Candidatus Hodgkinia cicadicola strain MAGTDC chromosome variant3, whole genome shotgun sequence.
type: Entry
definition: Candidatus Hodgkinia cicadicola strain MAGTDC chromosome variant3, whole genome shotgun sequence.
sequence version: NZ_CM008789.1
sequence date: 2023-04-10
sequence: sequence
division: CON
label: NZ_CM008789.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN07255135
keyword: WGS
keyword: RefSeq
source: Candidatus Hodgkinia cicadicola
organism: Candidatus Hodgkinia cicadicola
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Candidatus Hodgkinia.
reference: 1
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCM008789.1.\nBacteria and source DNA available from McCutcheon Lab.\n\nThis endosymbiotic bacterium typically consists of a single, highly\npolyploid (a few hundred copies of the genome) chromosome. In this\ncase however, the single chromosome has split into several dozen\nlineages, each with a different reduced version of the ancestral\nsingle chromosome. The chromosomes were named variantX to\ndistinguish them from each other. Some of the chromosomes are\ncomplete circular molecules, while others are likely circular\nmolecules but they still have a run of N's at the end of the\ncomponent contig to close the gap.\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 :: SPAdes v. 3.6.2\nExpected Final Version :: yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/20/2023 16:42:59\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) :: 964\nCDSs (total) :: 921\nGenes (coding) :: 887\nCDSs (with protein) :: 887\nGenes (RNA) :: 43\nrRNAs :: 16, 16 (16S, 23S)\ncomplete rRNAs :: 14, 14 (16S, 23S)\npartial rRNAs :: 2, 2 (16S, 23S)\ntRNAs :: 11\nncRNAs :: 0\nPseudo Genes (total) :: 34\nCDSs (without protein) :: 34\nPseudo Genes (ambiguous residues) :: 0 of 34\nPseudo Genes (frameshifted) :: 2 of 34\nPseudo Genes (incomplete) :: 32 of 34\nPseudo Genes (internal stop) :: 4 of 34\nPseudo Genes (multiple problems) :: 3 of 34\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000340
sequence length: 51873
topology: circular
so has quality: SO_0000988
location: 1..51873
location: region:1-51873:1
RO_0002162: 573658

NZ_CM008789
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN07255135
type: BioSample
SIO_000068: biosample

1
title: Direct Submission
author: Campbell, M.A.
author: Lukasik, P.
author: Simon, C.
author: McCutcheon, J.P.
journal: Submitted (25-SEP-2017) Division of Biological Sciences, University of Montana, 32 Campus Drive, HS104, Missoula, MT 59812, USA

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

position:51873:1
position: 51873
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-51873:1:source
so part of: sequence
organism: Candidatus Hodgkinia cicadicola
mol type: genomic DNA
strain: MAGTDC
isolation source: bacteriome tissue
host: Magicicada tredecula
chromosome: variant3
country: USA: Marshall County, Kentucky
lat lon: 37.0086 N 88.3308 W
collection date: 2015-06-04

573658
type: Taxonomy
SIO_000068: taxonomy

MAGTDC_RS01305
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS01305
old locus tag: magtdc_22
so part of: sequence
location: complement(1399..5436)
location: region:1399-5436:-1
so has part: feature:1399-5436:-1:exon
subclass of: SO_0000010

79947671
type: Gene
SIO_000068: ncbigene

position:1399:-1
position: 1399
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5436:-1
position: 5436
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1399-5436:-1:exon

