Difference between revisions of "Homology-modelling HEXA"

From Bioinformatikpedia
(Methods)
(Modeller)
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=== Modeller ===
 
=== 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]].
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  +
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.
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* Alignments:
  +
  +
3BC9:
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  +
POODLE-I predicted five disordered regions:
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{| border="1" style="text-align:center; border-spacing:0;"
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|-
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|3BC9:
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|SLFLIESEPSTGASVSKNLTEIILIFSNDINKVSQLALTDLITDSDIQGIDYNIEGNKVIINNFSL
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|HEXA:
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|------------------MTSSRLWFSLLLAAAFAGRATALWP-WP-QNFQTSDQRYVLYPNNFQF
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|-
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|3BC9:
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|EPTCNYRLSYEVIDIYDNHLQGYIEFLVNQSNYPQIPDQEVNHTILQAFYWEMNTGEYATEHPEEA
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|HEXA:
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|QYDVSSAAQPGCSVL-DEAFQRYRDLLFGSGSWPR-PYLTGKRHTLEKNVLVVSV---VT--PGCN
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|-
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|3BC9:
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|NLWNLLAERAPELAEAGFTAVWLPPANKGMAGIHDVGYGTYDLWDLGEFDQKGTVRTKYGTKGELE
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|HEXA:
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|QLPTLESVENYTLTINDDQCLLLSETVWG—ALRGLETFSQLVWKSAE-GTFFINKTEIEDFPRFPH
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|-
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|3BC9:
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|NAIDALHNNDIKVYFDAVLNHRMGADYAETVLLDENSRDKPGQYIKAWTGFNFPGRNGEYSNFTWN
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|HEXA:
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|RGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPEL-MRKGSYNPVTHIY
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|-
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|3BC9:
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|GQCFDGTDWDDYSKESGKYLFDEKSWDWTYNWDEDYLMGADVDYENEAVQNDVIDWGQWIINNIDF
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|HEXA:
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|TAQDVKEVIEYARLRGIRVLAEFDTPGHTLSW-GPGIPGLLTPCYSGSEPSGTFGPVNPSLNN-TY
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|-
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|3BC9:
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|DGFRLDAVKHIDYRFIDKWMSAVQNSSNRDVFFVGEAWVEDVDDLKGFLDTVGNPDLRVFDFPLRS
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|HEXA:
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|-EFMSTFFLEVSSVFPDFYLHLGG-----DEVDFT-CW-KSNPEIQDFMRKKGF--GEDF-KQLES
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|-
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|3BC9:
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|FFVDMLNGAYMADLRNAGLVNSPGYENRAVTFVDNHDTDRDEGSYTVSIYSRKYQAYAYILTRAEG
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|HEXA:
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|FYIQTL-LDIVSSYGKGYVVWQEVFDN-KVKIQP----DTIIQVWREDI-PVNYMKELELVTKA-G
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|-
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|3BC9:
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|VPTVYWKDYYIWEMKEGLDKLLTARRYYAYGPGYEVDNNDADIYSYVRSGFPDVAGDGLVLMISDG
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|HEXA:
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|FRALLSAPWYLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEY—VDNTNLVPRLWPR
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|-
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|3BC9:
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|TSGNVAGKWINSRQPDTEFYDLTGHIKEHVTTDSEGYGNFKVIKSEDKGWSIWVPVE
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|HEXA:
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|-AGAVAERLWSNKLTSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT-----
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|-
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|}
   
 
=== iTasser ===
 
=== iTasser ===

Revision as of 15:16, 11 June 2011

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:

iTasser

Analysis

RMSD

TM-Score