SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching O97394 from www.uniprot.org...

The NucPred score for your sequence is 0.56 (see score help below)

   1  MLKSAASSLRRRRPKTTITATLAIEMPSQPKLASLLAVLVLLCYCDSCFF    50
  51  CYADANLQQQNSIVQQQQLQAPRFTTHPSSSGSIVSEGSTKILQCHALGY   100
 101  PQPTYRWLKDGVPVGDFSSSQFYRFHSTRREDAGSYQCIARNDAGSIFSE   150
 151  KSDVVVAYMGIFENTTEGRLTVISGHPAIFDMPPIESIPVPSVMWQSEDG   200
 201  PLNYDIKYAFTHANQLIILSADENDRKGYRAKAINTQLGKEESSAFVHLN   250
 251  VSGDPYIEVAPEIIVRPQDVKVKVGTGVVELQCIANARPLHELETLWLKD   300
 301  GLAVETAGVRHTLNDPWNRTLALLQANSSHSGEYTCQVRLRSGGYPAVSA   350
 351  SARLQILEPPLFFTPMRAETFGEFGGQVQLTCDVVGEPTPQVKWFRNAES   400
 401  VDAHIESGRYTLNTDNTLVIKKLILDDAAMFQCLAINEAGENSASTWLRV   450
 451  KTSAPIMELPPQNVTALDGKDATISCRAVGSPNPNITWIYNETQLVDISS   500
 501  RVQILESGDLLISNIRSVDAGLYICVRANEAGSVKGEAYLSVLVRTQIIQ   550
 551  PPVDTTVLLGLTATLQCKVSSDPSVPYNIDWYREGQSSTPISNSQRIGVQ   600
 601  ADGQLEIQAVRASDVGSYACVVTSPGGNETRAARLSVIELPFPPSNVKVE   650
 651  RLPEPQQRSINVSWTPGFDGNSPISKFIIQRREVSELEKFVGPVPDPLLN   700
 701  WITELSNVSADQRWILLENLKAATVYQFRVSAVNRVGEGSPSEPSNVVEL   750
 751  PQEAPSGPPVGFVGSARSMSEIITQWQPPLEEHRNGQILGYILRYRLFGY   800
 801  NNVPWSYQNITNEAQRNFLIQELITWKDYIVQIAAYNNMGVGVYTEGSKI   850
 851  KTKEGVPEAPPTNVKVEAINSTAARCRWTPPNPQQINGINQGYKIQAWQR   900
 901  RLIDGEWRDIERRMKTVPPSLIDPLAEQTAILGGLEKFTEYNISVLCFTD   950
 951  PGDGVASSQVAVMTMDDVPDEVTGLHFDDVSDRSVKVLWAPPRASNGILT  1000
1001  GYTVRYQVKDRPDTLKSFNLTADDTELTVNQLQATTHYWFEIVAWTRVGS  1050
1051  GIPKTATIQSGVEPVLPHAPTALALSNIEAFSVVLQFTPGFDGNSSITKW  1100
1101  KVEGQTARNMTWFTICEINDPDAETLTVTGLVPFTQYRLRLSASNVVGSS  1150
1151  KPSEATKDFQTIQARPKHPPFNVTVRAMSAQQLRVRWIPLQQTEWYGNPR  1200
1201  GYNISYKQLVKTPGTIKYVPRSVVIEDHTANSHVLDSLEEWTLYEVKMNA  1250
1251  CNDVGCSKESDTAVERTREAVPSYGPLDVQANATSSTTVVVQWGEVPRQH  1300
1301  RNGQIDGYKVFYAAADRGQQVLHKTIPNNATFTTTLTELKKYVVYHVQVL  1350
1351  AYTRLGNGALSTPPIRVQTFEDTPGVPSNVSFPDVSLTMARIIWDVPVDP  1400
1401  NGKILAYQVTYTLNGSAMLNYSREFPPSDRTFRATELLPGKYYSFSCTAQ  1450
1451  TRLGWGKIATALVYTTNNRERPQAPSVPQISRSQIQAHQITFSWTPGRDG  1500
1501  FAPLRYYTVEMRENEGRWQPLPERVDPSLSSFTAVGLRPYMTYQFRIQAT  1550
1551  NDLGPSAFSRESVIVRTLPAAPAVGVGGLKVVPITTTSVRVQWSALETAL  1600
1601  WNGDASTGGYRILYQQLSDFPTALQSTPKTDVHGINENSVVLSDLQQDRN  1650
1651  YEIVVLPFNSQGPGPATPPAAVYVGEAVPTGEPRAVDAAPISSTEVRLLW  1700
1701  KPPKQSMQNGDILGYKIYYLVTYSPQALEPGRKWEEEIEVVSATATSHSL  1750
1751  VFLDKFTEYRIQLLAFNPAGDGPRSAPITVKTLPGVPSAPLHLRFSDITM  1800
1801  QSLEVTWDPPKFLNGEILGYLVTYETTEENEKFSKQVKQKVSNTTLRVQN  1850
1851  LEEEVTYTFTVRAQTSVDYGPGISENVTTGPQDGSPVAPRDLILTKTLSS  1900
1901  VEMHWINGPSGRGPILGYLIEAKKRDDSRWTKIEQTRKGMMQDFTVSYHI  1950
1951  LMPSTAYTFRVIAYNRYGISFPVYSKDSILTPSKLHLEYGYLQHKPFYRQ  2000
2001  TWFMVSLAATSIVIIVMVIAVLCVKSKSYKYKQEAQKTLEESMAMSIDER  2050
2051  QELALELYRSRHGVGTGTLNSVGTLRSGTLGTLGRKSTSRPPPGVHLGKS  2100
2101  PPRPSPASVAYHSDEESLKCYDENPDDSSVTEKPSEVSSSEASQHSESEN  2150
2151  ESVRSDPHSFVNHYANVNDSLRQSWKKTKPVRNYSSYTDSEPEGSAVMSL  2200
2201  NGGQIIVNNMARSRAPLPGFSSFV                            2224

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

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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