 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching P39447 from www.uniprot.org...
The NucPred score for your sequence is 0.93 (see score help below)
1 MSARAAAAKSTAMEETAIWEQHTVTLHRAPGFGFGIAISGGRDNPHFQSG 50
51 ETSIVISDVLKGGPAEGQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGK 100
101 NAKITIRRKKKVQIPVSHPDPEPVSDNEDDSYDEEVHDPRAGRGALANRR 150
151 SEKSWARDRSASRERSLSPRSDRRSVASSQPAKPTKVTLVKSRKNEEYGL 200
201 RLASHIFVKEISQDSLAARDGNIQEGDVVLKINGTVTENMSLTDAKTLIE 250
251 RSKGKLKMVVQRDERATLLNVPDLSDSIHSANASERDDISEIQSLASDHS 300
301 GRSHDRPPRRSQSRSPDQRSEPSDHSTQSPQQPSNGSLRSREEERMSKPG 350
351 AISTPVKHVDDHPPKAVEEVTVEKNEKQTPTLPEPKPVYAQVGQPDVDLP 400
401 VSPSDGALPNSAHEDGILRPSMKLVKFRKGDSVGLRLAGGNDVGIFVAGV 450
451 LEDSPAAKEGLEEGDQILRVNNVDFTNIIREEAVLFLLDLPKGEEVTILA 500
501 QKKKDVYRRIVESDVGDSFYIRTHFEYEKESPYGLSFNKGEVFRVVDTLY 550
551 NGKLGSWLAIRIGKNHKEVERGIIPNKNRAEQLASVQYTLPKTAGGDRAD 600
601 FWRFRGLRSSKRNLRKSREDLSAQPVQTKFPAYERVVLREAGFLRPVTIF 650
651 GPIADVAREKLAREEPDIYQIAKSEPRDAGTDHRSSGIIRLHTIKQIIDQ 700
701 DKHALLDVTPNAVDRLNYAQWYPIVVFLNPDSKQGVKTMRMRLCPESRKS 750
751 ARKLYERSHKLRKNNHHLFTTTINLNSMNDGWYGALKEAIQQQQNQLVWV 800
801 SEGKADGATSDDLDLHDDRLSYLSAPGSEYSMYSTDSRHTSDYEDTDTEG 850
851 GAYTDQELDETLNDEVGTPPESAITRSSEPVREDSSGMHHENQTYPPYSP 900
901 QAQPQAIHRIDSPGLKPASQQKAEASSPVPYLSPETTPASSASAVNHNVS 950
951 VTNVSLEEPAPAPPTSHASQPGCLGAPSAEAAHVVLRGEGPPLPPHADPA 1000
1001 KVYRKEPYSEEMMRQNHILKQPALGHPGQRPDKEPNLAYEPQLPYIEKQA 1050
1051 SRDLEQPSYRYEVSSYTDQFSRNYDHRLRFEDRIPTYEDQWSYYDDKQPY 1100
1101 QPRPFENQHPRDLDSRQHPEEASERGYFQRFEEPAPLSYDSRTRYEQLPR 1150
1151 TSTLRHEEQPAPAYEVHNRYRPEAQPYSSTGPKSSEPKQYFDQYPRSYEQ 1200
1201 VPPPGFTSKTGHYEPLHGAAVVPPLIPSSQQKPEVLPSATKPQPPPPTLT 1250
1251 EEEEDPAMKPQSVLTRVKMFENKRSASLENKKDVNDTASFKPPEVASKPP 1300
1301 GASLAGPKPVPQSQFSEHDKTLYRLPEPQKPQVKPPEDIVRSNHYDPEED 1350
1351 EEYYRKQLSYFDRRSFESKPSAHLPAGHHSEPAKPVHSQSQPNFSSYSSK 1400
1401 GKPETDAVDRSFSEKRYDPAQATPPPPPLPSQYSQPAPPLSSSSLHIHSK 1450
1451 GAQGEGNSVSLDFQNSYMSKPDPPPSQSKPATFRPPTREDPPQTFYPQKS 1500
1501 FPDKAPVNGAEQTQKTITPVYNRFTPKPYTSSARPFERKFESPKFNHNLL 1550
1551 PSETVHKPELSSKTPTSPKTLMKAHSSTQPPEFDSGVETFSVHTDKPKYQ 1600
1601 MNNISTMPKAVPVSPSAVEEDEDEDGHTVVATARGIFNSNGGVLSSIETG 1650
1651 VSIIIPQGAIPEGIEQEIYFKVCRDNSILPPLDKEKGETLLSPLVMCGPH 1700
1701 GLKFLKPVELRLPHCDPKTWQNKCLPGDPNYLVGANCVSVLIDHF 1745
Positively and negatively influencing subsequences are coloured according to the following scale:
(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)
What does the NucPred score mean?
| You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper. |
| NucPred score threshold | Specificity | Sensitivity |
| see above | fraction of proteins predicted to be nuclear that actually are nuclear | fraction of true nuclear proteins that are predicted (coverage) |
| 0.10 | 0.45 | 0.88 |
| 0.20 | 0.52 | 0.83 |
| 0.30 | 0.57 | 0.77 |
| 0.40 | 0.63 | 0.69 |
| 0.50 | 0.70 | 0.62 |
| 0.60 | 0.71 | 0.53 |
| 0.70 | 0.81 | 0.44 |
| 0.80 | 0.84 | 0.32 |
| 0.90 | 0.88 | 0.21 |
| 1.00 | 1.00 | 0.02 |
| Sequences which score >= 0.8 with NucPred and which
are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.) |
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