Jnet secondary structure prediction

QUERY      : PTVERSTRMSNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVATGDQKLKDGGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFVMAGDQNSSYRHPAVYDEKEKTCHMLYLSAQENMGPRYCSPDAQNRDAVFCFKPDKNESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQPTQYEEEMTDYQKIQQGFRQNNREMIKSAFLPVGAFNSDNFKSKGRGFNWANFDSVKKKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIKKQSRNMNLYSVDGERIVLPRIFISNDKESIKCPCEPERISNSTCNFYVCNCVEKRAEIKENNQVVIKEEFRDYYENGEEKSNKQMLL : QUERY 
AMA1_PLACH : ---ERSHKLINPWEKFMEKYDIEKVHGSGIRVDLGEDARVENQDYRIPSGKCPVMGKGITIQNSKVSFLTRVATGNQKVREGGLAFPQTDVNISPITIDNLKLMYKDHKEILALNDMSLCAKHASFYVPGTNVNTAYRHPAVYDKSNKTCYILYVAAQENMGPRYCSNEEDNENQPFCFTPEKKDEYKNLSYLTKNLREDWETSCPNKSIQNAKFGVWVDGYCSEYQKKEVHDNKTLLECNQIVFNESASDQPKQYEKHLEDTAKIRRGIVDRNGKLIGEALLPIGSYRADQVKSKGKGYNWANYDKKTKKCYIFNKKPTCLINDKDFVATTALSSLEEGPQEFPCDIYKKKIAEEIKVMNVNRNNNGND--TIKFPRIFISDDKESLNCPCEPTQLTQSTCKFFVCNCVEKRQFISENNEVEIKDEFKSEYESP---------- : AMA1_PLACH
Q25657     : ---ERSTKLINPWEKYTEKYDIERMHGSGIRVDLGEDARVENRDYRIPSGKCPVIGKGITIQNSEVSFLTPVATGDQSVRSGGLALPKTDVHLSPITIDNLKTMYKEHTEIVKLNNMSLCAKHTSFYVPGNNANSAYRHPAVYDKSNSTCYMLYVAAQENMGPRYCSNNANNDNQPFCFTPEKIEKYKNLSYLTKNLRDDWETSCPNKSIKNAKFGIWVDGYCKDYQKHTVHDSDSLLKCNQIIFNESASDQPKQYEKHLEDTTKFRQGVAERNGKLIGEALLPIGSYKSDQIKSHGRGYNWGNYDSQNKKCYIFETKPTCLINDRNFIATTALSSTEEFEEQFPCDIYKNKINEEIKVLNKNI---SNGNNSIEFPRIFISTDKNSLNCPCEPTQLTESSCNFYVCNCVEKRQYIAENNDVEIKEEL----------------- : Q25657
Q9BIM8     : ---------------------------------------VAGTQYRLPSGKCPVFGKGIIIENSNTTFLKPVATGNQDLKDGGFAFPPTNPLISPMTLNGMRDFYKNNEYVKNLDELTLCSRHAGNMNPDNDKNSNYKYPAVYDYNDKKCHILYIAAQENNGPRYCNKDQSKRNSMFCFRPAKDKLFENYTYLSKNVVDNWEEVCPRKNLENAKFGLWVDGNCEDIPHVNEFSANDLFECNKLVFELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNRETQKCEIFNVKPTCLINNSSYIATTALSHPIEVEHNFPCSLYKDEIKKEIERESKRIKLNDNDDEKIIAPRIFISDDKDSLKCPCDPEMVSNSTCRFFVCKCVERRAEVTSNN------------------------- : Q9BIM8
Q25688     : --------LINPWEKFMEKYDIEKVHGSGIRVDLGEDARVENQDYRIPSGKCPVMGKGITIQNSKVSFLTRVATGNQKVREGGLAFPQTDVNISPITIANLKLMYKDHKEILALNDMSLCAKHASFYVPGTNVNTAYRHPAVYDKSNQTCYILYVAAQENMGPRYCSNEEDNENQPFCFTPEKKDEYKNLSYLTKNLREDWETSCPNKSIQNAKFGVWVDGYCSEYQKKEVRDSNSLSDCSKIVFDESASDQPKQYEKHLEDTAKIRRGIVDRNGKLIGEALLPIGSYRADQVKSKGKGYNWANYDKKEKKCYIFNKKPTCLINDKNFVATTALS-------------------------------------------------------------------------------------------------------------- : Q25688
O15681     : ---------GNPFKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRNFLEDVPT-EKEYKQSGNPLPPSGQRISPFPM----ELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKAYRYPFVYDSKKRLCHILYVSMQLMEGKKYCSVKGEPPDLTYCFKPRKSVTENHLIYGSAYVGENPDSKCPNQALRGYRFGVWKKGRCLDYTELTDTRVESKAQCWVKTFDGVASDQPHTYQASWNDWWPLHQ---------------------SDQPHSGGVGRNYGFYTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNF----------------------------------------------------------------------------------------------------- : O15681

