Task 3: odba human Sequence-based predictions

From Bioinformatikpedia
Revision as of 18:55, 12 May 2012 by Kiening (talk | contribs) (reprof with HHBlits - PSSM (up20))

secondary structure

To predict secondary structure we use the following tools and compare the results:

-reprof
-psipred
-DSSP_Server

reprof

to run reprof from the command line the following command is used:

reprof -i seq.fasta

reprof then calculates the secondary structure prediction and provides an output file "seq.fasta.reprof". Reprof can be run with a fasta file, or with a BLAST/HHBlits - PSSM file. We will try both variants, because the second variant promises more accurate results. Result: (H = Helix, E = Extended/Sheet, L = Loop)

reprof with fasta

obda_human
Reliability( 0-9 (most reliable) )
sec-structure
AA-sequence
9221124455554036207776653067862000247852012212357787787762666544200476501154066765467703167878778656
LLHHHHHHHHHHHHLLLLHHHHHHHLLLLLLLELLLLLLLLHLLLLLLLLLLLLLLLLHHHHHHHHLLLLLLELLLLEEEEELLLLLEELLLLLLLLLHH
MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE

7776655320100000301100557547888740466664011100046751342012001024530573233245541430113666535300255543
HHHHHHHHHHHHHLHLHHEEELLLLLEEEEEEELLLLLLLLELLLLELLLLLEEEEEELLLLEEEELLLLHHHHHHHHHLLHLLLLLLLLLLLELLLLLL
KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER

2565305212002477767777653177627888842564565652123003342344178887067503105676210256402047640478887567
EEEEELLLHHHHLHHHHHHHHHHHHLLLLEEEEEEELLLLLLLLLLLLLLEEEEELLLLEEEEEELLLEEELLLLLLLELLLLEELLLLLEEEEEEEELL
HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG

7234432321577765553267212200001212125776522000114312346677733555545324788866888888643278889998876138
LLEEEEELLLHHHHHHHHHLLLLEEEEHEEEEELLLLLLLLLLHLLLLLLLLLLLLLLLLHHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHHHHHHLL
NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK

898975011024431728777888989998887256688886799
LLLLLLEEELHHHHHLHHHHHHHHHHHHHHHHHHLLLLLLLLLLL
PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK
P10775
Reliability( 0-9 (most reliable) )
sec-structure
AA-sequence

9721000003610177776776314314516778775677778877514877115421004336431001011566864102210024543110024337
LLLLELHHLLLLLHHHHHHHHHHHLLEEEELLLLLLHHHHHHHHHHHHLLLLHHHHHHHHLLLLLLLHEEEHLLLLLLLLEEEEELLLLLLLLHLLLLLL
MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRTNELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGVL

0133000013330258887661566556631578202223423334201324622688888888877652057775225666664004000153444411
HHHHLHLHHHHHHLLLLLLLLHHHHHHHHHLLLLLHLLHHHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHLLLLLLHHHHHHHHHLLLLLLHHHHHHHHH
PSTLRSLPTLRELHLSDNPLGDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEAGARVLGQGLADSACQLETLR

1047778532245655530000101103476775603366543044581121001011000456101257888875566677776613656705677777
HLLLLLLLLLHHHHHHHHHLHLLHHHLLLLLLLLLHHHHHHHLLLLLLLHHHHLHHEEEHLLLLLHHHHHHHHHHHHHHHHHHHHHHLLLLLLHHHHHHH
LENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIAELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLC

7631777612221231100357767777776410311433210357677236888888842788636677614532246313688888875112001025
HHHLLLLLLHHHHHHHHLHHHHHHHHHHHHHHHLLHHHHHHHLLLLLLLLHHHHHHHHHHLLLLLEEEEEEELLLLLLLLLHHHHHHHHHHHLLHHHHLL
ESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQALSQPGTTLRVLCLGDCEVTNSGCSSLASLLLANRSLRELDL

65766771365554034675421654433056661778999988407888851138
LLLLLLLHHHHHHHLLLLLLLLHHHHHHHLLLLLLHHHHHHHHHHHLLLLLLLELL
SNNCVGDPGVLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS
Q08209
Reliability( 0-9 (most reliable) )
sec-structure
AA-sequence

9888511664455661466520588761225577627887133322010123575211247777614640222244420133525663200001133420
LLLLLLLLLLLLLLLLEEEEELLLLLLLEEEEEEELLLLLLEEEEEHHHELLLLLLLEEEEEEEEELLLLEEELLLLLLLLLLLEEEEELLLLHHHHHHE
MSEPKAIDPKLSTTDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMK

