Candidatus Hodgkinia cicadicola strain MAGTDC chromosome variant26, whole genome shotgun sequence.
type: Entry
definition: Candidatus Hodgkinia cicadicola strain MAGTDC chromosome variant26, whole genome shotgun sequence.
sequence version: NZ_CM008787.1
sequence date: 2023-04-10
sequence: sequence
division: CON
label: NZ_CM008787.1
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\nCM008787.1.\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: 13764
topology: circular
so has quality: SO_0000988
location: 1..13764
location: region:1-13764:1
RO_0002162: 573658

NZ_CM008787
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:13764:1
position: 13764
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-13764:1:source
so part of: sequence
organism: Candidatus Hodgkinia cicadicola
mol type: genomic DNA
strain: MAGTDC
isolation source: bacteriome tissue
host: Magicicada tredecula
chromosome: variant26
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_RS01205
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS01205
so part of: sequence
location: 1053..1433
location: region:1053-1433:1
so has part: feature:1053-1433:1:exon
subclass of: SO_0000010

79947656
type: Gene
SIO_000068: ncbigene

position:1053:1
position: 1053
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1433:1
position: 1433
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1053-1433:1:exon

MAGTDC_RS01205
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS01205
inference: COORDINATES: protein motif:HMM:NF013658.2
GO function: GO:0003824 - catalytic activity [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: phosphoadenosine phosphosulfate reductase family protein
translation: MCVNTRHICCNTRKLISLEKKLLNKNWFTGLRVAQSELRRINKTIIWDTTYNNIKLSPILLWNINQIINCISSIQVSYNFLQNIGFRSIGCAPCTRAVDPNESSRAGRWWWESFRKLGLECGLHKI
SIO_010081: MAGTDC_RS01205
subclass of: SO_0000673
so part of: MAGTDC_RS01205
location: 1053..1433
location: region:1053-1433:1
so has part: feature:1053-1433:1:exon

WP_146656697.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1053-1433:1:exon

MAGTDC_RS01210
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS01210
old locus tag: magtdc_168
so part of: sequence
location: complement(1518..1589)
location: region:1518-1589:-1
so has part: feature:1518-1589:-1:exon
subclass of: SO_0000663

79947657
type: Gene
SIO_000068: ncbigene

position:1518:-1
position: 1518
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1589:-1
position: 1589
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1518-1589:-1:exon

MAGTDC_RS01210
type: Transfer RNA
subclass of: SO_0000253
RO_0002162: 573658
locus tag: MAGTDC_RS01210
old locus tag: magtdc_168
product: tRNA-Ile
inference: COORDINATES: profile:tRNAscan-SE:2.0.12
note: Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
anticodon: (pos:complement(1555..1557),aa:Ile,seq:gat)
SIO_010081: MAGTDC_RS01210
subclass of: SO_0000673
so part of: MAGTDC_RS01210
location: complement(1518..1589)
location: region:1518-1589:-1
so has part: feature:1518-1589:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:1518-1589:-1:exon

MAGTDC_RS01215
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS01215
old locus tag: magtdc_169
so part of: sequence
location: 2371..3576
location: region:2371-3576:1
so has part: feature:2371-3576:1:exon
subclass of: SO_0000010

79947658
type: Gene
SIO_000068: ncbigene

position:2371:1
position: 2371
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3576:1
position: 3576
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2371-3576:1:exon

MAGTDC_RS01215
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS01215
old locus tag: magtdc_169
inference: COORDINATES: protein motif:HMM:NF012488.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: aminotransferase class V-fold PLP-dependent enzyme
translation: MISVIWLRTKFNALYCFNKPLIYFDNASTTQKPWFILNVFRYLNYNICSNPGRSQYYVAFLLSNILNESRTYLKHVFLKCTNYECVIYKSVTEIINAVYNNYWFIRKKTTILTCIDSHHSVIAPIYGKLDIFTLNVVGLDHDFIPNVRQYLNYIKNNISLLMFNHMSNVIGILIPIRLYSYFKGDNMTFIVDGSQSVPHFEVNIESINCNAYLLSAHKLYSFSNMGICFGRKNFLNDLNPLILGGGGVHKIKLKPFKCFLNNIPDKHESGSPTSFGLTCLSEIIRWKTKISSTHEKHICRYLWYKLSSIKGINLIGNWQPSSRLISFTIDNMPSYEVNKLLNKFMICIRSGYHCTTPLIEYLGKSTVCRISIGLYNTYKDADMLIYGIKILNINTTRKILC
SIO_010081: MAGTDC_RS01215
subclass of: SO_0000673
so part of: MAGTDC_RS01215
location: 2371..3576
location: region:2371-3576:1
so has part: feature:2371-3576:1:exon

WP_146656698.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2371-3576:1:exon

MAGTDC_RS01220
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS01220
old locus tag: magtdc_170
so part of: sequence
location: 3633..5732
location: region:3633-5732:1
so has part: feature:3633-5732:1:exon
subclass of: SO_0000010

