Task 3: odba human Sequence-based predictions

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:

obda_human - PSSM - UP20 HHBlits
Reliability( 0-9 (most reliable) )
sec-structure
AA-sequence
9011122245644236115555543116766654453556544557765555458776453234143366656786728986778724477557888978
LLHLLLHHHHHHHLLLLLHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLEEEEELLLLLELLLLLLLLLLHH
MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE

8888998898788888898885047875763577741478899998606897795021488998773998789899885003564567752011066777
HHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLHHHHHHHHHHHLLLLLEEEELLHHHHHHHHLLLLHHHHHHHHHLLLLLLLLLLLLLEELLLLLL
KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER

6100101256557999999988553178816889881350116558999999774499889998848703362023556840288988637982799855
LLLLLELEHHHHHHHHHHHHHHHHHLLLLLEEEEEEELLLHLLLHHHHHHHHHHHLLLLEEEEEELLLEEEEEELLLLLLLLHHHHHHHHLLLLEEEEEL
HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG

6878889899999988752489768999973032777776755657888999986047859999988886799997888889889899889888888736
LLHHHHHHHHHHHHHHHHHLLLLEEEEEEEELLLLLLLLLLLLLLLLHHHHHHHHHLLLHHHHHHHHHHHLLLLLHHHHHHHHHHHHHHHHHHHHHHHHL
NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK

674889999984266986689888988999872585477765789
LLLLHHHHHHHHLLLLLHHHHHHHHHHHHHHHHLLLLLLLLLLLL
PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK

P10775 - PSSM UP20 HHBlits
Reliability( 0-9 (most reliable) )
sec-structure
AA-sequence

9565456756800079887228884688850676780015788998731898358884146568446899988752215662788841464672215778
LEEELLLLLLLHHLHHHHHHLLLLLEEEEEELLLLLLLLHHHHHHHHHLLLLLEEEEEELLLLLLLLHHHHHHHHHLLLLLEEEEEEELLLLLLLLHHHH
MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRTNELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGVL

9887308884588830464683328888888862143407788542534755457889887128881688852465564557888877740054607888
HHHHHHLLLLEEEEEELLLLLLLLHHHHHHHHHHHLLLEEEEEEELLLLLLLLHHHHHHHHHLLLLLEEEEEELLLLLLLLHHHHHHHHHLHLLLEEEEE
PSTLRSLPTLRELHLSDNPLGDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEAGARVLGQGLADSACQLETLR

5235237654577642014523537877135656742178888877401756388886436667013788898873078807887046736732088888
EELLLLLLLLHHHHHHHLLLLLLEEEEEELLLLLLLLLHHHHHHHHHLLLLLEEEEEEELLLLLHHHHHHHHHHHHHLLLLEEEEELLLLLLLLLHHHHH
LENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIAELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLC

6630326755888851566674434568988711888168782056578645899987620337752788731675685427788988830888358783
HHHHLLLLLEEEEEEELLLLLLLLHHHHHHHHHLLLLLEEEEELLLLLLLLLHHHHHHHHLLLLLLEEEEEELLLLLLLLLHHHHHHHHHLLLLLEEEEE
ESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQALSQPGTTLRVLCLGDCEVTNSGCSSLASLLLANRSLRELDL

16768915799999887624877067785067688677999998898767846738
LLLLLLHHHHHHHHHHHHLLLLLEEEEEEELLLLLHHHHHHHHHHHHHLLLLEEEL
SNNCVGDPGVLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS

Q08209 - PSSM - UP20 HHBlits
Reliability( 0-9 (most reliable) )
sec-structure
AA-sequence

9877777751245775557766787777782220055787587899999852899898889999999999885489834700233453125510899999
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHHHLELLLLLLLHHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHLLLLEEEEELLEEEEEELLLLHHHHHH
MSEPKAIDPKLSTTDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMK

