Lactobacillus helsingborgensis strain ESL0183 plasmid unnamed.
type: Entry
definition: Lactobacillus helsingborgensis strain ESL0183 plasmid unnamed.
sequence version: NZ_CP029545.1
sequence date: 2023-03-23
sequence: sequence
division: CON
label: NZ_CP029545.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN07311026
keyword: RefSeq
source: Lactobacillus helsingborgensis
organism: Lactobacillus helsingborgensis
taxonomy: Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP029545.1.\nBacteria and source DNA available from Philipp Engel, University of\nLausanne, department of fundamental microbiology.\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 :: HGAP v. 2.3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 300.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/23/2023 02:37:29\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) :: 1,757\nCDSs (total) :: 1,686\nGenes (coding) :: 1,673\nCDSs (with protein) :: 1,673\nGenes (RNA) :: 71\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 56\nncRNAs :: 3\nPseudo Genes (total) :: 13\nCDSs (without protein) :: 13\nPseudo Genes (ambiguous residues) :: 0 of 13\nPseudo Genes (frameshifted) :: 5 of 13\nPseudo Genes (incomplete) :: 5 of 13\nPseudo Genes (internal stop) :: 6 of 13\nPseudo Genes (multiple problems) :: 3 of 13\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##

sequence
subclass of: SO_0000155
sequence length: 11217
topology: linear
so has quality: SO_0000987
location: 1..11217
location: region:1-11217:1
RO_0002162: 1218494

NZ_CP029545
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN07311026
type: BioSample
SIO_000068: biosample

1
title: Reference genomes for bee gut microbiota database
author: Ellegaard, K.M.
journal: Unpublished

2
title: Direct Submission
author: Ellegaard, K.M.
journal: Submitted (22-MAY-2018) Department of Fundamental Microbiology, University of Lausanne, Batiment Biophore, Lausanne 1015, Switzerland

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

position:11217:1
position: 11217
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-11217:1:source
so part of: sequence
organism: Lactobacillus helsingborgensis
mol type: genomic DNA
strain: ESL0183
isolation source: gut
host: Apis mellifera
plasmid: unnamed
country: Switzerland: Lausanne
lat lon: 46.52 N 6.58 E
collection date: 2014-12-12

1218494
type: Taxonomy
SIO_000068: taxonomy

DLD54_RS08770
type: Gene
subclass of: SO_0000704
RO_0002162: 1218494
locus tag: DLD54_RS08770
old locus tag: DLD54_08770
so part of: sequence
location: complement(315..1574)
location: region:315-1574:-1
so has part: feature:315-1574:-1:exon
subclass of: SO_0000010

78130147
type: Gene
SIO_000068: ncbigene

position:315:-1
position: 315
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1574:-1
position: 1574
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:315-1574:-1:exon

DLD54_RS08770
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1218494
locus tag: DLD54_RS08770
old locus tag: DLD54_08770
inference: COORDINATES: protein motif:HMM:NF019310.2
GO function: GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO process: GO:0055085 - transmembrane transport [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MFS transporter
translation: MDVFLRNKNYRKFSIAGFLSSAGNILFYLAFMTYASKLQNYALALSLISITEAIPDLLGSVAGYIADRTQNKFKMITWLAVIRFILYMLVGFLFTRNNIAGWNLVLIVIAINFISDLSGSYSGGLETPIIVNLVSEEEVAEAEGFTGGVSSILQMLAQFAGSGLLLFMSYSGLAVVNALTFLIAGLIFANVGHNYYKVHSEATQEAVNNQNFFKTMINSFKQLKKEKGIFTILITIALLNGVLGALEPLISIMIAANKTTMIIGTFSFTIALFGAIGSIGAAIGSILGTKLFKSTSLLIIALIDTIFSAGMVITIFSKNIILCMFMFFFLAFFAGTASPKLEQWIVTSVDRTILSSTIGAVNTILIVTSPLVTAVISTISAATSVYYSLGTLLIGSIIVFGVILHIIRKTNLDKQPVEN
SIO_010081: DLD54_RS08770
subclass of: SO_0000673
so part of: DLD54_RS08770
location: complement(315..1574)
location: region:315-1574:-1
so has part: feature:315-1574:-1:exon

WP_109919033.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:315-1574:-1:exon

DLD54_RS08775
type: Gene
subclass of: SO_0000704
RO_0002162: 1218494
locus tag: DLD54_RS08775
old locus tag: DLD54_08775
so part of: sequence
location: 1675..2523
location: region:1675-2523:1
so has part: feature:1675-2523:1:exon
subclass of: SO_0000010

78130148
type: Gene
SIO_000068: ncbigene

position:1675:1
position: 1675
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2523:1
position: 2523
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1675-2523:1:exon