79947659
type: Gene
SIO_000068: ncbigene

position:3633:1
position: 3633
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5732:1
position: 5732
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3633-5732:1:exon

MAGTDC_RS01220
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS01220
old locus tag: magtdc_170
inference: COORDINATES: protein motif:HMM:NF012361.2
GO function: GO:0004812 - aminoacyl-tRNA ligase activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
GO process: GO:0006418 - tRNA aminoacylation for protein translation [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: class I tRNA ligase family protein
translation: MYTKQVYSPYVNSLDTDQIIQVKKRFDLVTPPPNITGELHIGHIFNIVIQRVFLFWDNKHKMNCLIGVDHAGLATKCILLNRYNKTNPLNFWIWKQRISKQIIFQIKRFIWTLKSTKLRFTLDNPFNITVNYAFVKLWNRGMVISKKKLLWWDCGLQTTLSEMELGKKKGLGCWFGFKYVLLGTKLRWNGRWILNNYITLERSDVKMQISKIIINLNDISFIKFKSNVLIDPISLNYTDILVNVGCEHNLDIIDDVVEVSYNLLCISNKDLKLLLIKWIYIRIGICYHNKNEEIDIYFNKKTNSNVKLCLSNQWYIKLNLLKKTNLINEYKNLFKDGLDQNLKLWCISRFIEWGHKLPVLWQGSEVVINDSTTKAKYYSIAWYALPFVKTKTKFIQDISVFDTWFSSALWYLACLGWPHKTTQLRTCYGKSIVFTGIDITFFWVTKMILISNILMKERIPFERILIHPIICDSKGDKMSKTKGNVLSPSSLFNSYGLGALVLYFSGIELNSKRNKICLNSIILCKNMLNKLWNLNRINANEKKCIGFNICHWILSSIYCKHKKMIKYFNTFEFNKFQAELTKLIKYDVNNFISIHNCQKWDSIKLVIKSIFSCWIGGKPKHNLFTYTKKTYLMFGSLLKLIYLFELSGARFISNGSRLFKQVRYILERVSPVDVLFFKRLRITSNTGITLWNNTLILIH
SIO_010081: MAGTDC_RS01220
subclass of: SO_0000673
so part of: MAGTDC_RS01220
location: 3633..5732
location: region:3633-5732:1
so has part: feature:3633-5732:1:exon

WP_146656699.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3633-5732:1:exon

MAGTDC_RS01225
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS01225
old locus tag: magtdc_171
so part of: sequence
location: complement(6204..7706)
location: region:6204-7706:-1
so has part: feature:6204-7706:-1:exon
subclass of: SO_0000010

79947660
type: Gene
SIO_000068: ncbigene

position:6204:-1
position: 6204
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7706:-1
position: 7706
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6204-7706:-1:exon

MAGTDC_RS01225
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS01225
old locus tag: magtdc_171
inference: COORDINATES: protein motif:HMM:NF019604.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: electron-transfer flavoprotein:ubiquinone oxidoreductase
translation: MKDIIVVGAGPGGLTAAIELKKLEPKNNIIILEKSSEVGGHLVSGAILQRNEYYEYISKYSLKYNTVITNENIWRLTKNSYYNLTRFVPDEYRNKRNILIDIGEVCKALALEATRIGVKICTCCAVDGFLNYKDSIVGLTLAGGNKIKSDHVIVAEGACGTLTEKIFKHYNIKINKRYALGIREERRYEINKLTSNNVGSIYHTIGWPSDDNSNGGFVYCYKDKVVIGYVTYLDYSNCYINPYNEFERFKSHPKISELIKGTVKTKYSAKIIAINDMRNPTVACFHGCSIIGCAFGLLDSMKLKGLHNAIISGKMVAEKYITTTTKMVTNIIDYLTDIDLINNLKISNQTSTIFQKYGAVVAFIYKKINKIILSCLLNFKFKNKWFNYNKKPPRDWNVKDNRDDSLMFSDINYGPDSHISVMDEMKHKIYDLKLNNKMSSRFCPAGVFRWEKQFKHYVFKINHTNCLQCKACLVKTAEKTIDWNVCKNGDGPNFITENYK
SIO_010081: MAGTDC_RS01225
subclass of: SO_0000673
so part of: MAGTDC_RS01225
location: complement(6204..7706)
location: region:6204-7706:-1
so has part: feature:6204-7706:-1:exon

WP_146656700.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6204-7706:-1:exon

MAGTDC_RS05370
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS05370
pseudo: true
so part of: sequence
location: 7719..8240
location: region:7719-8240:1
so has part: feature:7719-8240:1:exon
subclass of: SO_0000010

79948343
type: Gene
SIO_000068: ncbigene

position:7719:1
position: 7719
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8240:1
position: 8240
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7719-8240:1:exon

