Difference between revisions of "Homology based structure predictions"
From Bioinformatikpedia
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Because we found no homologous structures in Task 2, we extended our list by using HHSearch. |
Because we found no homologous structures in Task 2, we extended our list by using HHSearch. |
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| − | + | HHSearch found just sequences with an indentity below 40% therefore we will use the 12 proteins shown below for creating a multiple alignment for homologous modeling. We choose sequences to cover the whole protein and we pay specific attention on the transmembrane region. |
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Revision as of 13:25, 9 June 2011
Contents
Homologous
Because we found no homologous structures in Task 2, we extended our list by using HHSearch.
HHSearch found just sequences with an indentity below 40% therefore we will use the 12 proteins shown below for creating a multiple alignment for homologous modeling. We choose sequences to cover the whole protein and we pay specific attention on the transmembrane region.
| PDB-ID | Identity | Description |
| 1s79 | 37% | Kram |
| 3p73 | 28% | Kram |
| 1kcg | 22% | Kram |
| 1jfm | 14% | Kram |
| 1bii | 22% | Kram |
| 2p24 | 21% | Kram |
| 1cd1 | 21% | Kram |
| 2wy3 | 29% | Kram |
| 1lqv | 14% | Kram |
| 3jts | 25% | Kram |
| 1ow0 | 22% | Kram |
| 1hxm | 18% | Kram |
With these Sequences inclcuding 1a6z, we did a multible algniment with t-coffee(EXPRESSO). This mutlible alignment is later used in the Alignment Mode of SwissModel and Modeller.
DSSP --EEEEEEEEEEB-SS-SSB--EEE
Q30201 MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEAL
1S79_A --------------------------------------------------
3P73_A -----------------------EFGSHSLRYFLTGMTDPGPGMPRFVIV
1KCG_C -------------------------DAHSLWYNFTIIHLPRHGQQWCEVQ
1JFM_A -------------------------DAHSLRCNLTIKDPTPADPLWYEAK
1BII_A -MGAMAPRTLLLLLAAALGPTQTRAGSHSLRYFVTAVSRPGFGEPRYMEV
2P24_A --------------------------------------------------
1CD1_A -----------------------QQKNYTFRCLQMSSFANR-SWSRTDSV
2WY3_A ------------------------MEPHSLRYNLMVLSQDESVQSGFLAE
1LQV_A -------------------SQDASDGLQRLHMLQISYFR-DPYHVWYQGN
3JTS_A -------------------------GSHSMRYFYTSMSRPGRWEPRFIAV
1OW0_A --------------------------------------------------
1HXM_A --------------------------------------------------
DSSP EEETTEEEEEEESSS--EEE--STTS-SSTTTTHHHHHHHHHHHHHHHHH
Q30201 GYVDDQLFVFYDHES--RRVE-PRTPWVSSRISSQMWLQLSQSLKGWDHM
1S79_A ------------------GRW-IL-KNDVKNRSVYIKGFPTDATLDDIKE
3P73_A GYVDDKIFGTYNSKS--RTAQ-PIVEML-PQEDQEHWDTQTQKAQGGERD
1KCG_C SQVDQKNFLSYDCGS--DKVLSMGHL-EEQLYATDAWGKQLEMLREVGQR
1JFM_A CFVGEILILHLSNIN--KTMT-SG-DPGETANATEVKKCLTQPLKNLCQK
1BII_A GYVDNTEFVRFDSDAENPRYE-PRARWIE-QEGPEYWERETRRAKGNEQS
2P24_A --------------------------M----AIMAPRTLVLLLSGALALT
1CD1_A VWLGDLQTHRWSNDS--ATIS-FTKPWSQGKLSNQQWEKLQHMFQVYRVS