           : 1---------11--------21--------31--------41--------51--------61--------71--------81--------91--------101-------111-------121-------131-------141-------151-------161-------171-------181-------191-------201-------211-------221-------231-------241-------251-------261-------271-------281-------291-------301-------311-------321-------331-------341-------351-------361-------371-------381-------391-------401-------411-------421-------431-------441-- :
OrigSeq    : PTVERSTRMSNPWKAFMEKYDIERTHSSGVRVDLGEDAEVENAKYRIPAGRCPVFGKGIVIENSDVSFLRPVATGDQKLKDGGFAFPNANDHISPMTLANLKERYKDNVEMMKLNDIALCRTHAASFVMAGDQNSSYRHPAVYDEKEKTCHMLYLSAQENMGPRYCSPDAQNRDAVFCFKPDKNESFENLVYLSKNVRNDWDKKCPRKNLGNAKFGLWVDGNCEEIPYVKEVEAEDLRECNRIVFGASASDQPTQYEEEMTDYQKIQQGFRQNNREMIKSAFLPVGAFNSDNFKSKGRGFNWANFDSVKKKCYIFNTKPTCLINDKNFIATTALSHPQEVDLEFPCSIYKDEIEREIKKQSRNMNLYSVDGERIVLPRIFISNDKESIKCPCEPERISNSTCNFYVCNCVEKRAEIKENNQVVIKEEFRDYYENGEEKSNKQMLL : OrigSeq

jalign     : ------------------------------E------EEEEEE--------------EEEEE---EEEEEEEE----E---------------------------------------HHHHHE---E----------------------EEEEEEE--------EEE---------E-----------EEEEEEE-----------------EE--EEE----------------------EEE-E---------HHHH----HHHHH-HH---------------------------------------------------EE---EEEEEEHH--------------H--HHHHHHHHH------------------------------------------------------------------------------------ : jalign
jfreq      : ---E---------HHHHH---EEE-----EEEE----HHHH------------E---EEEEE----EEEEEE------------E-----------HHHHHHHHHH--HHHHHH--HHHHHHH--EE-------------EEE------HHEHHHHHHH-----------------E-------H-H---EEEE-------------------EEEEEE----------EE----------EEEEE-------H-HHHHH--HHHHHHH-----HHHHHHH----------------------------EEEEEE-----EEE----EEEEEE--------------HHHH-HHHHHHHHHH-----------EE--EEEE--------------------EEEEEEEEH--EEEEE---HEHHHHHH-------HHH--HHH-- : jfreq
jhmm       : -----------HHHHHH-EE---E----EEEEE------------E-------E----EEEE-----------------------------------HHHHHHHHH----EE----HHHHHHHH-------------EEEEEEE----EEEEEEE--------------------EEEEE---------EEE---------------H-----EEEEEE------------------H---EEE--------HHHHHHH---HHHHHHHHHH--HHHHHH-------------------EEEEEE-----EEEEE-----EE----HHHHEEE----------------HHHHHHHHHHH-------------EEEEEEEE----------------------EEEEE----EEEE-----EEEE---HH------------EE- : jhmm
jnet       : ------------HHHHHHH---EEE----EEEE---HHHHH----------------EEEEE----EEEEEE------------------------HHHHHHHHHH--HHHHHH--HHHHHHH---E-------------EEE-----EEEEEEEEHHHH----------------EEE-----------EEEEE------------------EEEEEE----------EE----HHHHH--EEEE------HHHHHHH---HHHHHHHHHH--HHHHHHH------------------E----------EEEEEE----EEE----EEEEEE--------------HHHHHHHHHHHHHH-----------EEEEEEEEE---------------------EEEEEE----EEEEE---EEEEEHHHHH------------EE- : jnet
jpssm      : -----H------HHHHHHH---HHH-----EEE------------------------EEEEE----EEE------------------------------------------H-----HHHHHH-----------------EEE-----EEEEEEEE---------------------EEE----------EEE--------------------EEEEEE----------------HHHHHHHHHEE-------HHHHHH---HHHHHHHHHH--HHHHHH-------------------E----------EEEEEE----EEE-----EEE----------------HHHHHHHHHHHHH------------EEEE-EEEE----------------------EEEE-----EEEE-----EEEEHHHHH--------------- : jpssm

