User:Eric Martz/Sandbox 13
From Proteopedia
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| - | >tr| | + | >tr|Q83WM5|Q83WM5_CAMJE FlgE OS=Campylobacter jejuni GN=flgE PE=4 SV=1 |
MMRSLWSGVSGLQAHQVAMDVEGNNISNVNTTGFKYSRADFGTMFSQTVKIATAPTDGRG | MMRSLWSGVSGLQAHQVAMDVEGNNISNVNTTGFKYSRADFGTMFSQTVKIATAPTDGRG | ||
| - | + | GSNPLQIGLGVSVSSTTRIHSQGSVQTTDKNTDVAINGDGFFMVSDDGGLTRYLTRSGDF | |
| - | + | KLDAYGNFVNNAGFVVQGWNINWDTQSIDSSRTPQNIFIDPGMHIPAAKSTEVAIKANLN | |
| - | + | SGLSVGTAKTPIYGLDSVHGFNKKDGTAKNENDTGITQFYTTSKNSVEVTEKGVDCAALF | |
| - | + | NGKGDGLNLRDGQGIWVSYADSKFSTDVPNGVNVFNPNTQATQNGVIFWGDENNAVNLDI | |
| - | + | TLNGVRIQNNSIKSLDQAIEYINTFTAPTDTREGTGVKAVRKADGSGIEFINTNADGTTD | |
| - | + | NMKNIDLVVNQANTAGERHNLTWQANNNSFQATSRKQGANSVWIPGNNPVNGTERIQIVT | |
| - | + | AHKYVYSSTPVQLDPMYNPDGGPAFNQANINTPGTAENNYRNAVNGSLLNTTVRTFRTTE | |
| - | + | DLRELLQRDARYGVDYDGSGGFEADGSDVNEGVKVTVGATGEFIISNPNVQSTPPNGIVQ | |
| - | + | NNRRPHDISFNVTAYTDAKGKVSTNMAFTNIFKGFDGVLTVGNSNRQSEQLFLSAFSAGL | |
| - | + | EIYDSLGSKHTLEVQFVKQSTTQDGGNEWQMIIRVPEPAEINTTGEGPNNIIVGTARFNN | |
| - | + | DGSLANYSPKTINFSPNNGAAPNQQIKLSFGTSGSNDGLVSSNSASTLTGQATDGYTSGN | |
| - | + | LKPDAIRVDDKGNILGEFTNGKTFAVAKMAMASVANNSGLEEIGGNLFKVTANSGAIVVG | |
| - | + | EAGTGGRGEMKTSALEMSNVDLSRSLTELIIIQRGYQANSKTISTSDQMLQTLIQLKQ | |
| - | + | ||
>sp|P0A1J1|FLGE_SALTY Flagellar hook protein flgE OS=Salmonella typhimurium GN=flgE PE=1 SV=2 | >sp|P0A1J1|FLGE_SALTY Flagellar hook protein flgE OS=Salmonella typhimurium GN=flgE PE=1 SV=2 | ||
MSFSQAVSGLNAAATNLDVIGNNIANSATYGFKSGTASFADMFAGSKVGLGVKVAGITQD | MSFSQAVSGLNAAATNLDVIGNNIANSATYGFKSGTASFADMFAGSKVGLGVKVAGITQD | ||
Revision as of 06:01, 25 May 2011
Sequence Alignment Tools
What I want:
- % identity vs. length of each chain and number of identical residues/chain length for each chain
- colors that indicate identity/similarity/difference
- ability to block a region of the alignment and get identity and length for that region (could cut and paste a new job ...)
Contents |
Uniprot.org
- no % ident
- gray colors
Jalview
Seems to be mostly an alignment editing tool.
ClustalW2 at EBI
- has colors but no color key
- no % id (?!)
- give a score but doesn't explain it.
RCSB Compare Structures
- Smith-Waterman or Needleman-Wunsch does #1,#2 but only for sequences of 3D structures.
- Smith-Waterman shows only the aligned segments, while Needleman-Wunsch shows full length with gaps.
Swiss-Model
Why doesn't it make a model of FlgE CamJe using 1wlg?
>tr|Q83WM5|Q83WM5_CAMJE FlgE OS=Campylobacter jejuni GN=flgE PE=4 SV=1 MMRSLWSGVSGLQAHQVAMDVEGNNISNVNTTGFKYSRADFGTMFSQTVKIATAPTDGRG GSNPLQIGLGVSVSSTTRIHSQGSVQTTDKNTDVAINGDGFFMVSDDGGLTRYLTRSGDF KLDAYGNFVNNAGFVVQGWNINWDTQSIDSSRTPQNIFIDPGMHIPAAKSTEVAIKANLN SGLSVGTAKTPIYGLDSVHGFNKKDGTAKNENDTGITQFYTTSKNSVEVTEKGVDCAALF NGKGDGLNLRDGQGIWVSYADSKFSTDVPNGVNVFNPNTQATQNGVIFWGDENNAVNLDI TLNGVRIQNNSIKSLDQAIEYINTFTAPTDTREGTGVKAVRKADGSGIEFINTNADGTTD NMKNIDLVVNQANTAGERHNLTWQANNNSFQATSRKQGANSVWIPGNNPVNGTERIQIVT AHKYVYSSTPVQLDPMYNPDGGPAFNQANINTPGTAENNYRNAVNGSLLNTTVRTFRTTE DLRELLQRDARYGVDYDGSGGFEADGSDVNEGVKVTVGATGEFIISNPNVQSTPPNGIVQ NNRRPHDISFNVTAYTDAKGKVSTNMAFTNIFKGFDGVLTVGNSNRQSEQLFLSAFSAGL EIYDSLGSKHTLEVQFVKQSTTQDGGNEWQMIIRVPEPAEINTTGEGPNNIIVGTARFNN DGSLANYSPKTINFSPNNGAAPNQQIKLSFGTSGSNDGLVSSNSASTLTGQATDGYTSGN LKPDAIRVDDKGNILGEFTNGKTFAVAKMAMASVANNSGLEEIGGNLFKVTANSGAIVVG EAGTGGRGEMKTSALEMSNVDLSRSLTELIIIQRGYQANSKTISTSDQMLQTLIQLKQ >sp|P0A1J1|FLGE_SALTY Flagellar hook protein flgE OS=Salmonella typhimurium GN=flgE PE=1 SV=2 MSFSQAVSGLNAAATNLDVIGNNIANSATYGFKSGTASFADMFAGSKVGLGVKVAGITQD FTDGTTTNTGRGLDVAISQNGFFRLVDSNGSVFYSRNGQFKLDENRNLVNMQGMQLTGYP ATGTPPTIQQGANPAPITIPNTLMAAKSTTTASMQINLNSTDPVPSKTPFSVSDADSYNK KGTVTVYDSQGNAHDMNVYFVKTKDNEWAVYTHDSSDPAATAPTTASTTLKFNENGILES GGTVNITTGTINGATAATFSLSFLNSMQQNTGANNIVATNQNGYKPGDLVSYQINNDGTV VGNYSNEQEQVLGQIVLANFANNEGLASQGDNVWAATQASGVALLGTAGSGNFGKLTNGA LEASNVDLSKELVNMIVAQRNYQSNAQTIKTQDQILNTLVNLR