2WY3_A GHLDGQPFLRYDRQK--RRAK-PQGQWAEDVLGAETWDTETEDLTENGQD
1LQV_A ASLGGHLTHVLEGPDTNTTII-QLQPL----QEPESWARTQSGLQSYLLQ
3JTS_A GYVDDTQFVRFDSDAASQRME-PRAPWVE-QEGPEYWDRETRNMKAETQN
1OW0_A --------------------------------------------------
1HXM_A -----------------------------------AIELVPEHQTVPVSI
DSSP HHHHHHHHTTT-SSS--E--------EEEEEE-EEE-TTS-E-EEE-E--
Q30201 FTVDFWTIMENHN-HSKE--------SHTLQV-ILGCEMQED-NST-E--
1S79_A WLEDKGQV-LNIQMRRTL--------HKAFKG-SIFVVFDSI-ESA-KKF
3P73_A FDWNLNRLPERYN-KSKG--------SHTMQM-MFGCDILED-GSI-R--
1KCG_C LRLELADT---------ELEDFTPSGPLTLQV-RMSCECEAD-GYI-R--
1JFM_A LRNKVSNT-KVDTHKTNG--------YPHLQV-TMIYPQSQG-RTP-S--
1BII_A FRVDLRTALRYYNQSAGG--------SHTLQW-MAGCDVESD-GRLLR--
2P24_A QTWAGSHSRGEDD--IEA--------DHVGSYGIVVYQSP----GD-I--
1CD1_A FTRDIQELVKMMSPKEDY--------PIEIQL-SAGCEMYPG-NAS-E--
2WY3_A LRRTLTHI----KDQKGG--------LHSLQE-IRVCEIHED-SST-R--
1LQV_A FHGLVRLVHQERT--LAF--------PLTIRC-FLGCELPPEGSRA-H--
3JTS_A APVNLRNLRGYYNQSEAG--------SHTIQR-MYGCDLGPD-GRLLR--
1OW0_A -----ACHPRLSLHRPAL--------EDLLLG-SEANLTCTL-TGLRD--
1HXM_A GVPATLRCSMKGEAIGNY--------YINWYR-KTQGNTMTF-IYRE---
DSSP ----------EEEETTEE----------------EEEEEGGGTEEEES--
Q30201 ----------GYWKYGYD----------------GQDHLEFCPDTLDW--
1S79_A VETPGQKYKETDLLILFKDDYFAKKNEERKQNKVE---------------
3P73_A ----------GYDQYAFD----------------GRDFLAFDMDTMTF--
1KCG_C ----------GSWQFSFD----------------GRKFLLFDSNNRKW--
1JFM_A ----------ATWEFNIS----------------DSYFFTFYTENMSW--
1BII_A ----------GYWQFAYD----------------GCDYIALNEDLKTW--
2P24_A ----------GQYTFEFD----------------GDELFYVDLDKKET--
1CD1_A ----------SFLHVAFQ----------------GKYVVRFWG--TSWQT
2WY3_A ----------GSRHFYYN----------------GELFLSQNLETQES--
1LQV_A ----------VFFEVAVN----------------GSSFVSFRPERALW--
3JTS_A ----------GYHQSAYD----------------GKDYIALNEDLRSW--
1OW0_A ----------ASGVTFTW----------------TPSSGKSAV--QGPPE
1HXM_A ----------KDIYGPGF----------------KDNFQGDIDIAKNL--
DSSP SGG-G----HHH-HHHHHSSTHHH--HHHHHHHHTHHHHHHHHHHHHHTT
Q30201 RAA-E----PRA-WPTKLEWERHK--IRARQNRAYLERDCPAQLQQLLEL
1S79_A --------------------------------------------------
3P73_A TAA-D----PVA-EITKRRWETEG--TYAERWKHELGTVCVQNLRRYLEH
1KCG_C TVV-H----AGA-RRMKEKWEKDS--GLTTFFKMVSMRDCKSWLRDFLMH
1JFM_A RSA-N----DES-GVIMNKWKDDG--EFVKQLKFLI-HECSQKMDEFLKQ
1BII_A TAA-D----MAA-QITRRKWEQA---GAAERDRAYLEGECVEWLRRYLKN
2P24_A IWM-------------LPEFAQLR--SFDPQGGLQNIATGKHNLGVLTKR
1CD1_A VPGAP----SWL-DLPIKVLNADQ--GTSATVQMLLNDTCPLFVRGLLEA
2WY3_A TVP-QSSRAQTLAMNVTNFW-KEDAMKTKTHYRAMQ-ADCLQKLQRYLKS
1LQV_A QAD-TQVTSGVV-TFTLQQLNAYN--RTRYELREFLEDTCVQYVQKHISA
3JTS_A TAA-D----MAA-QNTQRKWEAA---GEAEQHRTYLEGECLEWLRRYLEN
1OW0_A R--DL----CGC-YSVSSVLPGCA--EPWNHGKTFTCTAAYPESKTPLTA
1HXM_A AVL-K----ILA-PSERDEGSYYC--ACDTLGMGGEYTDKLIFGKGTRVT
DSSP TSS--B--EEEEEEEE-SS-----E-EEEEEEEEEBSS--EEEEEETTEE
Q30201 GRGVLDQQVPPLVKVTHHVT----S-SVTTLRCRALNYYPQNITMKWLKD
1S79_A --------------------------------------------------
3P73_A GKAALKRRVQPEVRVWGKEA----D-GILTLSCHAHGFYPRPITISWMKD
