User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods
From Proteopedia
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* When I received nothing back after several minutes I looked at the end of the sequences to see if they matched identially and noticed they didn't have the same C-terminus or even N-terminus. In fact what I thought were the same protein have several differences: | * When I received nothing back after several minutes I looked at the end of the sequences to see if they matched identially and noticed they didn't have the same C-terminus or even N-terminus. In fact what I thought were the same protein have several differences: | ||
| - | <small><font face = 'courier'> | + | <small><font face = 'courier'><code> |
1ig8 1 ---DVPKELMQQIENFEKIFTVPTETLQAVTKHFISELEKGLSKKGGNIP 47 | 1ig8 1 ---DVPKELMQQIENFEKIFTVPTETLQAVTKHFISELEKGLSKKGGNIP 47 | ||
| - | |||||||.:|...|.:|||.:|||:.|.||||.||.|||:||||||| | + | <nowiki>|||||||.:|...|.:|||.:|||:.|.||||.||.|||:|||||||</nowiki> |
3b8a 1 SMADVPKELMDEIHQLEDMFTVDSETLRKVVKHFIDELNKGLTKKGGNIP 50 | 3b8a 1 SMADVPKELMDEIHQLEDMFTVDSETLRKVVKHFIDELNKGLTKKGGNIP 50 | ||
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||||||::||||||||:||||| | ||||||::||||||||:||||| | ||
3b8a 449 AVIAALSEKRIAEGKSLGIIGA 470 | 3b8a 449 AVIAALSEKRIAEGKSLGIIGA 470 | ||
| + | </code> | ||
<br> | <br> | ||
</font></small><br/> | </font></small><br/> | ||
| - | According to help page, this shouldn't matter but they always seem to need to be identical to me for anything to work at the Yale Morph server. | + | According to help page for the Yale Morph server this task was submitted, this shouldn't matter because it will do a ClustalW alignment but they always seem to need to be identical to me for anything to work at the Yale Morph server. |
Revision as of 05:44, 7 January 2012
MORPH
- First I changed chain X of 3b8a to chain A to match 1ig8 using PDB Goodies for the protein. I knew PDB Goodies ignored and left out the heteroatoms so I changed the few lines of the glucose ligand to chain a by hand. Th heterotoms will not be used by the Yale Morph server but I need them in the original file in order to be able to use fit or compare to add them in later.
- Submitted 1gi8 and the altered 3b8a to the Yale Morph beta server
- When I received nothing back after several minutes I looked at the end of the sequences to see if they matched identially and noticed they didn't have the same C-terminus or even N-terminus. In fact what I thought were the same protein have several differences:
1ig8 1 ---DVPKELMQQIENFEKIFTVPTETLQAVTKHFISELEKGLSKKGGNIP 47
|||||||.:|...|.:|||.:|||:.|.||||.||.|||:|||||||
3b8a 1 SMADVPKELMDEIHQLEDMFTVDSETLRKVVKHFIDELNKGLTKKGGNIP 50
1ig8 48 MIPGWVMDFPTGKESGDFLAIDLGGTNLRVVLVKLGGDRTFDTTQSKYRL 97
|||||||:||||||||::|||||||||||||||||.|:.|||||||||:|
3b8a 51 MIPGWVMEFPTGKESGNYLAIDLGGTNLRVVLVKLSGNHTFDTTQSKYKL 100
1ig8 98 PDAMRTTQNPDELWEFIADSLKAFIDEQFPQGISEPIPLGFTFSFPASQN 147
|..||||::.:|||.|||||||.|:.||.... ::.:|||||||:|||||
3b8a 101 PHDMRTTKHQEELWSFIADSLKDFMVEQELLN-TDTLPLGFTFSYPASQN 149
1ig8 148 KINEGILQRWTKGFDIPNIENHDVVPMLQKQITKRNIPIEVVALINDTTG 197
||||||||||||||||||:|.|||||:||.:|:||.:|||:|||||||.|
3b8a 150 KINEGILQRWTKGFDIPNVEGHDVVPLLQNEISKRELPIEIVALINDTVG 199
1ig8 198 TLVASYYTDPETKMGVIFGTGVNGAYYDVCSDIEKLQGKLSDDIPPSAPM 247
||:||||||||||||||||||||||:|||.||||||:|||:||||.::||
3b8a 200 TLIASYYTDPETKMGVIFGTGVNGAFYDVVSDIEKLEGKLADDIPSNSPM 249
1ig8 248 AINCEYGSFDNEHVVLPRTKYDITIDEESPRPGQQTFEKMSSGYYLGEIL 297
|||||||||||||:||||||||:.:||:|||||||.||||:|||||||:|
3b8a 250 AINCEYGSFDNEHLVLPRTKYDVAVDEQSPRPGQQAFEKMTSGYYLGELL 299
1ig8 298 RLALMDMYKQGFIFKNQDLSKFDKPFVMDTSYPARIEEDPFENLEDTDDL 347
||.|:::.::|.:.|:|||||..:|::||||||||||:|||||||||||:
3b8a 300 RLVLLELNEKGLMLKDQDLSKLKQPYIMDTSYPARIEDDPFENLEDTDDI 349
1ig8 348 FQNEFGINTTVQERKLIRRLSELIGARAARLSVCGIAAICQKRGYKTGHI 397
||.:||:.||:.||||||||.||||.|||||:||||||||||||||||||
3b8a 350 FQKDFGVKTTLPERKLIRRLCELIGTRAARLAVCGIAAICQKRGYKTGHI 399
1ig8 398 AADGSVYNRYPGFKEKAANALKDIYGWTQTSLDDYPIKIVPAEDGSGAGA 447
||||||||:||||||.||..|:||||||..:..| ||.||||||||||||
3b8a 400 AADGSVYNKYPGFKEAAAKGLRDIYGWTGDASKD-PITIVPAEDGSGAGA 448
1ig8 448 AVIAALAQKRIAEGKSVGIIGA 469
||||||::||||||||:|||||
3b8a 449 AVIAALSEKRIAEGKSLGIIGA 470
According to help page for the Yale Morph server this task was submitted, this shouldn't matter because it will do a ClustalW alignment but they always seem to need to be identical to me for anything to work at the Yale Morph server.
