Mannheimia pernigra strain 16CN0041 plasmid pMP1, complete sequence.
type: Entry
definition: Mannheimia pernigra strain 16CN0041 plasmid pMP1, complete sequence.
sequence version: NZ_CP055303.1
sequence date: 2023-02-13
sequence: sequence
division: CON
label: NZ_CP055303.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN15211747
keyword: RefSeq
source: Mannheimia pernigra
organism: Mannheimia pernigra
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Mannheimia.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP055303.1.\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 :: HGAP v. 4\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 418x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/13/2023 10:51:14\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) :: 2,274\nCDSs (total) :: 2,183\nGenes (coding) :: 2,139\nCDSs (with protein) :: 2,139\nGenes (RNA) :: 91\nrRNAs :: 8, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 6, 6 (5S, 16S, 23S)\ntRNAs :: 67\nncRNAs :: 4\nPseudo Genes (total) :: 44\nCDSs (without protein) :: 44\nPseudo Genes (ambiguous residues) :: 0 of 44\nPseudo Genes (frameshifted) :: 15 of 44\nPseudo Genes (incomplete) :: 29 of 44\nPseudo Genes (internal stop) :: 6 of 44\nPseudo Genes (multiple problems) :: 6 of 44\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 6872
topology: circular
so has quality: SO_0000988
location: 1..6872
location: region:1-6872:1
RO_0002162: 111844

NZ_CP055303
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN15211747
type: BioSample
SIO_000068: biosample

1
title: Mannheimia pernigra sp. nov. isolated from bovine respiratory tract
author: Kuhnert, P.
author: Akarsu-Egger, H.
journal: Unpublished

2
title: Direct Submission
author: Kuhnert, P.
author: Akarsu-Egger, H.
journal: Submitted (15-JUN-2020) Institute of Veterinary Bacteriology, University of Bern, Laenggassstr. 122, Bern 3012, Switzerland

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

position:6872:1
position: 6872
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6872:1:source
so part of: sequence
organism: Mannheimia pernigra
mol type: genomic DNA
strain: 16CN0041
isolation source: upper respiratory tract
host: cattle
plasmid: pMP1
country: Switzerland
collection date: 2017-10-21

111844
type: Taxonomy
SIO_000068: taxonomy

HV561_RS11505
type: Gene
subclass of: SO_0000704
RO_0002162: 111844
locus tag: HV561_RS11505
so part of: sequence
location: complement(268..750)
location: region:268-750:-1
so has part: feature:268-750:-1:exon
subclass of: SO_0000010

position:268:-1
position: 268
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:750:-1
position: 750
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:268-750:-1:exon

HV561_RS11505
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 111844
locus tag: HV561_RS11505
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: MSKILDLAQTFQQTSQKELESTSEIVQNAIKRHEQNLIQQLQHAGNNLAENIQIEQAKLIKNTVKMYRLPTLIALTILTLIAITAGVLTWQAKNAYQEMTEWQSSAEIAKEQSGGIKLSTCKTEKGIKPCVAVDKDFINSMWGENLKVIEIHETKKQGKK
SIO_010081: HV561_RS11505
subclass of: SO_0000673
so part of: HV561_RS11505
location: complement(268..750)
location: region:268-750:-1
so has part: feature:268-750:-1:exon

WP_012209822.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:268-750:-1:exon

HV561_RS11510
type: Gene
subclass of: SO_0000704
RO_0002162: 111844
locus tag: HV561_RS11510
pseudo: true
so part of: sequence
location: complement(<758..1438)
location: region:758-1438:-1
so has part: feature:758-1438:-1:exon
subclass of: SO_0000010

position:758:-1
position: 758
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:1438:-1
position: 1438
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:758-1438:-1:exon

HV561_RS11510
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 111844
locus tag: HV561_RS11510
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: HV561_RS11510
subclass of: SO_0000673
so part of: HV561_RS11510
location: complement(<758..1438)
location: region:758-1438:-1
so has part: feature:758-1438:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:758-1438:-1:exon

