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PROMALS output alignment format PROMALS web server provides links to alignments in the following two formats. 1. Colored alignment The first line in each block shows conservation indices for positions with a conservation index above 5. Each representative sequence has a magenta name and is colored according to PSIPRED [7] secondary structure predictions (red: alpha-helix, blue: beta-strand). A representative sequence and the immediate sequences below it with black names, if there are any, form a closely related group (determined by option "Identity threshold"). Sequences within each group are aligned in a fast way. The groups are aligned using profile consistency with predicted secondary structures. In the example below, seq8, seq1, seq6, seq5 and seq9 are representative sequences; seq8, seq10 and seq7 form a closely related group, and seq6 is a group by itself. The consensus predicted secondary structures are shown in the last line in each block. If the fraction of helix or strand predictions among representative sequences in a position is larger than 0.5, the consensus letter is "h" or "e", respectively.
Colored alignment example: Conservation: 9669 6 6 9 9 99 9 7 6 9 696 66 6 6 67 99 seq8 ----SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKKMEKLNNIFFT seq10 --FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKKMEK------- seq7 ----SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKKMEKLNNIFF- seq1 -KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMR seq4 ------EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSV-VSYE-----------------MR seq3 -MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK----------- seq2 EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK--- seq0 --FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF------ seq6 --FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKKLEKLSSTLLR seq5 ----SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKKIEKLTTLLMR seq9 ---KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK---------- Consensus_ss: hhhhhhhhhhhhh eeeeeeeee eeeeee eeeeeee hhhhhhhhhhhhhhh Conservation: seq8 LM----------------------------------- seq10 ------------------------------------- seq7 ------------------------------------- seq1 LMELKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM seq4 LFGVQKDNFALEHSLL--------------------- seq3 ------------------------------------- seq2 ------------------------------------- seq0 ------------------------------------- seq6 SI----------------------------------- seq5 ------------------------------------- seq9 ------------------------------------- Consensus_ss: h 2. CLUSTAL format alignment
Each sequence and its name are on the same line and the sequences can be partitioned into a number of blocks separated by empty lines. The word "CLUSTAL" indicating the format can begin in the first line, but such a first line is optional.
CLUSTAL format alignment Example: seq8 ----SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKK
seq1 -KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKK
seq6 --FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKK
seq5 ----SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKK
seq9 ---KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
seq10 --FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKK
seq7 ----SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKK
seq4 ------EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSV-VSYE---------
seq3 -MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK-
seq2 EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKK
seq0 --FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKK
seq8 MEKLNNIFFTLM-----------------------------------
seq1 IEKFHSQLMRLMELKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
seq6 LEKLSSTLLRSI-----------------------------------
seq5 IEKLTTLLMR-------------------------------------
seq9 -----------------------------------------------
seq10 MEK--------------------------------------------
seq7 MEKLNNIFF--------------------------------------
seq4 ------MRLFGVQKDNFALEHSLL-----------------------
seq3 -----------------------------------------------
seq2 VEKLHGK----------------------------------------
seq0 IEKF-------------------------------------------
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