLNQLDGLTPTERVSLLAVLNSLDRNLGELLEQHRDH
SIO_010081: K9N75_RS22705
subclass of: SO_0000673
so part of: K9N75_RS22705
location: complement(1441..1767)
location: region:1441-1767:-1
so has part: feature:1441-1767:-1:exon

WP_116362722.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1441-1767:-1:exon

K9N75_RS22710
type: Gene
subclass of: SO_0000704
RO_0002162: 546367
locus tag: K9N75_RS22710
old locus tag: K9N75_22710
so part of: sequence
location: 2524..3666
location: region:2524-3666:1
so has part: feature:2524-3666:1:exon
subclass of: SO_0000010

69640915
type: Gene
SIO_000068: ncbigene

position:2524:1
position: 2524
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3666:1
position: 3666
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2524-3666:1:exon

K9N75_RS22710
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 546367
locus tag: K9N75_RS22710
old locus tag: K9N75_22710
EC number: 2.7.7.49
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005761319.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: reverse transcriptase family protein
translation: MMKPLFNGTQLASQDSLAAMLGVTTERLNKIVLSIPKSYKSFNIETGKNKKVRTLFEPKKGLKHIQKKINKEIFENVNYPNYLHGGLKERDYVSNAGTHAGKKTIISLDIENFYPSISKRDILNIFKNMMRFSPSISETLTELVTLDGKLPQGACCSSYIANLIFFNDEHNIVRKINNMGMNYTRLLDDVTISSDKKLSKEEETKAITTVVGMINRHRLSLNDAKTVIEKSDHPNSKLHVTGLWVKHKTPKINKENRRYIRYLVFICEKESAVDRTSTEYHTLWNKASGKVAQMSRVGHEQSVELREKLGKILPLYDEFKIRKIVFLANNYIKNFSLPLSEEQVSKVNKIIYDVGIVGRSNKKLSNELRKKLRSILPKDA
SIO_010081: K9N75_RS22710
subclass of: SO_0000673
so part of: K9N75_RS22710
location: 2524..3666
location: region:2524-3666:1
so has part: feature:2524-3666:1:exon

WP_224452649.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2524-3666:1:exon

K9N75_RS22715
type: Gene
subclass of: SO_0000704
RO_0002162: 546367
locus tag: K9N75_RS22715
old locus tag: K9N75_22715
so part of: sequence
location: 3670..3873
location: region:3670-3873:1
so has part: feature:3670-3873:1:exon
subclass of: SO_0000010

69640916
type: Gene
SIO_000068: ncbigene

position:3670:1
position: 3670
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3873:1
position: 3873
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3670-3873:1:exon

K9N75_RS22715
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 546367
locus tag: K9N75_RS22715
old locus tag: K9N75_22715
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000427298.1
GO function: GO:0003676 - nucleic acid binding [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: cold shock domain-containing protein
translation: MDHGFVNFFDSVKGYGFIRREQGRDVMFRSDDIPNENYTVDIPKGTKVQFNTVKTAKGLKAIDILFI
SIO_010081: K9N75_RS22715
subclass of: SO_0000673
so part of: K9N75_RS22715
location: 3670..3873
location: region:3670-3873:1
so has part: feature:3670-3873:1:exon

WP_224452644.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3670-3873:1:exon

K9N75_RS22720
type: Gene
subclass of: SO_0000704
RO_0002162: 546367
locus tag: K9N75_RS22720
old locus tag: K9N75_22720
so part of: sequence
location: complement(3862..4752)
location: region:3862-4752:-1
so has part: feature:3862-4752:-1:exon
subclass of: SO_0000010

69640917
type: Gene
SIO_000068: ncbigene

position:3862:-1
position: 3862
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4752:-1
position: 4752
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3862-4752:-1:exon

K9N75_RS22720
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 546367
locus tag: K9N75_RS22720
old locus tag: K9N75_22720
inference: COORDINATES: similar to AA sequence:RefSeq:WP_019725130.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MTNPALDLFNDRLPNKPYFSDDLHFGVRIAGKERAILAKYIQFNQPHAMFWLGFDVDRLGAAIDWSDRNAPAPTLTITNPENGHAHLLYALKTSIRTAPDGKMKPLKYAAAVENALRKKLDADVGYSGLICKNPNHGYWKIAVWQPELYTLDWLADSLDLNAANDKEIVTDYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERASAYNLQFPFPLDESEVKGISNSIAKWTIKNFSEYSFDDFVKKTHAPEIQSLRGKKSKGGGRPSLGEPWIIMGVSRRTYFRMKSSDK
SIO_010081: K9N75_RS22720
subclass of: SO_0000673
so part of: K9N75_RS22720
location: complement(3862..4752)
location: region:3862-4752:-1
so has part: feature:3862-4752:-1:exon

WP_224452645.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3862-4752:-1:exon

K9N75_RS22725
type: Gene
subclass of: SO_0000704
RO_0002162: 546367
gene: nadS
locus tag: K9N75_RS22725
old locus tag: K9N75_22725
so part of: sequence
location: complement(4947..5231)
location: region:4947-5231:-1
so has part: feature:4947-5231:-1:exon
subclass of: SO_0000010

69640918
type: Gene
SIO_000068: ncbigene

position:4947:-1
position: 4947
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5231:-1
position: 5231
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4947-5231:-1:exon

K9N75_RS22725
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 546367
gene: nadS
locus tag: K9N75_RS22725
old locus tag: K9N75_22725
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000007431.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: NadS family protein
translation: MSFFDELKASLEEAVEIKKGVKAPARVTRYELADVKALRAQLNVTQDEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELASH
SIO_010081: K9N75_RS22725
subclass of: SO_0000673
so part of: K9N75_RS22725
location: complement(4947..5231)
location: region:4947-5231:-1
so has part: feature:4947-5231:-1:exon

WP_012442910.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4947-5231:-1:exon

K9N75_RS22730
type: Gene
subclass of: SO_0000704
RO_0002162: 546367
locus tag: K9N75_RS22730
old locus tag: K9N75_22730
so part of: sequence
location: complement(5233..5565)
location: region:5233-5565:-1
so has part: feature:5233-5565:-1:exon
subclass of: SO_0000010

69640919
type: Gene
SIO_000068: ncbigene

position:5233:-1
position: 5233
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5565:-1
position: 5565
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5233-5565:-1:exon

K9N75_RS22730
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 546367
locus tag: K9N75_RS22730
old locus tag: K9N75_22730
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015873600.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system RelE/ParE family toxin
translation: MSHAIEFIETPMFTRQIKQIATDDELKELQKTLIESPDKGDLIRQTGGLRKIRMATGTQGKSGSARVIYFLATEEIIYLVMAYPKSTKDSLTDAEKSDLKKLTKLLKDEV
SIO_010081: K9N75_RS22730
subclass of: SO_0000673
so part of: K9N75_RS22730
location: complement(5233..5565)
location: region:5233-5565:-1
so has part: feature:5233-5565:-1:exon

WP_224452646.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5233-5565:-1:exon