Spiroplasma kunkelii CR2-3x plasmid pSKU76, complete sequence.
type: Entry
definition: Spiroplasma kunkelii CR2-3x plasmid pSKU76, complete sequence.
sequence version: NZ_CP012425.1
sequence date: 2022-12-13
sequence: sequence
division: CON
label: NZ_CP012425.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN03269975
keyword: RefSeq
source: Spiroplasma kunkelii CR2-3x
organism: Spiroplasma kunkelii CR2-3x
taxonomy: Bacteria; Mycoplasmatota; Mollicutes; Entomoplasmatales; Spiroplasmataceae; Spiroplasma.
reference: 1
references: 26494665
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP012425.1.\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##Assembly-Data-START##\nAssembly Method :: SMRT Portal v. 2.3\nSequencing Technology :: PacBio\n##Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/12/2022 23:04:56\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\nGenes (total) :: 1,961\nCDSs (total) :: 1,922\nGenes (coding) :: 1,836\nCDSs (with protein) :: 1,836\nGenes (RNA) :: 39\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 33\nncRNAs :: 3\nPseudo Genes (total) :: 86\nCDSs (without protein) :: 86\nPseudo Genes (ambiguous residues) :: 0 of 86\nPseudo Genes (frameshifted) :: 41 of 86\nPseudo Genes (incomplete) :: 55 of 86\nPseudo Genes (internal stop) :: 46 of 86\nPseudo Genes (multiple problems) :: 45 of 86\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7576
topology: circular
so has quality: SO_0000988
location: 1..7576
location: region:1-7576:1
RO_0002162: 273035

NZ_CP012425
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN03269975
type: BioSample
SIO_000068: biosample

1
title: Complete Genome Sequence of Spiroplasma kunkelii Strain CR2-3x, Causal Agent of Corn Stunt Disease in Zea mays L
author: Davis, R.E.
author: Shao, J.
author: Dally, E.L.
author: Zhao, Y.
author: Gasparich, G.E.
author: Gaynor, B.J.
author: Athey, J.C.
author: Harrison, N.A.
author: Donofrio, N.
journal: Genome Announc 3 (5), e01216-15 (2015)
pubmed: 26494665
comments: Publication Status: Online-Only

26494665
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Davis, R.E.
author: Shao, J.Y.
author: Dally, E.L.
author: Zhao, Y.
author: Gasparich, G.E.
author: Gaynor, B.J.
author: Athey, J.C.
author: Harrison, N.A.
author: Donofrio, N.
journal: Submitted (20-AUG-2015) USDA, United States Department of Agriculture, Molecular Plant Pathology Laboratory, 10300 Baltimore Ave., Beltsville, MD 20705, USA

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

position:7576:1
position: 7576
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7576:1:source
so part of: sequence
organism: Spiroplasma kunkelii CR2-3x
mol type: genomic DNA
strain: CR2-3x
host: Zea mays L.
plasmid: pSKU76
country: Costa Rica
collection date: 2004

273035
type: Taxonomy
SIO_000068: taxonomy

SKUN_RS08060
type: Gene
subclass of: SO_0000704
RO_0002162: 273035
locus tag: SKUN_RS08060
old locus tag: SKUN_001752
so part of: sequence
location: join(7162..7576,1..311)
location: region:1-7576:1
so has part: feature:7162-7576:1:exon
so has part: feature:1-311:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:7162-7576:1:exon

position:7162:1
position: 7162
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-311:1:exon

position:311:1
position: 311
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

SKUN_RS08060
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 273035
locus tag: SKUN_RS08060
old locus tag: SKUN_001752
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MFKWKLKNNKGIAIPLDTDNLNSQNETEVNNNDLYVIENKNNAEKTIKLSHKSNKTLYFGLGILASNVILLLVVFYVRLWLLFPITILFSSFSLLFIFDYLVNSRKKTELDRWYFRNKWIIILNRVSVMFYPLTIFFYVFGILFSNKEIIFFFKEYNYAFGNNILFLTLLSVLIVVNITVNILIYFFYKVDVPHNELNNQTYLLSKLNTVKKAMNIFTICWYVLILLIFIILILLIKKIKK
SIO_010081: SKUN_RS08060
subclass of: SO_0000673
so part of: SKUN_RS08060
location: join(7162..7576,1..311)
location: region:1-7576:1
so has part: feature:7162-7576:1:exon
so has part: feature:1-311:1:exon

WP_053391625.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7162-7576:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-311:1:exon

SKUN_RS08065
type: Gene
subclass of: SO_0000704
RO_0002162: 273035
locus tag: SKUN_RS08065
old locus tag: SKUN_001753
so part of: sequence
location: 324..1922
location: region:324-1922:1
so has part: feature:324-1922:1:exon
subclass of: SO_0000010

position:324:1
position: 324
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1922:1
position: 1922
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:324-1922:1:exon

