Staphylococcus pasteuri strain FDAARGOS_1069 plasmid unnamed.
type: Entry
definition: Staphylococcus pasteuri strain FDAARGOS_1069 plasmid unnamed.
sequence version: NZ_CP067015.1
sequence date: 2023-05-06
sequence: sequence
division: CON
label: NZ_CP067015.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN16357238
keyword: RefSeq
source: Staphylococcus pasteuri
organism: Staphylococcus pasteuri
taxonomy: Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP067015.1.\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 :: Canu v. 1.8\nGenome Coverage :: 1188.39x\nSequencing Technology :: Pacbio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/06/2023 05:02:28\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,441\nCDSs (total) :: 2,357\nGenes (coding) :: 2,321\nCDSs (with protein) :: 2,321\nGenes (RNA) :: 84\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 62\nncRNAs :: 4\nPseudo Genes (total) :: 36\nCDSs (without protein) :: 36\nPseudo Genes (ambiguous residues) :: 0 of 36\nPseudo Genes (frameshifted) :: 13 of 36\nPseudo Genes (incomplete) :: 10 of 36\nPseudo Genes (internal stop) :: 17 of 36\nPseudo Genes (multiple problems) :: 4 of 36\n##Genome-Annotation-Data-END##

sequence
subclass of: SO_0000155
sequence length: 7946
topology: linear
so has quality: SO_0000987
location: 1..7946
location: region:1-7946:1
RO_0002162: 45972

NZ_CP067015
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN16357238
type: BioSample
SIO_000068: biosample

1
title: FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS): Supporting development and validation of Infectious Disease Dx tests
author: Sproer, C.
author: Gronow, S.
author: Severitt, S.
author: Schroder, I.
author: Tallon, L.
author: Sadzewicz, L.
author: Zhao, X.
author: Boylan, J.
author: Ott, S.
author: Bowen, H.
author: Vavikolanu, K.
author: Mehta, A.
author: Aluvathingal, J.
author: Nadendla, S.
author: Lowell, S.
author: Myers, T.
author: Yan, Y.
author: Sichtig, H.
journal: Unpublished

2
title: Direct Submission
author: Sproer, C.
author: Gronow, S.
author: Severitt, S.
author: Schroder, I.
author: Tallon, L.
author: Sadzewicz, L.
author: Zhao, X.
author: Boylan, J.
author: Ott, S.
author: Bowen, H.
author: Vavikolanu, K.
author: Mehta, A.
author: Aluvathingal, J.
author: Nadendla, S.
author: Lowell, S.
author: Myers, T.
author: Yan, Y.
author: Sichtig, H.
journal: Submitted (08-DEC-2020) Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993-0002, USA

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

position:7946:1
position: 7946
reference: sequence
type: ForwardStrandPosition
type: ExactPosition
type: FuzzyPosition

feature:1-7946:1:source
so part of: sequence
organism: Staphylococcus pasteuri
mol type: genomic DNA
strain: FDAARGOS_1069
culture collection: DSM:10657
plasmid: unnamed
country: Germany: Braunschweig
collected by: DSMZ

45972
type: Taxonomy
SIO_000068: taxonomy

I6I26_RS12110
type: Gene
subclass of: SO_0000704
RO_0002162: 45972
locus tag: I6I26_RS12110
old locus tag: I6I26_12110
pseudo: true
so part of: sequence
location: complement(<1..237)
location: region:1-237:-1
so has part: feature:1-237:-1:exon
subclass of: SO_0000010

72471484
type: Gene
SIO_000068: ncbigene

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

position:237:-1
position: 237
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-237:-1:exon

I6I26_RS12110
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 45972
locus tag: I6I26_RS12110
old locus tag: I6I26_12110
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000638665.1
note: incomplete; too short partial abutting assembly gap; missing C-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: I6I26_RS12110
subclass of: SO_0000673
so part of: I6I26_RS12110
location: complement(<1..237)
location: region:1-237:-1
so has part: feature:1-237:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:1-237:-1:exon

I6I26_RS12115
type: Gene
subclass of: SO_0000704
RO_0002162: 45972
locus tag: I6I26_RS12115
old locus tag: I6I26_12115
so part of: sequence
location: 639..1241
location: region:639-1241:1
so has part: feature:639-1241:1:exon
subclass of: SO_0000010

72471485
type: Gene
SIO_000068: ncbigene

position:639:1
position: 639
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1241:1
position: 1241
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:639-1241:1:exon

I6I26_RS12115
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 45972
locus tag: I6I26_RS12115
old locus tag: I6I26_12115
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002447413.1
GO function: GO:0016491 - oxidoreductase activity [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: short chain dehydrogenase
translation: MKIVVIGATGTIGKSVSKKLKENNHEVIEVGSKSGDYQLDITSPTEVEQMYKDIKDIDAVVSATGGATFKSLSDISLEENNVAIKSKLLGQINLVLIGQHYLNKNGSFTLTSGIMMDDPILLGSSAAMANGGVAGFVTSAAIELKNGLRINNVSPNVVEEALDKYGEFFKGFTAVPVDKVANAFIKSVEGAQTGQTYKIY
SIO_010081: I6I26_RS12115
subclass of: SO_0000673
so part of: I6I26_RS12115
location: 639..1241
location: region:639-1241:1
so has part: feature:639-1241:1:exon

