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

NucPred

Fetching P53049 from www.uniprot.org...

The NucPred score for your sequence is 0.58 (see score help below)

   1  MTITVGDAVSETELENKSQNVVLSPKASASSDISTDVDKDTSSSWDDKSL    50
  51  LPTGEYIVDRNKPQTYLNSDDIEKVTESDIFPQKRLFSFLHSKKIPEVPQ   100
 101  TDDERKIYPLFHTNIISNMFFWWVLPILRVGYKRTIQPNDLFKMDPRMSI   150
 151  ETLYDDFEKNMIYYFEKTRKKYRKRHPEATEEEVMENAKLPKHTVLRALL   200
 201  FTFKKQYFMSIVFAILANCTSGFNPMITKRLIEFVEEKAIFHSMHVNKGI   250
 251  GYAIGACLMMFVNGLTFNHFFHTSQLTGVQAKSILTKAAMKKMFNASNYA   300
 301  RHCFPNGKVTSFVTTDLARIEFALSFQPFLAGFPAILAICIVLLIVNLGP   350
 351  IALVGIGIFFGGFFISLFAFKLILGFRIAANIFTDARVTMMREVLNNIKM   400
 401  IKYYTWEDAYEKNIQDIRTKEISKVRKMQLSRNFLIAMAMSLPSIASLVT   450
 451  FLAMYKVNKGGRQPGNIFASLSLFQVLSLQMFFLPIAIGTGIDMIIGLGR   500
 501  LQSLLEAPEDDPNQMIEMKPSPGFDPKLALKMTHCSFEWEDYELNDAIEE   550
 551  AKGEAKDEGKKNKKKRKDTWGKPSASTNKAKRLDNMLKDRDGPEDLEKTS   600
 601  FRGFKDLNFDIKKGEFIMITGPIGTGKSSLLNAMAGSMRKTDGKVEVNGD   650
 651  LLMCGYPWIQNASVRDNIIFGSPFNKEKYDEVVRVCSLKADLDILPAGDM   700
 701  TEIGERGITLSGGQKARINLARSVYKKKDIYLFDDVLSAVDSRVGKHIMD   750
 751  ECLTGMLANKTRILATHQLSLIERASRVIVLGTDGQVDIGTVDELKARNQ   800
 801  TLINLLQFSSQNSEKEDEEQEAVVAGELGQLKYESEVKELTELKKKATEM   850
 851  SQTANSGKIVADGHTSSKEERAVNSISLKIYREYIKAAVGKWGFIALPLY   900
 901  AILVVGTTFCSLFSSVWLSYWTENKFKNRPPSFYMGLYSFFVFAAFIFMN   950
 951  GQFTILCAMGIMASKWLNLRAVKRILHTPMSYIDTTPLGRILNRFTKDTD  1000
1001  SLDNELTESLRLMTSQFANIVGVCVMCIVYLPWFAIAIPFLLVIFVLIAD  1050
1051  HYQSSGREIKRLEAVQRSFVYNNLNEVLGGMDTIKAYRSQERFLAKSDFL  1100
1101  INKMNEAGYLVVVLQRWVGIFLDMVAIAFALIITLLCVTRAFPISAASVG  1150
1151  VLLTYVLQLPGLLNTILRAMTQTENDMNSAERLVTYATELPLEASYRKPE  1200
1201  MTPPESWPSMGEIIFENVDFAYRPGLPIVLKNLNLNIKSGEKIGICGRTG  1250
1251  AGKSTIMSALYRLNELTAGKILIDNVDISQLGLFDLRRKLAIIPQDPVLF  1300
1301  RGTIRKNLDPFNERTDDELWDALVRGGAIAKDDLPEVKLQKPDENGTHGK  1350
1351  MHKFHLDQAVEEEGSNFSLGERQLLALTRALVRQSKILILDEATSSVDYE  1400
1401  TDGKIQTRIVEEFGDCTILCIAHRLKTIVNYDRILVLEKGEVAEFDTPWT  1450
1451  LFSQEDSIFRSMCSRSGIVENDFENRS                         1477

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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