Homology based structure predictions
From Bioinformatikpedia
Contents
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|PDBID|CHAIN|SEQUENCE RL---------------------LRSHSLHYLFMGASEQDLGLS-L-FEA
1S79_A|PDBID|CHAIN|SEQUENCE GR--------------------------------------------WILK
3P73_A|PDBID|CHAIN|SEQUENCE EF----------------------GSHSLRYFLTGMTDPGPGMP-R-FVI
1KCG_C|PDBID|CHAIN|SEQUENCE ------------------------DAHSLWYNFTIIHLPRHGQQ-W-CEV
1JFM_A|PDBID|CHAIN|SEQUENCE DAHS------------------------LRCNLTI-KDPTPADP-LWYEA
1BII_A|PDBID|CHAIN|SEQUENCE MGAMAPRTLLLLLAAALGPTQTRAGSHSLRYFVTAVSRPGFGEP-R-YME
2P24_A|PDBID|CHAIN|SEQUENCE MAIMA---------------------------------PRT-------LV
1CD1_A|PDBID|CHAIN|SEQUENCE QQKN----------------------YTFRCLQMS-SFANRSWS-R-TDS
2WY3_A|PDBID|CHAIN|SEQUENCE M-----------------------EPHSLRYNLMVLSQDESVQS-G-FLA
1LQV_A|PDBID|CHAIN|SEQUENCE SQDAS---------------------DGLQR-------LHM-------LQ
3JTS_A|PDBID|CHAIN|SEQUENCE ------------------------GSHSMRYFYTSMSRPGRWEP-R-FIA
1OW0_A|PDBID|CHAIN|SEQUENCE ACHP------------------------R---LSL-HRPAL-ED-LL--L
1HXM_A|PDBID|CHAIN|SEQUENCE AIEL---------------------------------VPEHQTVPVS--I
3LMY_A|PDBID|CHAIN|SEQUENCE MELC------------------------G---LGL-PRPPMLLA-LL--L
1A6Z_A|PDBID|CHAIN|SEQUENCE LGYVD-DQ---LFVFYDHE----------------SRR--VEPRTPWVSS
1S79_A|PDBID|CHAIN|SEQUENCE NDVKN-RS---VYIKGF----------------PTDAT--LDDIKEWLE-
3P73_A|PDBID|CHAIN|SEQUENCE VGYVD-DK---IFGTYNSK----------------SRT--AQPIVEMLPQ
1KCG_C|PDBID|CHAIN|SEQUENCE QSQVD-QK---NFLSYDCG----------------SDK--VLSMGHLEEQ
1JFM_A|PDBID|CHAIN|SEQUENCE KCFVG-EI---LILHLS----------------NINKT--MTSGDPGET-
1BII_A|PDBID|CHAIN|SEQUENCE VGYVD-NT---EFVRFDSDA--------------ENPR--YEPRARWIEQ
2P24_A|PDBID|CHAIN|SEQUENCE LLLS--GALALTQTWAGSH-SRGED-------------------DI----
1CD1_A|PDBID|CHAIN|SEQUENCE VVWLG-DL---QTHRWS----------------NDSAT--ISFTKPWSQG
2WY3_A|PDBID|CHAIN|SEQUENCE EGHLD-GQ---PFLRYDRQ----------------KRR--AKPQGQWAED
1LQV_A|PDBID|CHAIN|SEQUENCE ISYFR-DP---YHVWYQGNASLGGHLTHVLEGPDTNTT--IIQLQP----
3JTS_A|PDBID|CHAIN|SEQUENCE VGYVD-DT---QFVRFDSDA--------------ASQR--MEPRAPWVEQ
1OW0_A|PDBID|CHAIN|SEQUENCE GSEA----------------------------------------------
1HXM_A|PDBID|CHAIN|SEQUENCE GV------------------------------------------------
3LMY_A|PDBID|CHAIN|SEQUENCE ATLLAAML---ALLTQV----------------ALVVQVAEAARAPSVSA
1A6Z_A|PDBID|CHAIN|SEQUENCE RISSQMW-------------------------------------------
1S79_A|PDBID|CHAIN|SEQUENCE D-------------------------------------------------
3P73_A|PDBID|CHAIN|SEQUENCE -EDQEHW-------------------------------------------
1KCG_C|PDBID|CHAIN|SEQUENCE LYATDAW-------------------------------------------
