Candidatus Ishikawaella capsulata Mpkobe plasmid pAst, complete sequence.
type: Entry
definition: Candidatus Ishikawaella capsulata Mpkobe plasmid pAst, complete sequence.
sequence version: NZ_AP010873.1
sequence date: 2022-12-24
sequence: sequence
division: CON
label: NZ_AP010873.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMD00061091
keyword: RefSeq
source: Candidatus Ishikawaella capsulata Mpkobe
organism: Candidatus Ishikawaella capsulata Mpkobe
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Candidatus Ishikawaella.
reference: 1
references: 21737395
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nAP010873.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/24/2022 01:57:08\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) :: 675\nCDSs (total) :: 626\nGenes (coding) :: 601\nCDSs (with protein) :: 601\nGenes (RNA) :: 49\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 37\nncRNAs :: 3\nPseudo Genes (total) :: 25\nCDSs (without protein) :: 25\nPseudo Genes (ambiguous residues) :: 0 of 25\nPseudo Genes (frameshifted) :: 10 of 25\nPseudo Genes (incomplete) :: 15 of 25\nPseudo Genes (internal stop) :: 5 of 25\nPseudo Genes (multiple problems) :: 4 of 25\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 9139
topology: circular
so has quality: SO_0000988
location: 1..9139
location: region:1-9139:1
RO_0002162: 476281

NZ_AP010873
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMD00061091
type: BioSample
SIO_000068: biosample

1
title: Reductive evolution of bacterial genome in insect gut environment
author: Nikoh, N.
author: Hosokawa, T.
author: Oshima, K.
author: Hattori, M.
author: Fukatsu, T.
journal: Genome Biol Evol 3, 702-714 (2011)
pubmed: 21737395

21737395
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Nikoh, N.
author: Hosokawa, T.
author: Shimada, M.
author: Yamashita, A.
author: Ohshima, K.
author: Hattori, M.
author: Fukatsu, T.
journal: Submitted (12-SEP-2008) Contact:Naruo Nikoh The Open University of Japan; 2-11 Wakaba, Mihama, Chiba, Chiba 261-8586, Japan

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

position:9139:1
position: 9139
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9139:1:source
so part of: sequence
organism: Candidatus Ishikawaella capsulata Mpkobe
mol type: genomic DNA
strain: Mpkobe
host: Megacopta punctatissima
plasmid: pAst
note: rRNA phylotype Rs-D17

476281
type: Taxonomy
SIO_000068: taxonomy

ICMP_RS03280
type: Gene
subclass of: SO_0000704
RO_0002162: 476281
locus tag: ICMP_RS03280
so part of: sequence
location: 337..1245
location: region:337-1245:1
so has part: feature:337-1245:1:exon
subclass of: SO_0000010

position:337:1
position: 337
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1245:1
position: 1245
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:337-1245:1:exon

ICMP_RS03280
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 476281
locus tag: ICMP_RS03280
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007886110.1
GO function: GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO process: GO:0006270 - DNA replication initiation [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: RepB family plasmid replication initiator protein
translation: MMNIDIESKYLLEPFLSVTKNTGEIVYLSPNKNNTVQPVALMRLGLFVPTLKSTARRKSSFVVSTDATRAFKNLSLVRAEGYNKITIVGERLDMDSDFKTWIGIIQSFAKFASTKNSVTLPFINFIKMCGIPSAHSSSVLRKRLDASLRRIATNTLSFEGNGKAYHTHLVQSAYYNSEKDIVNIQADPNLFELYNFDHKVLLHLRAISFLKRKESSQALYTYLESLPLNPGPVSISRLRLRLNLSSKITTQNYIVRRALKQLQKIGYLDYSEVKSNNCIFFIIHRRTPKLKNIDVISNVDFE
SIO_010081: ICMP_RS03280
subclass of: SO_0000673
so part of: ICMP_RS03280
location: 337..1245
location: region:337-1245:1
so has part: feature:337-1245:1:exon

WP_041070253.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:337-1245:1:exon

