LOCUS KHJ47473.1 1591 aa PRT CON 17-DEC-2014
DEFINITION Trichuris suis Rap/ran-GAP protein.
ACCESSION KN538379-229
PROTEIN_ID KHJ47473.1
SOURCE Trichuris suis (pig whipworm)
ORGANISM Trichuris suis
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Enoplea; Dorylaimia;
Trichinellida; Trichuridae; Trichuris.
REFERENCE 1 (bases 1 to 2343098)
AUTHORS Mitreva,M.
TITLE Draft genome of Trichuris suis
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 2343098)
AUTHORS Mitreva,M., Pepin,K.H., Abubucker,S., Martin,J., Minx,P.,
Warren,C., Palsikar,V.B., Zhang,X., Rosa,B.A. and Wilson,R.K.
TITLE Direct Submission
JOURNAL Submitted (27-JAN-2014) The Genome Institute, Washington University
School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA
COMMENT Trichuris suis contaminated a dirt lot located at the USDA,
Agricultural Research Service, Beltsville Agricultural Research
Center, Animal Parasitic Disease Laboratory in Beltsville, MD since
the early 1960s. Adult worms were isolated for passage from pigs
placed on the lot and naturally infected. The T. suis adults were
manually removed from the cecum and proximal colon tissue and
cultured in vitro to release fertilized eggs that were removed
after 24-48 hours and embryonated to an infective stage (Hill et
al., Experimental Parasitology 77, 170-178, 1993). The strain has
been actively passed in pigs one to two times per year since that
time and characterized for pathogenesis in pigs (Mansfield and
Urban, Veterinary Immunology and Immunopathology 50, 1-17, 1996).
This strain of T. suis has also been used therapeutically in human
subjects with inflammatory bowel disease (Trichuris suis therapy in
Crohn's disease. Summers RW, Elliott DE, Urban JF Jr, Thompson R,
Weinstock JV. Gut. 2005 Jan;54(1):87-90. The Genome Institute
collaborators that provided material for the genome/transcriptome
sequencing are: USDA - Urban, Jr., J.F., Hill, D. E. and Michigan
State University - Mansfield L.S.
The repeat library was generated using Repeatmodeler (A. Smit, R.
Hubley http://www.systemsbiology.org/). The Ribosomal RNA genes
were identified using RNAmmer
((http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?rnammer ) and
transfer RNA's were identified with tRNAscan-SE (Lowe and Eddy,
1997). Non-coding RNAs, such as microRNAs, were identified by
sequence homology search of the Rfam database
(http://selab.janelia.org/software.html). Repeats and predicted
RNA's were then masked using RepeatMasker (A. Smit, R. Hubley & P.
Green http://repeatmasker.org). Protein-coding genes were predicted
using a combination of ab initio programs Snap (I. Korf, 2004),
Fgenesh (Softberry, Corp) and Augustus (M. Stanke, et. Al 2008) and
the annotation pipeline tool Maker (M. Yandell et. al., 2007) which
aligns mRNA, EST and protein information from same species or
cross-species to aid in gene structure determination and
modifications. A consensus gene set from the above prediction
algorithms was generated, using a logical, hierarchical approach
developed at the Genome institute. Gene product naming was
determined by BER (JCVI: http://ber.sourceforge.net).
Our goal is to explore this WGS draft sequence of Trichuris suis to
better define proteins involved in nematode parasitism that impact
health and disease and are relevant to both host-parasite
relationships and basic biological processes.
For information 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. For specific questions regarding the
Trichuris suis genome project contact Makedonka Mitreva
(mmitreva@genome.wustl.edu) at Washington University School of
Medicine. The National Human Genome Research Institute (NHGRI) of
the National Institutes of Health (NIH) provided funds for this
project.