1JFM_A|PDBID|CHAIN|SEQUENCE ANATEVK-------------------------------------------
1BII_A|PDBID|CHAIN|SEQUENCE -EGPEYW-------------------------------------------
2P24_A|PDBID|CHAIN|SEQUENCE EAD-----------------------------------------------
1CD1_A|PDBID|CHAIN|SEQUENCE KLSNQQW-------------------------------------------
2WY3_A|PDBID|CHAIN|SEQUENCE VLGAETW-------------------------------------------
1LQV_A|PDBID|CHAIN|SEQUENCE LQEPESW-------------------------------------------
3JTS_A|PDBID|CHAIN|SEQUENCE -EGPEYW-------------------------------------------
1OW0_A|PDBID|CHAIN|SEQUENCE -------------------------------------NLTCTLTGL--RD
1HXM_A|PDBID|CHAIN|SEQUENCE -----------------------------------PATLRCSMKGEAIGN
3LMY_A|PDBID|CHAIN|SEQUENCE KPGPALWPLPLSVKMTPNLLHLAPENFYISHSPNSTAGPSCTLLEEAFRR
1A6Z_A|PDBID|CHAIN|SEQUENCE -----------LQLSQSLKGWDHMFTV----DFWTI----------MENH
1S79_A|PDBID|CHAIN|SEQUENCE --------------------KGQVLNI----Q------------------
3P73_A|PDBID|CHAIN|SEQUENCE -----------DTQTQKAQGGERDFDW----NLNRL----------PERY
1KCG_C|PDBID|CHAIN|SEQUENCE -----------GKQLEMLREVGQRLRL----ELADT----------ELED
1JFM_A|PDBID|CHAIN|SEQUENCE -----------KCLTQPLKNLCQKLRN----KVSNT----------KVDT
1BII_A|PDBID|CHAIN|SEQUENCE -----------ERETRRAKGNEQSFRV----DLRTA----------LRYY
2P24_A|PDBID|CHAIN|SEQUENCE ----------------HV--------------------------------
1CD1_A|PDBID|CHAIN|SEQUENCE -----------EKLQHMFQVYRVSFTR----DIQEL----------VKMM
2WY3_A|PDBID|CHAIN|SEQUENCE -----------DTETEDLTENGQDLRR----TLTHI-------------K
1LQV_A|PDBID|CHAIN|SEQUENCE -----------ARTQSGLQSYLLQFHG-----LVRL----------VHQ-
3JTS_A|PDBID|CHAIN|SEQUENCE -----------DRETRNMKAETQNAPV----NLRNL----------RGYY
1OW0_A|PDBID|CHAIN|SEQUENCE ASGVTFTWTPS---SG----K-----------------------------
1HXM_A|PDBID|CHAIN|SEQUENCE YY---INW---YRKTQ---GN--------TMTFIYREKDIYGPGFKDNFQ
3LMY_A|PDBID|CHAIN|SEQUENCE YHGYIFGFYKWHHEPAEFQAKTQVQQLLVSITLQSE--------CDAFPN
1A6Z_A|PDBID|CHAIN|SEQUENCE NHS-KESHTLQVILGCEM--------------------------------
1S79_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
3P73_A|PDBID|CHAIN|SEQUENCE NK-SKGSHTMQMMFGCDI--------------------------------
1KCG_C|PDBID|CHAIN|SEQUENCE FT-PSGPLTLQVRMSCEC--------------------------------
1JFM_A|PDBID|CHAIN|SEQUENCE HKT-NGYPHLQVTMIYPQ--------------------------------
1BII_A|PDBID|CHAIN|SEQUENCE NQSAGGSHTLQWMAGCDV--------------------------------
2P24_A|PDBID|CHAIN|SEQUENCE -----------GSYGIVV--------------------------------
1CD1_A|PDBID|CHAIN|SEQUENCE SPKEDYPIEIQLSAGCEM--------------------------------
2WY3_A|PDBID|CHAIN|SEQUENCE DQK-GGLHSLQEIRVCEI--------------------------------
1LQV_A|PDBID|CHAIN|SEQUENCE ERTLAFPLTIRCFLGCEL--------------------------------