WP_002502820.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:639-1241:1:exon

I6I26_RS12120
type: Gene
subclass of: SO_0000704
RO_0002162: 45972
locus tag: I6I26_RS12120
old locus tag: I6I26_12120
so part of: sequence
location: 1314..2498
location: region:1314-2498:1
so has part: feature:1314-2498:1:exon
subclass of: SO_0000010

72471486
type: Gene
SIO_000068: ncbigene

position:1314:1
position: 1314
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2498:1
position: 2498
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1314-2498:1:exon

I6I26_RS12120
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 45972
locus tag: I6I26_RS12120
old locus tag: I6I26_12120
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002502819.1
GO function: GO:0016491 - oxidoreductase activity [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: FAD-dependent oxidoreductase
translation: MKKNYKLIIIGGGLVGLSTAYNLVTNYNGYSTVKGEDILVLEKNKFFNDKGSSAGSTRQFRYQYTEKYMTELVIQSIPDWQKLQQFTTNSLIEHVGSLWFGDPKLPTTEGGINPAEKTMDKTGVPYSNLNKTQIENWYQFKNLPDDYVGFYQKDGGAINLPETLKTFYSQASIAGVQMLENTPVLDIKKENGKYTIQTGEHEFTTEKILVSTGAYVNDITKYFDKQIKLDIWDMVSAYFEKTNPNIDYPTWFAFQQPNDENSNLYYGFPELDWKYKNYIRVAPDYPFAIYDSPSERKKPTSEDFKGTEEWVKNHMTDLDSNAKFKSTCMLGLPKNKNKLLYLDFITDDKNVVVQTGGWVAKFAPTFGKICSQLLINGRTDYNISHFKIESEDLK
SIO_010081: I6I26_RS12120
subclass of: SO_0000673
so part of: I6I26_RS12120
location: 1314..2498
location: region:1314-2498:1
so has part: feature:1314-2498:1:exon

WP_089413929.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1314-2498:1:exon

I6I26_RS12125
type: Gene
subclass of: SO_0000704
RO_0002162: 45972
locus tag: I6I26_RS12125
old locus tag: I6I26_12125
so part of: sequence
location: 2495..4219
location: region:2495-4219:1
so has part: feature:2495-4219:1:exon
subclass of: SO_0000010

72471487
type: Gene
SIO_000068: ncbigene

position:2495:1
position: 2495
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4219:1
position: 4219
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2495-4219:1:exon

I6I26_RS12125
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 45972
locus tag: I6I26_RS12125
old locus tag: I6I26_12125
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009385187.1
GO function: GO:0016491 - oxidoreductase activity [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: FAD-dependent oxidoreductase
translation: MTSKITMNDINYINGINDDLDIDIAIVGAGVSGIYSAYRFLEDDRYNNKKIGIFDLNDKIGGRLESIVLPESNVTGELGGMRYLTSQKITTSLIENIFKLKNKKFETGETSSHTFYLRGQRFKENEWEENQKKQDKFYTRYFMSEQLQGYHPDQLFNKVIAEVCLNDPWFNDSYNNKIEKQDDYNYSFKLSSEDWDNIKRNLIYYKDNSPYNQMKLYDIGFWNLLKDQLGNEGYEFLANAGSYYSNTLSWNSSEAFSYIVGDFTDGVEYKTIDEGYDQLAYSLAKRVSENDNVTLYLNSELKTFSKDKESYELELVNVNTTKTKKVKTREIILAMPKRSLELLDQDNFFFKDASHSKVSKLIDTVYAEPSLKLLLGFEYPWWRECLNSYYGKSTTDLPMRQCYYFGVDEDNQHSLLLASYNDMRTVNFWKSMIRSNDNKFIQHDEIKSKNNNLELFNEKYSDEVTNVMVEESINQLEELHDIKIPKPYASLVKDWSKDPFGGGYHAWHTGIDVQKTMKLIRKPYEYENIYIVGEAYSSDQGWTEGAFKTAEKMLQEHFGLERPEWLDSDYYLGW
SIO_010081: I6I26_RS12125
subclass of: SO_0000673
so part of: I6I26_RS12125
location: 2495..4219
location: region:2495-4219:1
so has part: feature:2495-4219:1:exon

WP_002502818.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2495-4219:1:exon

I6I26_RS12130
type: Gene
subclass of: SO_0000704
RO_0002162: 45972
gene: mobC
locus tag: I6I26_RS12130
old locus tag: I6I26_12130
so part of: sequence
location: 4443..4826
location: region:4443-4826:1
so has part: feature:4443-4826:1:exon
subclass of: SO_0000010

72471488
type: Gene
SIO_000068: ncbigene

position:4443:1
position: 4443
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4826:1
position: 4826
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4443-4826:1:exon