1KCG_C RKKRLE--------------------------------------------
1JFM_A SKEK----------------------------------------------
1BII_A GNATLLRTDPPKAHVTHHRR----PEGDVTLRCWALGFYPADITLTWQLN
2P24_A SNSTPATNEAPQATVFPKSP--VLLGQPNTLICFVDNIFPPVINITWLRN
1CD1_A GKSDLEKQEKPVAWLSSVP---SSAHGHRQLVCHVSGFYPKPVWVMWMRG
2WY3_A GVAIRRTVPPMVNVTCSEVS----EGNITVTCRASSFYPRNITLTWRQDG
1LQV_A ENTKGSQTSRSYTS------------------------------------
3JTS_A GKETLQRADPPKTHVTHHPV----SDQEATLRCWALGFYPAEITLTWQRD
1OW0_A TLSKSGNTFRPEVHLLPPPSEELALNELVTLTCLARGFSPKDVLVRWLQG
1HXM_A VEPRSQPHTKPSVFVMKNG---------TNVACLVKEFYPKDIRINLVSS
DSSP --GGGS---EEEE-TTS-E----EEEEEEEE-TTGGGGEE---EEEE-TT
Q30201 K-QPMDAKEFEPKDVLPNG----DGTYQGWITLAVPPGEE---QRYTCQV
1S79_A --------------------------------------------------
3P73_A --GMVRDQETRWGGIVPNS----DGTYHASAAIDVLPEDG---DKYWCRV
1KCG_C --------------------------------------------------
1JFM_A --------------------------------------------------
1BII_A --GEELTQEMELVETRPAG----DGTFQKWASVVVPLGKE---QKYTCHV
2P24_A --SKSVADGVYETSFFVNR----DYSFHKLSYLTFIPSDD---DIYDCKV
1CD1_A --DQ-EQQGTHRGDFLPNA----DETWYLQATLDVEAGEE---AGLACRV
2WY3_A --VSLSHNTQQWGDVLPDG----NGTYQTWVATRIRQGEE---QRFTCYM
1LQV_A --------------------------------------------------
3JTS_A --GEDQTQDTELVETRPAG----DGTFQKWAAVVVPSGKE---QRYTCHV
1OW0_A SQEL-PREKYLTW-ASRQEPSQGTTTFAVTSILRVAAEDWKKGDTFSCMV
1HXM_A -----KKITEFDPAIVISP----SGKYNAVKLGKYE--DS---NSVTCSV
DSSP SSS-EEE-E-
Q30201 EHPGLDQ-PLIVIWEPSPSGTLVIGVISGIAVFVVILFIGILFIILRKRQ
1S79_A --------------------------------------------------
3P73_A EHASLPQ-PGLFSWEPQ---------------------------------
1KCG_C --------------------------------------------------
1JFM_A --------------------------------------------------
1BII_A EHEGLPE-PLTLRWGKEEPPSSTKTNTVIIAVPVVLGAVVILGAVMAFVM
2P24_A EHWGLEE-PVLKHWEPEIPAPMSELTETSGSRLEVLFQ------------
1CD1_A KHSSLGG-QDIILYWDARQAPVGLIVFIVLIMLVVVGAVVYYIWRRRSAY
2WY3_A EHSGNHG-THPVPSGKVLVLQSQRTDFPYVSAAMPCFVIIIILCVPCCKK
1LQV_A --------------------------------------------------
3JTS_A QHEGLRE-PLTLRWEP----------------------------------
1OW0_A GHEALPLAFTQKTIDRLAGK------------------------------
1HXM_A QHDNK---TVHSTDFEVKTDSTDHVKPKETENTKQPSKS-----------
DSSP
Q30201 GSRGAMGHYVLAERE----------------
1S79_A -------------------------------
3P73_A -------------------------------
1KCG_C -------------------------------
1JFM_A -------------------------------
1BII_A KRRRNTGGKGGDYALAPGSQSSDMSLPDCKV
2P24_A -------------------------------
1CD1_A QDIR---------------------------
2WY3_A KTSAAEGP-----------------------
1LQV_A -------------------------------
3JTS_A -------------------------------
1OW0_A -------------------------------
1HXM_A -------------------------------
ITasser
Predicted Secondary Structure by I-Tasser