SKUN_RS08065
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 273035
locus tag: SKUN_RS08065
old locus tag: SKUN_001753
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MKNLHERLTKNLGRRLLIGAFFIFLGMVPAIYIWSCVPNNKPSPIPIPNSPIATSVSNIEFNTNNDYLYDYLKPYIANDFKVNNYISLNNNQYIYYDTENKIKFINSESKITPIENQKVAKAIGEFDNKELIILKNGNKFKLGLVDDKSIEYINLNSGTNFDIDLEPPFNAPFYINQASKTTFNIIYSNQRQEIKLFQFDFLTRNYYIHTLIYKNKPIIGKTITYQNGIIIIQIPEYKNKFYVISNESIKKDNQDLIINDSDLFINDEGTNYVFLLYFLPNNIYDYEKIDKAKIKIAGFNTNTNKLVIFNKQKTIYNYILENNVKTNYYIFKNYFITYSDVLKVVKKVIILDDLITDNYKYEIYNNISSYGQYFILSENDLYIGYNVYSEDGCMVILFYDKYLKKFVEKDFKNITDINLNKNLFNKNLFYIYQGNYYFTIYENNTLKVFTNDNNIANINIDKCKITRYKNNLVILTIDKCLLLNLDSKNTTEFNLKDFDFDNSNSEFINSNFDKSNILFRNVDNVSLFVLNV
SIO_010081: SKUN_RS08065
subclass of: SO_0000673
so part of: SKUN_RS08065
location: 324..1922
location: region:324-1922:1
so has part: feature:324-1922:1:exon

WP_053391616.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:324-1922:1:exon

SKUN_RS08070
type: Gene
subclass of: SO_0000704
RO_0002162: 273035
locus tag: SKUN_RS08070
old locus tag: SKUN_001754
so part of: sequence
location: 1953..2204
location: region:1953-2204:1
so has part: feature:1953-2204:1:exon
subclass of: SO_0000010

position:1953:1
position: 1953
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2204:1
position: 2204
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1953-2204:1:exon

SKUN_RS08070
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 273035
locus tag: SKUN_RS08070
old locus tag: SKUN_001754
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MKKDTKKFLNKNYIYLLGAFALFSLFGIVLILLGVITKNSNLQFGGIFVLIISILIGLTYVVIGILGLIKIIKERKLKKINNN
SIO_010081: SKUN_RS08070
subclass of: SO_0000673
so part of: SKUN_RS08070
location: 1953..2204
location: region:1953-2204:1
so has part: feature:1953-2204:1:exon

WP_053391617.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1953-2204:1:exon

SKUN_RS08075
type: Gene
subclass of: SO_0000704
RO_0002162: 273035
locus tag: SKUN_RS08075
old locus tag: SKUN_001755
so part of: sequence
location: 2927..3541
location: region:2927-3541:1
so has part: feature:2927-3541:1:exon
subclass of: SO_0000010

position:2927:1
position: 2927
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3541:1
position: 3541
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2927-3541:1:exon

SKUN_RS08075
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 273035
locus tag: SKUN_RS08075
old locus tag: SKUN_001755
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MQELLIQNEAQAFNQLNPNKDISNIFTSKKNVKKNYTEKSNMVRFGTIYISSSKKFCHLDKNKENYLIGIKPHYTYNVYDAEKNWKEKITGKELMKKYNLVGFHYLTVEQQRFKNMQKANPFFLQFKNVQESMEWHRQQAKEQREQLNALLMNRKQKTDTKVSENDVISKFNSDYENKKYQSTDKKRTVDINQLLTDLDDPMFN
SIO_010081: SKUN_RS08075
subclass of: SO_0000673
so part of: SKUN_RS08075
location: 2927..3541
location: region:2927-3541:1
so has part: feature:2927-3541:1:exon

WP_053391618.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2927-3541:1:exon

SKUN_RS08080
type: Gene
subclass of: SO_0000704
RO_0002162: 273035
locus tag: SKUN_RS08080
old locus tag: SKUN_001756
so part of: sequence
location: 3871..4110
location: region:3871-4110:1
so has part: feature:3871-4110:1:exon
subclass of: SO_0000010

position:3871:1
position: 3871
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4110:1
position: 4110
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3871-4110:1:exon

SKUN_RS08080
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 273035
locus tag: SKUN_RS08080
old locus tag: SKUN_001756
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MPITSEKNRKTLEKIEDTVAFKKENEKYWKQKIPTMTCEKKLVEAFKKEAKEKEWKYTTLMNKILRERYGKEKNNNEDD
SIO_010081: SKUN_RS08080
subclass of: SO_0000673
so part of: SKUN_RS08080
location: 3871..4110
location: region:3871-4110:1
so has part: feature:3871-4110:1:exon

WP_053391619.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3871-4110:1:exon

