Difference between revisions of "Homology-modelling HEXA"

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(Modeller)
(Modeller)
Line 118: Line 118:
 
|3BC9:
 
|3BC9:
 
|SLFLIESEPSTGASVSKNLTEIILIFSNDINKVSQLALTDLITDSDIQGIDYNIEGNKVIINNFSL
 
|SLFLIESEPSTGASVSKNLTEIILIFSNDINKVSQLALTDLITDSDIQGIDYNIEGNKVIINNFSL
  +
|-
 
|HEXA:
 
|HEXA:
 
|------------------MTSSRLWFSLLLAAAFAGRATALWP-WP-QNFQTSDQRYVLYPNNFQF
 
|------------------MTSSRLWFSLLLAAAFAGRATALWP-WP-QNFQTSDQRYVLYPNNFQF
Line 123: Line 124:
 
|3BC9:
 
|3BC9:
 
|EPTCNYRLSYEVIDIYDNHLQGYIEFLVNQSNYPQIPDQEVNHTILQAFYWEMNTGEYATEHPEEA
 
|EPTCNYRLSYEVIDIYDNHLQGYIEFLVNQSNYPQIPDQEVNHTILQAFYWEMNTGEYATEHPEEA
  +
|-
 
|HEXA:
 
|HEXA:
 
|QYDVSSAAQPGCSVL-DEAFQRYRDLLFGSGSWPR-PYLTGKRHTLEKNVLVVSV---VT--PGCN
 
|QYDVSSAAQPGCSVL-DEAFQRYRDLLFGSGSWPR-PYLTGKRHTLEKNVLVVSV---VT--PGCN
Line 128: Line 130:
 
|3BC9:
 
|3BC9:
 
|NLWNLLAERAPELAEAGFTAVWLPPANKGMAGIHDVGYGTYDLWDLGEFDQKGTVRTKYGTKGELE
 
|NLWNLLAERAPELAEAGFTAVWLPPANKGMAGIHDVGYGTYDLWDLGEFDQKGTVRTKYGTKGELE
  +
|-
 
|HEXA:
 
|HEXA:
 
|QLPTLESVENYTLTINDDQCLLLSETVWG—ALRGLETFSQLVWKSAE-GTFFINKTEIEDFPRFPH
 
|QLPTLESVENYTLTINDDQCLLLSETVWG—ALRGLETFSQLVWKSAE-GTFFINKTEIEDFPRFPH
  +
|-
 
|-
 
|-
 
|3BC9:
 
|3BC9:
 
|NAIDALHNNDIKVYFDAVLNHRMGADYAETVLLDENSRDKPGQYIKAWTGFNFPGRNGEYSNFTWN
 
|NAIDALHNNDIKVYFDAVLNHRMGADYAETVLLDENSRDKPGQYIKAWTGFNFPGRNGEYSNFTWN
  +
|-
 
|HEXA:
 
|HEXA:
 
|RGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPEL-MRKGSYNPVTHIY
 
|RGLLLDTSRHYLPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPEL-MRKGSYNPVTHIY
Line 138: Line 143:
 
|3BC9:
 
|3BC9:
 
|GQCFDGTDWDDYSKESGKYLFDEKSWDWTYNWDEDYLMGADVDYENEAVQNDVIDWGQWIINNIDF
 
|GQCFDGTDWDDYSKESGKYLFDEKSWDWTYNWDEDYLMGADVDYENEAVQNDVIDWGQWIINNIDF
  +
|-
 
|HEXA:
 
|HEXA:
 
|TAQDVKEVIEYARLRGIRVLAEFDTPGHTLSW-GPGIPGLLTPCYSGSEPSGTFGPVNPSLNN-TY
 
|TAQDVKEVIEYARLRGIRVLAEFDTPGHTLSW-GPGIPGLLTPCYSGSEPSGTFGPVNPSLNN-TY
Line 143: Line 149:
 
|3BC9:
 
|3BC9:
 
|DGFRLDAVKHIDYRFIDKWMSAVQNSSNRDVFFVGEAWVEDVDDLKGFLDTVGNPDLRVFDFPLRS
 
|DGFRLDAVKHIDYRFIDKWMSAVQNSSNRDVFFVGEAWVEDVDDLKGFLDTVGNPDLRVFDFPLRS
  +
|-
 
|HEXA:
 
|HEXA:
 
|-EFMSTFFLEVSSVFPDFYLHLGG-----DEVDFT-CW-KSNPEIQDFMRKKGF--GEDF-KQLES
 
|-EFMSTFFLEVSSVFPDFYLHLGG-----DEVDFT-CW-KSNPEIQDFMRKKGF--GEDF-KQLES
Line 148: Line 155:
 
|3BC9:
 
|3BC9:
 
|FFVDMLNGAYMADLRNAGLVNSPGYENRAVTFVDNHDTDRDEGSYTVSIYSRKYQAYAYILTRAEG
 
|FFVDMLNGAYMADLRNAGLVNSPGYENRAVTFVDNHDTDRDEGSYTVSIYSRKYQAYAYILTRAEG
  +
|-
 
|HEXA:
 
|HEXA:
 
|FYIQTL-LDIVSSYGKGYVVWQEVFDN-KVKIQP----DTIIQVWREDI-PVNYMKELELVTKA-G
 
|FYIQTL-LDIVSSYGKGYVVWQEVFDN-KVKIQP----DTIIQVWREDI-PVNYMKELELVTKA-G
Line 153: Line 161:
 
|3BC9:
 
|3BC9:
 
|VPTVYWKDYYIWEMKEGLDKLLTARRYYAYGPGYEVDNNDADIYSYVRSGFPDVAGDGLVLMISDG
 
|VPTVYWKDYYIWEMKEGLDKLLTARRYYAYGPGYEVDNNDADIYSYVRSGFPDVAGDGLVLMISDG
  +
|-
 
|HEXA:
 
|HEXA:
 
|FRALLSAPWYLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEY—VDNTNLVPRLWPR
 
|FRALLSAPWYLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEY—VDNTNLVPRLWPR
Line 158: Line 167:
 
|3BC9:
 
|3BC9:
 
|TSGNVAGKWINSRQPDTEFYDLTGHIKEHVTTDSEGYGNFKVIKSEDKGWSIWVPVE
 
|TSGNVAGKWINSRQPDTEFYDLTGHIKEHVTTDSEGYGNFKVIKSEDKGWSIWVPVE
  +
|-
 
|HEXA:
 
|HEXA:
 
|-AGAVAERLWSNKLTSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT-----
 
|-AGAVAERLWSNKLTSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT-----

Revision as of 15:17, 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