Homology based structure predictions
From Bioinformatikpedia
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Homologous
Because we found no homologous structures in Task 2, we extended our list by using HHSearch.
We will use 13 proteins for creating a multiple alignment for homologous modeling. We choosen sequences to cover the whole protein and we payed specific attention on the transmembrane region.
| PDB-ID | Identity | Description |
| 1s79 | 37% | Kram |
| 2yc6 | 32% | 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 |
| 3lmy | 19% | Kram |
With these Sequences inclcuding 1a6z, we did a multible algniment with t-coffee.
1A6Z_A RL---------------------LRSHSLHYLFMGASEQDLGLS-L-FEALGYVD-DQ---LFVFYDHE----------------SRR--VEPRTPWVSS
1S79_A GR--------------------------------------------WILKNDVKN-RS---VYIKGF----------------PTDAT--LDDIKEWLE-
3P73_A EF----------------------GSHSLRYFLTGMTDPGPGMP-R-FVIVGYVD-DK---IFGTYNSK----------------SRT--AQPIVEMLPQ
1KCG_C ------------------------DAHSLWYNFTIIHLPRHGQQ-W-CEVQSQVD-QK---NFLSYDCG----------------SDK--VLSMGHLEEQ
1JFM_A DAHS------------------------LRCNLTI-KDPTPADP-LWYEAKCFVG-EI---LILHLS----------------NINKT--MTSGDPGET-
1BII_A MGAMAPRTLLLLLAAALGPTQTRAGSHSLRYFVTAVSRPGFGEP-R-YMEVGYVD-NT---EFVRFDSDA--------------ENPR--YEPRARWIEQ
2P24_A MAIMA---------------------------------PRT-------LVLLLS--GALALTQTWAGSH-SRGED-------------------DI----
1CD1_A QQKN----------------------YTFRCLQMS-SFANRSWS-R-TDSVVWLG-DL---QTHRWS----------------NDSAT--ISFTKPWSQG
2WY3_A M-----------------------EPHSLRYNLMVLSQDESVQS-G-FLAEGHLD-GQ---PFLRYDRQ----------------KRR--AKPQGQWAED
1LQV_A SQDAS---------------------DGLQR-------LHM-------LQISYFR-DP---YHVWYQGNASLGGHLTHVLEGPDTNTT--IIQLQP----
3JTS_A ------------------------GSHSMRYFYTSMSRPGRWEP-R-FIAVGYVD-DT---QFVRFDSDA--------------ASQR--MEPRAPWVEQ
1OW0_A ACHP------------------------R---LSL-HRPAL-ED-LL--LGSEA----------------------------------------------
1HXM_A AIEL---------------------------------VPEHQTVPVS--IGV------------------------------------------------
3LMY_A MELC------------------------G---LGL-PRPPMLLA-LL--LATLLAAML---ALLTQV----------------ALVVQVAEAARAPSVSA
1A6Z_A RISSQMW------------------------------------------------------LQLSQSLKGWDHMFTV----DFWTI----------MENH
1S79_A D---------------------------------------------------------------------KGQVLNI----Q------------------
3P73_A -EDQEHW------------------------------------------------------DTQTQKAQGGERDFDW----NLNRL----------PERY
1KCG_C LYATDAW------------------------------------------------------GKQLEMLREVGQRLRL----ELADT----------ELED
1JFM_A ANATEVK------------------------------------------------------KCLTQPLKNLCQKLRN----KVSNT----------KVDT
1BII_A -EGPEYW------------------------------------------------------ERETRRAKGNEQSFRV----DLRTA----------LRYY
2P24_A EAD---------------------------------------------------------------HV--------------------------------
1CD1_A KLSNQQW------------------------------------------------------EKLQHMFQVYRVSFTR----DIQEL----------VKMM
2WY3_A VLGAETW------------------------------------------------------DTETEDLTENGQDLRR----TLTHI-------------K
1LQV_A LQEPESW------------------------------------------------------ARTQSGLQSYLLQFHG-----LVRL----------VHQ-
3JTS_A -EGPEYW------------------------------------------------------DRETRNMKAETQNAPV----NLRNL----------RGYY
1OW0_A -------------------------------------NLTCTLTGL--RDASGVTFTWTPS---SG----K-----------------------------
1HXM_A -----------------------------------PATLRCSMKGEAIGNYY---INW---YRKTQ---GN--------TMTFIYREKDIYGPGFKDNFQ
3LMY_A KPGPALWPLPLSVKMTPNLLHLAPENFYISHSPNSTAGPSCTLLEEAFRRYHGYIFGFYKWHHEPAEFQAKTQVQQLLVSITLQSE--------CDAFPN
1A6Z_A NHS-KESHTLQVILGCEM----------------------------------------------------------------------------------
1S79_A ----------------------------------------------------------------------------------------------------
3P73_A NK-SKGSHTMQMMFGCDI----------------------------------------------------------------------------------