HV561_RS11220
type: Gene
subclass of: SO_0000704
RO_0002162: 111844
locus tag: HV561_RS11220
old locus tag: HV561_11215
so part of: sequence
location: complement(1435..1740)
location: region:1435-1740:-1
so has part: feature:1435-1740:-1:exon
subclass of: SO_0000010

position:1435:-1
position: 1435
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1740:-1
position: 1740
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1435-1740:-1:exon

HV561_RS11220
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 111844
locus tag: HV561_RS11220
old locus tag: HV561_11215
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005618548.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobC family plasmid mobilization relaxosome protein
translation: MKREKEIKIRLTENEYQALLERKTKARLAEWVREIALEQQPNRQPKVIDPALLFELNRIGVNLNQIARQCNSQKPSIDLVSVLATLREIEKNLKKLRELSL
SIO_010081: HV561_RS11220
subclass of: SO_0000673
so part of: HV561_RS11220
location: complement(1435..1740)
location: region:1435-1740:-1
so has part: feature:1435-1740:-1:exon

WP_012209820.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1435-1740:-1:exon

HV561_RS11225
type: Gene
subclass of: SO_0000704
RO_0002162: 111844
locus tag: HV561_RS11225
old locus tag: HV561_11220
pseudo: true
so part of: sequence
location: complement(2829..>3620)
location: region:2829-3620:-1
so has part: feature:2829-3620:-1:exon
subclass of: SO_0000010

position:2829:-1
position: 2829
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3620:-1
position: 3620
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2829-3620:-1:exon

HV561_RS11225
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 111844
locus tag: HV561_RS11225
old locus tag: HV561_11220
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011453049.1
note: incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: IS982-like element IS1592 family transposase
SIO_010081: HV561_RS11225
subclass of: SO_0000673
so part of: HV561_RS11225
location: complement(2829..>3620)
location: region:2829-3620:-1
so has part: feature:2829-3620:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:2829-3620:-1:exon

HV561_RS11230
type: Gene
subclass of: SO_0000704
RO_0002162: 111844
gene: tet(H)
locus tag: HV561_RS11230
old locus tag: HV561_11225
so part of: sequence
location: complement(3611..4789)
location: region:3611-4789:-1
so has part: feature:3611-4789:-1:exon
subclass of: SO_0000010

position:3611:-1
position: 3611
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4789:-1
position: 4789
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3611-4789:-1:exon

HV561_RS11230
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 111844
gene: tet(H)
locus tag: HV561_RS11230
old locus tag: HV561_11225
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006248867.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: tetracycline efflux MFS transporter Tet(H)
translation: MNKSIIIILLITVLDAIGIGLIMPVLPTLLNEFVSENSLATHYGVLLALYATMQVIFAPILGRLSDKYGRKPILLFSLLGAALDYLLMAFSTTLWMLYIGRIIAGITGATGAVCASAMSDVTPAKNRTRYFGFLGGAFGVGLIIGPMLGGLLGDISAHMPFIFAAISHSILLILSLLFFRETQKREALVDNRTPENQTASNTVTVFFKKSLYFWLATYFIIQLIGQIPATIWVLFTQYRFDWNTTSIGMSLAVLGVLHIFFQAIVAGKLAQKWGEKTTIMISMSIDMMGCLLLAWIGHVWVILPALICLAAGGMGQPALQGYLSKSVDDNAQGKLQGTLVSLTNITGIIGPLLFAFIYSYSVAYWDGLLWLMGAILYAMLLITAYFHQRKSD
SIO_010081: HV561_RS11230
subclass of: SO_0000673
so part of: HV561_RS11230
location: complement(3611..4789)
location: region:3611-4789:-1
so has part: feature:3611-4789:-1:exon

WP_176809055.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3611-4789:-1:exon

