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

NucPred

Fetching P38671 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MLPRTASATRTPHLNRLVSAGSRRVLPRCSSSLGIRGSLAATPRLLSTIT    50
  51  TQQPSPLKRQPAPRATVGFERHLATVLDEPAQTATTPLYELRSFSPQAPL   100
 101  TVRDHTKVYAKQRVNYHGIPGDVNEMFLVFEACLQVGRLERAAQVLKRLA   150
 151  NLDVVPPADYLDLFNQYLDAKVSQLLQEPDVDKADDIHKAFETMVSDGRE   200
 201  LPVGGETVALLLKASLTSTDPETMQRYVTRYLSLLPTQIALETVFNTEIL   250
 251  TYEELTKVAELCPKYNMPDNVDPDTFAQQQQQQQQQQQQQQEQQQQQDTS   300
 301  IDQSEVSIEPLLTSSEPSAIPEVLGTPQKGFGLQFVKRTVSMFKDIPDGF   350
 351  DISTLPMSQQREIQSKLEKDCVDASLARWREENESLQKMGLNTSLDTPSL   400
 401  NSRLYQWQKDLETRLRTMLVEVEKSEMVSKKNKDDLDRCIYGPFIRQSNP   450
 451  ERLAAVTIISTLSSLAMGGAHKGSTIASLITHIAKFAEEDIRVQKAEALI   500
 501  SKRNLRKAKSKQHNPRSVLRFKNSTASAGSSDMADSNNVAVEMDDEAWTT   550
 551  TIRTKVGAALLSALLDTAKITLVREDPVTKTLITQNQPAFSHVMQLRKGK   600
 601  KIGTIIPNKAVVELLVREPVPDFLARHLPMVTPPDPWVSFEKGAYLETKT   650
 651  PVLRLKNGEREQRLYTEAAIARGDMDQVFKGLDVLGKTGWKINSPVFKVM   700
 701  LDVWNSGKQVANIPPLDPIFDLPPEPASTEDPTVKRAWLKEIKVIENERS   750
 751  GLHSQRCFMNFQLEIARAYRDQTFYFPHNVDFRGRAYPIPPYLNHMGADH   800
 801  VRGLMLFAKGKPLGESGLRWLKVHLANVYGFDKASLQERQDFADENIENI   850
 851  RDSVNNPLNGNQWWLQAEDPWQCLATCFELAAALELEDPTKYVSHLPIHQ   900
 901  DGTCNGLQHYAALGGDTWGAQQVNLVPGDRPADVYSAVAKLVIKGIEDDL   950
 951  AKDNEFAKAMHGKITRKVVKQTVMTNVYGVTYVGARKQVLKQIEAAYPNI  1000
1001  TAESGIEAALLASYVTQHIFRAMSTMFKGAHDIQNWLGEIGGRVCRALTP  1050
1051  EQLDEFERSERSPHGDGTASGENITLAGNPRKSSAHKNDEILNNFQSTII  1100
1101  WTTPLRMPVVQPYRKHGTKTVSTCMQDLVMTIPERSDPVNRRKQLQAFPP  1150
1151  NFIHSLDASHMILSALHCDELGLTFAAVHDSFWTHASDIDSMNAVLRDAF  1200
1201  IRIHSEDVIGRLAAEFQARYKNSLYLAKIETGTKVAQEIQRWRVRNKLGP  1250
1251  RKELLLEKERQELLRSSNPEDVERGKKMISPASLYELYSSAEDLTVPEDL  1300
1301  KEVTIGNLAGVEETKVRRGREMDEEGEVDGSEEAVEHEDGMHEDEMLADE  1350
1351  PRDMDGNSGLDELSELRNTNHFALSQKRAKASIASGGKQKHYLDIWLPLV  1400
1401  FPPIPEKGDFDVRSLKDSTYFFS                             1423

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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