Difference between revisions of "Homology-modelling HEXA"
From Bioinformatikpedia
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|3BC9: |
|3BC9: |
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|SLFLIESEPSTGASVSKNLTEIILIFSNDINKVSQLALTDLITDSDIQGIDYNIEGNKVIINNFSL |
|SLFLIESEPSTGASVSKNLTEIILIFSNDINKVSQLALTDLITDSDIQGIDYNIEGNKVIINNFSL |
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|HEXA: |
|HEXA: |
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|------------------MTSSRLWFSLLLAAAFAGRATALWP-WP-QNFQTSDQRYVLYPNNFQF |
|------------------MTSSRLWFSLLLAAAFAGRATALWP-WP-QNFQTSDQRYVLYPNNFQF |
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|3BC9: |
|3BC9: |
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|EPTCNYRLSYEVIDIYDNHLQGYIEFLVNQSNYPQIPDQEVNHTILQAFYWEMNTGEYATEHPEEA |
|EPTCNYRLSYEVIDIYDNHLQGYIEFLVNQSNYPQIPDQEVNHTILQAFYWEMNTGEYATEHPEEA |
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|HEXA: |
|HEXA: |
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|QYDVSSAAQPGCSVL-DEAFQRYRDLLFGSGSWPR-PYLTGKRHTLEKNVLVVSV---VT--PGCN |
|QYDVSSAAQPGCSVL-DEAFQRYRDLLFGSGSWPR-PYLTGKRHTLEKNVLVVSV---VT--PGCN |
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|3BC9: |
|3BC9: |
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|NLWNLLAERAPELAEAGFTAVWLPPANKGMAGIHDVGYGTYDLWDLGEFDQKGTVRTKYGTKGELE |
|NLWNLLAERAPELAEAGFTAVWLPPANKGMAGIHDVGYGTYDLWDLGEFDQKGTVRTKYGTKGELE |
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|HEXA: |
|HEXA: |
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|QLPTLESVENYTLTINDDQCLLLSETVWG—ALRGLETFSQLVWKSAE-GTFFINKTEIEDFPRFPH |
|QLPTLESVENYTLTINDDQCLLLSETVWG—ALRGLETFSQLVWKSAE-GTFFINKTEIEDFPRFPH |
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|3BC9: |
|3BC9: |
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|NAIDALHNNDIKVYFDAVLNHRMGADYAETVLLDENSRDKPGQYIKAWTGFNFPGRNGEYSNFTWN |
|NAIDALHNNDIKVYFDAVLNHRMGADYAETVLLDENSRDKPGQYIKAWTGFNFPGRNGEYSNFTWN |
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|HEXA: |
|HEXA: |
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|RGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPEL-MRKGSYNPVTHIY |
|RGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPEL-MRKGSYNPVTHIY |
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|3BC9: |
|3BC9: |
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|GQCFDGTDWDDYSKESGKYLFDEKSWDWTYNWDEDYLMGADVDYENEAVQNDVIDWGQWIINNIDF |
|GQCFDGTDWDDYSKESGKYLFDEKSWDWTYNWDEDYLMGADVDYENEAVQNDVIDWGQWIINNIDF |
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|HEXA: |
|HEXA: |
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|TAQDVKEVIEYARLRGIRVLAEFDTPGHTLSW-GPGIPGLLTPCYSGSEPSGTFGPVNPSLNN-TY |
|TAQDVKEVIEYARLRGIRVLAEFDTPGHTLSW-GPGIPGLLTPCYSGSEPSGTFGPVNPSLNN-TY |
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|3BC9: |
|3BC9: |
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|DGFRLDAVKHIDYRFIDKWMSAVQNSSNRDVFFVGEAWVEDVDDLKGFLDTVGNPDLRVFDFPLRS |
|DGFRLDAVKHIDYRFIDKWMSAVQNSSNRDVFFVGEAWVEDVDDLKGFLDTVGNPDLRVFDFPLRS |
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|HEXA: |
|HEXA: |
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|-EFMSTFFLEVSSVFPDFYLHLGG-----DEVDFT-CW-KSNPEIQDFMRKKGF--GEDF-KQLES |
|-EFMSTFFLEVSSVFPDFYLHLGG-----DEVDFT-CW-KSNPEIQDFMRKKGF--GEDF-KQLES |
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|3BC9: |
|3BC9: |
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|FFVDMLNGAYMADLRNAGLVNSPGYENRAVTFVDNHDTDRDEGSYTVSIYSRKYQAYAYILTRAEG |
|FFVDMLNGAYMADLRNAGLVNSPGYENRAVTFVDNHDTDRDEGSYTVSIYSRKYQAYAYILTRAEG |
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|HEXA: |
|HEXA: |
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|FYIQTL-LDIVSSYGKGYVVWQEVFDN-KVKIQP----DTIIQVWREDI-PVNYMKELELVTKA-G |
|FYIQTL-LDIVSSYGKGYVVWQEVFDN-KVKIQP----DTIIQVWREDI-PVNYMKELELVTKA-G |
