QL Secondary Structure Prediction
Using Homologues
No more than
80
characters per line
Single-letter
residue codes
Arbitrary white spaces between proteins, but
not
between residues.
Maximum of
50
homologues
Maximum of
2000
residues per protein
Gaps are represented by '-' (hyphens)
Characters b,j,o,u,x, and z are treated as unknown residues
You can save the results as plain text by clicking on the link at the bottom of the results page (loading the plain text up on another page), then using the save option on your web browser
The following is an example of the appropriate format:
OUTPUT format:
All 3 probabilities
Predicted sec. structure
Predicted sec. structure w/ prob.
Eye-Friendly: Seq. followed by prediction in rows
INPUT format:
CLUSTAL
CLUSTAL
format only: Sequence begins in column:
Number of proteins in alignment:
Type in your alignment here:
Gap fixed = 10 Gap vary. = 10 * :=> match across all seqs. . :=> conservative substitutions pbdg GETSEQ fr MTKT------LPKDFIFGGATAAYQAEGATHTDGKGPVAWDKYLEDNYWY----TAEPAS lacg_staau P111 MTKT------LPEDFIFGGATAAYQAEGATNTDGKGRVAWDTYLEENYWY----TAEPAS lacg_lacca P146 MSKQ------LPQDFVMGGATAAYQVEGATKEDGKGRVLWDDFLDKQGRF----KPDPAA bgla_clotm P262 MS--KIT---FPKDFIWGSATAAYQIEGAYNEDGKGESIWDRFSHTPGNIADGHTGDVAC bgla_bacci Q035 MS--IHM---FPSDFKWGVATAAYQIEGAYNEDGRGMSIWDTFAHTPGKVKNGDNGNVAC bgls_calsa P104 MD--M-S---FPKGFLWGAATASYQIEGAWNEDGKGESIWDRFTHQKRNILYGHNGDVAC bgla_bacpo P220 MT--IFQ---FPQDFMWGTATAAYQIEGAYQEDGRGLSIWDTFAHTPGKVFNGDNGNVAC bgls_agrsp P126 MTDPNTLAARFPGDFLFGVATASFQIEGSTKADGRKPSIWDAFCNMPGHVFGRHNGDIAC bglb_bacpo P225 MSENTFI---FPATFMWGTSTSSYQIEGGTDEGGRTPSIWDTFCQIPGKVIGGDCGDVAC *. .* .* * .*...* **. ...*. ** . . . * pbdg GETSEQ fr DFYHKYPVDLELAEEYGVNGIRISIAWSRIFPTGYGEVNEKGVEFYHKLFAECHKRHVEP lacg_staau P111 DFYNRYPVDLELSEKFGVNGIRISIAWSRIFPNGYGEVNPKGVEYYHKLFAECHKRHVEP lacg_lacca P146 DFYHRYDEDLALAEKYGHQVIRVSIAWSRIFPDGAGEVEPRGVAFYHKLFADCAAHHIEP bgla_clotm P262 DHYHRYEEDIKIMKEIGIKSYRFSISWPRIFPEGTGKLNQKGLDFYKRLTNLLLENGIMP bgla_bacci Q035 DSYHRVEEDVQLLKDLGVKVYRFSISWPRVLPQGTGEVNRAGLDYYHRLVDELLANGIEP bgls_calsa P104 DHYHRFEEDVSLMKELGLKAYRFSIAWTRIFPDGFGTVNQKGLEFYDRLINKLVENGIEP bgla_bacpo P220 DSYHRYEEDIRLMKELGIRTYRFSVSWPRIFPNGDGEVNQEGLDYYHRVVDLLNDNGIEP bgls_agrsp P126 DHYNRWEEDLDLIKEMGVEAYRFSLAWPRIIPDGFGPINEKGLDFYDRLVDGCKARGIKT bglb_bacpo P225 DHFHHFKEDVQLMKQLGFLHYRFSVAWPRIMPAA-GIINEEGLLFYEHLLDEIELAGLIP * ... *. . .. * * *..