3JTS_A|PDBID|CHAIN|SEQUENCE NQSEAGSHTIQRMYGCDL--------------------------------
1OW0_A|PDBID|CHAIN|SEQUENCE ------------------------------------------S-------
1HXM_A|PDBID|CHAIN|SEQUENCE GDI-DI--------------------------------------------
3LMY_A|PDBID|CHAIN|SEQUENCE ISS-DESYTLLVKEPVAVLKANRVWGALRGLETFSQLVYQDSYGTFTINE
1A6Z_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1S79_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
3P73_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1KCG_C|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1JFM_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1BII_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
2P24_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1CD1_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
2WY3_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1LQV_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
3JTS_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1OW0_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1HXM_A|PDBID|CHAIN|SEQUENCE -------------------------------------------------A
3LMY_A|PDBID|CHAIN|SEQUENCE STIIDSPRFSHRGILIDTSRHYLPVKIILKTLDAMAFNKFNVLHWHIVDD
1A6Z_A|PDBID|CHAIN|SEQUENCE --------------------QEDNS-------------------------
1S79_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
3P73_A|PDBID|CHAIN|SEQUENCE --------------------LEDGS-------------------------
1KCG_C|PDBID|CHAIN|SEQUENCE --------------------EADGY-------------------------
1JFM_A|PDBID|CHAIN|SEQUENCE --------------------SQ-GRT------------------------
1BII_A|PDBID|CHAIN|SEQUENCE --------------------ESDGRL------------------------
2P24_A|PDBID|CHAIN|SEQUENCE --------------------YQSPGD------------------------
1CD1_A|PDBID|CHAIN|SEQUENCE --------------------YP-GNA------------------------
2WY3_A|PDBID|CHAIN|SEQUENCE --------------------HEDSS-------------------------
1LQV_A|PDBID|CHAIN|SEQUENCE --------------------PPEGSR------------------------
3JTS_A|PDBID|CHAIN|SEQUENCE --------------------GPDGRL------------------------
1OW0_A|PDBID|CHAIN|SEQUENCE ------AVQGPPERDLCGCYSV-SSV------------------------
1HXM_A|PDBID|CHAIN|SEQUENCE KNLAVLKILAPSERD-EGSYYC-A--------------------------
3LMY_A|PDBID|CHAIN|SEQUENCE QSFPYQSITFPELSN-KGSYSL-SHVYTPNDVRMVIEYARLRGIRVLPEF
1A6Z_A|PDBID|CHAIN|SEQUENCE -TEGYWKYGYDGQDHLEFCPDTL--DWRAA-----EPRAWPTKLEWERHK
1S79_A|PDBID|CHAIN|SEQUENCE -MRRTLHKAFKGSIF-----------------------------------
3P73_A|PDBID|CHAIN|SEQUENCE -IRGYDQYAFDGRDFLAFDMDTM--TFTAA-----DPVAEITKRRWETEG
1KCG_C|PDBID|CHAIN|SEQUENCE -IRGSWQFSFDGRKFLLFDSNNR--KWTVV-----HAGARRMKEKWEKDS
1JFM_A|PDBID|CHAIN|SEQUENCE -PSATWEFNISDSYF-----------------------------------
1BII_A|PDBID|CHAIN|SEQUENCE -LRGYWQFAYDGCDYIALNEDLK--TWTAA-----DMAAQITRRKWEQAG