MAGTDC_RS01305
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS01305
old locus tag: magtdc_22
inference: COORDINATES: protein motif:HMM:NF016859.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MLSVFSKNISNLRFKITSPETILSWSYGEICNADTYDNDGKPIIGGLFCPKIFGSRKKNECICSIPKIDNKMICQTCGIYLGADRLQTRSRFGHIVLSTPVMHTLFYKPTPNILAELLNMDVEIIQGIIDCELHVITESNLDEYRSGQIISTETYRNMWMRNDRCSVTSGGQAIMELLSNVQVKKIKTELTKEIKHIKSEELLDRIKNRLEIVEGFISNNISLDWLVIRILPVLPAELRPTIVLDDDTLVNSDLNILYKHIIIANNNHLITTNEIESNNIDKFDSYIEGLKLLQKVVDDLIDNSSNVGNPNKYNTPALKSLAEMLKGKRGRFRYNILGKRVDYSGRSVIVSGPNLSINECSIPRSMAVELFKPFIYSKLMLKSNLNDRGSIKKILEDDIHLTYKILEEVVSYCPVLLNRAPTLHKLSIRAFWVKLTNEKVIRLHPLVCSGFNADFDGDQMAVHVPLSFSARIEATTLLMANNNVMHPAHGDPCILPSQDMILGLYYMSLISPEHKDICLSSYNEVHKILFFKKINLHTKVKFRIIVNGKITEILSTPGRLLISELVPSECNFLYEWNYPEFSKQLIFDIIELVKNKCGLKQMTTFCEKLMRLGFKYATQSGMSLSDSDFTNQSYKRKLLRDIQSKTTKSWSKISNKQKISMPLLIWPKVLDAINNNINLEITGYSSKQTSIQLIVNSGARGTLSQIKQLIGSRGYIVGFDGKLCRLPILNSYNEGLSLIQFFYCTFSSRRGLIDTTLKTASSGYFTRKLVESTREWIISEDDCDTDTGLHVKPIINFEFIKNRLIGRFIAKPILINKKIIIKRNELITEYNICNILMNCNGGLWIRSPLTCQARLGICKRCYGIELGSGNIAQYGDSVGVLAAQSISEPGTQLTLRTFHGLTNGEDKTHREVIENCLISPFSGIVKIKDVTCIVSKSDDIIVVNSNSVLSIVKNGIELWKYKLLRGTHLLVSNNKYVEAEEILCFNCIKSKNLLSLVSGILFFENLVYYLNIKKQTHNITKKIITNIKPDVIRKEMSLIGLDVGRKKRLHYVSVNSRNKFIINPNEKINLFDGILEVSIEDEDEDEDENDMALTEGFERLSKLFDNSIDDDNISIISPIAGLLKHGTDSNGNRSFIIDPKKINEYPVVYSDLDVKLFIKENKMIKQGQIILHGDHDLSNYAEVYGFNDLFNYFISIVQEIYGNQGVNVNSKHIEMVLRQMTNTVSISNPGNSLLKVGCCYNWQDVSRINNYIKILRGKMVIGDRQIVGITNACVNLKSILSAISFQGAIKSVIKAIISNNNYEISMIKDKIMLGKVPLVGTGFINEHRLIESKLLNKSDPVNRKI
SIO_010081: MAGTDC_RS01305
subclass of: SO_0000673
so part of: MAGTDC_RS01305
location: complement(1399..5436)
location: region:1399-5436:-1
so has part: feature:1399-5436:-1:exon

WP_146656716.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1399-5436:-1:exon

MAGTDC_RS01310
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS01310
old locus tag: magtdc_23
so part of: sequence
location: complement(5442..9221)
location: region:5442-9221:-1
so has part: feature:5442-9221:-1:exon
subclass of: SO_0000010

79947672
type: Gene
SIO_000068: ncbigene

position:5442:-1
position: 5442
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9221:-1
position: 9221
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5442-9221:-1:exon

