[modeller_usage] RE : help with residues numbering
To: <>
Subject: [modeller_usage] RE : help with residues numbering
From: "BESSADOK Anis" <>
Date: Fri, 27 Feb 2009 12:43:15 +0100
Hi all,
I'm a new user of modeller, I want to know how to conserve residue numbering between my target sequence and the MODEL?
I will try to build a final Model using two parts of my protein sequence but I want to conserve the numbering.
One of my alignment files looks like this:
>P1;2hydA
structureX:2hydA:1:A:578:::::
----------------------------------------------MIKRYLQFVKPYKY
RIFATIIVGIIKFGIPMLIPLLIKYAIDGVINNHA----------------LTTDEKVHH
LTIAIGIALFIFVIVRPPIEFIRQYLAQWTSNKILYDIRKKLYNHLQALSARFYA--NNQ
VGQVISRVINDVEQTKDFILTGLMNIWLDCITIIIALSIMFFLDVKLTLAALFIFPFYIL
TVYVFFGRLRKLTRERSQALAEVQGFLHERVQGISVVKSFAIEDNEAKNFDKKNTNFLTR
ALKHTRWNAYSFAAINTVTDIGPIIVIGVGAYLAISGSITVGTLAAFVGYLELLFGPLRR
LVASFTTLTQSFASMDRVFQLIDEDYDIKNG-VGAQPIEIKQGRIDIDHVSFQYNDN-EA
PILKDINLSIEKGETVAFVGMSGGGKSTLINLIPRFYDVTSGQILIDGHNIKDFLTGSLR
NQIGLVQQDNILFSDTVKENILLG-RPTATDEE-VVEAAKMANAHDFIMNLPQGYDTEVG
ERGVKLSGGQKQRLSIARIFLNNPPILILDEATSALDLESESIIQEALDVLSKDRTTLIV
AHRLSTITHADKIVVIENGHIVETGTHRELIAKQGAYEHLYSIQNL----*
>P1;1pgp
sequence:1pgp:43: :630:::::
--------------------------------------------SNWLDKLYMVVGTLAA
IIHGAGLPLMMLVFGEMTDIFANAGNLEDLMSNITNRSDINDT---GFFMNLEEDMTR--
----YAYYYSGIGAGVLVAAYIQVSFWCLAAGRQIHKIRKQFFHAIMRQEIGWFD--VHD
VGELNTRLTDDVSKINEGIGDKIGMFFQSMATFFTGFIVGFTRGWKLTLVILAISPVLGL
SAAVWAKILSSFTDKELLAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNKNLEEAKRI
GIKKAITANISIGAAFLLIYASYALAFWYGTTLVLSGEYSIGQVLTVFFSVLIGAFSVGQ
ASPSIEAFANARGAAYEIFKIIDNKPSIDSYSKSGHKPDNIKGNLEFRNVHFSYPSRKEV
KILKGLNLKVQSGQTVALVGNSGCGKSTTVQLMQRLYDPTEGMVSVDGQDIRTINVRFLR
EIIGVVSQEPVLFATTIAENIRYGREN--VTMDEIEKAVKEANAYDFIMKLPHKFDTLVG
ERGAQLSGGQKQRIAIARALVRNPKILLLDEATSALDTESEAVVQVALDKARKGRTTIVI
AHRLSTVRNADVIAGFDDGVIVEKGNHDELMKEKGIYFKLVTMQT-----*
Regards,
A
Anis
PhD Student
iBiTec-S/SB2SM
Laboratoire Stress oxydant et Détoxication
CEA-SACLAY, 91191 Gif-sur-Yvette cedex
e-mail:
Tel (33)1-69084432, Fax (33)1-69088717