*.*..* . * .. *. .*... . . . pbdg GETSEQ fr FVTLHHFDTPEALHSNGDFLNRENIEHFIDYAAFCFEEFPE-VNYWTTFNEIGPIGDGQY lacg_staau P111 FVTLHHFDTPEVLHKDGDFLNRKTIDYFVDYAEYCFKEFPE-VKYWTTFNEIGPIGDGQY lacg_lacca P146 FVTLHHFDTPERLHEAGDWLSQEMLDDFVAYAKFCFEEFSE-VKYWITINEPTSMAVQQY bgla_clotm P262 AITLYHWDLPQKLQDKGGWKNRDTTDYFTEYSEVIFKNLGDIVPIWFTHNEPGVVSLLGH bgla_bacci Q035 FCTLYHWDLPQALQDQGGWGSRITIDAFAEYAELMFKELGGKIKQWITFNEPWCMAFLSN bgls_calsa P104 VVTLYHWDLPQKLQDIGGWANPEIVNYYFDYAMLVINRYKDKVKKWITFNEPYCIAFLGY bgla_bacpo P220 FCTLYHWDLPQALQDAGGWGNRRTIQAFVQFAETMFREFHGKIQHWLTFNEPWCIAFLSN bgls_agrsp P126 YATLYHWDLPLTLMGDGGWASRSTAHAFQRYAKTVMARLGDRLDAVATFNEPWCAVWLSH bglb_bacpo P225 MLTLYHWDLPQWIEDEGGWTQRETIQHFKTYASVIMDRFGERINWWNTINEPYCASILGY **.*.* * . *.. . . . .. . . . * ** pbdg GETSEQ fr LVGKFPPGIKYDLAKVFQSHHNMMVSHARAVKLYKDKGYKGEIGVVHALPTKY------P lacg_staau P111 LVGKFPPGIKYDFEKVFQSHHNMMVAHARAVKLFKDGGYKGEIGVVHALPTKY------P lacg_lacca P146 TTGTFPPAESGRFDKTFQAEHNQMVAHARIVNLYKSMQLGGQIGIVHALQTVY------P bgla_clotm P262 FLGIHAPGIK-DLRTSLEVSHNLLLSHGKAVKLFREMNIDAQIGIALNLSYHY------P bgla_bacci Q035 YLGVHAPGNK-DLQLAIDVSHHLLVAHGRAVTLFRELGISGEIGIAPNTSWAV------P bgls_calsa P104 FHGIHAPGIK-DFKVAMDVVHSLMLSHFKVVKAVKENNIDVEVGITLNLTPVYLQTERLG bgla_bacpo P220 MLGVHAPGLT-NLQTAIDVGHHLLVAHGLSVRRFRELGTSGQIGIAPNVSWAV------P bgls_agrsp P126 LYGVHAPGER-NMEAALAAMHHINLAHGFGVEASRHVAPKVPVGLVLNAHSA------IP bglb_bacpo P225 GTGEHAPGHE-NWREAFTAAHHILMCHGIASNLHKEKGLTGKIGITLNMEHVDAASER-- * .*. . * . * . .*.. . pbdg GETSEQ fr YDPENPADVRAAELEDIIHNKFILDATYLGHYSDKTMEGVNHIL-AENGGELDLRDEDFQ lacg_staau P111 FDPSNPEDVRAAELEDIIHNKFILDATYLGKYSRETMEGVQHIL-SVNGGKLNITDEDYA lacg_lacca P146 Y-SDSAVDHHAAELQDALENRLYLDGTLAGEYHQETLALVKEILDANHQPMFQSTPQEMK bgla_clotm P262 A-SEKAEDIEAAELSFSLAGRWYLDPVLKGRYPENALKLYKKKGI-----ELSFPEDDLK bgla_bacci Q035 Y-RRTKEDMEACLRVNGWSGDWYLDPIYFGEYPKFMLDWYENLGY-----KPPIVDGDME bgls_calsa P104 Y-KVSEIEREMVSLSSQLDNQLFLDPVLKGSYPQKLLDYLVQKDLLDSQKALSMQQEVKE bgla_bacpo P220 Y-STSEEDKAACARTISLHSDWFLQPIYQGSYPQFLVDWFAEQGA-----TVPIQDGDMD bgls_agrsp P126 A-SDGEADLKAAERAFQFHNGAFFDPVFKGEYPAEMMEALGD-------RMPVVEAEDLG bglb_bacpo P225 -----PEDVAAAIRRDGFINRWFAEPLFNGKYPEDMVEWYGT--YLNGLD--FVQPGDME . . . * * . pbdg GETSEQ fr ALDAAKDLNDFLGINYYMSDWMQAFDGETEIIHNGKGEKGSSKYQIKGVGRRVAPDYVPR lacg_staau P111 ILDAAKDLNDFLGINYYMSDWMRGYDGESEITHNATGDKGGSKYQLKGVGQREFDVDVPR lacg_lacca P146 