COMBOSA

COMBOSA (Coloring Of Molecules Based On Sequence Alignment) is used to color a three dimensional representation of a protein according to the results of a sequence alignment. The program accepts a group of aligned sequences in FASTA or GDE format (one of the sequences must have a solved three dimensional structure), and it generates a script that can be used by a molecular visualization program (RasMol). The script adjusts the color and appearance of the molecule so that conserved residues are highlighted.

Paste the aligned sequences (in FASTA or GDE format) into the text area below. If you include the solved sequence in this text area the identity and similarity calculations will include the solved sequence. >CbrigsFEM-2 MSGPPPPKTNEKSSQPVTG-RSQEPTRKGQLGPNYLRIIEEDEEYGHALL EPSEEQIKFEREALFEDLHLDRQRSARSFIEETFEEEMLGPQN-GIPPTT ESPQSYIPIRYRNPPAAAPVHDVFGDAVHAIFQKLMTRGPPVEYCHWMSY WIAKQID-KDSPVKYHECRFTPDQYVTENTAEAKKTYMDNMWKAAEKNLW MYTYNSPLLRTKWTGIHVSAEQIKGQRHKQEDRFVA-YPNSLYMDTSRSD HIALLGVFDGHGGHECSQYAAGHMWETWIETRASHFEE------PLEKQL KTSLDLLDERMTVRSTKE--CWKGGTTAVCCAIDMNKKELAFAWLGDSPG YIMDNLEVRKVTRDHSPSDPEEGRRVEEAGGQLFVIGGELRVNGVLNLTR ALGDV---------PGRPMISNQAETCQRDIEVG---DYLVILACDGISD VFNTSDLYNLVQAYVNENPVEEYNDLAHYICHEAIAHGSTDNVTVV-IGF LRPPQDLWRMMKIDEESDEEEDEVDDE----------------------- ------------------------------------------- >CremFEM-2 ----MSDSLNHPSSSTVHADDGFEPPTSP----------EDNNK------ KPSLEQIKQEREALFTDLFADRRRSARSVIEEAFQNELMSAE--PVQPNV PNPHS-IPIRFRHQPVAGPAHDVFGDAVHSIFQKIMSRGVNADYSHWMSY WIALGID-KKTQMNYHMKPFCKDTYATEGSLEAKQTFTDKIRSAVEEIIW KSAEYCDILSEKWTGIHVSADQLKGQRNKQEDRFVA-YPNGQYMNRGQSD -ISLLAVFDGHGGHECSQYAAAHFWEAWSDAQHHHSQDM-----KLDELL EKALETLDERMTVRSVRE--SWKGGTTAVCCAVDLNTNQIAFAWLGDSPG YIMSNLEFRKFTTEHSPSDPEECRRVEEVGGQIFVIGGELRVNGVLNLTR ALGDV---------PGRPMISNKPDTLLKTIEPA---DYLVLLACDGISD VFNTSDLYNLVQAFVNEYDVEDYHELARYICNQAVSAGSADNVTVV-IGF LRPPEDVWRVMK--TDSDDEESELEEEDDNE------------------- ------------------------------------------- >CeleFEM-2 -------------------------------------------------- ---MEKVNEERDAVFEDHIGDRRRSVRSLLEEAFADEMEKTSYDVEVADT PQPH--IPIRFRHPPIAGPVHDVFGDAIHDIFQKMMKRGQAVDFCHWVSH LIATEIDEKFSEVAFRDVQYNPDIYVTDSTTEAKKLFNDKIWPAIDKILQ QNAETCPILSEKWSGIHVSGDQLKGQRHKQEDRFLA-YPNGQYMDRGEDP -ISVLAVFDGHGGHECSQYAAGHLWETWLEVRKSRDPSD-----SLEDQL RKSLELLDERMTVRSVKE--CWKGGSTAVCCAIDMDQKLMALAWLGDSPG YVMSNIEFRQLTRGHSPSDEREARRVEEAGGQLFVIGGELRVNGVLNLTR ALGDV---------PGRPMISNEPETCQVPIESS---DYLVLLACDGISD VFNERDLYQLVEAFANDYPVEDYAELSRFICTKAIEAGSADNVSVV-IGF LRPPQDVWKLMK--HESDDEDSDVTDEE---------------------- -------------------------------------------

Paste the aligned solved sequence into the text area below (be sure to include the sequence title). The script that is generated should only be used when examining the structure of the molecule described by this sequence.

Use the following two selections to alter the appearance of the accompanying multiple alignment figure.

• Show 100 90 80 70 60 50 40 30 residues per line.
• Use bold regular text.

Choose the colors you wish to use for highlighting. Gaps (amino acids in the solved sequence that align with gaps in the other sequences) have the highest priority for coloring, followed by identical amino acids, and then similar amino acids.

• Color gaps white very light gray light gray medium gray dark gray very dark gray black lightest red very light red light red medium red dark red very dark red darkest red lightest yellow very light yellow light yellow medium yellow dark yellow very dark yellow darkest yellow lighest blue very light blue light blue medium blue dark blue very dark blue darkest blue lighest green very light green light green medium green dark green very dark green darkest green , identical amino acids white very light gray light gray medium gray dark gray very dark gray black lightest red very light red light red medium red dark red very dark red darkest red lightest yellow very light yellow light yellow medium yellow dark yellow very dark yellow darkest yellow lighest blue very light blue light blue medium blue dark blue very dark blue darkest blue lighest green very light green light green medium green dark green very dark green darkest green , and similar amino acids white very light gray light gray medium gray dark gray very dark gray black lightest red very light red light red medium red dark red very dark red darkest red lightest yellow very light yellow light yellow medium yellow dark yellow very dark yellow darkest yellow lighest blue very light blue light blue medium blue dark blue very dark blue darkest blue lighest green very light green light green medium green dark green very dark green darkest green
• Percentage of sequences that must agree for gap, identity, or similarity coloring to be added: 10 20 30 40 50 60 70 80 90 100
• The default color (the color used if no gap, identity, or similarity coloring is added): white very light gray light gray medium gray dark gray very dark gray black lightest red very light red light red medium red dark red very dark red darkest red lightest yellow very light yellow light yellow medium yellow dark yellow very dark yellow darkest yellow lighest blue very light blue light blue medium blue dark blue very dark blue darkest blue lighest green very light green light green medium green dark green very dark green darkest green

Enter the groups of similar amino acids separated by commas to be used for the similarity calculation. ILV,FWY,KRH,DE,GAS,P,C,TNQM