ICMP_RS03285
type: Gene
subclass of: SO_0000704
RO_0002162: 476281
locus tag: ICMP_RS03285
so part of: sequence
location: 1323..1964
location: region:1323-1964:1
so has part: feature:1323-1964:1:exon
subclass of: SO_0000010

position:1323:1
position: 1323
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1964:1
position: 1964
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1323-1964:1:exon

ICMP_RS03285
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 476281
locus tag: ICMP_RS03285
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017167677.1
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO process: GO:0006310 - DNA recombination [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: recombinase family protein
translation: MSQSKKLIQAVRIYLRVSTDKQDLKRQEMVVMNTLSSDYYIAGIYREKASGARTDRPELMRMISDLKFGEIVIAEKIDRISRLPLEEAEILIDSIRNKGVKLVIPGIVDLTDLIHEVKGVNNIIISCMQNMLLKIALQMARDDYETRRDRIRQGVNIAKKAGKYKGRPPKKMIHEYIVSLRKKGHSIYNTAKMAQCSVSQVKRIWAMNKINKI
SIO_010081: ICMP_RS03285
subclass of: SO_0000673
so part of: ICMP_RS03285
location: 1323..1964
location: region:1323-1964:1
so has part: feature:1323-1964:1:exon

WP_041070256.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1323-1964:1:exon

ICMP_RS03290
type: Gene
subclass of: SO_0000704
RO_0002162: 476281
gene: map
locus tag: ICMP_RS03290
so part of: sequence
location: 2040..2792
location: region:2040-2792:1
so has part: feature:2040-2792:1:exon
subclass of: SO_0000010

position:2040:1
position: 2040
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2792:1
position: 2792
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2040-2792:1:exon

ICMP_RS03290
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 476281
gene: map
locus tag: ICMP_RS03290
EC number: 3.4.11.18
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002209416.1
GO process: GO:0036211 - protein modification process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type I methionyl aminopeptidase
translation: MKKVKLHNKEEINKVREAGHAAACVLDMIQSHIVIGITTKKLDKICHNFIVNKLKVIPANLGYNGFAHTICTSINEVVCHGIPSDRKLRDGDIINIDVAVIKDGWYGDTSRMYFVGTPSIKAKCLVNTCYEAMIAGINVVKPEVTINNIGIAIQRIAKQKGFSVVREYCGHGIGQTYHTYPQIIHYNSLENTSKLKTGMIFTIEPMLNEGKAKTVVLSDGWTVETRDHSLSAQWEHTIAVTDNGFEVLTK
SIO_010081: ICMP_RS03290
subclass of: SO_0000673
so part of: ICMP_RS03290
location: 2040..2792
location: region:2040-2792:1
so has part: feature:2040-2792:1:exon

WP_041070260.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2040-2792:1:exon

ICMP_RS03295
type: Gene
subclass of: SO_0000704
RO_0002162: 476281
locus tag: ICMP_RS03295
so part of: sequence
location: 2863..4071
location: region:2863-4071:1
so has part: feature:2863-4071:1:exon
subclass of: SO_0000010

position:2863:1
position: 2863
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4071:1
position: 4071
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2863-4071:1:exon

ICMP_RS03295
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 476281
locus tag: ICMP_RS03295
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012989335.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: bifunctional succinylornithine transaminase/acetylornithine transaminase
translation: MFFQPKREDFDKYIVPCFSPAPFILVKGRGSRLWDQENKEYIDFASGIAVTSLGHSNVKLINALNTQLNKLWHVSNIYTNEPVLKLAKKLVELTFADKVFFCNSGAEANEAALKLARKYANEYYDKTKNEIIAFENSFHGRTLFTVTVGGQSKYSDNFGPLPPAITHLPYNDLKTFEQHISSKTCAVIVELIIGEGGVIPIDPFFLEQVRKICTNYDITLIFDEIQTGMGRTGYLYAYQEYNIVPDILTSAKGLGGGFPIGAMLTKEKWAQIFQPGTHGTTFGGNLLAATVAETVLSQLDYEMLSGVLQRHDIIMNELIKLNKKYNIFQIIRGKGLLIGAQLSSIYYGKAKKLTQLASEEGLLILIAGSNVVRFTPALNIPLDDIYEGFQYFEQAIIRFKDK
SIO_010081: ICMP_RS03295
subclass of: SO_0000673
so part of: ICMP_RS03295
location: 2863..4071
location: region:2863-4071:1
so has part: feature:2863-4071:1:exon

