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[GUSDEV] Error with GBParser plugin
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From: Alberto D. <da...@io...> - 2005-08-18 19:18:28
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Hi All,
Our problem to use GBParser with some GenBank (should I say GenPept ?)
entries persist... some entries as the one listed below are probably
causing the problem ... Has anybody been faced to this problem while
trying to load that kind of sequence into GUS ? Meaning it has "SecStr"
and "Region" features that are probably not represented in the GUS
tables (such as suggested by Jeetendra)... the error generated by the
GBParser plugin was posted a couple of days ago by Henrique.
Any tips to help to solve this would be greatly appreciated.
Thanks, Alberto
LOCUS 1WCS_A 641 aa linear INV 21-
NOV-2004
DEFINITION Chain A, A Mutant Of Trypanosoma Rangeli Sialidase
Displaying
Trans- Sialidase Activity.
ACCESSION 1WCS_A
VERSION 1WCS_A GI:58177176
DBSOURCE pdb: molecule 1WCS, chain 65, release Nov 21, 2004;
deposition: Nov 21, 2004;
class: Hydrolase;
source: Mol_id: 1; Expression_system: Escherichia Coli;
Expression_system_strain: Bl21; Organism_scientific:
Trypanosoma
Rangeli;
Exp. method: X-Ray Diffraction.
KEYWORDS .
SOURCE Trypanosoma rangeli
ORGANISM Trypanosoma rangeli
Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
Trypanosoma.
REFERENCE 1 (residues 1 to 641)
AUTHORS Paris,G., Ratier,L., Amaya,M.F., Nguyen,T., Alzari,P.M. and
Frasch,A.C.
TITLE A sialidase mutant displaying trans-sialidase activity
JOURNAL J. Mol. Biol. 345 (4), 923-934 (2005)
PUBMED 15588836
REFERENCE 2 (residues 1 to 641)
AUTHORS Paris,G., Ratier,L., Amaya,M.F., Nguyen,T., Alzari,P.M. and
Frasch,C.
TITLE Direct Submission
JOURNAL Submitted (21-NOV-2004)
COMMENT Revision History:
DEC 15 4 Initial Entry.
FEATURES Location/Qualifiers
source 1..641
/organism="Trypanosoma rangeli"
/db_xref="taxon:5698"
Region join(1..40,341..409)
/region_name="Domain 1"
/note="NCBI Domains"
SecStr 7..16
/sec_str_type="sheet"
/note="strand 1"
SecStr 21..26
/sec_str_type="sheet"
/note="strand 2"
SecStr 28..33
/sec_str_type="sheet"
/note="strand 3"
SecStr 36..40
/sec_str_type="sheet"
/note="strand 4"
Region 41..229
/region_name="Domain 2"
/note="NCBI Domains"
SecStr 41..47
/sec_str_type="sheet"
/note="strand 5"
SecStr 48..58
/sec_str_type="sheet"
/note="strand 6"
SecStr 65..75
/sec_str_type="sheet"
/note="strand 7"
SecStr 80..87
/sec_str_type="sheet"
/note="strand 8"
SecStr 95..107
/sec_str_type="sheet"
/note="strand 9"
SecStr 108..119
/sec_str_type="sheet"
/note="strand 10"
SecStr 132..142
/sec_str_type="sheet"
/note="strand 11"
SecStr 143..148
/sec_str_type="sheet"
/note="strand 12"
SecStr 149..159
/sec_str_type="sheet"
/note="strand 13"
SecStr 160..163
/sec_str_type="sheet"
/note="strand 14"
SecStr 169..172
/sec_str_type="sheet"
/note="strand 15"
SecStr 173..176
/sec_str_type="sheet"
/note="strand 16"
SecStr 177..182
/sec_str_type="sheet"
/note="strand 17"
SecStr 183..190
/sec_str_type="sheet"
/note="strand 18"
SecStr 192..203
/sec_str_type="sheet"
/note="strand 19"
SecStr 205..215
