Thermococcus indicus strain IOH1 plasmid pTI1, complete sequence.
type: Entry
definition: Thermococcus indicus strain IOH1 plasmid pTI1, complete sequence.
sequence version: NZ_CP040847.1
sequence date: 2023-03-28
sequence: sequence
division: CON
label: NZ_CP040847.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN11959431
keyword: RefSeq
source: Thermococcus indicus
organism: Thermococcus indicus
taxonomy: Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; Thermococcus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP040847.1.\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 :: SMRT v. -\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 294.43x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/28/2023 02:24:04\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) :: 2,452\nCDSs (total) :: 2,400\nGenes (coding) :: 2,357\nCDSs (with protein) :: 2,357\nGenes (RNA) :: 52\nrRNAs :: 2, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 1, 1 (5S, 16S, 23S)\ntRNAs :: 46\nncRNAs :: 2\nPseudo Genes (total) :: 43\nCDSs (without protein) :: 43\nPseudo Genes (ambiguous residues) :: 0 of 43\nPseudo Genes (frameshifted) :: 28 of 43\nPseudo Genes (incomplete) :: 15 of 43\nPseudo Genes (internal stop) :: 0 of 43\nCRISPR Arrays :: 5\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7674
topology: circular
so has quality: SO_0000988
location: 1..7674
location: region:1-7674:1
RO_0002162: 2586643

NZ_CP040847
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN11959431
type: BioSample
SIO_000068: biosample

1
title: Thermococcus indicus sp. nov., a Fe(III)-reducing hyperthermophilic archaeon isolated from the Onnuri vent field of the Central Indian Ocean ridge
author: Lim, J.K.
author: Kim, Y.J.
author: Kwon, K.K.
journal: Unpublished

2
title: Direct Submission
author: Lim, J.K.
author: Kim, Y.J.
author: Kwon, K.K.
journal: Submitted (05-JUN-2019) Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology (KIOST), 3426, Resarch building 4, 385, Heaeyang-ro, Yeongdo-gu, Busan 49111, South Korea

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

position:7674:1
position: 7674
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7674:1:source
so part of: sequence
organism: Thermococcus indicus
mol type: genomic DNA
strain: IOH1
isolation source: hydrothermal vent area derived sediment
type material: type strain of Thermococcus indicus
plasmid: pTI1
country: Indian Ocean: Onnuri Vent Field, Central Indian Ocean ridge
lat lon: 11.24 S 66.25 E
collection date: 2018-06
collected by: Yun Jae Kim

2586643
type: Taxonomy
SIO_000068: taxonomy

FH039_RS12040
type: Gene
subclass of: SO_0000704
RO_0002162: 2586643
locus tag: FH039_RS12040
old locus tag: FH039_12040
so part of: sequence
location: 1..192
location: region:1-192:1
so has part: feature:1-192:1:exon
subclass of: SO_0000010

40475926
type: Gene
SIO_000068: ncbigene

position:192:1
position: 192
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-192:1:exon

FH039_RS12040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2586643
locus tag: FH039_RS12040
old locus tag: FH039_12040
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004067399.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ribbon-helix-helix domain-containing protein
translation: MGKMMVSISDEVEQEFRELVAKRYGLRRGALSIAVEEALRLWIIRTKAELEAMENSKAVEEVR
SIO_010081: FH039_RS12040
subclass of: SO_0000673
so part of: FH039_RS12040
location: 1..192
location: region:1-192:1
so has part: feature:1-192:1:exon

WP_206206179.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-192:1:exon

FH039_RS12045
type: Gene
subclass of: SO_0000704
RO_0002162: 2586643
locus tag: FH039_RS12045
old locus tag: FH039_12045
so part of: sequence
location: 195..3341
location: region:195-3341:1
so has part: feature:195-3341:1:exon
subclass of: SO_0000010

40475927
type: Gene
SIO_000068: ncbigene

position:195:1
position: 195
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3341:1
position: 3341
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:195-3341:1:exon

