LOCUS KHJ47435.1 1022 aa PRT CON 17-DEC-2014
DEFINITION Trichuris suis zinc carboxypeptidase protein.
ACCESSION KN538379-191
PROTEIN_ID KHJ47435.1
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JOURNAL Unpublished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_02295"
/inference="protein motif:HMMPfam:IPR000834"
/note="KEGG: dme:Dmel_CG32627 5.4e-68 CG32627 gene product
from transcript CG32627-RA"
/db_xref="InterPro:IPR000834"
intron_pos 22:0 (1/19)
intron_pos 37:0 (2/19)
intron_pos 61:1 (3/19)
intron_pos 113:1 (4/19)
intron_pos 155:1 (5/19)
intron_pos 211:1 (6/19)
intron_pos 259:1 (7/19)
intron_pos 339:1 (8/19)
intron_pos 354:0 (9/19)
intron_pos 519:2 (10/19)
intron_pos 565:2 (11/19)
intron_pos 593:0 (12/19)
intron_pos 646:1 (13/19)
intron_pos 729:0 (14/19)
intron_pos 799:1 (15/19)
intron_pos 879:0 (16/19)
intron_pos 918:0 (17/19)
intron_pos 977:0 (18/19)
intron_pos 1011:2 (19/19)
BEGIN
1 MSYRSVLWVL RNHFPRVTFL QLPKYEIPFG GKELLGHCRT PEVITLLARI LIEYINPSSE
61 ESKQRLQLLA KMNGASYLAK SLRSQLQIYD GSAVMNNSLA ALIKVTLLVG GVDGRFYIKV
121 RFGGLLALAA NVIATREGQR CIELLQFLTS VCHSVRGTWL TNYCLGKNAA FLSKHEKFIL
181 FIKSTFKDYA NEEINVIHHC AKLLYLMAKP KSTRLILVTN GIVQSVMELF QAFFAKEEEN
241 AWTVCMAALG TVRLLTSTMA GRQTLVECNG LTIFREAVKS FNVAEQSNRN CSFLYHAMSS
301 LCLRCLPMCS LPVDSVEHPI TVHLPVTRTD HTPADILSDS EEELSIAAGF LTDTDDETMV
361 VQKPGLEGPP TRLKLFQSEM HLYRFLCREL EFGMDENTES ASQANHDVDE AVEFNDTIRK
421 CLPRRRRNSL SEVSGLRFSI HKKDESDAEK ALYASLGRRA SLDSGPRPDP VWYSWMDYVF
481 QAASTHSVYQ FVTIAFPDYH GLYPNLSRQR LKFCPNTLLE MLEPLIDRVE VESFPAKVVY
541 DLDALLKQPK TELPAHSLLS DDLIRLGKVD AHTTSLKFES RFESGNLRKA IQVGPYEYDL
601 ILTPDTNQIN EYFHTFYFKV WNMVSNVPYT FNIINCVKTR SLYNSGMQPV VFSVTEALLG
661 RPGWVRSGRS CVYYRNFYSR SHAKVVARSK APQTITSYYT ASFTVHFRHA YDMCYFAYHY
721 PYTYTMLKTH LVKLSHLLSC VSDVRFRIDT LCRSIAGNPV KLLTITNAAC RTTLQERDVI
781 VISSRVHPGE SNSSWMMHGL LNYLVSPQPR ACLARSLFIF KIIPMLNVDG VVNGNHRCSL
841 AGEDLNRQWV HPDKSLFPSV YHTKNLIGYL HHIGKTPLVY CDFHGHSRKK NIFAYGNNPN
901 LSWYSGDRKS QHQFEFYQLP EILDDISPAF HLKYCSFDIK KNKEGSARVA VWRDTSLCRA
961 YTMEASYAGF DHGPYEGYQM TTKDLIEMGE KFIDALVCLK ESIRNNEMAT RKFELGSKNS
1021 KK
//