LOCUS DS499576 3644 bp DNA linear CON 16-SEP-2013
DEFINITION Alistipes putredinis DSM 17216 Scfld_02_6 genomic scaffold, whole
genome shotgun sequence.
ACCESSION DS499576 ABFK02000000
VERSION DS499576.1
DBLINK BioProject: PRJNA19655
BioSample: SAMN00000002
KEYWORDS WGS.
SOURCE Alistipes putredinis DSM 17216
ORGANISM Alistipes putredinis DSM 17216
Bacteria; Pseudomonadati; Bacteroidota; Bacteroidia; Bacteroidales;
Rikenellaceae; Alistipes.
REFERENCE 1 (bases 1 to 3644)
AUTHORS Sudarsanam,P., Ley,R., Guruge,J., Turnbaugh,P.J., Mahowald,M.,
Liep,D. and Gordon,J.
TITLE Draft genome sequence of Alistipes putredinis (DSM 17216)
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 3644)
AUTHORS Fulton,L., Clifton,S., Fulton,B., Xu,J., Minx,P., Pepin,K.H.,
Johnson,M., Thiruvilangam,P., Bhonagiri,V., Nash,W.E., Mardis,E.R.
and Wilson,R.K.
TITLE Direct Submission
JOURNAL Submitted (23-OCT-2007) Genome Sequencing Center, Washington
University School of Medicine, 4444 Forest Park, St. Louis, MO
63108, USA
COMMENT Alistipes putredinis (GenBank Accession Number for 16S rDNAgene:
L16497) is a member of the Bacteroidetes division of the domain
bacteria and has been isolated from human feces. It has been found
in 16S rDNA sequence-based enumerations of the colonic microbiota
of adult humans (Eckburg et. al.(2005), Ley et. al. (2006)). The
sequenced strain was obtained from Deutsche Sammlung von
Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 17216).
We have collected 11.6X coverage in plasmid end reads and454 reads.
We have performed one round of automated sequence
improvement(pre-finishing), along with manual improvement that
includes breaking apart any mis-assembly, and making manual joins
where possible. Manual edits also are made where the consensus
appears to be incorrect. All low quality data on the ends of
contigs is removed. Contigs are ordered and oriented where
possible.
Sequencing/Assembly: The genomic DNA was purified from liquid
culture derived from a single bacterial colony. A hybrid sequencing
strategy that utilized reads from both 454 GS-20 and ABI 3730xl
sequencers was devised and implemented to generate the draft genome
sequences. 454 reads were assembled using Newbler (454 Life
Sciences) into 454 de novo contigs. These de novo contigs were
converted in silico to 800 base paired reads ('superreads') with
400 base overlaps with neighboring superreads. Finally, PCAP
(Huang, et al, Genome Research, 13:2164, (2003)) was used to
assemble the super-reads and the conventional 3730xl capillary
reads.
This sequenced strain is part of a comprehensive, sequence-based
survey of members of the normal human gut microbiota. A joint
effort of the WU-GSC and the Center for Genome Sciences at
Washington University School of Medicine, the purpose of this
survey is to provide the general scientific community with a broad
view of the gene content of 100 representatives of the major
divisions represented in the intestine's microbial community. This
information should provide a frame of reference for analyzing
metagenomic studies of the human gut microbiome. Further details of
this effort are described in a white paper entitled 'Extending Our
View of Self: the Human Gut Microbiome Initiative (HGMI)'
(http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMIS
eq.pdf). These studies are supported by National Human Genome
Research Institute.
For answers to your questions regarding this assembly or project,
or any other GSC genome project, please visit our Genome Groups web
page (http://genome.wustl.edu/genome_group_index.cgi) and email the
designated contact person.
