Task3 protocol

Secondary Structure Prediction

Information on Proteins

Sequences obtained from UniProt.

P45381

>sp|P45381|ACY2_HUMAN Aspartoacylase OS=Homo sapiens GN=ASPA PE=1 SV=1
MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKK
CTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTS
NMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVG
PQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIA
AIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK
LTLNAKSIRCCLH

P10775

>sp|P10775|RINI_PIG Ribonuclease inhibitor OS=Sus scrofa GN=RNH1 PE=1 SV=1
MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRT
NELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGVLPSTLRSLPTLRELHLSDNPL
GDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEA
GARVLGQGLADSACQLETLRLENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIA
ELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLC
ESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQAL
SQPGTTLRVLCLGDCEVTNSGCSSLASLLLANRSLRELDLSNNCVGDPGVLQLLGSLEQP
GCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS

Q08209

>sp|Q08209|PP2BA_HUMAN Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform OS=Homo sapiens GN=PPP3CA PE=1 SV=1
MSEPKAIDPKLSTTDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESV
ALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYV
DRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMD
AFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFG
NEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFP
SLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEK
VTEMLVNVLNICSDDELGSEEDGFDGATAAARKEVIRNKIRAIGKMARVFSVLREESESV
LTLKGLTPTGMLPSGVLSGGKQTLQSATVEAIEADEAIKGFSPQHKITSFEEAKGLDRIN
ERMPPRRDAMPSDANLNSINKALTSETNGTDSNGSNSSNIQ

Q9X0E6

>sp|Q9X0E6|CUTA_THEMA Divalent-cation tolerance protein CutA OS=Thermotoga maritima GN=cutA PE=1 SV=1
MILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEE
KEKELYEELRKLHPYETPAIFTLKVENVLTEYMNWLRESVL

reprof calls

reprof -i P45381.fasta
reprof -i P10775.fasta
reprof -i Q08209.fasta
reprof -i Q9X0E6.fasta

PsiPred

For the PsiPred predictions, we employed the PsiPred Webserver using default settings (i.e.,mask low complexity regions).

DSSP

For the DSSP predictions, we used the DSSP Webserver. As an input, we provided following pdb files:

• P45381: 2o53
• P10775: 2bnh
• Q08209: 1aui
• Q9X0E6: 1o5j

Disorder Prediction

The following calls were applied to protein sequences P10775, Q08209, Q9X0E6, and P45381 (Aspartoacylase).

iupred ./../P10775_ribInh.fa long > P10775_long.out
iupred ./../P10775_ribInh.fa short > P10775_short.out
iupred ./../P10775_ribInh.fa glob > P10775_glob.out

Transmembrane Helix Prediction

Information on Proteins

P35462

>sp|P35462|DRD3_HUMAN D(3) dopamine receptor OS=Homo sapiens GN=DRD3 PE=1 SV=2
MASLSQLSSHLNYTCGAENSTGASQARPHAYYALSYCALILAIVFGNGLVCMAVLKERAL
QTTTNYLVVSLAVADLLVATLVMPWVVYLEVTGGVWNFSRICCDVFVTLDVMMCTASILN
LCAISIDRYTAVVMPVHYQHGTGQSSCRRVALMITAVWVLAFAVSCPLLFGFNTTGDPTV
CSISNPDFVIYSSVVSFYLPFGVTVLVYARIYVVLKQRRRKRILTRQNSQCNSVRPGFPQ
QTLSPDPAHLELKRYYSICQDTALGGPGFQERGGELKREEKTRNSLSPTIAPKLSLEVRK
LSNGRLSTSLKLGPLQPRGVPLREKKATQMVAIVLGAFIVCWLPFFLTHVLNTHCQTCHV
SPELYSATTWLGYVNSALNPVIYTTFNIEFRKAFLKILSC

Blastget found 50 homologues, which were used for the multiple alignment and the Polyphobius TMH prediction.

