[modeller_usage] Advice on best template for Modelling

[KEVIN KARIUKI WAMAE <>]

Hi..I am trying to model two proteins (Plasmodium reticulocyte-binding protein homologue 4 and 5). From Literature review, I have found out that the protein "Py235 of P.yoelii" (http://www.rcsb.org/pdb/explore/explore.do?structureId=3HGF) is the closest there is to finding a template theoretically.

Attached are the alignments that have been generated by MODELLER, and visually I could detect so many gaps.

From the tutorials in the MODELLER website, i saw tutorial number 4 "Difficult Modeling. Model a sequence based on a low identity to a template" that employs the use of mGenThreader.

Is this the best option? Please assist.

Regards....kevinkariuki

 _aln.pos         10        20        30        40        50        60
3GFHA     ---------------------------P---------------------------------------- 
PfRh4     MNKNILWITFFYFLFFLLDMYQGNDAIPSKEKKNDPEADSKNSQNQHDINKTHHTNNNYDLNIKDKDE 
 _consrvd                            *

 _aln.p   70        80        90       100       110       120       130
3GFHA     ---------------MVK---------------------------------------EIE-------- 
PfRh4     KKRKNDNLINNYDYSLLKLSYNKNQDIYKNIQNGQKLKTDIILNSFVQINSSNILMDEIENYVKKYTE 
 _consrvd                  *                                       ***

 _aln.pos  140       150       160       170       180       190       200
3GFHA     -------------------------------------------------------------------- 
PfRh4     SNRIMYLQFKYIYLQSLNITVSFVPPNSPFRSYYDKNLNKDINETCHSIQTLLNNLISSKIIFKMLET 
 _consrvd

 _aln.pos    210       220       230       240       250       260       270
3GFHA     -----------KKI-------EN--------------------------------------------- 
PfRh4     TKEQILLLWNNKKISQQNYNQENQEKSKMIDSENEKLEKYTNKFEHNIKPHIEDIEKKVNEYINNSDC 
 _consrvd            ***       **

 _aln.pos      280       290       300       310       320       330       340
3GFHA     -----------------IVT------------------------------------------------ 
PfRh4     HLTCSKYKTIINNYIDEIITTNTNIYENKYNLPQERIIKNYNHNGINNDDNFIEYNILNADPDLRSHF 
 _consrvd                  * *

 _aln.pos        350       360       370       380       390       400
3GFHA     -------------------------------KIDKKKYI----------------------------- 
PfRh4     ITLLVSRKQLIYIEYIYFINKHIVNKIQENFKLNQNKYIHFINSNNAVNAAKEYEYIIKYYTTFKYLQ 
 _consrvd                                *    ***

 _aln.p  410       420       430       440       450       460       470
3GFHA     -------------------------------------------------------------------- 
PfRh4     TLNKSLYDSIYKHKINNYSHNIEDLINQLQHKINNLMIISFDKNKSSDLMLQCTNIKKYTDDICLSIK 
 _consrvd

 _aln.pos  480       490       500       510       520       530       540
3GFHA     ---------------------------------------------YDN-------------------- 
PfRh4     PKALEVEYLRNINKHINKNEFLNKFMQNETFKKNIDDKIKEMNNIYDNIYIILKQKFLNKLNEIIQNH 
 _consrvd                                              ***

 _aln.pos    550       560       570       580       590       600       610
3GFHA     ---------------MKKLLNEIAEI------------------------------------------ 
PfRh4     KNKQETKLNTTTIQELLQLLKDIKEIQTKQIDTKINTFNMYYNDIQQIKIKINQNEKEIKKVLPQLYI 
 _consrvd                   **  * **

 _aln.pos      620       630       640       650       660       670       680
3GFHA     -------------------------------------------------------------------- 
PfRh4     PKNEQEYIQIYKNELKDRIKETQTKINLFKQILELKEKEHYITNKHTYLNFTHKTIQQILQQQYKNNT 
 _consrvd