jpred      : ------------HHHHHHH---EE-----EEEE----HHHH----------------EEEEE----EEEEEE-------------------------HHHHHHHHH----------HHHHHHH---E-------------EEE-----EEEEEEEE--------------------EEE-----------EEEE-------------------EEEEEE----------------------EEEEE-------HHHHHH---HHHHHHHHHH--HHHHHH-------------------E----------EEEEE-----EEE----EEEEEE--------------HHHHHHHHHHHHHH------------EEE-EEEE----------------------EEEEE----EEEE-----EEEEHHHHH------------E-- : jpred

Lupas 14   : ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- : Lupas 14
Lupas 21   : ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- : Lupas 21
Lupas 28   : ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- : Lupas 28

Jnet_25    : -BB--B--BBBBB--BB--B-B--BB-BBBBBBBB----B----B-BBBB-BBBBB-BBBB------BB--BB-----B--BBB-BB-----BBBBBB--B--BB-----B--B--BBBBB-BBB-BBB------BB-BBBBBB-----BBBBBBBBB------BB----------BBB-B-----B--BBBBB-BB---B---BB---B--B-BBBB--B-B--B--B--B-B--B--BB-BBB--BB--B---B---B--B--B--BB------BB--BBBBBBBB-B--B-B-B-BBBBBBB-----BBBBB---B-BBB----BBBBBBBBB---B---BBB-BB---B---B------B-BB-----BBBBBBBBBB-----B-B-B----BB-B-B-BBBB-BB-----B-----B-B---B---B----------BBB : Jnet_25
Jnet_5     : ---------------B-------------B-B-B----------B------B---B--B-B-------------------------------BB-B-B--B---------B--------BB--BB--------------BBBB------BBBBBBBB--------------------B-----------B--BB--------------------BBBB------------------B--B---B---------------------B---B------------B---B-----------B---B--------B---------B-----BBBBBBB-----------B--B-------B----------------B-BB-BBB--------B-----------B--BBB-B------------------B---------------BB : Jnet_5
Jnet_0     : ----------------------------------------------------------------------------------------------------B--------------------------------------------------BB-B-------------------------------------B----------------------------------------------B------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- : Jnet_0
Jnet Rel   : 4230022578945888642385341498558864652542145754578987514653899479814665414888644578994899999766871653677531871676418554443364430779999888633167539997489988613328998657789999998322411566384961124313799999878997999945654551356447643114510502114135644898880564440164525776987317478876345445545677667885301203546671689981157178808861686635788887899985416588999999851476544489841771358885999864788888767678842899831100578718982776166751068894339931454 : Jnet Rel


Notes
Key:
Colour code for alignment:
Blue            - Complete identity at a position
Shades of red   - The more red a position is, the higher the level of
                  conservation of chemical properties of the amino acids
jalign          - Jnet alignment prediction
jfreq           - Jnet PSIBLAST frequency profile prediction
jhmm            - Jnet hmm profile prediction
jnet            - Jnet prediction
jpssm           - Jnet PSIBLAST pssm profile prediction
jpred           - Consensus prediction over all methods

MCoil           - MultiCoil prediction (and dimer and trimer predictions)
Lupas           - Lupas Coil prediction (window size of 14, 21 and 28)

Note on coiled coil predictions  - = less than 50% probability
                                 c = between 50% and 90% probability
                                 C = greater than 90% probability

Jnet_25         - Jnet prediction of burial, less than 25% solvent accesibility
Jnet_5          - Jnet prediction of burial, less than 5% exposure
Jnet_0          - Jnet prediction of burial, 0% exposure
Jnet Rel        - Jnet prediction of prediction accuracy, ranges from 0 to 9, bigger is better.