1331577766237775323055315633101345543037640577623532202211441221344665000134433220422233320340467624
EEEELLLLLLLEEEEEEEELLLLEEEEEEEHHHHHHHLLLLLEEEEEELLLLLLEEEEEEEEEEEEEEEEELHHHHHHHHHLLLLLHHHHHLLLEEEEEL
LFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMDAFDCLPLAALMNQQFLCVHG

6474436343554310157887757611246217755467764332010220100255530521010002254110100100235413777501557763
LLLLLLLLHHHHHHHHLLLLLLLLLLLEEEEELLLLLLLLLLLLLLELLLLLELLEEEEELLLLEEEEHLLLLHHHHEHHHLLLLLLEEEEEELLLLLLL
GLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFP

2577760664021214631678750541456651137786315542201455324354045676554101135675567656767301776667777554
EEEEEEELLLEEEEELLLEEEEEELLLEEEEEEELLLLLLLLLLLLLEEEEEELLLLLHHHHHHHHHHHEELLLLLLLLLLLLLLLHHHHHHHHHHHHHH
SLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLNICSDDELGSEEDGFDGATAAARKEVIRNKI

4421010235433046662477622277652464221277133333243232000332155875402001230153121135788877678876434554
HHHLHHEEEEEEEELLLLLEEEEELLLLLLLLLLLEELLLLEEEEEEEEEEELLHHHHLLLLLLLEEEEHHHHLLLLHHLLLLLLLLLLLLLLLLHHHHH
RAIGKMARVFSVLREESESVLTLKGLTPTGMLPSGVLSGGKQTLQSATVEAIEADEAIKGFSPQHKITSFEEAKGLDRINERMPPRRDAMPSDANLNSIN

331156787677886677889
HHHLLLLLLLLLLLLLLLLLL
KALTSETNGTDSNGSNSSNIQ
Q9X0E6
Reliability( 0-9 (most reliable) )
sec-structure
AA-sequence

7687613771687888888888877787530020104624520132330256774264687898899987508777820100246778889988877524
LEEEEELLLLHHHHHHHHHHHHHHHHHHHHLHLHHHLLLEEELEEELLHHHHHHHLLLHHHHHHHHHHHHHLLLLLLLHHEHHHHHHHHHHHHHHHHHHL
MILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEEKEKELYEELRKLHPYETPAIFTLKVENVLTEYMNWLRESV

9
L
L

reprof with HHBlits - PSSM (up20)

To retrieve PSSM-files from hhblits, the tool hhblits_pssm.pl from the hhsuite is used( we used the version installed in "/opt/hhblits/hhblits/" on jobtest ). It is started from the command line with the following command:

hhblits_pssm.pl --infile query.fasta --outfile query.pssm -h "/mnt/project/rost_db/data/hhblits/uniprot20_current"

now reprof is run using the created pssm's. Results:

psipred

the version from [1] was used to predict secondary structure with psipred. Results:

obda_human
confidence
sec-structure
AA-sequence
915554344652010125789986408888898888999867679889999999999943
CHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAE

345544347897889982787589997259999999999999999999799999999999
CCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
FIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILY

984258734444798615999998531399982418689312241328998999998626
HHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEECCCCCCHHHHHCCCCHHHHHHHHCC
ESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYG

978889988877778888776122353334681566759888767099958999818886
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCC
NISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGA

670358878577674079759999579823236884113641143204567987321028
CCHHHHHHHHHHHHHHCCCEEEEEECCCEEECCCCCCCCCCCHHHHHCCCCCCCCCEECC
ASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG

209999999999999999089974998642117999999999999997788866514995
CCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHCCCC
NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHP

799999999779999999999999999999999999992999996677866421799789
HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHH
ISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQL

9999999999998299899998789
HHHHHHHHHHHHHHCCCCCCCCCCC
RKQQESLARHLQTYGEHYPLDHFDK
P10775
confidence
sec-structure
AA-sequence

989828999999999999677137869971179999887999999643699967898647
CEEECCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCEEECCC
MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRT

999958999999760499984138982169999455648999723799858897979999
CCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCEEECCCCCC
NELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGVLPSTLRSLPTLRELHLSDNPL

926999999884299986488981148899014899999871699979997869999968
CHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCEEECCCCCCCHH
GDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEA

999999750299985368971389999776999999882199979796999999918999
HHHHHHHHCCCCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHH
GARVLGQGLADSACQLETLRLENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIA

998530499984148970289999665999999860499969996889999907999999
HHHHHHCCCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHH
ELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLC

980499986458961189789888999999882499749896999999925899999851
HHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCCHHHHHHHHHC
ESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQAL

899961119980268899666999999984399979885999999938999999840699
CCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHCCC
SQPGTTLRVLCLGDCEVTNSGCSSLASLLLANRSLRELDLSNNCVGDPGVLQLLGSLEQP