 _aln.pos        690       700       710       720       730       740
3GFHA     -EKD---------------------------------------------------------------- 
PfRh4     QEKNTLAQFLYNADIKKYIDELIPITQQIQTKMYTTNNIEHIKQILINYIQECKPIQNISEHTIYTLY 
 _consrvd  **

 _aln.p  750       760       770       780       790       800       810
3GFHA     ---KTSLEEV----------------------------------KNIN-------------------- 
PfRh4     QEIKTNLENIEQKIMQNIQQTTNRLKINIKKIFDQINQKYDDLTKNINQMNDEKIGLRQMENRLKGKY 
 _consrvd    ** **                                    ****

 _aln.pos  820       830       840       850       860       870       880
3GFHA     ------------MSY------------------G---------------------------------- 
PfRh4     EEIKKANLQDRDIKYIVQNNDANNNNNNIIIINGNNQTGDYNHILFDYTHLWDNAQFTRTKENINNLK 
 _consrvd               *                  *

 _aln.pos    890       900       910       920       930       940       950
3GFHA     -------------------------------------------------------------------- 
PfRh4     DNIQININNIKSIIRNLQNELNNYNTLKSNSIHIYDKIHTLEELKILTQEINDKNVIRKIYDIETIYQ 
 _consrvd

 _aln.pos      960       970       980       990      1000      1010      1020
3GFHA     -------------------------------------KSLNKLFLE---------------K------ 
PfRh4     NDLHNIEEIIKNITSIYYKINILNILIICIKQTYNNNKSIESLKLKINNLTNSTQEYINQIKAIPTNL 
 _consrvd                                      **   * *                *

 _aln.pos       1030      1040      1050      1060      1070      1080
3GFHA     ----IKKKS----------------------------------------------------------- 
PfRh4     LPEHIKQKSVSELNIYMKQIYDKLNEHVINNLYTKSKDSLQFYINEKNYNNNHDDHNDDHNDVYNDIK 
 _consrvd     ** **

 _aln.p 1090      1100      1110      1120      1130      1140      1150
3GFHA     -------------------------------------------------------------------- 
PfRh4     ENEIYKNNKLYECIQIKKDVDELYNIYDQLFKNISQNYNNHSLSFVHSINNHMLSIFQDTKYGKHKNQ 
 _consrvd

 _aln.pos 1160      1170      1180      1190      1200      1210      1220
3GFHA     ------ENMIKSME--------------------KY-------------------------------- 
PfRh4     QILSDIENIIKQNEHTESYKNLDTSNIQLIKEQIKYFLQIFHILQENITTFENQYKDLIIKMNHKINN 
 _consrvd       ** **  *                    **

 _aln.pos   1230      1240      1250      1260      1270      1280      1290
3GFHA     -------------------------------------------------------------------- 
PfRh4     NLKDITHIVINDNNTLQEQNRIYNELQNKIKQIKNVSDVFTHNINYSQQILNYSQAQNSFFNIFMKFQ 
 _consrvd

 _aln.pos     1300      1310      1320      1330      1340      1350      1360
3GFHA     ---------------------------------IKD------------------LDEIK--------- 
PfRh4     NINNDINSKRYNVQKKITEIINSYDIINYNKNNIKDIYQQFKNIQQQLNTTETQLNHIKQNINHFKYF 
 _consrvd                                  ***                  *  **

 _aln.pos       1370      1380      1390      1400      1410      1420
3GFHA     -------------------------------------------------------------------- 
PfRh4     YESHQTISIVKNMQNEKLKIQEFNKKIQHFKEETQIMINKLIQPSHIHLHKMKLPITQQQLNTILHRN 
 _consrvd

 _aln.p 1430      1440      1450      1460      1470      1480      1490
3GFHA     EQSPKA-----------EMN------------------------------------------------ 
PfRh4     EQTKNATRSYNMNEEENEMGYGITNKRKNSETNDMINTTIGDKTNVLKNDDQEKGKRGTSRNNNIHTN 
 _consrvd **   *           **