Q9YDF8

>sp|Q9YDF8|KVAP_AERPE Voltage-gated potassium channel OS=Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) GN=APE_0955 PE=1 SV=1
MSVERWVFPGCSVMARFRRGLSDLGGRVRNIGDVMEHPLVELGVSYAALLSVIVVVVEYT
MQLSGEYLVRLYLVDLILVIILWADYAYRAYKSGDPAGYVKKTLYEIPALVPAGLLALIE
GHLAGLGLFRLVRLLRFLRILLIISRGSKFLSAIADAADKIRFYHLFGAVMLTVLYGAFA
IYIVEYPDPNSSIKSVFDALWWAVVTATTVGYGDVVPATPIGKVIGIAVMLTGISALTLL
IGTVSNMFQKILVGEPEPSCSPAKLAEMVSSMSEEEFEEFVRTLKNLRRLENSMK

No homologues have been found with the blastget search.

P47863

>sp|P47863|AQP4_RAT Aquaporin-4 OS=Rattus norvegicus GN=Aqp4 PE=1 SV=1
MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAMLIFVLLSVGSTINWG
GSENPLPVDMVLISLCFGLSIATMVQCFGHISGGHINPAVTVAMVCTRKISIAKSVFYIT
AQCLGAIIGAGILYLVTPPSVVGGLGVTTVHGNLTAGHGLLVELIITFQLVFTIFASCDS
KRTDVTGSVALAIGFSVAIGHLFAINYTGASMNPARSFGPAVIMGNWENHWIYWVGPIIG
AVLAGALYEYVFCPDVELKRRLKEAFSKAAQQTKGSYMEVEDNRSQVETEDLILKPGVVH
VIDIDRGDEKKGKDSSGEVLSSV

Blastget found 34 homologues, which were used for the multiple alignment and the Polyphobius TMH prediction.

Command

blastget -db /mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot -ix /mnt/project/pracstrucfunc12/data/index_pp/uniprot_sprot.idx p35462.fa > p35462.out
kalign p35462.out > p35462_kalign.out
jphobius -poly p35462_kalign.out > p35462_phobius.out

Signal Peptide Prediction

Information on Proteins

P02768

>sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2
MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
AASQAALGL

P47863

>sp|P47863|AQP4_RAT Aquaporin-4 OS=Rattus norvegicus GN=Aqp4 PE=1 SV=1
MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAMLIFVLLSVGSTINWG
GSENPLPVDMVLISLCFGLSIATMVQCFGHISGGHINPAVTVAMVCTRKISIAKSVFYIT
AQCLGAIIGAGILYLVTPPSVVGGLGVTTVHGNLTAGHGLLVELIITFQLVFTIFASCDS
KRTDVTGSVALAIGFSVAIGHLFAINYTGASMNPARSFGPAVIMGNWENHWIYWVGPIIG
AVLAGALYEYVFCPDVELKRRLKEAFSKAAQQTKGSYMEVEDNRSQVETEDLILKPGVVH
VIDIDRGDEKKGKDSSGEVLSSV

P11279

>sp|P11279|LAMP1_HUMAN Lysosome-associated membrane glycoprotein 1 OS=Homo sapiens GN=LAMP1 PE=1 SV=3
MAAPGSARRPLLLLLLLLLLGLMHCASAAMFMVKNGNGTACIMANFSAAFSVNYDTKSGP
KNMTFDLPSDATVVLNRSSCGKENTSDPSLVIAFGRGHTLTLNFTRNATRYSVQLMSFVY
NLSDTHLFPNASSKEIKTVESITDIRADIDKKYRCVSGTQVHMNNVTVTLHDATIQAYLS
NSSFSRGETRCEQDRPSPTTAPPAPPSPSPSPVPKSPSVDKYNVSGTNGTCLLASMGLQL
NLTYERKDNTTVTRLLNINPNKTSASGSCGAHLVTLELHSEGTTVLLFQFGMNASSSRFF
LQGIQLNTILPDARDPAFKAANGSLRALQATVGNSYKCNAEEHVRVTKAFSVNIFKVWVQ
AFKVEGGQFGSVEECLLDENSMLIPIAVGGALAGLVLIVLIAYLVGRKRSHAGYQTI

Command

signalp -t euk p02768.fa
signalp -t euk p11279.fa
signalp -t euk p47863.fa

SignalP4.0 prediction: server was used at http://www.cbs.dtu.dk/services/SignalP/