Exiguobacterium profundum strain TSS-3 plasmid pEprTSS-3, complete sequence.
type: Entry
definition: Exiguobacterium profundum strain TSS-3 plasmid pEprTSS-3, complete sequence.
sequence version: NZ_CP109618.1
sequence date: 2023-03-09
sequence: sequence
division: CON
label: NZ_CP109618.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN31184852
keyword: RefSeq
source: Exiguobacterium profundum
organism: Exiguobacterium profundum
taxonomy: Bacteria; Bacillota; Bacilli; Bacillales; Bacillales Family XII. Incertae Sedis; Exiguobacterium.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP109618.1.\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 Date :: 20-JUN-2022\nAssembly Method :: unicycler v. 0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 420.0x\nSequencing Technology :: Illumina NovaSeq; Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/08/2023 16:15:19\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) :: 3,005\nCDSs (total) :: 2,907\nGenes (coding) :: 2,876\nCDSs (with protein) :: 2,876\nGenes (RNA) :: 98\nrRNAs :: 9, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 9, 9 (5S, 16S, 23S)\ntRNAs :: 67\nncRNAs :: 4\nPseudo Genes (total) :: 31\nCDSs (without protein) :: 31\nPseudo Genes (ambiguous residues) :: 0 of 31\nPseudo Genes (frameshifted) :: 13 of 31\nPseudo Genes (incomplete) :: 20 of 31\nPseudo Genes (internal stop) :: 5 of 31\nPseudo Genes (multiple problems) :: 6 of 31\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4645
topology: circular
so has quality: SO_0000988
location: 1..4645
location: region:1-4645:1
RO_0002162: 307643

NZ_CP109618
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN31184852
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequence of Exiguobacterium profundum TSS-3 isolated from an extremely saline-alkaline spring located in Ixtapa, Chiapas-Mexico
author: Rincon-Rosales, R.
author: Rogel, M.A.
author: Rincon-Molina, C.I.
author: Guerrero, G.
author: Manzano-Gomez, L.A.
author: Lopez-Lopez, A.
author: Rincon Molina, F.A.
author: Martinez-Romero, E.
journal: Unpublished

2
title: Direct Submission
author: Rincon-Rosales, R.
author: Rogel, M.A.
author: Rincon-Molina, C.I.
author: Guerrero, G.
author: Manzano-Gomez, L.A.
author: Lopez-Lopez, A.
author: Rincon Molina, F.A.
author: Martinez-Romero, E.
journal: Submitted (13-OCT-2022) Ecological Genomics, Center for Genomic Sciences, Av. Universidad, Cuernavaca, Morelos 62210, Mexico

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

position:4645:1
position: 4645
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4645:1:source
so part of: sequence
organism: Exiguobacterium profundum
mol type: genomic DNA
strain: TSS-3
isolation source: sediment of an extremely saline-alkaline spring
plasmid: pEprTSS-3
country: Mexico: Ixtapa, Chiapas
lat lon: 16.47 N 92.54 W
altitude: 1063 m
collection date: 2018-02-16
collected by: Claribel Orquidea Zenteno Alegria

307643
type: Taxonomy
SIO_000068: taxonomy

OE059_RS15000
type: Gene
subclass of: SO_0000704
RO_0002162: 307643
locus tag: OE059_RS15000
old locus tag: OE059_15025
so part of: sequence
location: complement(join(4489..4645,1..8))
location: region:1-4645:-1
so has part: feature:1-8:-1:exon
so has part: feature:4489-4645:-1:exon
subclass of: SO_0000010

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

position:4645:-1
position: 4645
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-8:-1:exon

position:8:-1
position: 8
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:4489-4645:-1:exon

position:4489:-1
position: 4489
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

OE059_RS15000
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 307643
locus tag: OE059_RS15000
old locus tag: OE059_15025
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: MRDPSVRQRESRLGELMTEMEGVFKIPMLKNTTWEKENPQVIELYRKVSDSRNL
SIO_010081: OE059_RS15000
subclass of: SO_0000673
so part of: OE059_RS15000
location: complement(join(4489..4645,1..8))
location: region:1-4645:-1
so has part: feature:1-8:-1:exon
so has part: feature:4489-4645:-1:exon

WP_214803937.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-8:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:4489-4645:-1:exon

OE059_RS15005
type: Gene
subclass of: SO_0000704
RO_0002162: 307643
locus tag: OE059_RS15005
old locus tag: OE059_15030
so part of: sequence
location: complement(83..295)
location: region:83-295:-1
so has part: feature:83-295:-1:exon
subclass of: SO_0000010

position:83:-1
position: 83
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:295:-1
position: 295
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:83-295:-1:exon

OE059_RS15005
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 307643
locus tag: OE059_RS15005
old locus tag: OE059_15030
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: MKKMLVVFLSAVLLLQGCSTNESEQKLVEWGEYSTSQEERLKKNGIDFKVEDDTIYIEEKDLNKAAACCS
SIO_010081: OE059_RS15005
subclass of: SO_0000673
so part of: OE059_RS15005
location: complement(83..295)
location: region:83-295:-1
so has part: feature:83-295:-1:exon

