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

NucPred

Fetching Q94636 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MIKHILQVEETKKIFEEIDDNEYEKIQDSRKNDDFIVDDDGYGYRDHGGE    50
  51  IWDRDGDVEEVGKKKKKKQNNHDPNENIMNYMMPASTLKKKSNAASTNPS   100
 101  AQQKPKVSVEQSRDIMNNLFQQLDAKDVDELEDVNEAKNMFVQEMNRPVA   150
 151  FNKEEDFNNRYSVTLESREEQERRRQSEQLKQQANIGQNQSDVNPFSKKR   200
 201  KLDEFQQVQANSYQSKQNSHSVSKSKPGDHEMANHADGVDLNLLAIDDTK   250
 251  MTDSHPSEIITQNQRASAVSSVNQQIMESTNGKNQLEKNDTEWQQMKEKN   300
 301  AVFNQDLRMNDNALMSNQQDYPLPLNEDGTLSFYWIDAHEENNGADLFVF   350
 351  GKIYQHEERKFVSCSIKVNGMQRELFVLPKMSGKSRAAMTTEEEKEQARK   400
 401  VMMELEGVRKRFPAITKWRCKPVTRKYAFELPIQHGEHQFVKIKYDATFP   450
 451  SLPSTVQGNTFECIFGANQSMLESFILKRKIRGPCWMTIRNPQKVTDFRR   500
 501  TWCKQEILVSNPKDIEITLDDLNKTELPPLTSVTFAIKTCRSSQNTNEIA   550
 551  MLSCIVNENISQEGPSKIDVHKSFTLLRKLDGKPMPIEYERAFRDKKDSF   600
 601  IQFFQHERQLIEAFVAKIYQLDPDLMVAHNLCGGMFDLLLARIQMLKISH   650
 651  WSRIGRLKKNQIPNKKSDQSGANYGGSQWIPRQVTCGRLLVDTFLTAKEL   700
 701  IRETNYDLTHLAKVQLQKDRIDFDDDLLPTFYVQMAKLFQLIDHTEKDAY   750
 751  LTLQLMNHLQVIPLTKQLTNIAGNLWFRSLQNARAERNEMLLLHEFKKKK   800
 801  FVLPDKKQLNAKDLKKNMFADEYEEGDGKTKGGKRKKAAYAGGLVIEPKA   850
 851  GFYDNIILLLDFNSLYPSIIQEYNLCFTTVNRRPTKNFDGSEMKNQYKKG   900
 901  ENGEEEVDIEEADLPDKNVNLKDAVLPMVLRDLVQKRKAVKDKMKTEKDH   950
 951  VKLSQLEIRQKAIKLTANSMYGCLGFGSSRFHAQAIAALITRTGRETLLR  1000
1001  TKDIAENKLGFNVVYGDTDSIMINTGSNQLQQALEMGKRLKGEVNCLYKC  1050
1051  LEIEIDGVFKSLLLLKKKKYAALKYENFLSPAEVKVVQEMKGLDMVRRDW  1100
1101  CPLSKRVGRYVLDQILSGKQREEVVLNLNEFLSNIGNELKEGTIKLNEFI  1150
1151  ITKQITKAISDYNDIKGQPHVAVAKRLRDQGKSENQLVNNFIPYVICQQT  1200
1201  YGDTTKSSTALSDKAYHPDEVISSRGKVTIDSDWYVSTQLLPPITRLIEH  1250
1251  IEGIEVEFVAQCLGLDPKKYRYHSEKKNTDNPTDDPLIVSNPVLQTETER  1300
1301  SLKNRTVAELNIKCPHCAHNYHFPGILVPSSNNTELTGLACVKCNQRIPD  1350
1351  AYMLNRLNLFLKQLTALYYLGMKECKEPQCGMKTNQLLLNNKCIVKGCKG  1400
1401  KMNSEYSELRINDTLRYLEGLFNVKKFLIENEKYRKKYEKPELVPNFQSF  1450
1451  KELQKKVESFMIRSGYNKVDLGNIFGFMSKGANPHQQKMSIF          1492

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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