SKUN_RS08085
type: Gene
subclass of: SO_0000704
RO_0002162: 273035
locus tag: SKUN_RS08085
old locus tag: SKUN_001757
so part of: sequence
location: 4097..4870
location: region:4097-4870:1
so has part: feature:4097-4870:1:exon
subclass of: SO_0000010

position:4097:1
position: 4097
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4870:1
position: 4870
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4097-4870:1:exon

SKUN_RS08085
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 273035
locus tag: SKUN_RS08085
old locus tag: SKUN_001757
inference: COORDINATES: protein motif:HMM:NF013793.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: AAA family ATPase
translation: MKMISFCNKKGGVGKTTLCKNVAYKFALDNKKVLVIDLDPQATITFELKGNEINLDKTIAECFILNKNSSLKRIIQKTKYKEIDYIVGGEKVKKVNFLLKEFYENNHKFFVAENIYLTNKETFDSYDYVLIDYPPTVDELSLNWLIISDLIIIPINEGLGAFKGILDLINTLKYICEKEKRQIPEYKIILNNIKSDKNLILINEWLDEKGFLNYCSKIILKSSETFLTSENELSSIWDSQYYWRQKQAYEEFIKEIK
SIO_010081: SKUN_RS08085
subclass of: SO_0000673
so part of: SKUN_RS08085
location: 4097..4870
location: region:4097-4870:1
so has part: feature:4097-4870:1:exon

WP_053391620.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4097-4870:1:exon

SKUN_RS08090
type: Gene
subclass of: SO_0000704
RO_0002162: 273035
locus tag: SKUN_RS08090
old locus tag: SKUN_001758
so part of: sequence
location: 4959..5477
location: region:4959-5477:1
so has part: feature:4959-5477:1:exon
subclass of: SO_0000010

position:4959:1
position: 4959
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5477:1
position: 5477
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4959-5477:1:exon

SKUN_RS08090
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 273035
locus tag: SKUN_RS08090
old locus tag: SKUN_001758
inference: COORDINATES: protein motif:HMM:NF038029.1
GO component: GO:0016020 - membrane [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: lipoprotein
translation: MKKILSILKAIILITTGASSIISCGVEKVKTNKDLDNLDNQDENKKLQDENKKLQDENKKLQDENKKLKWKIEKNILFINSINSPIKVEATKPDEVKEYEVFNALKPKVLEAIKTIDNSLTENDFIIGFKDYFNHMQLRHIDLSTSKKITIIISGKNKATGEKEFVVVLPKI
SIO_010081: SKUN_RS08090
subclass of: SO_0000673
so part of: SKUN_RS08090
location: 4959..5477
location: region:4959-5477:1
so has part: feature:4959-5477:1:exon

WP_053391621.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4959-5477:1:exon

SKUN_RS08095
type: Gene
subclass of: SO_0000704
RO_0002162: 273035
locus tag: SKUN_RS08095
old locus tag: SKUN_001759
so part of: sequence
location: 6112..6321
location: region:6112-6321:1
so has part: feature:6112-6321:1:exon
subclass of: SO_0000010

position:6112:1
position: 6112
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

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

urn:…
SIO_000300: 1
SIO_000628: feature:6112-6321:1:exon

SKUN_RS08095
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 273035
locus tag: SKUN_RS08095
old locus tag: SKUN_001759
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MGGIVIKKTQIVSNAINRNTKEVKKLQNLIETMKKKLNLIKNIEPQLKNAEKELELITKSRKNLEELFK
SIO_010081: SKUN_RS08095
subclass of: SO_0000673
so part of: SKUN_RS08095
location: 6112..6321
location: region:6112-6321:1
so has part: feature:6112-6321:1:exon

WP_053391622.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6112-6321:1:exon

SKUN_RS08100
type: Gene
subclass of: SO_0000704
RO_0002162: 273035
locus tag: SKUN_RS08100
old locus tag: SKUN_001760
so part of: sequence
location: 6422..6880
location: region:6422-6880:1
so has part: feature:6422-6880:1:exon
subclass of: SO_0000010

position:6422:1
position: 6422
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6880:1
position: 6880
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6422-6880:1:exon

SKUN_RS08100
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 273035
locus tag: SKUN_RS08100
old locus tag: SKUN_001760
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MALNANQLKLNKEQQQLLNQRINLARNKGINKGSIKEKKKSRLKVFITFFATLLLCTGGFVGGYYGVQYSQNHNKNVVNKIATKELGEITIPKDDKTPNINQILVALYGKNTSINIKDYAVKDIKDTSAVIYSAYMFDNSTITVTYTVKNAG
SIO_010081: SKUN_RS08100
subclass of: SO_0000673
so part of: SKUN_RS08100
location: 6422..6880
location: region:6422-6880:1
so has part: feature:6422-6880:1:exon

WP_053391623.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6422-6880:1:exon