997678830589887899999999995599831219
CCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCEECC
GCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS
Q08209
confidence
sec-structure
AA-sequence

999988999887776433454799998899321139899989999999996317799999
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHH
MSEPKAIDPKLSTTDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESV

999999999997219880321498447446663057899999816999998630024543
HHHHHHHHHHHHHHCCCCEEECCCEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
ALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYV

689971899999999834099957772157432122131554799995408989999985
CCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHH
DRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMD

429830331043915485046798999911110268999999999741002589999889
HCCCCHHHHHCCCCEEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCCCHHCCCCCCCCCC
AFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFG

976434567889874069747689999987549803433323114013201134467999
CCCCCCCCCCCCCCCCEEECCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC
NEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFP

469980378752345882379998376020786434899998898885444531367899
CEEEEECCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHH
SLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEK

999999984067865568988888820389999999997775556788889999842100
HHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
VTEMLVNVLNICSDDELGSEEDGFDGATAAARKEVIRNKIRAIGKMARVFSVLREESESV

000137999999886667723566666677776665430699998898548887401200
HHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH
LTLKGLTPTGMLPSGVLSGGKQTLQSATVEAIEADEAIKGFSPQHKITSFEEAKGLDRIN

38999989998864522211113457789999999999999
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
ERMPPRRDAMPSDANLNSINKALTSETNGTDSNGSNSSNIQ
Q9X0E6
confidence
sec-structure
AA-sequence

999999079999999999998635611237776532476544610112148789766711
CEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEECCCEEECCEEEEEEECCCC
MILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEE
 
19999999986599966418998366555778899875229
CHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHCC
KEKELYEELRKLHPYETPAIFTLKVENVLTEYMNWLRESVL

DSSP_Server

to use DSSP_Server we first had to determine which pdb-ID's are associated with the uniprot ID's P12694, P10775, Q9X0E6, Q08209

uniprot IDpdb ID's
P126941DTW, 1OLS, 1OLU, 1OLX, 1U5B, 1V11, 1V16, 1V1M, 1V1R, 1WCI, 1X7W, 1X7Y, 1X7Z, 1X80, 2BEU, 2BEV, 2BEW, 2BFB, 2BFC, 2BFD, 2BFE, 2BFF, 2J9F
P107751DFJ, 2BNH
Q082091AUI, 1M63, 1MF8, 2JOG, 2JZI, 2P6B, 2R28, 2W73, 3LL8
Q9X0E61KR4, 1O5J, 1VHF

now DSSP_Server is run for each uniprot ID with the corresponding pdb ID with the best resolution or greates span over the protein. Results:

P12694 - 2BFD - Position 46-445
sec-structure 
( H = alpha helix
B = residue in isolated beta-bridge
E = extended strand, participates in beta ladder
G = 3-helix (3/10 helix)
I = 5 helix (pi helix)
T = hydrogen bonded turn
S = bend )
aa-sequence

S    TT      SS        SS S EE SB TTS BS GGG     HHHHHHHHHHHHHHHHHHHHHHHHHHTTSSS     TT HHHHHHHHHTS 
AKPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALD

TTSEEE  S  HHHHHHTT  HHHHHHHHHT TT TTTT S SS   BTTTTB    SSTTTHHHHHHHHHHHHHHHT    EEEEEETTGGGSHHHHHH
NTDLVFGQAREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAG

HHHHHHTT  EEEEEEE SEETTEEGGGT SSSTTGGGTGGGT EEEEEETT HHHHHHHHHHHHHHHHHHT  EEEEEE           HHHHHHHHH
FNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDGNDVFAVYNATKEARRRAVAENQPFLIEAMTYRIG!ST!DHPISRLRHYL

TTTT   HHHHHHHHHHHHHHHHHHHHHHHHS B  GGGGSTTSSSS  HHHHHHHHHHHHHHHHHGGGS GGGB         S EEEE HHHHHHHHH
LSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK!AHF!EYGQTQKMNLFQSVTSAL

HHHHHH TT EEEETTTTTT TTSTTTTHHHHH TTTEEE  S HHHHHHHHHHHHHTT  EEEE SSGGG GGGHHHHHTTGGGHHHHTTTSS  TTEE
DNSLAKDPTAVIFGEDVAFGGVFRCTVGLRDKYGKDRVFNTPLCEQGIVGFGIGIAVTGATAIAEIQFADYIFPAFDQIVNEAAKYRYRSGDLFNCGSLT

EEEEES  SS GGGSS   HHHHHTSTT EEE  SSHHHHHHHHHHHHHSSS EEEEEEGGGTTS  EEEESS     SS  EEEE  SSEEEEE TTHH
IRSPWGCVGHGALYHSQSPEAFFAHCPGIKVVIPRSPFQAKGLLLSCIEDKNPCIFFEPKILYRAAAEEVPIEPYNIPLSQAEVIQEGSDVTLVAWGTQV