HV561_RS11235
type: Gene
subclass of: SO_0000704
RO_0002162: 111844
gene: tetR(H)
locus tag: HV561_RS11235
old locus tag: HV561_11230
so part of: sequence
location: 4881..5504
location: region:4881-5504:1
so has part: feature:4881-5504:1:exon
subclass of: SO_0000010

position:4881:1
position: 4881
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5504:1
position: 5504
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4881-5504:1:exon

HV561_RS11235
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 111844
gene: tetR(H)
locus tag: HV561_RS11235
old locus tag: HV561_11230
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006248868.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: tetracycline resistance transcriptional repressor TetR(H)
translation: MAKLDKEQVIDNALILLNEVGIEGLTTRKLAQKIGVEQPTLYWHVKNKRALLDALAETILQKHHHHVLPLPNETWQDFLRNNAKSFRQALLMYRDGGKIHAGTRPSESQFETSEQQLQFLCDAGFSLSQAVYALSSIAHFTLGSVLETQEHQESQKEREKVETDTVAYPPLLTQAVAIMDSDNGDAAFLFVLDVMISGLETVLKSAK
SIO_010081: HV561_RS11235
subclass of: SO_0000673
so part of: HV561_RS11235
location: 4881..5504
location: region:4881-5504:1
so has part: feature:4881-5504:1:exon

WP_006248868.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4881-5504:1:exon

HV561_RS11240
type: Gene
subclass of: SO_0000704
RO_0002162: 111844
locus tag: HV561_RS11240
old locus tag: HV561_11235
pseudo: true
so part of: sequence
location: complement(5507..>5767)
location: region:5507-5767:-1
so has part: feature:5507-5767:-1:exon
subclass of: SO_0000010

position:5507:-1
position: 5507
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5767:-1
position: 5767
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5507-5767:-1:exon

HV561_RS11240
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 111844
locus tag: HV561_RS11240
old locus tag: HV561_11235
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004245619.1
note: incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: hypothetical protein
SIO_010081: HV561_RS11240
subclass of: SO_0000673
so part of: HV561_RS11240
location: complement(5507..>5767)
location: region:5507-5767:-1
so has part: feature:5507-5767:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:5507-5767:-1:exon

HV561_RS11245
type: Gene
subclass of: SO_0000704
RO_0002162: 111844
locus tag: HV561_RS11245
old locus tag: HV561_11240
pseudo: true
so part of: sequence
location: <5764..>6096
location: region:5764-6096:1
so has part: feature:5764-6096:1:exon
subclass of: SO_0000010

position:5764:1
position: 5764
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

position:6096:1
position: 6096
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5764-6096:1:exon

HV561_RS11245
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 111844
locus tag: HV561_RS11245
old locus tag: HV561_11240
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009874826.1
GO function: GO:0046872 - metal ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
note: incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: iron-containing alcohol dehydrogenase
SIO_010081: HV561_RS11245
subclass of: SO_0000673
so part of: HV561_RS11245
location: <5764..>6096
location: region:5764-6096:1
so has part: feature:5764-6096:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:5764-6096:1:exon

HV561_RS11250
type: Gene
subclass of: SO_0000704
RO_0002162: 111844
locus tag: HV561_RS11250
old locus tag: HV561_11245
so part of: sequence
location: complement(6468..6668)
location: region:6468-6668:-1
so has part: feature:6468-6668:-1:exon
subclass of: SO_0000010

position:6468:-1
position: 6468
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6668:-1
position: 6668
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6468-6668:-1:exon

HV561_RS11250
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 111844
locus tag: HV561_RS11250
old locus tag: HV561_11245
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: MEIDKIIEKRIQAIKTAHASNRIECTVNEEEHLAMLERAKEPISNEEFAEREVRRIYAKYGVEYKP
SIO_010081: HV561_RS11250
subclass of: SO_0000673
so part of: HV561_RS11250
location: complement(6468..6668)
location: region:6468-6668:-1
so has part: feature:6468-6668:-1:exon

WP_039768363.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6468-6668:-1:exon