 _aln.pos 1500      1510      1520      1530      1540      1550      1560
3GFHA     -------------------------------------------------------------------- 
PfRh4     ENNINNEHTNENNINNEHTNEKNINNEHANEKNIYNEHTNENNINYEHPNNYQQKNDEKISLQHKTIN 
 _consrvd

 _aln.pos   1570      1580      1590      1600      1610      1620      1630
3GFHA     -------------------------------------------------------------------- 
PfRh4     TSQRTIDDSNMDRNNRYNTSSQQKNNLHTNNNSNSRYNNNHDKQNEHKYNQGKSSGKDNAYYRIFYAG 
 _consrvd

 _aln.pos     1640      1650      1660      1670      1680      1690      1700
3GFHA     -----------T-------------------------------------------------------- 
PfRh4     GITAVLLLCSSTAFFFIKNSNEPHHIFNIFQKEFSEADNAHSEEKEEYLPVYFDEVEDEVEDEVEDED 
 _consrvd            *

 _aln.pos       1710
3GFHA     ---------------- 
PfRh4     ENENEVENENEDFNDI 
 _consrvd

 _aln.pos         10        20        30        40        50        60
3GFHA     ------------------------------------------PM---------V---KEIEKKI---- 
PfRh5     MIRIKKKLILTIIYIHLFILNRLSFENAIKKTKNQENNLTLLPIKSTEEEKDDIKNGKDIKKEIDNDK 
 _consrvd                                           *              * * * *

 _aln.p   70        80        90       100       110       120       130
3GFHA     ENIVT--KIDKKKYIYDNMKK-------------------------------LLNE------------ 
PfRh5     ENIKTNNAKDHSTYIKSYLNTNVNDGLKYLFIPSHNSFIKKYSVFNQINDGMLLNEKNDVKNNEDYKN 
 _consrvd *** *    *   **                                     ****

 _aln.pos  140       150       160       170       180       190       200
3GFHA     -------------------------------------------------------------------- 
PfRh5     VDYKNVNFLQYHFKELSNYNIANSIDILQEKEGHLDFVIIPHYTFLDYYKHLSYNSIYHKSSTYGKCI 
 _consrvd

 _aln.pos    210       220       230       240       250       260       270
3GFHA     ---------------------------IAEIEK------------------------DKT-----SLE 
PfRh5     AVDAFIKKINETYDKVKSKCNDIKNDLIATIKKLEHPYDINNKNDDSYRYDISEEIDDKSEETDDETE 
 _consrvd                            ** * *                        **        *

 _aln.pos      280       290       300       310       320       330       340
3GFHA     EVKN-----------------------------------------------------INM-SYG---- 
PfRh5     EVEDSIQDTDSNHTPSNKKKNDLMNRTFKKMMDEYNTKKKKLIKCIKNHENDFNKICMDMKNYGTNLF 
 _consrvd **                                                         *  **

 _aln.pos        350       360       370       380       390       400
3GFHA     ---------------------------------KSLNKLFLE--KIKKKSE----NMIKSMEKYI--- 
PfRh5     EQLSCYNNNFCNTNGIRYHYDEYIHKLILSVKSKNLNKDLSDMTNILQQSELLLTNLNKKMGSYIYID 
 _consrvd                                  * ***       *   **    *  * *  **

 _aln.p  410       420       430       440       450       460       470
3GFHA     -------------------------------------------KD------LD--------------- 
PfRh5     TIKFIHKEMKHIFNRIEYHTKIINDKTKIIQDKIKLNIWRTFQKDELLKRILDMSNEYSLFITSDHLR 
 _consrvd                                            **      **

 _aln.pos  480       490       500       510       520
3GFHA     ----------E----------------------IK---EQSPKAEMN-T- 
PfRh5     QMLYNTFYSKEKHLNNIFHHLIYVLQMKFNDVPIKMEYFQTYKKNKPLTQ 
 _consrvd           *                      **    *  *     *