2P24_A|PDBID|CHAIN|SEQUENCE --IGQYTFEFDGDELFYVDLDKKETIWM-----LPEFA-Q--LRSFDPQ-
1CD1_A|PDBID|CHAIN|SEQUENCE -SESFLHVAFQGKYVVRFWGT----SWQTVP--GAPSWLDLPIKVLNADQ
2WY3_A|PDBID|CHAIN|SEQUENCE -TRGSRHFYYNGELFLSQNLETQ--ESTVPQSSRAQTLAMNVTNFWKEDA
1LQV_A|PDBID|CHAIN|SEQUENCE -AHVFFEVAVNGSSFVSFRPERA--LWQ-----ADTQV------------
3JTS_A|PDBID|CHAIN|SEQUENCE -LRGYHQSAYDGKDYIALNEDLR--SWTAA-----DMAAQNTQRKWEAAG
1OW0_A|PDBID|CHAIN|SEQUENCE -LPGCAEPWNHGKTF------------TCTA---A---------------
1HXM_A|PDBID|CHAIN|SEQUENCE ----CDTLGM----------------------------------------
3LMY_A|PDBID|CHAIN|SEQUENCE DTPGHTLSWGKGQKD------------LLTP---C---------------
1A6Z_A|PDBID|CHAIN|SEQUENCE IRARQNRAYL-----ERDCPAQLQQLLELGRGV--LDQQVPPLVKVT-H-
1S79_A|PDBID|CHAIN|SEQUENCE -------------------------------------VVFDSIES-----
3P73_A|PDBID|CHAIN|SEQUENCE TYAERWKHEL-----GTVCVQNLRRYLEHGKAA--LKRRVQPEVRVW-G-
1KCG_C|PDBID|CHAIN|SEQUENCE GLTTFFKMVS-----MRDCKSWLRDFLMHRKK------------------
1JFM_A|PDBID|CHAIN|SEQUENCE -------------------------------------FTFYTENM-----
1BII_A|PDBID|CHAIN|SEQUENCE -AAERDRAYL-----EGECVEWLRRYLKNGNAT--LLRTDPPKAHVT-H-
2P24_A|PDBID|CHAIN|SEQUENCE GGLQNI---A-----TGK--HNLGVLTKRSNST--PATNEAPQATVF---
1CD1_A|PDBID|CHAIN|SEQUENCE GTSATVQMLL-----NDTCPLFVRGLLEAGKSD--LEKQEKPVAWLS-SV
2WY3_A|PDBID|CHAIN|SEQUENCE MKTKTHYRAM-----QADCLQKLQRYLKSGVA---IRRTVPPMVNVT-C-
1LQV_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
3JTS_A|PDBID|CHAIN|SEQUENCE -EAEQHRTYL-----EGECLEWLRRYLENGKET--LQRADPPKTHVT-H-
1OW0_A|PDBID|CHAIN|SEQUENCE --------YP-----ESKTP--LTATL--SKS---G-NTFRPEVHLL-PP
1HXM_A|PDBID|CHAIN|SEQUENCE ---------------GG--E--YTDKLIFGKGT--R-VTVEPRSQPH-TK
3LMY_A|PDBID|CHAIN|SEQUENCE --------YSRQNKLDSFGP--INPTL--NTTYSFL-TTFFKEISEVFPD
1A6Z_A|PDBID|CHAIN|SEQUENCE ---H-VTSSVTTLRCRAL--------------------------------
1S79_A|PDBID|CHAIN|SEQUENCE ------------------AKKFVETP------------------------
3P73_A|PDBID|CHAIN|SEQUENCE ---K-EADGILTLSCHAH--------------------------------
1KCG_C|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1JFM_A|PDBID|CHAIN|SEQUENCE ------------------SWRSANDE------------------------
1BII_A|PDBID|CHAIN|SEQUENCE ---HRRPEGDVTLRCWAL--------------------------------
2P24_A|PDBID|CHAIN|SEQUENCE PKSPVLLGQPNTLICFVD--------------------------------
1CD1_A|PDBID|CHAIN|SEQUENCE ---PSSAHGHRQLVCHVS--------------------------------
2WY3_A|PDBID|CHAIN|SEQUENCE ---SEVSEGNITVTCRAS--------------------------------
1LQV_A|PDBID|CHAIN|SEQUENCE ------TSGVVTFTLQQL--------------------------------
3JTS_A|PDBID|CHAIN|SEQUENCE ---HPVSDQEATLRCWAL--------------------------------
1OW0_A|PDBID|CHAIN|SEQUENCE PSEELALNELVTLTCLAR--------------------------------