MAGTDC_RS05370
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS05370
inference: COORDINATES: protein motif:HMM:NF013398.2
note: internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 4
product: GTP cyclohydrolase I
SIO_010081: MAGTDC_RS05370
subclass of: SO_0000673
so part of: MAGTDC_RS05370
location: 7719..8240
location: region:7719-8240:1
so has part: feature:7719-8240:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:7719-8240:1:exon

MAGTDC_RS01240
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS01240
old locus tag: magtdc_172
so part of: sequence
location: 8233..8550
location: region:8233-8550:1
so has part: feature:8233-8550:1:exon
subclass of: SO_0000010

79947661
type: Gene
SIO_000068: ncbigene

position:8233:1
position: 8233
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8550:1
position: 8550
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8233-8550:1:exon

MAGTDC_RS01240
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS01240
old locus tag: magtdc_172
inference: COORDINATES: protein motif:HMM:NF013653.2
GO function: GO:0004635 - phosphoribosyl-AMP cyclohydrolase activity [Evidence IEA]
GO process: GO:0000105 - histidine biosynthetic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: phosphoribosyl-AMP cyclohydrolase
translation: MNNLELNGLDLIPVIVIDFYSKEVVMFAYTNELCLRLTLITKFCHYYNRTDQFIWLKGWESGNLHLIQEIYTDCNSDCLIFSILILQTGLVCHTERPSCFYKLLK
SIO_010081: MAGTDC_RS01240
subclass of: SO_0000673
so part of: MAGTDC_RS01240
location: 8233..8550
location: region:8233-8550:1
so has part: feature:8233-8550:1:exon

WP_146656704.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8233-8550:1:exon

MAGTDC_RS01245
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS01245
old locus tag: magtdc_173
so part of: sequence
location: complement(10335..13340)
location: region:10335-13340:-1
so has part: feature:10335-13340:-1:exon
subclass of: SO_0000010

79947662
type: Gene
SIO_000068: ncbigene

position:10335:-1
position: 10335
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:13340:-1
position: 13340
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10335-13340:-1:exon

MAGTDC_RS01245
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS01245
old locus tag: magtdc_173
EC number: 2.7.7.7
inference: COORDINATES: protein motif:HMM:TIGR00594.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: DNA polymerase III subunit alpha
translation: MINFVNLKVHSIYSILESTLKVDRIAELAFEKKQKAVCLTDNNLHGSLEFCLKCIELGIKPIIGCKLAINHKHTLFSYGKRKKSNLIITVLIQSELGYKNLLKLINQSDCKHNYHVVNLKDIHSLSKGLICLMGGFGSLSWDVYNTIGPNKTIDRLNVIKNIFDNNLCIELERNIFTNPDYEKFMIDYAKTNGLVVAAINETYFESPEDIEVIEILQSISKQKLTHISKNNYFNDYKNILTRFPDVIEAVKNTTTISNLCNFHLEKRIVHLPSILKNKKTENKILYLKSIEALEYMFYSVGKKNKEIYYDRLLKELSIILVTSYSGYFLIVSDFTLWAKYNNIYVGSGRGSASGSLIAYCLGITVVDPMVHELLFERFLNVNRISLPDIDVDFCHEGREKIIRYIQLKYGIRNIGQIITFGSLQVKVAIKDVGRYLSISYNTLNLLCKSLPTFDHETNSILDVLYKTKLISSPLFEKVMNIILKLIGLYRQISTHAAGLVIYDTPLVNDTPIVWSKEDRVGVVQHSMNWVDSAGLPKFDLLGLKTLTAIDETIEYITINRIHIDLECYTDNKTFELICNGTVLGTFQLESQGMKEHIKHIRPSSIIDLTALIALYRPGPIKHIKLYSDAKWKRTKRTSLHKSIDYILDETYGIIIYQEQVMLIAQELAGYSLSEADVLRRVMAKKDRKEMSEQRTRFVNGVVANKIDHNLAREIFDTLLRFADYGFNKSHAVAYSSLAYLTSYLKANFPLEFYVANMNTEIMDLERVSALYYDAIDMGIKFLLPSVCLPVDKFIIGNNLIYFPLSVIKGLNDQIIDSINKSMNNKKFKNLLDFCIRSDAKIITKTVLKSLIYSGALDCFNISRKQLVSLINTIIICLTSKHDPNNLLGNYTSNNNEEIPLALLYKEYLMLNCYVSKCSIIEIDEGSKPNLKGLCIVVSHNKDIATVIIGNKRLNVLFKSKKRIELGNVYRYTFEKIAGKLCCISFVLFKFKRNKSLISIKL
SIO_010081: MAGTDC_RS01245
subclass of: SO_0000673
so part of: MAGTDC_RS01245
location: complement(10335..13340)
location: region:10335-13340:-1
so has part: feature:10335-13340:-1:exon

WP_146656703.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:10335-13340:-1:exon