GDE alignment format

GDE alignment format is one of standard alignment formats. A popular program for sequence alignment, Clustal, for example, can save alignment in this format. In this format, all letters indicating amino acids are in lower case, gaps are indicated by dashes. Sequences are placed one after another, name of each sequence is placed onto a separate line and begins with %. The sequence is placed afterwards beginning on the next line and may be broken into several lines. Thus the alignment might look like this:

%EC_RbsR
-------------------------MATMKDVARLAGVSTSTVSHVINKD---RFVSEAI
TAKVEAAIKELNYAP---SALARSLKLNQTHTIGMLITASTN-----PFYSELVRGVERS
CFERGYSLVLCNTEGD-EQRMNRNLETLMQK-RVDGLLLLCTETHQPSREIMQRYPTVPT
--VMMDW--APFDGDSDLIQDNSLLGGDLATQYLIDKGHTR-IACITG-PLDKTPARLR-
-----LEGYRAAMKRAGLNIPDGYEVTG---DFEFNGGFDAMRQLLSHP--LRPQAVFTG
NDAMAVGVYQALYQAE-LQVPQDIAVIGYDDIE---LASFMTPPLTTIHQPKDELGELAI
DVLIHRITQPT------LQQQRLQLTPILMERGSA------------------------
%Pp_RbsR
-------------------------MATIKDVAALAGISYTTVSHVLNKT---RPVSEQV
RLKVEAAIIELDYVP---SAVARSLKARSTATIGLLVPNSVN-----PYFAELARGIEDA
CERNGYCVILCNSDDN-PQKQRSYLRVLLEK-RIDGLVVASVGQDD---DLLQSLASVRT
PMVIVDR--ELEGVDADLVRIDHEQGAYLATRHLLELGHRD-VAYIGG-PAETGVTQLR-
-----LSGFRRAMAEAGAPVPGSRVLHC---DFTSPGGHAAAAQVLEG---KRPSAIFAG
NDMIGFGVLRAAAERN-ISVPGELSVIGFDDIE---LSRYVYPSLTTVGQSIRELGESAA
SLLLTRIATPRQG----AAEQRIVAPRIVLRESTGPRPDLFNDY---------------
%BS_RbsR
-------------------------MATIKDVAGAAGVSVATVSRNLNDN---GYVHEET
RTRVIAAMAKLNYYP---NEVARSLYKRESRLIGLLLPDITN-----PFFPQLARGAEDE
LNREGYRLIFGNSDEE-LKKELEYLQTFKQN-HVAGIIAAT------NYPDLEEYSGMNY
PVVFLDR--TLEG-APSVSS-DGYTGVKLAAQAIIHGKSQR-ITLLRG-PAHLPTAQDR-
-----FNGALEILKQA--EVDFQVIETA---SFSIKDAQSMAKELFASY--PATDGVIAS
NDIQAAAVLHEALRRG-KNVPEDIQIIGYDDIP---QSGLLFPPLSTIKQPAYDMGKEAA
KLLLGIIKKQP------LAETAIQMPVTYIGRKTTRKED--------------------
%SACR_LACLA
-------------------------MIKLEDVANKAGVSVTTVSRVINRK---GYLSDAT
ISKVEKAMQDLHYIP---NAAARSLQGKSLKLIGLVFPTIKN-----IFYAELIEKIEQA
LFIRGYKAMLATTEHD-EQKERDYLALLLSN-QVDGIIYGS------HNLKAHDYIAIEA
PIVAFDR--LLTP-ETTVVSSDNFEGGILATKALINSGSKK-IAIFTGNDNTNSPTYLR-
-----RDGYLLELERN--QLKTHIIKIP---SQWTLLRKKVEIKKILEN--NDFDGVFCT
DDLTAILVKDLAS-----NLKKSLNVVGFDGTE---FIENYYPNLTTIKQPINDLAELLV
DLIIRKIDGD-------NIDITYQLPVQLHYGID-------------------------