1HXM_A|PDBID|CHAIN|SEQUENCE PSVFV-MKNGTNVACLVK--------------------------------
3LMY_A|PDBID|CHAIN|SEQUENCE QFIHLG-GDEVEFKCWESNPKIQDFMRQKGFGTDFKKLESFYIQKVLDII
1A6Z_A|PDBID|CHAIN|SEQUENCE -------------------------------------------NYYPQNI
1S79_A|PDBID|CHAIN|SEQUENCE -------------------------GQKYKET----------------DL
3P73_A|PDBID|CHAIN|SEQUENCE -------------------------------------------GFYPRPI
1KCG_C|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1JFM_A|PDBID|CHAIN|SEQUENCE ---------------------SGVIMNKWKDD----------------GE
1BII_A|PDBID|CHAIN|SEQUENCE -------------------------------------------GFYPADI
2P24_A|PDBID|CHAIN|SEQUENCE -------------------------------------------NIFPPVI
1CD1_A|PDBID|CHAIN|SEQUENCE -------------------------------------------GFYPKPV
2WY3_A|PDBID|CHAIN|SEQUENCE -------------------------------------------SFYPRNI
1LQV_A|PDBID|CHAIN|SEQUENCE -------------------------------------------NAYNR--
3JTS_A|PDBID|CHAIN|SEQUENCE -------------------------------------------GFYPAEI
1OW0_A|PDBID|CHAIN|SEQUENCE -------------------------------------------GFSPKDV
1HXM_A|PDBID|CHAIN|SEQUENCE -------------------------------------------EFYPKDI
3LMY_A|PDBID|CHAIN|SEQUENCE ATINKGSIVWQEVFDDKAKLAPGTIVEVWKDSAYPEELSRVTASGFPVIL
1A6Z_A|PDBID|CHAIN|SEQUENCE ----TMKWLKDKQPMDAKEFEP--KDVLPNGDGT----------------
1S79_A|PDBID|CHAIN|SEQUENCE ----LILFKDDYF-------------------------------------
3P73_A|PDBID|CHAIN|SEQUENCE ----TISWMKDGMVRDQET-RW--GGIVPNSDGT----------------
1KCG_C|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1JFM_A|PDBID|CHAIN|SEQUENCE FVKQLKFLIHECS-------------------------------------
1BII_A|PDBID|CHAIN|SEQUENCE ----TLTWQLNGEELTQEM-EL--VETRPAGDGT----------------
2P24_A|PDBID|CHAIN|SEQUENCE ----NITWLRNSKSVADGV-YE--TSFFVNRDYS----------------
1CD1_A|PDBID|CHAIN|SEQUENCE ----WVMWMRGDQEQ-QGT-HR--GDFLPNADET----------------
2WY3_A|PDBID|CHAIN|SEQUENCE ----TLTWRQDGVSLSHNTQQW--GDVLPDGNGT----------------
1LQV_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
3JTS_A|PDBID|CHAIN|SEQUENCE ----TLTWQRDGEDQTQDT-EL--VETRPAGDGT----------------
1OW0_A|PDBID|CHAIN|SEQUENCE ----LVRWLQGSQELPREK-YLTWASRQEPSQGTTT--------------
1HXM_A|PDBID|CHAIN|SEQUENCE ----RINLVSSKKITEFD-----PA-IVISPSGK----------------
3LMY_A|PDBID|CHAIN|SEQUENCE ----SAPWYLDLISYGQDW-R-KYYKVEPLDFGGTQKQKQLFIGGEACLW
1A6Z_A|PDBID|CHAIN|SEQUENCE ----------YQG-----------WITLAVPP-----GEEQRYTCQVEHP
1S79_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
3P73_A|PDBID|CHAIN|SEQUENCE ----------YHA-----------SAAIDVLP-----EDGDKYWCRVEHA
1KCG_C|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1JFM_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1BII_A|PDBID|CHAIN|SEQUENCE ----------FQK-----------WASVVVPL-----GKEQKYTCHVEHE