FEATURES Location/Qualifiers
source 1..3644
/organism="Alistipes putredinis DSM 17216"
/mol_type="genomic DNA"
/strain="DSM 17216"
/type_material="type strain of Bacteroides putredinis"
/db_xref="taxon:445970"
gene complement(<1..132)
/locus_tag="ALIPUT_00021"
CDS complement(<1..132)
/locus_tag="ALIPUT_00021"
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="EDS04820.1"
/translation="MKKLHHIVLVLALAATLFTGCNKDEGVTPRPPVPETADQTIMFY
"
gene complement(310..1047)
/locus_tag="ALIPUT_00022"
CDS complement(310..1047)
/locus_tag="ALIPUT_00022"
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="EDS04821.1"
/translation="MRKLLVLLLFLPLMATAKIPVEEDIIRQTLDSESPYYYPNLMLR
YQSGDDSMTEEDYHYLYYGYAYQDAYKPLNANSDMDKAILIAQTVDFENPTHESLEKL
IAAVNDALVQDPFSPKLLNLLAFAYGALGDSKNEQINYNRMNSILATIEDSGNGLKEG
SAWHILMFGHALDLLAAHDRHYGKARVVSRSVEYVPLLEPVRTEEGRIKGYYFDYSRI
YRNKPDDYVFKRPRTWQFNNLRPREYK"
gene complement(1127..1579)
/locus_tag="ALIPUT_00023"
CDS complement(1127..1579)
/locus_tag="ALIPUT_00023"
/inference="protein motif:Gene3D:IPR013785"
/inference="protein motif:HMMPanther:IPR002220"
/inference="protein motif:HMMPfam:IPR002220"
/inference="similar to AA sequence:REFSEQ:YP_001300553.1"
/note="KEGG: bfs:BF2486 5.5e-28 dapA2; putative
dihydrodipicolinate synthase K01714;
COG: COG0329 Dihydrodipicolinate
synthase/N-acetylneuraminate lyase"
/codon_start=1
/transl_table=11
/product="dihydrodipicolinate synthetase family"
/protein_id="EDS04822.1"
/db_xref="InterPro:IPR002220"
/db_xref="InterPro:IPR013785"
/translation="MTAATTIRIAGDFPNVIGIKEASGKIDQIQEILDWRSRDFLVLS
GDDALTLDLMSRGADGVISVAVNAFPRKMMTCIDLAKKGDFEGAHKAYECLEEAVTAL
FAEGNPTGVKCAMSVLGLIGNTLRLPLVPGTPQLEARFKELIAKYDLN"
gene complement(1702..1899)
/locus_tag="ALIPUT_00024"
CDS complement(1702..1899)
/locus_tag="ALIPUT_00024"
/note="KEGG: bfs:BF3862 0.0034 dapA1; putative
dihydrodipicolinate synthase K01714;
Psort location: Cytoplasmic, score: 8.96"
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="EDS04823.1"
/translation="MWISSCNSARRQNPDPLPARTGRCRHVHQNHIAGRVPLVIGVGG
NSTSEVLDQLREFDRGGRMRS"
gene complement(2368..3339)
/locus_tag="ALIPUT_00019"
CDS complement(2368..3339)
/locus_tag="ALIPUT_00019"
/inference="protein motif:HMMPfam:IPR001357"
/inference="protein motif:HMMSmart:IPR001357"
/inference="protein motif:superfamily:IPR010994"
/inference="similar to AA sequence:INSD:ABR40932.1"
/note="KEGG: bfs:BF2485 1.1e-54 ligA, dnaL, lig, lop,
pdeC; putative DNA ligase K01972;
COG: COG0272 NAD-dependent DNA ligase (contains BRCT
domain type II);
Psort location: Cytoplasmic, score: 8.96"
/codon_start=1
/transl_table=11
/product="BRCA1 C-terminal domain protein"
/protein_id="EDS04824.1"
/db_xref="InterPro:IPR001357"
/db_xref="InterPro:IPR010994"
/translation="MDIEGLGEETVELLFENGLLHDIADLYDLRAEQLACLPRLGEKS
AENIIRSIRGSVEVPFQRVLFALGIRFVGETTAKYLAAHFRTLDAVMHATREELIEAD
EVGGKIADAIIDYFADAENLRIIERLRKAGLQTEAAHKALESESLAGKNFVITGRFSG
HSRDELKELIEAHGGKNLAGVSGNVEFLVAGKKIGPGKIQKATQLGVRLIPEEELLAM
NASGGTLPVTKKSFRREHLCGPPPRLRETTDKNDGGGHGKRGRCFLGGNGTPRGRENT
QYYFPGACPGHRNNDVEIRIIRTNPFSLLRSPGFWAGSFPLLPKRKF"
gene 3358..>3644
/locus_tag="ALIPUT_00020"
CDS 3358..>3644
/locus_tag="ALIPUT_00020"
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="EDS04825.1"
/translation="MDDAAQYLRPAVALIGTVVLAFALVFHQRSAAFRTAGDVLEGTA
VRRTGRKIDARDLGDDLAAFFDIYHIAYANVQQGDLFGVVQRGPNPPQCELA"
CONTIG join(ABFK02000014.1:1..2106,gap(unk100),ABFK02000013.1:1..1438)
//