1KCG_C FT-PSGPLTLQVRMSCEC----------------------------------------------------------------------------------
1JFM_A HKT-NGYPHLQVTMIYPQ----------------------------------------------------------------------------------
1BII_A NQSAGGSHTLQWMAGCDV----------------------------------------------------------------------------------
2P24_A -----------GSYGIVV----------------------------------------------------------------------------------
1CD1_A SPKEDYPIEIQLSAGCEM----------------------------------------------------------------------------------
2WY3_A DQK-GGLHSLQEIRVCEI----------------------------------------------------------------------------------
1LQV_A ERTLAFPLTIRCFLGCEL----------------------------------------------------------------------------------
3JTS_A NQSEAGSHTIQRMYGCDL----------------------------------------------------------------------------------
1OW0_A ------------------------------------------S---------------------------------------------------------
1HXM_A GDI-DI---------------------------------------------------------------------------------------------A
3LMY_A ISS-DESYTLLVKEPVAVLKANRVWGALRGLETFSQLVYQDSYGTFTINESTIIDSPRFSHRGILIDTSRHYLPVKIILKTLDAMAFNKFNVLHWHIVDD
1A6Z_A --------------------QEDNS--------------------------TEGYWKYGYDGQDHLEFCPDTL--DWRAA-----EPRAWPTKLEWERHK
1S79_A ---------------------------------------------------MRRTLHKAFKGSIF-----------------------------------
3P73_A --------------------LEDGS--------------------------IRGYDQYAFDGRDFLAFDMDTM--TFTAA-----DPVAEITKRRWETEG
1KCG_C --------------------EADGY--------------------------IRGSWQFSFDGRKFLLFDSNNR--KWTVV-----HAGARRMKEKWEKDS
1JFM_A --------------------SQ-GRT-------------------------PSATWEFNISDSYF-----------------------------------
1BII_A --------------------ESDGRL-------------------------LRGYWQFAYDGCDYIALNEDLK--TWTAA-----DMAAQITRRKWEQAG
2P24_A --------------------YQSPGD--------------------------IGQYTFEFDGDELFYVDLDKKETIWM-----LPEFA-Q--LRSFDPQ-
1CD1_A --------------------YP-GNA-------------------------SESFLHVAFQGKYVVRFWGT----SWQTVP--GAPSWLDLPIKVLNADQ
2WY3_A --------------------HEDSS--------------------------TRGSRHFYYNGELFLSQNLETQ--ESTVPQSSRAQTLAMNVTNFWKEDA
1LQV_A --------------------PPEGSR-------------------------AHVFFEVAVNGSSFVSFRPERA--LWQ-----ADTQV------------
3JTS_A --------------------GPDGRL-------------------------LRGYHQSAYDGKDYIALNEDLR--SWTAA-----DMAAQNTQRKWEAAG
1OW0_A ------AVQGPPERDLCGCYSV-SSV-------------------------LPGCAEPWNHGKTF------------TCTA---A---------------
1HXM_A KNLAVLKILAPSERD-EGSYYC-A------------------------------CDTLGM----------------------------------------
3LMY_A QSFPYQSITFPELSN-KGSYSL-SHVYTPNDVRMVIEYARLRGIRVLPEFDTPGHTLSWGKGQKD------------LLTP---C---------------
1A6Z_A IRARQNRAYL-----ERDCPAQLQQLLELGRGV--LDQQVPPLVKVT-H----H-VTSSVTTLRCRAL--------------------------------
1S79_A -------------------------------------VVFDSIES-----------------------AKKFVETP------------------------
3P73_A TYAERWKHEL-----GTVCVQNLRRYLEHGKAA--LKRRVQPEVRVW-G----K-EADGILTLSCHAH--------------------------------
1KCG_C GLTTFFKMVS-----MRDCKSWLRDFLMHRKK--------------------------------------------------------------------
1JFM_A -------------------------------------FTFYTENM-----------------------SWRSANDE------------------------
1BII_A -AAERDRAYL-----EGECVEWLRRYLKNGNAT--LLRTDPPKAHVT-H----HRRPEGDVTLRCWAL--------------------------------
2P24_A GGLQNI---A-----TGK--HNLGVLTKRSNST--PATNEAPQATVF---PKSPVLLGQPNTLICFVD--------------------------------
1CD1_A GTSATVQMLL-----NDTCPLFVRGLLEAGKSD--LEKQEKPVAWLS-SV---PSSAHGHRQLVCHVS--------------------------------
2WY3_A MKTKTHYRAM-----QADCLQKLQRYLKSGVA---IRRTVPPMVNVT-C----SEVSEGNITVTCRAS--------------------------------
1LQV_A --------------------------------------------------------TSGVVTFTLQQL--------------------------------
3JTS_A -EAEQHRTYL-----EGECLEWLRRYLENGKET--LQRADPPKTHVT-H----HPVSDQEATLRCWAL--------------------------------