FH039_RS12045
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2586643
locus tag: FH039_RS12045
old locus tag: FH039_12045
inference: COORDINATES: protein motif:HMM:NF020811.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: bifunctional DNA primase/polymerase
translation: MREAPEVGVSSGTAPLRSNNSPHLTNELNPYINAPSPKSSLYEWAKFYYAVGLTPLPAKAKAKNPIVNWKDYEEKRPTPEELSKWFKGKTLRQVNIGTLAGKVSSNLIILDFESVEAYKTFMDILDRINPNVATKLENETWIVKTGKGYHLYFRTFRELPYAKVPGVVEVRGDSKHFTVLPPSIHPSGRRYSFSNHPAVGIAELDGEELLAVYTALNEAFGVPIPEDINPTAKAVEVETTATNEPIREVRGGVKAPKEFKTLPSVEVYNLLGPYYVPGTRQDLTLYLSGYLAKAKVDIFNAVDIVLTFVENDLQPDAKTKEEVERRLEALFYSYGKVFGLEELKAHYGEDLTDKLADYLNNLLQRYNLSISKGFIEGRLRAKSSPVKGKEGLREIIEKVLRSKGFSEEDAHDEGLNVLSELSNLLKVDVERTITIPVKVGSTYYANDPKRGILYLTRKRVRVGNDEIIVWEKEYILGYYIKELRVLINPSEDIDRYYNIVFEHPVTKDTLTYTEATIEEVSRDLLTKAGVRNPYKLKGAISSIVEAFVIKGLAEVEIKAPATGFFEVEGELKFFESPKFRLNLPPVNIEKTKEAFKKLEELLEFYHFSDRALANLYFDIQAPLGLIRKQYGRENKILFNFGTPHVGKTLIRKLMGYLWGLREDKSVIGASNITAPQLSHKLNQTTLAITLDEVRNALSNPHIADLLKTATTNIHVKSRIDKNRGYRMTEFHAYASPVIITNYVPQLYIGLEDRLIPVEWDITDKRTKEEVSRFEGRLAQYKEDLAYIGSYLRAFYLQNWDRIKPLILNEDQIEAGRKLLVMVYESLGLSVPEWLRPITLEYEIEQPSEEELFLTTIREDLLEKCRMVGVVEVIDPTTEEERTIKESILNLPWRERIKHLAKRGALPEYMVLGRRKIYIKPTIIRAIRKRTGFELAGGLKNLAQLLGYKYDNFKPIGKAMAISIDDLVEKLPQRIPEEEEDLALIQDLEEVLEATKDNTGFSPVDRVMEGLLKRGWSERDIRHILYKLHDKGELLEFNGRVKLRRDRGE
SIO_010081: FH039_RS12045
subclass of: SO_0000673
so part of: FH039_RS12045
location: 195..3341
location: region:195-3341:1
so has part: feature:195-3341:1:exon

WP_139681891.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:195-3341:1:exon

FH039_RS12235
type: Gene
subclass of: SO_0000704
RO_0002162: 2586643
locus tag: FH039_RS12235
so part of: sequence
location: 4050..4202
location: region:4050-4202:1
so has part: feature:4050-4202:1:exon
subclass of: SO_0000010

54129881
type: Gene
SIO_000068: ncbigene

position:4050:1
position: 4050
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4202:1
position: 4202
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4050-4202:1:exon

FH039_RS12235
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2586643
locus tag: FH039_RS12235
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: MSREPQERDDEEKEFIEGMLRLLEPLLAEDWNTEADEWWDYVKGRRHKHI
SIO_010081: FH039_RS12235
subclass of: SO_0000673
so part of: FH039_RS12235
location: 4050..4202
location: region:4050-4202:1
so has part: feature:4050-4202:1:exon

WP_168188426.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4050-4202:1:exon

FH039_RS12050
type: Gene
subclass of: SO_0000704
RO_0002162: 2586643
locus tag: FH039_RS12050
old locus tag: FH039_12050
so part of: sequence
location: 4234..4473
location: region:4234-4473:1
so has part: feature:4234-4473:1:exon
subclass of: SO_0000010

40475928
type: Gene
SIO_000068: ncbigene

position:4234:1
position: 4234
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4473:1
position: 4473
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4234-4473:1:exon

FH039_RS12050
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2586643
locus tag: FH039_RS12050
old locus tag: FH039_12050
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012819831.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: addiction module protein
translation: MSEAINPNMLLQRIDEMEKELEKLRLEVLKMRAESLPVEEVDEETLKDLEKRFEEYKSGKAEVVSGDEAVKILSEMLED
SIO_010081: FH039_RS12050
subclass of: SO_0000673
so part of: FH039_RS12050
location: 4234..4473
location: region:4234-4473:1
so has part: feature:4234-4473:1:exon

WP_139681892.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4234-4473:1:exon

FH039_RS12055
type: Gene
subclass of: SO_0000704
RO_0002162: 2586643
locus tag: FH039_RS12055
old locus tag: FH039_12055
so part of: sequence
location: complement(4470..4757)
location: region:4470-4757:-1
so has part: feature:4470-4757:-1:exon
subclass of: SO_0000010

40475929
type: Gene
SIO_000068: ncbigene

position:4470:-1
position: 4470
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4757:-1
position: 4757
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4470-4757:-1:exon

FH039_RS12055
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2586643
locus tag: FH039_RS12055
old locus tag: FH039_12055
inference: COORDINATES: protein motif:HMM:NF016876.2
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: MFRVDVDKRVFVEAKRWLKPAHIRKLVEFIEALKIDPNSPVPKGYDVRRVKGMKIKGFPAYALRLGGYRVFYGVDWENKVIYLSKIEPRGRAYKR
SIO_010081: FH039_RS12055
subclass of: SO_0000673
so part of: FH039_RS12055
location: complement(4470..4757)
location: region:4470-4757:-1
so has part: feature:4470-4757:-1:exon

WP_168188427.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4470-4757:-1:exon