2P24_A|PDBID|CHAIN|SEQUENCE ----------FHK-----------LSYLTFIP-----SDDDIYDCKVEHW
1CD1_A|PDBID|CHAIN|SEQUENCE ----------WYL-----------QATLDVEA-----GEEAGLACRVKHS
2WY3_A|PDBID|CHAIN|SEQUENCE ----------YQT-----------WVATRIRQ-----GEEQRFTCYMEHS
1LQV_A|PDBID|CHAIN|SEQUENCE ------------------------TRYELREF-----LED---TC-----
3JTS_A|PDBID|CHAIN|SEQUENCE ----------FQK-----------WAAVVVPS-----GKEQRYTCHVQHE
1OW0_A|PDBID|CHAIN|SEQUENCE ----------FAV-----------TSILRVAAEDW--KKGDTFSCMVGHE
1HXM_A|PDBID|CHAIN|SEQUENCE ----------YN--------------AVKLG--KY--EDSNSVTCSVQHD
3LMY_A|PDBID|CHAIN|SEQUENCE GEYVDATNLTPRLWPRASAVGERLWSSKDVRDMDDAYDRLTRHRCRMVER
1A6Z_A|PDBID|CHAIN|SEQUENCE GLD-QPL-------------------------------------------
1S79_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
3P73_A|PDBID|CHAIN|SEQUENCE SLP-QPGLFSW---------------------------------------
1KCG_C|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1JFM_A|PDBID|CHAIN|SEQUENCE --------------------------------------------------
1BII_A|PDBID|CHAIN|SEQUENCE GLP-EPLTLRWGKEEPPSSTKTNTVII----AVPVVLGAVVILGAVMAFV
2P24_A|PDBID|CHAIN|SEQUENCE GLE-EPVLKHWEPE-IPAPMS-----------------------------
1CD1_A|PDBID|CHAIN|SEQUENCE SLGGQDIILYWDARQAPVGLIVFIV-----------LIMLVVVGAVV---
2WY3_A|PDBID|CHAIN|SEQUENCE GNH-GTHPVPSGKVLVLQSQRTDFPYVSAAMPCFVIIIILC-----VPC-
1LQV_A|PDBID|CHAIN|SEQUENCE -------VQYVQKH-ISAENT-----------------------------
3JTS_A|PDBID|CHAIN|SEQUENCE GLR-EPLTLRW---------------------------------------
1OW0_A|PDBID|CHAIN|SEQUENCE ALP-L---------------------------------------------
1HXM_A|PDBID|CHAIN|SEQUENCE NKT-VHSTDF----EVKTDSTDH-----------------------V---
3LMY_A|PDBID|CHAIN|SEQUENCE GIA-----------------------------------------------
1A6Z_A|PDBID|CHAIN|SEQUENCE ----------------------------IVIW
1S79_A|PDBID|CHAIN|SEQUENCE -------------------AKKNEERKQNKVE
3P73_A|PDBID|CHAIN|SEQUENCE -----------------------------EPQ
1KCG_C|PDBID|CHAIN|SEQUENCE -----------------------------RLE
1JFM_A|PDBID|CHAIN|SEQUENCE -------------------QKMDEFLKQSKEK
1BII_A|PDBID|CHAIN|SEQUENCE MKRRRNTGGKGGDYALAPGSQSSDMSLPDCKV
2P24_A|PDBID|CHAIN|SEQUENCE -----------------ELTETSGSRLEVLFQ
1CD1_A|PDBID|CHAIN|SEQUENCE -----------------Y-YIWRRRSAYQDIR
2WY3_A|PDBID|CHAIN|SEQUENCE CKKK---------------------TSAAEGP
1LQV_A|PDBID|CHAIN|SEQUENCE -----------------KGSQT----SRSYTS
3JTS_A|PDBID|CHAIN|SEQUENCE ------------------------------EP
1OW0_A|PDBID|CHAIN|SEQUENCE -------------------AFTQKTIDRLAGK
1HXM_A|PDBID|CHAIN|SEQUENCE -----------------K-PKETENTKQPSKS
3LMY_A|PDBID|CHAIN|SEQUENCE ----------------------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.