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|3BC9: |
|3BC9: |
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|VPTVYWKDYYIWEMKEGLDKLLTARRYYAYGPGYEVDNNDADIYSYVRSGFPDVAGDGLVLMISDG |
|VPTVYWKDYYIWEMKEGLDKLLTARRYYAYGPGYEVDNNDADIYSYVRSGFPDVAGDGLVLMISDG |
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|HEXA: |
|HEXA: |
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|FRALLSAPWYLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEY—VDNTNLVPRLWPR |
|FRALLSAPWYLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEY—VDNTNLVPRLWPR |
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|3BC9: |
|3BC9: |
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|TSGNVAGKWINSRQPDTEFYDLTGHIKEHVTTDSEGYGNFKVIKSEDKGWSIWVPVE |
|TSGNVAGKWINSRQPDTEFYDLTGHIKEHVTTDSEGYGNFKVIKSEDKGWSIWVPVE |
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|HEXA: |
|HEXA: |
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|-AGAVAERLWSNKLTSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT----- |
|-AGAVAERLWSNKLTSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT----- |
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Revision as of 14:17, 11 June 2011
Contents
Homology structure groups
We decided to choose every 5% one protein:
| > 60% sequence identity | |||
| PDB id | name | similarity | single template |
| 1ht6_A | AMY1, alpha-amylase iso | 95% | |
| 3aj7_A | Oligo-1,6-glucosidase | 90% | |
| 1h4p_A | Glucan 1,3-beta-glucosidase | 85.2% | |
| 3bc9_A | AMYB, alpha amylase, ca | 80.8% | X |
| 2zum_A | 458AA long hypothetical | 75% | |
| 3bmv_A | Cyclomaltodextrin gluca | 70.3% | |
| 2f2h_A | Putative family 31 gluc | 64.8% | |
| 3emz_A | Xylanase, endo-1,4-beta | 61% | |
| > 40% | |||
| 2dep_A | Xylanase B, thermostabl | 54.9% | |
| 3cui_A | EXO-beta-1,4-glucanase; | 49.5% | X |
| 1vhc_A | Putative KHG/KDPG aldol | 45.1% | |
| 2hk0_A | D-psicose 3-epimerase | 40.8% | |
| < 40% | |||
| 2g0w_A | LMO2234 protein; putati | 35.5% | |
| 3q94_A | Fructose-bisphosphate a | 30.0% | |
| 3hn3_A | Beta-G1, beta-glucuroni | 25.1% | |
| 3lut_A | Voltage-gated potassium | 20.1% | X |
Results
Swissmodel
Modeller
We used Modeller from the command line. Therefore we followed the instructions, described here https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Task_4:_Homology_based_structure_predictions#Homology_modelling_with_Modeller.
First of all, we created an alignment for each of our three selected sequences. In the next step we used Modeller to model the 3D structure of the protein.
- Alignments:
3BC9:
POODLE-I predicted five disordered regions:
| 3BC9: | SLFLIESEPSTGASVSKNLTEIILIFSNDINKVSQLALTDLITDSDIQGIDYNIEGNKVIINNFSL |
| HEXA: | |
| 3BC9: | EPTCNYRLSYEVIDIYDNHLQGYIEFLVNQSNYPQIPDQEVNHTILQAFYWEMNTGEYATEHPEEA |
| HEXA: | QYDVSSAAQPGCSVL-DEAFQRYRDLLFGSGSWPR-PYLTGKRHTLEKNVLVVSV---VT--PGCN |
| 3BC9: | NLWNLLAERAPELAEAGFTAVWLPPANKGMAGIHDVGYGTYDLWDLGEFDQKGTVRTKYGTKGELE |
| HEXA: | QLPTLESVENYTLTINDDQCLLLSETVWG—ALRGLETFSQLVWKSAE-GTFFINKTEIEDFPRFPH |
| 3BC9: | NAIDALHNNDIKVYFDAVLNHRMGADYAETVLLDENSRDKPGQYIKAWTGFNFPGRNGEYSNFTWN |
| HEXA: | RGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPEL-MRKGSYNPVTHIY |
| 3BC9: | GQCFDGTDWDDYSKESGKYLFDEKSWDWTYNWDEDYLMGADVDYENEAVQNDVIDWGQWIINNIDF |
| HEXA: | TAQDVKEVIEYARLRGIRVLAEFDTPGHTLSW-GPGIPGLLTPCYSGSEPSGTFGPVNPSLNN-TY |
| 3BC9: | DGFRLDAVKHIDYRFIDKWMSAVQNSSNRDVFFVGEAWVEDVDDLKGFLDTVGNPDLRVFDFPLRS |
| HEXA: | |
| 3BC9: | FFVDMLNGAYMADLRNAGLVNSPGYENRAVTFVDNHDTDRDEGSYTVSIYSRKYQAYAYILTRAEG |
| HEXA: | FYIQTL-LDIVSSYGKGYVVWQEVFDN-KVKIQP----DTIIQVWREDI-PVNYMKELELVTKA-G |
| 3BC9: | VPTVYWKDYYIWEMKEGLDKLLTARRYYAYGPGYEVDNNDADIYSYVRSGFPDVAGDGLVLMISDG |
| HEXA: | FRALLSAPWYLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEY—VDNTNLVPRLWPR |
| 3BC9: | TSGNVAGKWINSRQPDTEFYDLTGHIKEHVTTDSEGYGNFKVIKSEDKGWSIWVPVE |
| HEXA: |