WP_041070263.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2863-4071:1:exon

ICMP_RS03300
type: Gene
subclass of: SO_0000704
RO_0002162: 476281
locus tag: ICMP_RS03300
so part of: sequence
location: 4074..5120
location: region:4074-5120:1
so has part: feature:4074-5120:1:exon
subclass of: SO_0000010

position:4074:1
position: 4074
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5120:1
position: 5120
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4074-5120:1:exon

ICMP_RS03300
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 476281
locus tag: ICMP_RS03300
inference: COORDINATES: protein motif:HMM:NF016822.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: arginine N-succinyltransferase
translation: MILFRPIQEKDLPDIIKLSTNTGIGLTSLPYDPGYLENRILCSTNTFNGKLPRSEQYYMFGLEDLNSNQIVGISAIESAVGLKDLFLNIYIEKINNVSSLIYLHHKLSMLSIHAHYTGNTELCTLFLHRNYQKNKNGLLLSKARFLFIACFKHLFSSRLIAEMRGIVNKKDESIYWNAIGRHFFNISFAEADYLSNTGIKSFMSNLIPYYPIYLDLLPSKVKNIIGKTHLDSLPAQKFLEQEGFYWNQSIDVFDAGPILEANTDRVHSICNSKVFKITEKNKNLPISGKGFTLISNEKFNNFRALLLENNCINQLIKLNSAQYDALEVEIGDTLRFVNLYPENKKYEC
SIO_010081: ICMP_RS03300
subclass of: SO_0000673
so part of: ICMP_RS03300
location: 4074..5120
location: region:4074-5120:1
so has part: feature:4074-5120:1:exon

WP_041070266.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4074-5120:1:exon

ICMP_RS03305
type: Gene
subclass of: SO_0000704
RO_0002162: 476281
gene: astD
locus tag: ICMP_RS03305
so part of: sequence
location: 5110..6537
location: region:5110-6537:1
so has part: feature:5110-6537:1:exon
subclass of: SO_0000010

position:5110:1
position: 5110
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6537:1
position: 6537
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5110-6537:1:exon

ICMP_RS03305
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 476281
gene: astD
locus tag: ICMP_RS03305
EC number: 1.2.1.71
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008805093.1
GO function: GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Evidence IEA]
GO process: GO:0006527 - arginine catabolic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: succinylglutamate-semialdehyde dehydrogenase
translation: MNVNSNFINGKWKSGHGTIINKIAPEDKSVIWRAHSADYDDVNEACESASNAFNYWSKINIEQRMGYINHYVTLLHKYKQQIATIISQETSKPLWETYIEVQSMIDKVLISKVSWEKRTGYGEIKISNKRILLHHKAHGVMAVFGPYNFPGHLPNGHIIPALIAGNTVVFKPSELTPATAEIITKIWQETNLPDGVLNLIQGDKKTGQMLLMNKNINGVLFTGSTKVGCYFHRYFAGQPEKILVLEMGGNNALIIDNFEDEYINYVVDLIIQSAFISAGQRCTCARRLLIKSGKKGDNLILNLIEKSKQLSIGHWNNQPQPFMGGVISHKHVDNMLQIQNNLQLLGGRILLQMKQIEKNATFLTPGIMETTNINLPDEEYFCPFIKITRYEHFDQAVDIANNTKYGLAVGLVSNDESLFNSLIIKSQAGIVNWNNALTGASSRMPFGGIKSSGNHRPSGYYAADYCAWPVVSLIN
SIO_010081: ICMP_RS03305
subclass of: SO_0000673
so part of: ICMP_RS03305
location: 5110..6537
location: region:5110-6537:1
so has part: feature:5110-6537:1:exon