DLD54_RS08775
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1218494
locus tag: DLD54_RS08775
old locus tag: DLD54_08775
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: Rgg/GadR/MutR family transcriptional regulator
translation: MTIGELLKKYRIEHEKTQKEWVGNIVSPSFYAKVEKNLSRISAEDLLGILRNNQVSIVSFVNSLDSREESVKNQESEVDKLITEAYYQGSKSDLEKISHLIKDSDLPDKDEQLMFITAYIALLNDDLKSLDEQIKSKLKNKIFSIVNFNETNAELYSNFMELYDLDSNLLITKRILQQFKGTNDVELQSLILAMISNLLFICVENKRYDGLEFFIKNANEIIVTPELFFYKNVLVFVEDLIDYHVRHDKASLEKCKLIIENIKLTGMTSYGNELSKFLKITE
SIO_010081: DLD54_RS08775
subclass of: SO_0000673
so part of: DLD54_RS08775
location: 1675..2523
location: region:1675-2523:1
so has part: feature:1675-2523:1:exon

WP_109919034.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1675-2523:1:exon

DLD54_RS08780
type: Gene
subclass of: SO_0000704
RO_0002162: 1218494
locus tag: DLD54_RS08780
old locus tag: DLD54_08780
so part of: sequence
location: 3137..5728
location: region:3137-5728:1
so has part: feature:3137-5728:1:exon
subclass of: SO_0000010

78130149
type: Gene
SIO_000068: ncbigene

position:3137:1
position: 3137
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5728:1
position: 5728
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3137-5728:1:exon

DLD54_RS08780
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1218494
locus tag: DLD54_RS08780
old locus tag: DLD54_08780
inference: COORDINATES: protein motif:HMM:NF017000.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: lipopolysaccharide core heptose(II) kinase RfaY
translation: MDNFIQLEKKIRSSDKFTELVKSMNFKDYKVIDDDVWIYFNPIECDVPDSGWKGHLSVQSKDIEDVFLISSQILSIENCAFKVARSRQVYEMLSDTHASVTEANKFMTFYPKNVEEFKLIVFKLDKALQRYSAPKIFTDFQLPKNSCVQFRYGAFKKMTCRDKEHNKIIDLVRLPTGKLIPDDRTKSFHMLPGTSWPFKANKYKDKKVYCPELNKYRFSEILSRKNKGGVYKGITINDVPIVMKTANELVGSNPKKLSAKQLLNNEIKYMKVLNKSPYIPELIETFSQGKTLVEIMRFISGPQLINIKIEDKEKVIRSLIKTVYSLHKQGIIIGDLTNTNFIYSNQKCYLVDLEYMASVNTPQKREAQTRFYLPDYKKEGYETQIEDVYSLAVTVITIIFNRVPKYHANNLFDGAVCLMRQLVIAEKLNPEEMKIINLAKYLLNIILSNDEYDPEQLNTFDNCKKYSLENFSKKEKISLLKNTIERKVLPIETKYSEYGLAKHMKNITNFGTMTSPISIQSGSVGINVFKGNSINLNNYKWRSIVAGLTSLKKYEYYDSYLFGYTGVLWEAGNNFLRNEITKNQLKEVVTAFLSMEKNCNNHKIDFALGISGKLYTAIRTLICQNNENLFSYSKKMGERLYMKLKKVHVIESNNFNQINFAHGLAGEAYSLLVSGLYFKKYNFQNKALEILNEIDQFMMKNLNRIKLLGTDTLEYSWCEGASGIGIALIRAVRLTNNSFAARSLNDIYKFCIHGYIELESNICHGRNSVIDFLNDYNQVVKSTKLKNDINMLIEFDLVSSYDESRSVLDFFDETGFTNCWDYGVGQIGSICSDLHALNGENRDFYLTDEQEHELSKNLIMKGN
SIO_010081: DLD54_RS08780
subclass of: SO_0000673
so part of: DLD54_RS08780
location: 3137..5728
location: region:3137-5728:1
so has part: feature:3137-5728:1:exon

WP_109919035.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3137-5728:1:exon

DLD54_RS08785
type: Gene
subclass of: SO_0000704
RO_0002162: 1218494
locus tag: DLD54_RS08785
old locus tag: DLD54_08785
so part of: sequence
location: 5732..7360
location: region:5732-7360:1
so has part: feature:5732-7360:1:exon
subclass of: SO_0000010

78130150
type: Gene
SIO_000068: ncbigene

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

position:7360:1
position: 7360
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5732-7360:1:exon