##Genome-Assembly-Data-START##
Finishing Goal :: High-Quality Draft
Current Finishing Status :: High-Quality Draft
Assembly Method :: ALLPATHS_LG v. 2012-11-02
Assembly Name :: T_suis_1.0.allpaths
Genome Coverage :: 392x
Sequencing Technology :: Illumina
##Genome-Assembly-Data-END##
FEATURES Qualifiers
source /organism="Trichuris suis"
/mol_type="genomic DNA"
/submitter_seqid="T_suis-1.0_Cont4"
/isolation_source="cecum and proximal colon of infected
animals which were naturally infected"
/host="Sus scrofa (pig)"
/db_xref="taxon:68888"
/chromosome="Unknown"
/dev_stage="adult"
/country="USA: Beltsville, MD"
protein /locus_tag="D918_02333"
/inference="protein motif:HMMPfam:IPR000331"
/note="KEGG: edi:EDI_016520 3.7e-09 rap GTPase-activating
protein"
/db_xref="InterPro:IPR000331"
intron_pos 88:0 (1/2)
intron_pos 705:0 (2/2)
BEGIN
1 MGISINILRN APHRFKPQRG LIFLAICGEE SSADKEGPIY VNFATSALQR YQFAELVPEE
61 KLSPKQIYNA QFLSPHVINV GNVYIDREIC EHPGYRVLSV TSSANEECQF YSRNVQALPV
121 AVQTKRIASK AMITQSFMEK ALEFISSDFT KVLWPKQGRE FKQICCLRCL IDSVYSHYVA
181 LCCPSVQYFN IDTVAKSVSF DPFCESEQSI AIPCGQQYAD EGDEYRRICV HVLIRWIALY
241 ASSYKHSTAG EETMNASDCS FVGAQKTNSI VDSFSPLKSA ESPRLPSNYS LVRKTLLTYL
301 PLCSRTYSIL RESFLLPLNH VGTIARVFRV LREWLLQQGE EEESQSTEAT SDVVSFRMHT
361 SHGMKLAIVI LVSFFDSPYL NFTNDFAQQN TTLVAQICVR ILTLFKHLAC SGSAFRISQD
421 TWHFLLKALL HIVHRVLPPL PADCSPVSTI VASQIYQTLL VTWVFASLNA PLPVQLWDNL
481 VDTCQKRTDW SALVFEWGKV MESITRALAL EVYSVDLLDP PLERPVEHRL KQKQALARQL
541 FKSVTQESGT SMFSSDTDSP SAKNSQELNS QQNPLSLLLS NSSRRQSEHP LAICFTVQNS
601 SDLVIELPSQ KSPSNASNCC CDSLNEAAEH LREAESAIEC LAEEVAISED SDSYDSGSAQ
661 FCSAESNSIA GMKSMLLSED ILTESTIMST NDADTVSDEF SYSQEVEQPS AQSMPQRIAL
721 LSEQDGGNGS GTAPEALGVV WKRILCCLGD VNRVTSAEIH VHMMEVIRSV LSLLVKIRNN
781 QDSCPSLVPP TVLLIPWLSE TLRLPEPFAA SRMIATRLYC FLLSQRRDIP LSDVTIADFF
841 CIASSILTGR EDALINTFLV SCSTSLVREL WPSCLLLLPD LVAASARIMK LATMDCVDSV
901 DKVNVVHFVG SVVLLAPHRP TFPTCQDSQK VMDSNMLQVE IFRCLVNSLH SDSVNDGDDR
961 LSTALALRGL SVLLHSLLRN TKLNGIVEGC FETILNYFAC NACSFSSIVC QLLNSLFPFC
1021 RDLSENHFRL MRHLFSVYNA AAEQLLGKES VNETEKKEVV ALLERICNDL VEWLLLIPAL
1081 VVGSYVGQEP PPLLSVLRLA ELLMMYRQRC VKANVDSGQG IVLEDYFQVL SISLFAILNC
1141 CFDQKTFYAY PAVTPSEIEQ LFGVGSRQKK FIIAKLSHLP GHSEDKLQTV MCSRTVVGQH
1201 LWKVRRLKLQ SRWKSAANEW LHDSVVNFQD KSFRTPPEEF CRFPDDQQVD NHTMDYSSEK
1261 HHCPLNCLID YLHQFCIDCL PSPSRLSCDG YYSDYVPSKA NYQTCDRKLV TGTTLLVEVG
1321 SSKFDAFDLA FSNSVMSLSC LDNLDDVVLL DQTQQAERHF RHIDGTASRE LHKIAVIYVA
1381 AGQEDKQSIL ENRDGSPRFE EFVSGLGWQV ELRTHSGYAG GLPTEGTIPY YCTPLIEVVF
1441 HVSTRLSCEE ITRKLRHIGN DEVHIVWSEH WRDYRRSIIP TEFCDVLIVI YPLADDLFRI
1501 QIDYDDTEID EFGPLFNDAI VHWSVLACLV RSTAINASRL KRRSISGYRN AHHLRLTSIS
1561 EMLKEAPHPT SLSHILTNLY SPIVPTLSTL C
//