Sequence: MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDF Predicted: CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCCCCCCCCSSSSSSSCCCSSSSCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Conf-Score: 985028899999999899875122045421036641367999985269985643743686068998778788540145583478888887676654315558 Sequence: WTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQ Predicted: HHHHHHHCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCSSSSCCCHHHCHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCHHHHHC Conf-Score: 888755315777644463525565898763541000558873365263022202455666677878887004598888767064299999999747666642 Sequence: QVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPSPSGTLV Predicted: CCCCCCCCCCCCCCCHHHHCHHHHCCCCCCSSSSSSSCCCCCCCCCCSSSSCCCCCCCCCCCSSSSSCCCCCCCCSSSSCCCCCCCCCSSSSCCCCCCCCCC Conf-Score: 599877567699854442101541541332479864358754456553541024888652112699807986310267512589998726840688766531 Sequence: IGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE Prediction: CCCCCCHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCHCCCC Conf-Score: 010211112222100246665443013678898651020169
Secondary structure elements are shown as H for Alpha helix,S for Beta sheet & C for Coil
Predicted Solvent Accessibility by I-Tasser
Sequence: MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVFYDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDF Prediction: 723312000000000101112222011200120120023333331200000102322003123724434241311436413610352044144313323230 Sequence: WTIMENHNHSKESHTLQVILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNRAYLERDCPAQLQQLLELGRGVLDQ Prediction: 220132133351310001010021136231211333023032003016303403102321432433044143404422010333005103400630351154 Sequence: QVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPSPSGTLV Prediction: 342353313321443300000100101014010203346564435434135233334221320000000347533120214264144202020214542200 Sequence: IGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE Prediction: 000001100000011100000001334446443132333438
Values range from 0 (buried residue) to 9 (highly exposed residue)
I-Tasser predicted five Models with a C-Score from -0.557 to -3.298. They are ranked from one to five as seen below.
Model1 has a TM-Score of about 0.64 and a RMSD of 7.7Å. For the prediction, I-Tasser used 10 Templates found on PDB which are:
SwissModel
SwissProt is a server based tool provided by the SIB. It combines tools like PSI-PRED and DISOPRED for secondary structure and disordered region prediction.
The model created by SwissModel is based on a self hit, but we had no chance to exclude the protein itself from the prediction. Therefore we also run SwissModel in Alignment-Mode.(TODO)
Automated Mode
Model information:
Modelled residue range: 26 to 297
Based on template: 1a6zC (2.60 Å)
Sequence Identity [%]: 100
Evalue: 7.66e-163
Quality information:
QMEAN Z-Score: -1.035
Even though the model is based on a self hit, the Z-Score is about -1, which means that the model is one standard deviation from the mean. The model is not quite unlikely but also not the most probable one.
