Task3 protocoll

Secondary Structure Prediction

Information on Proteins

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

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/