WP_052456854.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5110-6537:1:exon

ICMP_RS03310
type: Gene
subclass of: SO_0000704
RO_0002162: 476281
gene: astB
locus tag: ICMP_RS03310
so part of: sequence
location: 6573..7916
location: region:6573-7916:1
so has part: feature:6573-7916:1:exon
subclass of: SO_0000010

position:6573:1
position: 6573
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7916:1
position: 7916
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6573-7916:1:exon

ICMP_RS03310
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 476281
gene: astB
locus tag: ICMP_RS03310
EC number: 3.5.3.23
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002903055.1
GO function: GO:0009015 - N-succinylarginine dihydrolase activity [Evidence IEA]
GO process: GO:0006527 - arginine catabolic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: N-succinylarginine dihydrolase
translation: MSNIEVNFDGLVGPTHHYAGLSIDNNASFNNRYKLSNPRKAALQGLEKMKFLFDRGFFQGVFPPQLRPNIFALRKLGFSGTEKQILNSVANTSIDLLSAFTSASSMWLANAATISPSNDSLDRKVHFTVANLNNYLHRSQEHLFNAMILKKIFHNEKFFSHHSALIQQKSFSDEGSANHMRISWDEINQGIQIFVYGNSVFNHLKSKDFNYRQTLEASTAISRLHQLDPNYTLFFKQNPFAIKHGVFHNDVIAVSNKNLLFYHEYAFTNQNENIDKIISKSYKLNLPFIAIEVLEKDVKLSEAISSYLFNSQILSKNNGKMIILVPDECYYIENIWNYLNKIIANDLYPIDEIQTINLHESMCNGGGPACLRLKVMLNQEQFKSINANFLLNDLLYEKLKKWINKYYRDQLCINDLIDVQLLTEVYQALDELTQILKIGSIYKFQSI
SIO_010081: ICMP_RS03310
subclass of: SO_0000673
so part of: ICMP_RS03310
location: 6573..7916
location: region:6573-7916:1
so has part: feature:6573-7916:1:exon

WP_041070275.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6573-7916:1:exon

ICMP_RS03315
type: Gene
subclass of: SO_0000704
RO_0002162: 476281
locus tag: ICMP_RS03315
so part of: sequence
location: complement(7943..9139)
location: region:7943-9139:-1
so has part: feature:7943-9139:-1:exon
subclass of: SO_0000010

position:7943:-1
position: 7943
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9139:-1
position: 9139
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7943-9139:-1:exon

ICMP_RS03315
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 476281
locus tag: ICMP_RS03315
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014606080.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: cupin domain-containing protein
translation: MKKISRRTFLMLATGGATAFITKKFLIDRPHKEKIYKFPIKNIPLINEKPDMINPPTTDSGTLPNLRFAFDDAHIRKSTGGWTRQITKRELAISNTIAGVNMRLYKGGIRELHWHKEAEWAYMLYGKARITAIDIKGKWFIKDVNVGDLWYFPPGIPHSIQGLSKDGCEFLLVFDNGNFDEESTFLLSDWFKHIPIDILAKNFNTRKEIFKNLPSPEKKYIFSGEINNKIYYKNIKMTQNSRYKFSYKLMNNNIIKTKKGEIYIADSSTFHISKNISAALVLLEPGSIRELHWHPNNDEWQYYISGQGRMGVFASSGQARTFDFKSRDVGYVPFAMGHYIQNTGPERLIFLEIFNSNYYADISLNQWLAVTPPYLVQQHLNLNNEFIENLNRKKCPII
SIO_010081: ICMP_RS03315
subclass of: SO_0000673
so part of: ICMP_RS03315
location: complement(7943..9139)
location: region:7943-9139:-1
so has part: feature:7943-9139:-1:exon

WP_041070269.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7943-9139:-1:exon