Difference between revisions of "Task3 protocoll"
From Bioinformatikpedia
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== Secondary Structure Prediction == |
== Secondary Structure Prediction == |
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MILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEE |
MILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEE |
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KEKELYEELRKLHPYETPAIFTLKVENVLTEYMNWLRESVL |
KEKELYEELRKLHPYETPAIFTLKVENVLTEYMNWLRESVL |
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| + | |||
| + | == Disorder Prediction == |
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| + | The following calls were applied to protein sequences P10775, Q08209, Q9X0E6, and P45381 (Aspartoacylase). |
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| + | iupred ./../P10775_ribInh.fa long > P10775_long.out |
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| + | iupred ./../P10775_ribInh.fa short > P10775_short.out |
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| + | iupred ./../P10775_ribInh.fa glob > P10775_glob.out |
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SPELYSATTWLGYVNSALNPVIYTTFNIEFRKAFLKILSC |
SPELYSATTWLGYVNSALNPVIYTTFNIEFRKAFLKILSC |
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| + | Blastget found 50 homologues, which were used for the multiple alignment and the Polyphobius TMH prediction. |
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==== Q9YDF8 ==== |
==== Q9YDF8 ==== |
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IGTVSNMFQKILVGEPEPSCSPAKLAEMVSSMSEEEFEEFVRTLKNLRRLENSMK |
IGTVSNMFQKILVGEPEPSCSPAKLAEMVSSMSEEEFEEFVRTLKNLRRLENSMK |
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| + | No homologues have been found with the blastget search. |
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==== P47863 ==== |
==== P47863 ==== |
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AVLAGALYEYVFCPDVELKRRLKEAFSKAAQQTKGSYMEVEDNRSQVETEDLILKPGVVH |
AVLAGALYEYVFCPDVELKRRLKEAFSKAAQQTKGSYMEVEDNRSQVETEDLILKPGVVH |
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VIDIDRGDEKKGKDSSGEVLSSV |
VIDIDRGDEKKGKDSSGEVLSSV |
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| + | |||
| + | Blastget found 34 homologues, which were used for the multiple alignment and the Polyphobius TMH prediction. |
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| + | |||
| + | === Command === |
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| + | |||
| + | blastget -db /mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot -ix /mnt/project/pracstrucfunc12/data/index_pp/uniprot_sprot.idx p35462.fa > p35462.out |
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| + | kalign p35462.out > p35462_kalign.out |
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| + | jphobius -poly p35462_kalign.out > p35462_phobius.out |
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== Signal Peptide Prediction == |
== Signal Peptide Prediction == |
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==== P02768 ==== |
==== P02768 ==== |
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| + | >sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 |
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| + | MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF |
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| + | EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP |
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| + | ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF |
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| + | FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV |
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| + | ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK |
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| + | ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR |
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| + | RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE |
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| + | QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV |
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| + | LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL |
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| + | SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV |
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| + | AASQAALGL |
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| + | |||
==== P47863 ==== |
==== P47863 ==== |
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| + | >sp|P47863|AQP4_RAT Aquaporin-4 OS=Rattus norvegicus GN=Aqp4 PE=1 SV=1 |
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| + | MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAMLIFVLLSVGSTINWG |
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| + | GSENPLPVDMVLISLCFGLSIATMVQCFGHISGGHINPAVTVAMVCTRKISIAKSVFYIT |
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| + | AQCLGAIIGAGILYLVTPPSVVGGLGVTTVHGNLTAGHGLLVELIITFQLVFTIFASCDS |
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| + | KRTDVTGSVALAIGFSVAIGHLFAINYTGASMNPARSFGPAVIMGNWENHWIYWVGPIIG |
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| + | AVLAGALYEYVFCPDVELKRRLKEAFSKAAQQTKGSYMEVEDNRSQVETEDLILKPGVVH |
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| + | VIDIDRGDEKKGKDSSGEVLSSV |
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| + | |||
==== P11279 ==== |
==== P11279 ==== |
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| + | >sp|P11279|LAMP1_HUMAN Lysosome-associated membrane glycoprotein 1 OS=Homo sapiens GN=LAMP1 PE=1 SV=3 |
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| + | MAAPGSARRPLLLLLLLLLLGLMHCASAAMFMVKNGNGTACIMANFSAAFSVNYDTKSGP |
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| + | KNMTFDLPSDATVVLNRSSCGKENTSDPSLVIAFGRGHTLTLNFTRNATRYSVQLMSFVY |
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| + | NLSDTHLFPNASSKEIKTVESITDIRADIDKKYRCVSGTQVHMNNVTVTLHDATIQAYLS |
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| + | NSSFSRGETRCEQDRPSPTTAPPAPPSPSPSPVPKSPSVDKYNVSGTNGTCLLASMGLQL |
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| + | NLTYERKDNTTVTRLLNINPNKTSASGSCGAHLVTLELHSEGTTVLLFQFGMNASSSRFF |
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| + | LQGIQLNTILPDARDPAFKAANGSLRALQATVGNSYKCNAEEHVRVTKAFSVNIFKVWVQ |
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| + | AFKVEGGQFGSVEECLLDENSMLIPIAVGGALAGLVLIVLIAYLVGRKRSHAGYQTI |
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| + | |||
| + | ==== Command ==== |
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| + | signalp -t euk p02768.fa |
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| + | signalp -t euk p11279.fa |
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| + | signalp -t euk p47863.fa |
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| + | |||
| + | SignalP4.0 prediction: server was used at http://www.cbs.dtu.dk/services/SignalP/ |
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Latest revision as of 16:56, 18 May 2012
Contents
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/