I6I26_RS12130
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 45972
gene: mobC
locus tag: I6I26_RS12130
old locus tag: I6I26_12130
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002449121.1
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: MSEQNTFVASDETVGRNRKPNRKEPKQISFRVSESEYLKLQQSAETLNMSVPAFVKKKAQGARLVAPKLDQATRQSVAKDLSMLGANANQIAKYCNQHQHEAPNYEALERNISELRERLNDIWEKLN
SIO_010081: I6I26_RS12130
subclass of: SO_0000673
so part of: I6I26_RS12130
location: 4443..4826
location: region:4443-4826:1
so has part: feature:4443-4826:1:exon

WP_049366051.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4443-4826:1:exon

I6I26_RS12135
type: Gene
subclass of: SO_0000704
RO_0002162: 45972
locus tag: I6I26_RS12135
old locus tag: I6I26_12135
so part of: sequence
location: 4992..6002
location: region:4992-6002:1
so has part: feature:4992-6002:1:exon
subclass of: SO_0000010

72471489
type: Gene
SIO_000068: ncbigene

position:4992:1
position: 4992
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6002:1
position: 6002
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4992-6002:1:exon

I6I26_RS12135
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 45972
locus tag: I6I26_RS12135
old locus tag: I6I26_12135
inference: COORDINATES: similar to AA sequence:RefSeq:WP_020366464.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: relaxase/mobilization nuclease domain-containing protein
translation: MATTKISATKSTSRAINYAEERAVEKSGLNCDVDYAKSSFKATRELYGKTDGNQGHVIIQSFKPGEVTPEQCNQLGLALAEKLVPNHQVAVYTHNDTDHVHNHIVINSIDLETGKKFNNNKQALRNVRNFNDEVCMEHGLSVPEKNTARLRYTQTEKAIADPNTKSTAQYSWKDEIREAIDQSQATNMDEFKDHLNQHGIEIERVTPKSITYRHLAEDKKVRGRKLGEDYNKGGIEDGFERQIQRRRQQERDSDTECQPKRPTSNRDEATEQDTGVTQSDWDQFAQDTNELERSRQAAESARLAHEKARRDREERARAKQASRRIINNDRDHGLEL
SIO_010081: I6I26_RS12135
subclass of: SO_0000673
so part of: I6I26_RS12135
location: 4992..6002
location: region:4992-6002:1
so has part: feature:4992-6002:1:exon

WP_200271366.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4992-6002:1:exon

I6I26_RS12140
type: Gene
subclass of: SO_0000704
RO_0002162: 45972
locus tag: I6I26_RS12140
old locus tag: I6I26_12140
so part of: sequence
location: 5905..6510
location: region:5905-6510:1
so has part: feature:5905-6510:1:exon
subclass of: SO_0000010

72471490
type: Gene
SIO_000068: ncbigene

position:5905:1
position: 5905
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6510:1
position: 6510
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5905-6510:1:exon

I6I26_RS12140
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 45972
locus tag: I6I26_RS12140
old locus tag: I6I26_12140
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002440619.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: mobilization protein
translation: MKRLEEIEKREHERNKRHDELLTTIETTASNFNQATEITQKRFISVAKHYIERINNDNLKQDFQTAIQEELKDVKTDTHKAIEQLQTNQAELRQANKDYKTTLDERIKHNDTAMKQYDQAFHRLTQGITAMFFIIALVMVAFLVLSPLGDWLGVQHFYEWLNYVLKTGHSAWRYFILIFYLVPYALFGGLIYAILSAYKRI
SIO_010081: I6I26_RS12140
subclass of: SO_0000673
so part of: I6I26_RS12140
location: 5905..6510
location: region:5905-6510:1
so has part: feature:5905-6510:1:exon

WP_246456636.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5905-6510:1:exon

I6I26_RS12145
type: Gene
subclass of: SO_0000704
RO_0002162: 45972
locus tag: I6I26_RS12145
old locus tag: I6I26_12145
so part of: sequence
location: 7267..>7946
location: region:7267-7946:1
so has part: feature:7267-7946:1:exon
subclass of: SO_0000010

72471491
type: Gene
SIO_000068: ncbigene

position:7267:1
position: 7267
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7267-7946:1:exon

I6I26_RS12145
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 45972
locus tag: I6I26_RS12145
old locus tag: I6I26_12145
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002440631.1
GO function: GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO process: GO:0006270 - DNA replication initiation [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: RepB family plasmid replication initiator protein
translation: MSGETVIYKNEMNLVPLRRFTATEINLFFAMCNKLKEQDTNTLHLSFDELKELSNYSPETRNINRFVDDLQRVYDKMLDIRYTIRTETKIKKFVLFYKYEIDISEKYLEIATSPDLKYILNSITDNFTKFELKEMTHLKSTYSKNMFRLLKQYKHTGYMKIKIEDFRERLDIPESYRMSNINQFVLTPIIKELSPIFSNLNINKIKAKKGRKIEWLEFTFDAEKTHS
SIO_010081: I6I26_RS12145
subclass of: SO_0000673
so part of: I6I26_RS12145
location: 7267..>7946
location: region:7267-7946:1
so has part: feature:7267-7946:1:exon

WP_200271381.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7267-7946:1:exon