HHHHHHHHHHHHHH   EEEEE  EEES  HHHHHHHHHHHS EEEEEEEESTT HHHHHHHHHHHHHGGG SS  EEEEE SS   STTHHHHS  HHH
HVIREVASMAKEKLGVSCEVIDLRTIIPWDVDTICKSVIKTGRLLISHEAPLTGGFASEISSTVQEECFLNLEAPISRVCGYDTPFPHIFEPFYIPDKWK

HHHHHHHHHT 
CYDALRKMINY
P10775 - 2BNH - position 1-456
sec-structure 
( H = alpha helix
B = residue in isolated beta-bridge
E = extended strand, participates in beta ladder
G = 3-helix (3/10 helix)
I = 5 helix (pi helix)
T = hydrogen bonded turn
S = bend )
aa-sequence

S B  EES    HHHHHHHHHHHTT SEEEEET    HHHHHHHHHHHTT TT  EEE  S   HHHHHHHHHHHHSSTT    EEE TTS   GGGGGS
AMNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRTNELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGV

HHHHHHH TT  EEE  S   HHHHHHHHHHHHHSTT    EEE TT   BHHHHHHHHHHHHH S   EEE TTSB HHHHHHHHHHHHHT  S   EE
LPSTLRSLPTLRELHLSDNPLGDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEAGARVLGQGLADSACQLETL

E TTS   HHHHHHHHHHHHH TT  EEE  SS  HHHHHHHHHHHHT TT    EEE TTS   HHHHHHHHHHHHH SS  EEE TTS  HHHHHHHH
RLENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIAELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLL

HHHHTSTT    EEE TTS  BGGGHHHHHHHHHH SS  EEE  SSB HHHHHHHHHHHTTSSS    EEE TTS   HHHHHHHHHHHHH  S  EEE
CESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQALSQPGTTLRVLCLGDCEVTNSGCSSLASLLLANRSLRELD

 TTSS  HHHHHHHHHHHTSSS    EEE TT    HHHHHHHHHHHHH SS EEE 
LSNNCVGDPGVLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS
Q08209 - 1AUI - position 1-521
sec-structure 
( H = alpha helix
B = residue in isolated beta-bridge
E = extended strand, participates in beta ladder
G = 3-helix (3/10 helix)
I = 5 helix (pi helix)
T = hydrogen bonded turn
S = bend )
aa-sequence

S   SSTTS       B HHHHB TTS B HHHHHHHHHTT  B HHHHHHHHHHHHHHHHTS SEEEE SSEEEE   TT HHHHHHHHHHH  TTT  
ATDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTR

EEE S  SSSSS HHHHHHHHHHHHHHSTTTEEE   TTSSHHHHHHSSHHHHHHHHS HHHHHHHHHHHTTS  EEEETTTEEEESS   TT  SHHHH
YLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMDAFDCLPLAALMNQQFLCVHGGLSPEINTLDDI

HHS  SSS  SSSHHHHHHH EE TTTTS SS   EEE TTTTSSEEE HHHHHHHHHHTT SEEEE  S  TTSEEE  B TTTSSBSEEEE   SSGG
RKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFPSLITIFSAPNYL

GTS   EEEEEEETTEEEEEEE         GGG  HHHHHHHHHHHHHHHHHHHHHTT    HHHHHHHHGGGGS             S  HHHHHHHH
DVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLNICS!SFEEAKGLDRINERMPPR!SYPLEMCSHFDADEIKRLG

HHHHHH TT  SEE HHHHTTSHHHHT TTHHHHHHHH TT SSSEEHHHHHHHHGGG TT  HHHHHHHHHHHH TT SSEE HHHHHHHHHHHHTTSS
KRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVDFKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNL

 HHHHHHHHHHHHHHH TTSSSSEEHHHHHHHHGGG GGGG     
KDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLDIHKKMVVDV
Q9X0E6 - 1KR4 - position 1-101
sec-structure 
( H = alpha helix
B = residue in isolated beta-bridge
E = extended strand, participates in beta ladder
G = 3-helix (3/10 helix)
I = 5 helix (pi helix)
T = hydrogen bonded turn
S = bend )
aa-sequence

S  EE   EEEEEEEESSHHHHHHHHHHHHHTTS SEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHH SSSS  EEEE    EEHHH
AALYFXGHXILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEEKEKELYEELRKLHPYETPAIFTLKVENILTEY

HHHHHHHTS  
XNWLRESVLGS

Disorder

Transmembrane helices

Signal peptides

GO terms