1OW0_A --------YP-----ESKTP--LTATL--SKS---G-NTFRPEVHLL-PPPSEELALNELVTLTCLAR--------------------------------
1HXM_A ---------------GG--E--YTDKLIFGKGT--R-VTVEPRSQPH-TKPSVFV-MKNGTNVACLVK--------------------------------
3LMY_A --------YSRQNKLDSFGP--INPTL--NTTYSFL-TTFFKEISEVFPDQFIHLG-GDEVEFKCWESNPKIQDFMRQKGFGTDFKKLESFYIQKVLDII
1A6Z_A -------------------------------------------NYYPQNI----TMKWLKDKQPMDAKEFEP--KDVLPNGDGT----------------
1S79_A -------------------------GQKYKET----------------DL----LILFKDDYF-------------------------------------
3P73_A -------------------------------------------GFYPRPI----TISWMKDGMVRDQET-RW--GGIVPNSDGT----------------
1KCG_C ----------------------------------------------------------------------------------------------------
1JFM_A ---------------------SGVIMNKWKDD----------------GEFVKQLKFLIHECS-------------------------------------
1BII_A -------------------------------------------GFYPADI----TLTWQLNGEELTQEM-EL--VETRPAGDGT----------------
2P24_A -------------------------------------------NIFPPVI----NITWLRNSKSVADGV-YE--TSFFVNRDYS----------------
1CD1_A -------------------------------------------GFYPKPV----WVMWMRGDQEQ-QGT-HR--GDFLPNADET----------------
2WY3_A -------------------------------------------SFYPRNI----TLTWRQDGVSLSHNTQQW--GDVLPDGNGT----------------
1LQV_A -------------------------------------------NAYNR----------------------------------------------------
3JTS_A -------------------------------------------GFYPAEI----TLTWQRDGEDQTQDT-EL--VETRPAGDGT----------------
1OW0_A -------------------------------------------GFSPKDV----LVRWLQGSQELPREK-YLTWASRQEPSQGTTT--------------
1HXM_A -------------------------------------------EFYPKDI----RINLVSSKKITEFD-----PA-IVISPSGK----------------
3LMY_A ATINKGSIVWQEVFDDKAKLAPGTIVEVWKDSAYPEELSRVTASGFPVIL----SAPWYLDLISYGQDW-R-KYYKVEPLDFGGTQKQKQLFIGGEACLW
1A6Z_A ----------YQG-----------WITLAVPP-----GEEQRYTCQVEHPGLD-QPL-------------------------------------------
1S79_A ----------------------------------------------------------------------------------------------------
3P73_A ----------YHA-----------SAAIDVLP-----EDGDKYWCRVEHASLP-QPGLFSW---------------------------------------
1KCG_C ----------------------------------------------------------------------------------------------------
1JFM_A ----------------------------------------------------------------------------------------------------
1BII_A ----------FQK-----------WASVVVPL-----GKEQKYTCHVEHEGLP-EPLTLRWGKEEPPSSTKTNTVII----AVPVVLGAVVILGAVMAFV
2P24_A ----------FHK-----------LSYLTFIP-----SDDDIYDCKVEHWGLE-EPVLKHWEPE-IPAPMS-----------------------------
1CD1_A ----------WYL-----------QATLDVEA-----GEEAGLACRVKHSSLGGQDIILYWDARQAPVGLIVFIV-----------LIMLVVVGAVV---
2WY3_A ----------YQT-----------WVATRIRQ-----GEEQRFTCYMEHSGNH-GTHPVPSGKVLVLQSQRTDFPYVSAAMPCFVIIIILC-----VPC-
1LQV_A ------------------------TRYELREF-----LED---TC------------VQYVQKH-ISAENT-----------------------------
3JTS_A ----------FQK-----------WAAVVVPS-----GKEQRYTCHVQHEGLR-EPLTLRW---------------------------------------
1OW0_A ----------FAV-----------TSILRVAAEDW--KKGDTFSCMVGHEALP-L---------------------------------------------
1HXM_A ----------YN--------------AVKLG--KY--EDSNSVTCSVQHDNKT-VHSTDF----EVKTDSTDH-----------------------V---
3LMY_A GEYVDATNLTPRLWPRASAVGERLWSSKDVRDMDDAYDRLTRHRCRMVERGIA-----------------------------------------------
1A6Z_A ----------------------------IVIW
1S79_A -------------------AKKNEERKQNKVE
3P73_A -----------------------------EPQ
1KCG_C -----------------------------RLE
1JFM_A -------------------QKMDEFLKQSKEK
1BII_A MKRRRNTGGKGGDYALAPGSQSSDMSLPDCKV
2P24_A -----------------ELTETSGSRLEVLFQ
1CD1_A -----------------Y-YIWRRRSAYQDIR
2WY3_A CKKK---------------------TSAAEGP
1LQV_A -----------------KGSQT----SRSYTS
3JTS_A ------------------------------EP
1OW0_A -------------------AFTQKTIDRLAGK
1HXM_A -----------------K-PKETENTKQPSKS
3LMY_A ----------------------AQPLYAGYCN
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.
