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

NucPred

Fetching P21249 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MEKAREGAPSKERRSAEETISRETRHEIAGNDGDIGTDNIEYIDSMDSTG    50
  51  LGYGRTGEGISRILYEHPRDELINYKRRIDANTEQQREHADIMAALQRKI   100
 101  EEYRRRFAEIEGRLVVHDLNESGDLVNMKLKEEWLLSPKIKMEEISDVDF   150
 151  PNQLEDERRRAEDLAIQLQQERLQNDQLQSEIQRLRQQFGICIRDKERIY   200
 201  QTRERNFTRFLGEEQRKMMELWSELQRVRKQCAEYREQTERDLENQRNEF   250
 251  IKVIRHVSGIVRGLNIENGTHTLLSDLSSESGVEITQDTVLIEAVKRFHE   300
 301  SQQQTAPVIGPELITELRLARAEDAGLHDELMRKYEESAKRIIELEARDD   350
 351  ESHNKLVALESDLKRTRDRLAESQNALRKLYDMTYSYEINAEKETRSPSP   400
 401  TKGYVPPPEVVRSVRYVLNSRANDNNVLQRKLKNAEVQISELTTKNDSLE   450
 451  EIRRRLEKRIAEANRTITHRQRELDDAKHTVKDLEDRLKSLEQEKASIDS   500
 501  ARHHLEDEIRKMREQFNSTLLDVERRAAEDADERIRKIDEETKIRISELT   550
 551  NRIEMLLEENKRLKDENDGMKNRIQDIEKEYNTIIRKLEEKDNALKNLEN   600
 601  TRQRLVNELEEQRTRFDTMTSEFDNLRTNYDSANKNTVAIELTVKQIKEQ   650
 651  RDEIIKQKDKLAKELADLENKLNNETKMRGDAEKLNQRHLDEIDNFKKQI   700
 701  NEYITEVTIIRRQNDDFDTQMKTNQAKLSSMKNSLIAAKKEIEKLSEMNN   750
 751  RLQQDKNDLIGAKQKGDTELNLLTEKIRKVEIEFERIKKDNQELEDHERT   800
 801  ARDDLKQETNRNHLLAKELEEARADIVALNDRLAKMDANFKIKLDETIKK   850
 851  SPADHETIKSRESKSEKIIVKHETKIYEINKYRAELEKLESDKDDLEKRI   900
 901  IGLQDELNEKDRDTDRLNAEIDDLKRKLQTEIEKVRKETTTVQERYHIEW   950
 951  DEERDNHQKKIDSMNALIDELRSKLNDAERAMADLQNRDSILERENNDWK  1000
1001  EKSDALNMELDRLRDELLSVRRDAEKEINRYNTDLQTAARNEIKLLTPTN  1050
1051  NEMKSQLNAAEDKINSLNKVITDQQNKIRDLTGEVHHLEGELKDAKGNVA  1100
1101  NLESELDTTRERIHLLGEQNASLQTELNKIKGDIDSLFGENDMLKTAKES  1150
1151  NEAEIDRLKQKLQRSIENAKKYSDALDKLRPEYDRLQNLYREKIKQAENL  1200
1201  TQAVQDLESRLNQSRRELRDATDKLIASEGDRNALRSEVEKLQHEVQFMR  1250
1251  EQLLRKTDEYQAALSDLVNAHRTAEDGRVNAVQALEARKYEINDLQSRLD  1300
1301  NAEQYLVTLQQNYVAVENERDMLYDALRRLHSMIDRTVTINRFLIGVDES  1350
1351  MDEKKETVLQTQKSPDGKSKERFDISDLDTNIQKLIGRIEKLELERNEYR  1400
1401  DALDRIKKKSIESHIKINKQETIFTNIEDQLVDVEEEKRTLEMRLASAKQ  1450
1451  LLRSQEEALKQRDEERSHMKLKIAKFEMEARGKEAQLRQLNELVRNLRKD  1500
1501  LETAQGDLGVLHDHEERWYAHKFHLESKLKDQESESQQIRLLVANFETER  1550
1551  NSLNEKVRDLASRLQQTESKNADMKEDNDRLKKDLIKASTNEAELRRTID  1600
1601  QNSRVVSDNQILKDQLESAQNDLSNANNRKQQLENELLVVRSELRDLKQR  1650
1651  FSDNANRIIDLQRHLTDAENDKKRLTNRLNSLEKTVSQQRTIETEIRQQL  1700
1701  SLALNERNTLQNDLRDLQRRLARMETEKKIMNDKYDELEKIRASLIKRIE  1750
1751  LLDEEKRTMENILHETALQREAIESSLNALERENKELHRNCAQLQQQIAQ  1800
1801  LELENGNRLIQLTNKQREEYDKFAQNMRTEKIQIERIIENRERSLKSRIN  1850
1851  QLENQLNIMRDQLNSERRRRREISDKILSGEVNKLNVTLSGIPDAYEMYD  1900
1901  RTLYTYNTYFGSPSFTVGSSSFDPNITDDSKIILKHSDRLESSYAYGGGN  1950
1951  RTSDTAVTAPTGSSSYHGQRSDTHTVNESERGGNDSGKGTKQVDGEGGSL  2000
2001  SLSEIGQGATFEQQQQRRRKRQ                              2022

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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