FH039_RS12060
type: Gene
subclass of: SO_0000704
RO_0002162: 2586643
locus tag: FH039_RS12060
old locus tag: FH039_12060
so part of: sequence
location: 5152..5475
location: region:5152-5475:1
so has part: feature:5152-5475:1:exon
subclass of: SO_0000010

40475930
type: Gene
SIO_000068: ncbigene

position:5152:1
position: 5152
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5475:1
position: 5475
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5152-5475:1:exon

FH039_RS12060
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2586643
locus tag: FH039_RS12060
old locus tag: FH039_12060
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012819834.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSQDPITQILEFFESMHGKLSTKKKRKVAKCLLEAFQNHKGKIKAWEMGNEVIPKITQETGVSQVYTYKVLRELIALGIIARTITGYELSPTFRKRVYRLYKALGEL
SIO_010081: FH039_RS12060
subclass of: SO_0000673
so part of: FH039_RS12060
location: 5152..5475
location: region:5152-5475:1
so has part: feature:5152-5475:1:exon

WP_139681894.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5152-5475:1:exon

FH039_RS12240
type: Gene
subclass of: SO_0000704
RO_0002162: 2586643
locus tag: FH039_RS12240
so part of: sequence
location: 5589..5768
location: region:5589-5768:1
so has part: feature:5589-5768:1:exon
subclass of: SO_0000010

54129882
type: Gene
SIO_000068: ncbigene

position:5589:1
position: 5589
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5768:1
position: 5768
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5589-5768:1:exon

FH039_RS12240
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2586643
locus tag: FH039_RS12240
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: MKFSIEKIEWGCGDLKHNISKAQYEALMRKLEQMTIIVDGRRKIVIYQRRDENADIPKN
SIO_010081: FH039_RS12240
subclass of: SO_0000673
so part of: FH039_RS12240
location: 5589..5768
location: region:5589-5768:1
so has part: feature:5589-5768:1:exon

WP_168188428.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5589-5768:1:exon

FH039_RS12065
type: Gene
subclass of: SO_0000704
RO_0002162: 2586643
locus tag: FH039_RS12065
old locus tag: FH039_12065
so part of: sequence
location: 5967..6197
location: region:5967-6197:1
so has part: feature:5967-6197:1:exon
subclass of: SO_0000010

40475931
type: Gene
SIO_000068: ncbigene

position:5967:1
position: 5967
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6197:1
position: 6197
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5967-6197:1:exon

FH039_RS12065
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2586643
locus tag: FH039_RS12065
old locus tag: FH039_12065
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: MVEEKANRIIEEEEDDGVLVVKHVYSVEWTISTPTGKAFHVSIAHEDPEKAKAMALELFEKSKAFLEGGSHGAYSV
SIO_010081: FH039_RS12065
subclass of: SO_0000673
so part of: FH039_RS12065
location: 5967..6197
location: region:5967-6197:1
so has part: feature:5967-6197:1:exon

WP_139681895.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5967-6197:1:exon

FH039_RS12070
type: Gene
subclass of: SO_0000704
RO_0002162: 2586643
locus tag: FH039_RS12070
old locus tag: FH039_12070
so part of: sequence
location: 6178..6396
location: region:6178-6396:1
so has part: feature:6178-6396:1:exon
subclass of: SO_0000010

40475932
type: Gene
SIO_000068: ncbigene

position:6178:1
position: 6178
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6396:1
position: 6396
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6178-6396:1:exon

FH039_RS12070
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2586643
locus tag: FH039_RS12070
old locus tag: FH039_12070
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: MGLIQFRRLWGEKVIVERKNRDVVVGTLSGEDGMFIYLENGQLIRENQTIEVPTAIISKKSISMLRVAKNDS
SIO_010081: FH039_RS12070
subclass of: SO_0000673
so part of: FH039_RS12070
location: 6178..6396
location: region:6178-6396:1
so has part: feature:6178-6396:1:exon

WP_139681896.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6178-6396:1:exon

FH039_RS12075
type: Gene
subclass of: SO_0000704
RO_0002162: 2586643
locus tag: FH039_RS12075
old locus tag: FH039_12075
so part of: sequence
location: 6386..6865
location: region:6386-6865:1
so has part: feature:6386-6865:1:exon
subclass of: SO_0000010

40475933
type: Gene
SIO_000068: ncbigene

position:6386:1
position: 6386
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6865:1
position: 6865
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6386-6865:1:exon

FH039_RS12075
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2586643
locus tag: FH039_RS12075
old locus tag: FH039_12075
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: MTREGLYSDFLRGLYSGRITKIYERWITEQRRRYVRKNGEVIEKPYYTLTLPSSWVETWEEAPRSLIILETRTGDLIILHPETVEEVGGAIEGIIKANKIRIEMNYRLREGLLWRILRKYRGPWKSADKRRGMRRANYEDEMDRELARGPGSRKNVIGW
SIO_010081: FH039_RS12075
subclass of: SO_0000673
so part of: FH039_RS12075
location: 6386..6865
location: region:6386-6865:1
so has part: feature:6386-6865:1:exon

WP_139681897.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6386-6865:1:exon