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

NucPred

Fetching P53935 from www.uniprot.org...

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

   1  MPPNSKSKRRKNKSKQHNKKNGNSDPEQSINPTQLVPRMEPELYHTESDY    50
  51  PTSRVIKRAPNGDVIVEPINTDDDKKERTANLTHNKDSMDSASSLAFTLD   100
 101  SHWESLSPEEKKTILRIEKEEVFNVIRNYQDDHSCSCSVCGRRHLAMDQE   150
 151  MERIYNTLYAMDKDKDPETNPIKFHLGIIKELQISKNQQQNDLSSTKGEV   200
 201  VKNFLSSSTVGSLKEEVLHFKQKQLSKQEQAHNETADNTSLLEENLNNIH   250
 251  INKTSSEISANFNSVSDEELQQKYSNFTKTFISSHPKIAEEYVQKMMMYP   300
 301  NIRALTDDLMNSNGQGFLNAIEDFVRDGQIQASKKDDSITEDEASSTDLT   350
 351  DPKEFTTMLHSGKPLTEDEYADLQRNIAERMTNAYDTASKKFKDVSQLEK   400
 401  ELFTRFMSGRDKKSFRELIIQSFKNKFDGELGPSVLAATLSSCFSSQSKD   450
 451  TSLDTDSIYEDEDEEDYDDYSEYAEDSEEVSEYEGIEAVEKPEHDEKSNG   500
 501  IRETLHLSYDHDHKRQNHPHHHYHSTSTHSEDELSEEEYISDIELPHDPH   550
 551  KHFHRDDDILDGDEDEPEEEDENEGDDEEDTYDSGLDETDRLEEGRKLIQ   600
 601  IAITKLLQSRIMASYHEKQADNNRLKLLQELEEEKRKKREKEEKKQKKRE   650
 651  KEKEKKRLQQLAKEEEKRKREEEKERLKKELEEREMRRREAQRKKVEEAK   700
 701  RKKDEERKRRLEEQQRREEMQEKQRKQKEELKRKREEEKKRIREQKRLEQ   750
 751  EKLQKEKEEEERQRLIAEDALRKQKLNEEQTSANILSAKPFTENGVGNPV   800
 801  SSQSHPNMTNYQEDNSCSINDEILKMVNSVAASKPVSPTGFNVHDLLLPS   850
 851  TNNQMPAMEQSHLPQPGNQNNHFGTTTIPNALDLATKSSLQTENNYLMNS   900
 901  QTLENTSLLMHNNSSPTKLLPNDFGLSSWGGLTNTMSINPTCKPPVIQTS   950
 951  EMESQAHKSSPQATMPSFGLPNGGTHRKSFTDELNTLTSMLSSSGFADTS  1000
1001  LSSSGFPPSQRSVWNDQKSSFSGPSTAGNFNNSSIQSGMLLAPTLGSVES  1050
1051  FPNRTSIWDSSTTPMMNKSELSGRNITSTAQDSPAFMASNIWSSNSQYNS  1100
1101  PYLTSNVLQSPQISSGVDESHILDSIYNTYLAISPQDSLNPYIAIGTLFQ  1150
1151  NLVGLNLDYSTFINKLISMQGAYNCEFFTDNNGSITHVRFARQTPAGHSK  1200
1201  GLLNQLFSGLNDPTATPFTSRPHTSTRASFPIASSTTQTS            1240

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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