MAGTDC_RS01310
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS01310
old locus tag: magtdc_23
inference: COORDINATES: protein motif:HMM:NF012771.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MNKRFNLNNNLLEKPYLNHGGLQSRLYNNILWGQYNNEGIKISKLELNIRTLFPLDFEYWNIELVRIRNFIKSERSTMFELELNITWWYFENDIAFICYRHDFNVPLMNLPRLTKNGILIINNTKKILVMQLIKQSAVSFDQESESISLKDKYLDYLKINKSKIKHNTRESDLLASLLKLKTKHSHIFKNTYGTKEVMFYKGKWCYLTWSNCYQNKFKYNSKWSLRLKKTIITYLEIGNNIIVNGHSNRSENQFVNIGEKMVLNKNSVLTYSSSLTITKSNKIFHIINEIIEAKLRDKSEITYEDIDDVELTLPGRIFLNDLTNDSSNYGLELLTKRDLILIWKEISINRSNFKHVDCNVRVVKGSGDMIIDLVKKTLERELCVNDTNDPPDDVMMINIFLGCMKQIQKNIDKFFISSNLCQYLDQVNSLSELSHKGKLTCFGEGGVTQQNVEITIRDTKKWQLAKICPIESPEGQNIGLVLTLSTYANVDVNGYILTGYYKTCNGLINNRVIYLNHFEEKRLNVALSWDKFQKELVTCLTGNKIKIINNNKVDLNLVSNSQVFSPAVCLIPFLGHNDPTRALMAANMLKQAIPPLNPRPPLVGTGEEINVMRDTGHNIVASNYGVVVSLDSKRVVVYEPKDRKRRVYILPQSGTSNQEMYQRMRTVVNFGQILKQGDVIAECQSSYDGEMSLGANLLVAFMCWEGYNFEDSVIISDNIISKGIFKSFHITELETKIMKTPFGNELLSSDIIELPIKYRRYLDLNGIVKVGSNVREGDVLVGKLAPRSDAQRKKEEFKEICGDELSSDEENDVIDGKDGVIEEKMKVIDGINDIAEEKEYGDKVSMDLVYSTSLRVPSGIECATVLEIERSSNGEWSYQNKDLEDYIYCRNVVTRKYIRRCCLLLQVSNIESPNVTCSFLSENKVVQDGLNLLYKKYLDYLNKLEAVMLSKLTNRLTDETQDADSKVLEIIKIKLLVRKSIKIGDKICGRHGNKGVISRIVPKEDMPFMADGTPIDIILNPLGVPSRMNIGQLLEVSFGLISYKFGLEFKNVLNMFYKTNDERILRMVIPKLTEIYPNINNLTTNMILVLLTELSQGVKISCPLFNVSFETYLKDFNRRLLINSTRKVQLYNGITGLPFDRPTSVGIIYIYKLNHLVDNKLHARSTGSYSIVTQQPLKGKNNLGGQRLGEMEVWALQSYGVARCLNESLTAKCDDIVARREIQESILKGYSRYTPHQIEGMAVLVRELFSMCIEIEVTK
SIO_010081: MAGTDC_RS01310
subclass of: SO_0000673
so part of: MAGTDC_RS01310
location: complement(5442..9221)
location: region:5442-9221:-1
so has part: feature:5442-9221:-1:exon

WP_192573013.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5442-9221:-1:exon

MAGTDC_RS01315
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
gene: rplP
locus tag: MAGTDC_RS01315
old locus tag: magtdc_24
so part of: sequence
location: complement(9412..9834)
location: region:9412-9834:-1
so has part: feature:9412-9834:-1:exon
subclass of: SO_0000010

79947673
type: Gene
SIO_000068: ncbigene

position:9412:-1
position: 9412
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9834:-1
position: 9834
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9412-9834:-1:exon

MAGTDC_RS01315
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
gene: rplP
locus tag: MAGTDC_RS01315
old locus tag: magtdc_24
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005766912.1
GO component: GO:0022625 - cytosolic large ribosomal subunit [Evidence IEA]; GO:0000315 - organellar large ribosomal subunit [Evidence IEA]
GO function: GO:0003735 - structural constituent of ribosome [Evidence IEA]
GO process: GO:0006412 - translation [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: 50S ribosomal protein L16
translation: MLKPKATKYKKQFRGHYKTKSKAGCFIEYGTYGLRATSSGRINGIQIESARVAISKFIKKVGKLWIRVFPNIPITKKPIEVRMGKGKGEVYDWIFKVGIGRIIFEIQGTSEEVARAALRAASYKLGIDTSFVYRIMDLTC
SIO_010081: MAGTDC_RS01315
subclass of: SO_0000673
so part of: MAGTDC_RS01315
location: complement(9412..9834)
location: region:9412-9834:-1
so has part: feature:9412-9834:-1:exon

WP_146656721.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:9412-9834:-1:exon

MAGTDC_RS05390
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS05390
so part of: sequence
location: 27187..27309
location: region:27187-27309:1
so has part: feature:27187-27309:1:exon
subclass of: SO_0000010

79948347
type: Gene
SIO_000068: ncbigene

position:27187:1
position: 27187
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:27309:1
position: 27309
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:27187-27309:1:exon

MAGTDC_RS05390
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS05390
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: MIEPKRLYNSSITFFDNSTYVNTDILYGAANSLSIVWVVY
SIO_010081: MAGTDC_RS05390
subclass of: SO_0000673
so part of: MAGTDC_RS05390
location: 27187..27309
location: region:27187-27309:1
so has part: feature:27187-27309:1:exon

WP_278046899.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:27187-27309:1:exon

MAGTDC_RS01320
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
gene: rpsB
locus tag: MAGTDC_RS01320
old locus tag: magtdc_25
so part of: sequence
location: 30912..32000
location: region:30912-32000:1
so has part: feature:30912-32000:1:exon
subclass of: SO_0000010

79947674
type: Gene
SIO_000068: ncbigene

position:30912:1
position: 30912
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:32000:1
position: 32000
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:30912-32000:1:exon