/sec_str_type="sheet"
/note="strand 20"
SecStr 221..224
/sec_str_type="sheet"
/note="strand 21"
Region 230..290
/region_name="Domain 3"
/note="NCBI Domains"
SecStr 234..241
/sec_str_type="sheet"
/note="strand 22"
SecStr 242..252
/sec_str_type="sheet"
/note="strand 23"
SecStr 255..261
/sec_str_type="sheet"
/note="strand 24"
SecStr 267..270
/sec_str_type="sheet"
/note="strand 25"
SecStr 286..289
/sec_str_type="sheet"
/note="strand 26"
Region 291..340
/region_name="Domain 4"
/note="NCBI Domains"
SecStr 291..298
/sec_str_type="sheet"
/note="strand 27"
SecStr 301..310
/sec_str_type="sheet"
/note="strand 28"
SecStr 320..327
/sec_str_type="sheet"
/note="strand 29"
SecStr 330..338
/sec_str_type="sheet"
/note="strand 30"
SecStr 343..353
/sec_str_type="sheet"
/note="strand 31"
SecStr 354..365
/sec_str_type="sheet"
/note="strand 32"
SecStr 366..372
/sec_str_type="sheet"
/note="strand 33"
SecStr 373..376
/sec_str_type="sheet"
/note="strand 34"
SecStr 377..397
/sec_str_type="helix"
/note="helix 1"
Bond bond(400,414)
/bond_type="disulfide"
Region 410..641
/region_name="Domain 5"
/note="NCBI Domains"
SecStr 422..428
/sec_str_type="sheet"
/note="strand 35"
SecStr 430..433
/sec_str_type="sheet"
/note="strand 36"
SecStr 434..437
/sec_str_type="sheet"
/note="strand 37"
SecStr 444..448
/sec_str_type="sheet"
/note="strand 38"
SecStr 449..454
/sec_str_type="sheet"
/note="strand 39"
SecStr 455..460
/sec_str_type="sheet"
/note="strand 40"
SecStr 463..467
/sec_str_type="sheet"
/note="strand 41"
SecStr 468..471
/sec_str_type="sheet"
/note="strand 42"
SecStr 485..495
/sec_str_type="sheet"
/note="strand 43"
SecStr 500..505
/sec_str_type="sheet"
/note="strand 44"
SecStr 506..509
/sec_str_type="sheet"
/note="strand 45"
SecStr 518..524
/sec_str_type="sheet"
/note="strand 46"
SecStr 526..533
/sec_str_type="sheet"
/note="strand 47"
SecStr 545..550
/sec_str_type="sheet"
/note="strand 48"
SecStr 551..557
/sec_str_type="sheet"
/note="strand 49"
SecStr 558..565
/sec_str_type="sheet"
/note="strand 50"
SecStr 566..569
/sec_str_type="sheet"
/note="strand 51"
SecStr 572..576
/sec_str_type="sheet"
/note="strand 52"
SecStr 585..591
/sec_str_type="sheet"
/note="strand 53"
SecStr 603..606
/sec_str_type="sheet"
/note="strand 54"
SecStr 607..614
/sec_str_type="sheet"
/note="strand 55"
SecStr 618..626
/sec_str_type="helix"
/note="helix 2"
ORIGIN
1 aaslapgssr velfkrknst vpfeesngti rervvhsfri ptivnvdgvm
vaiadaryet
61 sfdnsfieta vkysvddgat wntqiaikns rassvsrvvd ptvivkgnkl
yilvgsfnkt
121 rnywtqhrdg sdwepllvvg evtksaangk ttatiswgkp vslkplfpae
fdgiltkefv
181 ggvgaaivas ngnlvypvqi admggrvftk imyseddgnt wkfaegrskf
gcsepavlew
241 egkliinnrv dynrrlvyes sdmgktwvea lgtlshvwtn sptsnqpdcq
ssfvavtieg
301 krvmlfthpl nlkgrwmrdr lhlwmtdnqr ifdvgqisig densgyssvl
ykddklyslh
361 eintndvysl vfvrligelq lmksvvrtwk eednhlasic tpvvpatpps
kgacgaavpt
421 aglvgflshs angsvwedvy rcvdanvana ervpnglkfn gvgggavwpv
arqgqtrryq
481 fanyrftlva tvtidelpkg tspllgagle gpgdakllgl sydknrqwrp
lygaapaspt
541 gswelhkkyh vvltmadrqg svyvdgqpla gsgntvvrga tlpdishfyi
ggprskgapt
601 dsrvtvtnvv lynrrlnsse irtlflsqdm igtdggagta a
//
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