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

NucPred

Fetching O14607 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MKSCAVSLTTAAVAFGDEAKKMAEGKASRESEEESVSLTVEEREALGGMD    50
  51  SRLFGFVRLHEDGARTKTLLGKAVRCYESLILKAEGKVESDFFCQLGHFN   100
 101  LLLEDYSKALSAYQRYYSLQADYWKNAAFLYGLGLVYFYYNAFHWAIKAF   150
 151  QDVLYVDPSFCRAKEIHLRLGLMFKVNTDYKSSLKHFQLALIDCNPCTLS   200
 201  NAEIQFHIAHLYETQRKYHSAKEAYEQLLQTENLPAQVKATVLQQLGWMH   250
 251  HNMDLVGDKATKESYAIQYLQKSLEADPNSGQSWYFLGRCYSSIGKVQDA   300
 301  FISYRQSIDKSEASADTWCSIGVLYQQQNQPMDALQAYICAVQLDHGHAA   350
 351  AWMDLGTLYESCNQPQDAIKCYLNAARSKRCSNTSTLAARIKFLQNGSDN   400
 401  WNGGQSLSHHPVQQVYSLCLTPQKLQHLEQLRANRDNLNPAQKHQLEQLE   450
 451  SQFVLMQQMRHKEVAQVRTTGIHNGAITDSSLPTNSVSNRQPHGALTRVS   500
 501  SVSQPGVRPACVEKLLSSGAFSAGCIPCGTSKILGSTDTILLGSNCIAGS   550
 551  ESNGNVPYLQQNTHTLPHNHTDLNSSTEEPWRKQLSNSAQGLHKSQSSCL   600
 601  SGPNEEQPLFSTGSAQYHQATSTGIKKANEHLTLPSNSVPQGDADSHLSC   650
 651  HTATSGGQQGIMFTKESKPSKNRSLVPETSRHTGDTSNGCADVKGLSNHV   700
 701  HQLIADAVSSPNHGDSPNLLIADNPQLSALLIGKANGNVGTGTCDKVNNI   750
 751  HPAVHTKTDHSVASSPSSAISTATPSPKSTEQRSINSVTSLNSPHSGLHT   800
 801  VNGEGLGKSQSSTKVDLPLASHRSTSQILPSMSVSICPSSTEVLKACRNP   850
 851  GKNGLSNSCILLDKCPPPRPPTSPYPPLPKDKLNPPTPSIYLENKRDAFF   900
 901  PPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQ   950
 951  LLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEK  1000
1001  RTQHKDHSDNESTSSENSGRRRKGPFKTIKFGTNIDLSDNKKWKLQLHEL  1050
1051  TKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFC  1100
1101  SVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEA  1150
1151  NVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAV  1200
1201  ERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQY  1250
1251  QTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKT  1300
1301  YIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSSSS     1347

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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