User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods
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| - | Turns out one is PI (3b8a) and the other is PII (1ig8). | + | Turns out they are not the same protein; one is yeast hexokinase PI (3b8a) and the other is hexokinase PII (1ig8). |
According to help page for the Yale Morph server this task was submitted, this shouldn't matter because it will do a ClustalW alignment. Frustratingly, though it does seem to matter because they always seem to need to be identical to me for anything to work at the Yale Morph server. And unfortunately when it fails, it doesn't tell you why it failed or even that it failed. A lot of stuff they talk about never got implemented and maybe the alignment was part of it? | According to help page for the Yale Morph server this task was submitted, this shouldn't matter because it will do a ClustalW alignment. Frustratingly, though it does seem to matter because they always seem to need to be identical to me for anything to work at the Yale Morph server. And unfortunately when it fails, it doesn't tell you why it failed or even that it failed. A lot of stuff they talk about never got implemented and maybe the alignment was part of it? | ||
Revision as of 22:19, 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, according to FASTA sequence obtained for each PDB file from PDBsum, differ quite a bit:
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
Turns out they are not the same protein; one is yeast hexokinase PI (3b8a) and the other is hexokinase PII (1ig8).
According to help page for the Yale Morph server this task was submitted, this shouldn't matter because it will do a ClustalW alignment. Frustratingly, though it does seem to matter because they always seem to need to be identical to me for anything to work at the Yale Morph server. And unfortunately when it fails, it doesn't tell you why it failed or even that it failed. A lot of stuff they talk about never got implemented and maybe the alignment was part of it?