9874046554058998856078976799999999864215760899860665688887742352656642488899989999871264064687267614
HHHHLLLLLLLEEEEEEEELLLLLLHHHHHHHHHHHHHHLLLLEEEEELLLLHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHLHHHEEELLLEEEEEL
LFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMDAFDCLPLAALMNQQFLCVHG

4468877624101025657787543410023305421124444555301256567542128789999988769817898434133301220477656630
LLLLLLLLHHHLHHLLLLLLLLLLLLLHEEEELLLLLLLLLLLLLLLEELLLLLLLLLELLHHHHHHHHHHLLLLEEEEELLLLLLLEEELLLLLLLLLL
GLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFP

6999984654465668357999981884238986037887888976653121332023457888998531456765455553223355057788999999
EEEEEEELLLLLLLLLLEEEEEEEELLLLEEEEEELLLLLLLLLLLLLLLLEELLLHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLHHHHHHHHHHHH
SLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLNICSDDELGSEEDGFDGATAAARKEVIRNKI

9999998788876551124787312477874554102476332344445542100135665766532426788752502146888766555656657666
HHHHHHHHHHHHHHHHLLLHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLHLLLLLLLLLLLLLLLHHHHHHLLLHLLLLLLLLLLLLLLLLLLLLL
RAIGKMARVFSVLREESESVLTLKGLTPTGMLPSGVLSGGKQTLQSATVEAIEADEAIKGFSPQHKITSFEEAKGLDRINERMPPRRDAMPSDANLNSIN

554655567766555544559
LLLLLLLLLLLLLLLLLLLLL
KALTSETNGTDSNGSNSSNIQ

Q9X0E6 - PSSM - UP20 HHBlits
Reliability( 0-9 (most reliable) )
sec-structure
AA-sequence

9999996599688889999999956312676518237898878224320588999844887899899999729988980788864026878999999843
LEEEEEELLLHHHHHHHHHHHHHHLLEEEEEELLLEEEEEELLELLLLLEEEEEEEELHHHHHHHHHHHHHLLLLLLLLEEEEELLLLLHHHHHHHHHHL
MILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEEKEKELYEELRKLHPYETPAIFTLKVENVLTEYMNWLRESV

9
L
L

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 ID	pdb ID's
P12694	1DTW, 1OLS, 1OLU, 1OLX, 1U5B, 1V11, 1V16, 1V1M, 1V1R, 1WCI, 1X7W, 1X7Y, 1X7Z, 1X80, 2BEU, 2BEV, 2BEW, 2BFB, 2BFC, 2BFD, 2BFE, 2BFF, 2J9F
P10775	1DFJ, 2BNH
Q08209	1AUI, 1M63, 1MF8, 2JOG, 2JZI, 2P6B, 2R28, 2W73, 3LL8
Q9X0E6	1KR4, 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

Comparison

method	query	helices	sheets	loops
reprof - fasta	obda_human	138	86	221
reprof - PSSM - HHBlits	obda_human	191	46	208
reprof - PSSM - psiBLAST	obda_human	helices	sheets	loops
psipred	obda_human	helices	sheets	loops
DSSP_Server	obda_human	helices	sheets	loops
reprof - fasta	P10775	138	86	221
reprof - PSSM - HHBlits	P10775	191	46	208
reprof - PSSM - psiBLAST	P10775	helices	sheets	loops
psipred	P10775	helices	sheets	loops
DSSP_Server	P10775	helices	sheets	loops
reprof - fasta	Q08209	138	86	221
reprof - PSSM - HHBlits	Q08209	191	46	208
reprof - PSSM - psiBLAST	Q08209	helices	sheets	loops
psipred	Q08209	helices	sheets	loops
DSSP_Server	Q08209	helices	sheets	loops
reprof - fasta	Q9X0E6	138	86	221
reprof - PSSM - HHBlits	Q9X0E6	191	46	208
reprof - PSSM - psiBLAST	Q9X0E6	helices	sheets	loops
psipred	Q9X0E6	helices	sheets	loops
DSSP_Server	Q9X0E6	helices	sheets	loops