AIDEAAHQLDFVGVNNYFSKWLRAYHGKSETIHNGDGTKGSSVARLQGVGEEKLPDGIET bgla_clotm P262 LISQP---IDFIAFNNYSSEFIK-YDPSSESGFSPA--------------NSIL-EKFEK bgla_bacci Q035 LIHQP---IDFIGINYYTSSMNR-YNPGEAGGMLSS--------------EAIS-MGAPK bgls_calsa P104 NFIFP----DFLGINYYTRAVRL-YDENSSWIFPIR--------------WEHP-AG-EY bgla_bacpo P220 IIGEP---IDMIGINYYSMSVNR-FNP--EAGFLQS--------------EEIN-MGLPV bgls_agrsp P126 IISQK---LDWWGLNYYTPMRVA-DDATPGVEFPAT--------------MPAPAVSDVK bglb_bacpo P225 LIQQP---GDFLGINYYTRSIIR---STNDASLLQV--------------EQVH-MEEPV . * . * * . pbdg GETSEQ fr TDWDWIIYPEGLYDQIMRVKNDYPNYKKIYITENGLGYKDEFVDN-----TVYDDGRIDY lacg_staau P111 TDWDWMIYPQGLYDQIMRVVKDYPNYHKIYITENGLGYKDEFIES---EKTVHDDARIDY lacg_lacca P146 TDWDWSIYPRGMYDILMRIHNDYPLVPVTYVTENGIGLKESLPENATPDTVIEDPKRIDY bgla_clotm P262 TDMGWIIYPEGLYDLLMLLDRDYGK-PNIVISENGAAFKDEIGSNGK----IEDTKRIQY bgla_bacci Q035 TDIGWEIYAEGLYDLLRYTADKYGN-PTLYITENGACYNDGLSLDGR----IHDQRRIDY bgls_calsa P104 TEMGWEVFPQGLFDLLIWIKESYPQ-IPIYITENGAAYNDIVTEDGK----VHDSKRIEY bgla_bacpo P220 TDIGWPVESRGLYEVLHYL-QKYGN-IDIYITENGACINDEV-VNGK----VQDDRRISY bgls_agrsp P126 TDIGWEVYAPALHTLVETLYERYDL-PECYITENGACYNMGVE-NGQ----VNDQPRLDY bglb_bacpo P225 TDMGWEIHPESFYKLLTRIEKDFSKGLPILITENGAAMRDEL-VNGQ----IEDTGRHGY *. .* . . .. . . . ..*** . . . * * * pbdg GETSEQ fr VKQHLEVLSDAIADGANVKGYFIWSLMDVFSWSNGYEKRYGLFYVDFDTQERYPKKSAHW lacg_staau P111 VRQHLNVIADAIIDGANVKGYFIWSLMDVFSWSNGYEKRYGLFYVDFETQERYPKKSAYW lacg_lacca P146 VKKYLSAMADAIHDGANVKGYFIWSLQDQFSWTNGYSKRYGLFFVDFPTQNRYIKQSAEW bgla_clotm P262 LKDYLTQAHRAIQDGVNLKAYYLWSLLDNFEWAYGYNKRFGIVHVNFDTLERKIKDSGYW bgla_bacci Q035 LAMHLIQASRAIEDGINLKGYMEWSLMDNFEWAEGYGMRFGLVHVDYDTLVRTPKDSFYW bgls_calsa P104 LKQHFEAARKAIENGVDLRGYFVWSLMDNFEWAMGYTKRFGIIYVDYETQKRIKKDSFYF bgla_bacpo P220 MQQHLVQVHRTIHDGLHVKGYMAWSLLDNFEWAEGYNMRFGMIHVDFRTQVRTPKESYYW bgls_agrsp P126 YAEHLGIVADLIRDGYPMRGYFAWSLMDNFEWAEGYRMRFGLVHVDYQTQVRTVKNSGKW bglb_bacpo P225 IEEHLKACHRFIEEGGQLKGYFVWSFLDNFEWAWGYSKRFGIVHINYETQERTPKQSALW .. * .* ...* **. * *.*. ** .*.*. ... * * *.* . pbdg GETSEQ fr YKKLAET------QVI-E lacg_staau P111 YKELAET------KEI-K lacg_lacca P146 FKSVSET------HIIPD bgla_clotm P262 YKEVI----KNNGF---- bgla_bacci Q035 YKGVI----SRGWLDL-- bgls_calsa P104 YQQYI----KEN-----S bgla_bacpo P220 YRNVV----SNNWLETRR bgls_agrsp P126 YSALASGFPKGNHGVAKG bglb_bacpo P225 FKQMM----AKNGF----
You can look at the
references
or the
Quadratic Logistic Algorithm
Last updated : 1/20/2000