DLD54_RS08785
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1218494
locus tag: DLD54_RS08785
old locus tag: DLD54_08785
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012845425.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ABC transporter ATP-binding protein
translation: MKYLFKYVRQEPLRVLLVVILQVICSLFRVANSIFNIFILNSLVKFDFRAFVSYILLNILLFVVMTVFLFLNLVEQAKVIQLLSLHVKQDIISHISKYSVEKFNEYDTSVYSSWLTNDMNLIEGNGFGNLFQSIQIITDPLFSIIALIKFHWTFVPLILLMTVLTIFLPQLVRKQLATSNLSMTKANANVLDIINDCLRGFSTLSVFGVEYQLERRITASMLKMIKVKVHQAKISTFATCIAQVSNIIAQMLILLWTGLLIFRHMVTIGVFSSASNLSFNVFNSLAAAAPILTELRSLDPVFEKYHLNENTNTINNSNNVRVDKYAEISDPIDVDAKELQVSYQDNKSVFAEPLTFSITAGEKVAICGDSGSGKSTLLRLISGQLREYRGSLRLNKLEMQKISYSAIRDKVIYVDQSPYLFNDTIRYNLELGQKFTKKELTAALEKSDLLDFVNQLPQKLDTSVGEGGTSLSGGQKQRLALARGLLRKKEIFLFDESTSSLDKNSALKVENDFLSQPDITVLFVSHQIHSENKNKFDQIIYV
SIO_010081: DLD54_RS08785
subclass of: SO_0000673
so part of: DLD54_RS08785
location: 5732..7360
location: region:5732-7360:1
so has part: feature:5732-7360:1:exon

WP_109919036.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5732-7360:1:exon

DLD54_RS08790
type: Gene
subclass of: SO_0000704
RO_0002162: 1218494
locus tag: DLD54_RS08790
old locus tag: DLD54_08790
so part of: sequence
location: complement(7377..7865)
location: region:7377-7865:-1
so has part: feature:7377-7865:-1:exon
subclass of: SO_0000010

78130151
type: Gene
SIO_000068: ncbigene

position:7377:-1
position: 7377
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7865:-1
position: 7865
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7377-7865:-1:exon

DLD54_RS08790
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1218494
locus tag: DLD54_RS08790
old locus tag: DLD54_08790
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: helix-turn-helix transcriptional regulator
translation: MQKTIKQLADELHVSKQTIRYHLKSLPVNFTGKDNKNRITVNAIGARLIKEKVVNKSGNVTGKKVQQKSSLPVNDNEQLKLLLQRIDTLEQTYHEQLLSKDQEIARLHDTLDQTQKLLNQSQQLQLMAEKKINKLKEISSNKTNKRASRKKGWWHLIINRND
SIO_010081: DLD54_RS08790
subclass of: SO_0000673
so part of: DLD54_RS08790
location: complement(7377..7865)
location: region:7377-7865:-1
so has part: feature:7377-7865:-1:exon

WP_109919037.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7377-7865:-1:exon

DLD54_RS08795
type: Gene
subclass of: SO_0000704
RO_0002162: 1218494
locus tag: DLD54_RS08795
old locus tag: DLD54_08795
so part of: sequence
location: 9936..10544
location: region:9936-10544:1
so has part: feature:9936-10544:1:exon
subclass of: SO_0000010

78130152
type: Gene
SIO_000068: ncbigene

position:9936:1
position: 9936
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10544:1
position: 10544
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9936-10544:1:exon

DLD54_RS08795
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1218494
locus tag: DLD54_RS08795
old locus tag: DLD54_08795
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005722279.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKFKYVVGLGVAAATFATVATPLAVTSVKAEATSDSVESPVSKYDINPVANYDNDSLRQIAINNNLDLSVVEALNDNIDPDKALPNGTPIYLPQNVGSVENVVGPQAFGPYDGVPASIKKKYYDSLSSAERSAKLWIAKRESGYNYYVSNGTHYGRFQLDKAYLNGDYSIANQEKAATIYIHKRYSGSWVKAKAFWQAHGWY
SIO_010081: DLD54_RS08795
subclass of: SO_0000673
so part of: DLD54_RS08795
location: 9936..10544
location: region:9936-10544:1
so has part: feature:9936-10544:1:exon

WP_038521159.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:9936-10544:1:exon

DLD54_RS08800
type: Gene
subclass of: SO_0000704
RO_0002162: 1218494
locus tag: DLD54_RS08800
old locus tag: DLD54_08800
so part of: sequence
location: 10566..11207
location: region:10566-11207:1
so has part: feature:10566-11207:1:exon
subclass of: SO_0000010

78130153
type: Gene
SIO_000068: ncbigene

position:10566:1
position: 10566
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:11207:1
position: 11207
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10566-11207:1:exon

DLD54_RS08800
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1218494
locus tag: DLD54_RS08800
old locus tag: DLD54_08800
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: MKRSLSIAAFAAVFGASLIFSATSSNYVPVKAADVSDTNTVVNNQGVSDKTWSNKLTKAGYVFKLAKNIATTDGGLYQRKNGLLKKYSLKHAKKVFAKNMLFKIDRAISVENGSLVHIVSQNGKYKFWTNFLTGTYNVNGHKKSLKPLIKTEVEMITNTSKEKIAKKLVTAEKLANKLKGSDKKLAQESITQLKQWIDNEVFANIPVLLIGSL
SIO_010081: DLD54_RS08800
subclass of: SO_0000673
so part of: DLD54_RS08800
location: 10566..11207
location: region:10566-11207:1
so has part: feature:10566-11207:1:exon

WP_038521162.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:10566-11207:1:exon