MAGTDC_RS01320
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
gene: rpsB
locus tag: MAGTDC_RS01320
old locus tag: magtdc_25
inference: COORDINATES: protein motif:HMM:NF012538.2
GO component: GO:0022627 - cytosolic small ribosomal subunit [Evidence IEA]; GO:0000314 - organellar small ribosomal subunit [Evidence IEA]
GO function: GO:0003735 - structural constituent of ribosome [Evidence IEA]
GO process: GO:0006412 - translation [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: 30S ribosomal protein S2
translation: MFGDRISLTDINTFIVNGIHYDKKISLNKAILKPIMLGIWHDVGILNMNKIILSLESALNLIFTKISQGKRLLFIGNEHLDLNSIGYYLSNTNQYFVMKPIGGLLSNWNTFRTAKTWSTHYQERSIRTRDRRLSDFYHRKSSDIISLFANSSKLEELPDVIVLFCNEGSEVIIKDANTIGIPIIGVTSLESNLDGIKYPILINNDSKQAISFICKLFWNIIEKANMIWRKYLNESDTKNILNNIGKHKLNSVCLRFRKKFIEDKRLIISVYNNPNMIHKILDLNLENIFTLLRNYNKFTPLKVVVNNLKHKIISMLKTNDSRYVNLVLFVNKIIKDLEIMMALVKNKYNKYLLNNQVVTYRF
SIO_010081: MAGTDC_RS01320
subclass of: SO_0000673
so part of: MAGTDC_RS01320
location: 30912..32000
location: region:30912-32000:1
so has part: feature:30912-32000:1:exon

WP_146656718.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:30912-32000:1:exon

MAGTDC_RS01325
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS01325
old locus tag: magtdc_26
so part of: sequence
location: 32006..32683
location: region:32006-32683:1
so has part: feature:32006-32683:1:exon
subclass of: SO_0000010

79947675
type: Gene
SIO_000068: ncbigene

position:32006:1
position: 32006
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:32683:1
position: 32683
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:32006-32683:1:exon

MAGTDC_RS01325
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS01325
old locus tag: magtdc_26
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: MDGNYIKLIITLRKQTGLSISYCKEVISKHNGNYIDALRTAQIESNRLLTYDVNGDHFISWIGTRFGLYIFKLTTKSEVYNNRSIWELRNKLNKIIQNHQLNSEKILNINVVNDLVIASCVGLKYSNNTFGLYFHEKINEFICKKFAISVISSYPCNRKKLIVLARIFSRQVLSYYVIYKKVVDIKTILKSECLYNTKQTMGNIINKFSSLNKCFVGIQRVFIMA
SIO_010081: MAGTDC_RS01325
subclass of: SO_0000673
so part of: MAGTDC_RS01325
location: 32006..32683
location: region:32006-32683:1
so has part: feature:32006-32683:1:exon

WP_146656719.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:32006-32683:1:exon

MAGTDC_RS01330
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS01330
old locus tag: magtdc_27
so part of: sequence
location: complement(43579..44517)
location: region:43579-44517:-1
so has part: feature:43579-44517:-1:exon
subclass of: SO_0000010

79947676
type: Gene
SIO_000068: ncbigene

position:43579:-1
position: 43579
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:44517:-1
position: 44517
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:43579-44517:-1:exon

MAGTDC_RS01330
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS01330
old locus tag: magtdc_27
EC number: 2.5.1.-
inference: COORDINATES: protein motif:HMM:NF012512.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: cysteine synthase family protein
translation: MRTKKIYSSITEVIGNTPIVRLKKIEEKYNVKTQLYAKLEYLNPFGSINDRVAETMVEDAWKRNKYNKNTIIVEVSYGNIGVSVAAVAARKGLGCLIVVHEGVSDAEINMLDLLGAKIIFSSNGIEEAIRTAKEFTKQVKHAIMTRQFENKIVVKTHKKTTAKEITRSMNNIDYFVCGVGTGGTITGVGEVLKKKKNSNTSIVAVEPWKASVLSGKQVQPHSIHGMGVGFLPKILNIKIIDYIFRVKDYEAVEYARIMANTEGMAVGLSSGAAICAGIKLGEVINNPLKKILIMVPSSAERYTLTDLSDNNH
SIO_010081: MAGTDC_RS01330
subclass of: SO_0000673
so part of: MAGTDC_RS01330
location: complement(43579..44517)
location: region:43579-44517:-1
so has part: feature:43579-44517:-1:exon

WP_146656720.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:43579-44517:-1:exon