WP_275060641.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:83-295:-1:exon

OE059_RS15010
type: Gene
subclass of: SO_0000704
RO_0002162: 307643
locus tag: OE059_RS15010
old locus tag: OE059_15035
so part of: sequence
location: complement(319..792)
location: region:319-792:-1
so has part: feature:319-792:-1:exon
subclass of: SO_0000010

position:319:-1
position: 319
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:792:-1
position: 792
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:319-792:-1:exon

OE059_RS15010
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 307643
locus tag: OE059_RS15010
old locus tag: OE059_15035
inference: COORDINATES: similar to AA sequence:RefSeq:WP_016510962.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKNMELTIYEVTELNERMKFLDLAKEHAPVGKEKLREALKSAGATFDQRTKRWHIDRSHPNADKKVLDFVQSSRVSIPKPKKIASEPLKIDPVTGQSQLDDDYFAIETRPEHIIRKKVSLDMDVALHKQLKQIALENDMKLYELVEGVLRDYVRKKT
SIO_010081: OE059_RS15010
subclass of: SO_0000673
so part of: OE059_RS15010
location: complement(319..792)
location: region:319-792:-1
so has part: feature:319-792:-1:exon

WP_275060642.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:319-792:-1:exon

OE059_RS15015
type: Gene
subclass of: SO_0000704
RO_0002162: 307643
locus tag: OE059_RS15015
old locus tag: OE059_15040
so part of: sequence
location: 2449..2733
location: region:2449-2733:1
so has part: feature:2449-2733:1:exon
subclass of: SO_0000010

position:2449:1
position: 2449
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2733:1
position: 2733
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2449-2733:1:exon

OE059_RS15015
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 307643
locus tag: OE059_RS15015
old locus tag: OE059_15040
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: MQRSRMTKPSDIPKLLTIADLSVRWDMPRQSLHDKKGENKFPLPVQYVANNRTALFLESDIIEYEKENPYIKTRAQREARRNFIFKLYMDANDE
SIO_010081: OE059_RS15015
subclass of: SO_0000673
so part of: OE059_RS15015
location: 2449..2733
location: region:2449-2733:1
so has part: feature:2449-2733:1:exon

WP_275060638.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2449-2733:1:exon

OE059_RS15020
type: Gene
subclass of: SO_0000704
RO_0002162: 307643
locus tag: OE059_RS15020
old locus tag: OE059_15045
so part of: sequence
location: complement(2778..3569)
location: region:2778-3569:-1
so has part: feature:2778-3569:-1:exon
subclass of: SO_0000010

position:2778:-1
position: 2778
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3569:-1
position: 3569
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2778-3569:-1:exon

OE059_RS15020
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 307643
locus tag: OE059_RS15020
old locus tag: OE059_15045
inference: COORDINATES: protein motif:HMM:NF020904.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: SMI1/KNR4 family protein
translation: MNFWKGISEYYTVETDFTKRDIEFIESELDISIPENYLNVLQDQNGGLLVCDSLKVDFKNSWADDHLPFNNLYGISKDSTVNDTKNTLSEWGITGKNLLIGGDGTYIYFLNFDSADTAPTVCYLDISTGDSKEVAESFDELISNLYVQDDFETFDFDGGTNPRTGTNFRDLVTSKDQEEVISGFIHWIGVDGPTKEVIEEMTRQLKNSSDPSMTMFLAEQLTQFIVNEEALTYLEPKDVMLIFESKNDENLQVYIEMIKESID
SIO_010081: OE059_RS15020
subclass of: SO_0000673
so part of: OE059_RS15020
location: complement(2778..3569)
location: region:2778-3569:-1
so has part: feature:2778-3569:-1:exon

WP_275060639.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2778-3569:-1:exon

OE059_RS15025
type: Gene
subclass of: SO_0000704
RO_0002162: 307643
locus tag: OE059_RS15025
old locus tag: OE059_15050
so part of: sequence
location: complement(3869..4441)
location: region:3869-4441:-1
so has part: feature:3869-4441:-1:exon
subclass of: SO_0000010

position:3869:-1
position: 3869
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4441:-1
position: 4441
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3869-4441:-1:exon

OE059_RS15025
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 307643
locus tag: OE059_RS15025
old locus tag: OE059_15050
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012726182.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: SMI1/KNR4 family protein
translation: MLATVSSQSPKNGQKSTDFTNFFMKNMDGVSLLLALETFKKRLINDRLEVQREEGYLSNEVFSFGSPASENELSKLPNKTPNEMIEFLKSHNGAEIFIHPEYGGGIIFFSVDEILEYIDIWECPENCIPVGVGRDGEWIICEVDRTGGNRIWVGESISFEDEYERLPMGFADWFDYLLVAQGAHFWDWFR
SIO_010081: OE059_RS15025
subclass of: SO_0000673
so part of: OE059_RS15025
location: complement(3869..4441)
location: region:3869-4441:-1
so has part: feature:3869-4441:-1:exon

WP_275060640.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3869-4441:-1:exon