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

NucPred

Fetching Q05854 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MGRPRKNVSQEKIQQLKRELELAGNRTDVLLQDKKGRSRSCLLCRRRKQR    50
  51  CDHKLPSCTACLKAGIKCVQPSKYSSSTSNSNTNNNTPTAGTVPPTPHPV   100
 101  IKRELQDSSIGAGAGAATSLNDMTIIKPISTSNSNVDAGDANEFRKTIKS   150
 151  VTTNSNPNLMRQDKDQYTIFLEKKLKSLETLLDLSPGCNQYNYELSQYKK   200
 201  VSHLFSNNTSDYSRPNSSNMVILPLPSPSNKPLENTNNNGSNVNAATNDT   250
 251  SASTNNINNNNAICQSASLLNDPLETLDFTKCIFAKYNLKKEFLMYDPIF   300
 301  ELNEKLSRSFLDTFFTRLQFKYPILDEQEIYTFYDHYLHNKILIPPSSPA   350
 351  TSSAAPPSNSHSYSEIEFHFLSGRMWLVFSISAYLLMTTGKYKGFPPHRY   400
 401  FSTAIRHITKCGLHLNYVQQIELLTLLVLYIIRTDRDSLILYDIIKDVMG   450
 451  ISKKKLHLNQWYPNDPFANKKLRLFWCVYLLERMICVAVGKPYTIKESEI   500
 501  NLPLFNNDSFYTKGVHAAAPSTNDHGVQFINQSLKLRRIESQFVETLQLL   550
 551  KNDSRSVKQSIDQLPLVRKFFEDLEVWRKSYSTLDVKNFENETLKLYYYR   600
 601  SVRLLIQPYLEFFAPEDRLFRECQAAAGQICQLYKIFHQKTLNGHSTPAV   650
 651  HTVFVAGVTLIYCMWLARNFDDQRRKKLGDASKHTRPLISASLFSTMDDL   700
 701  RACSVCLYVMTERSNFARTFRDTFDQLMNATVGNLIERCGPDSSELIFMA   750
 751  SSVAKRTEPKNINDEANKAISSGDTLHDSNSANAANLSNSNDKNISHNGG   800
 801  MPPAVARIFGKGQAEEHAGFVENSQVDLAEQEKFKKKQGVLEKTSVPKSL   850
 851  AHLLTKMDDRSRISNSSMSYTTSSSSSSSSSSSSSTLSFPSSQEKNLKIN   900
 901  VNNDNNGMTISSVNREHNNNHNNNNDNNNNNNNNNNNSNNNNNVNNNDNE   950
 951  SNSRSTTNNSCNNGNNSQYVRNNNVTMENDVERPIQDQYIVKKPTNQTEF  1000
1001  DWQVFQQQAFLQQQLAQHNLQAYLSSLNTDTMTNRSPSKSSSISTASSHS  1050
1051  DPIPIAMTQSPTPYPQTSNMLPQQHVSRPLPQQQREQPQQHITSPQRFSE  1100
1101  SNFTNQLNNGMINSNPLQSAIFSNHTSENKQLRDVEESNFSTSPLRADYG  1150
1151  NNIISSIPASFTSNSIPVSVKQARNGSSSGDILFSNGAHDMINNISTWTN  1200
1201  NSVLDALNSKSILQTIFPQSQEPSSLSMDKQQQQHQQQNMCSENNVTANN  1250
1251  FQQTQNDPSYNRNLFMMSNQEGVQYNLDETEKNGPKTQVEANTSANLHFD  1300
1301  NVIPTVTNADIRKKRSNWDNMMTSGPVEDFWTINDDYGFLT           1341

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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