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

NucPred

Fetching O55196 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MLLLQCRNPTSPPKPCGLVPNVKMSLLVFLGLLGVSAAMPFQMPMPRMPG    50
  51  FSSKSEEMMRYNQFNFMNAPPMMPMGPYGNGMPMPPHMPPQYPPYQMPMW   100
 101  PPPVPNGWQQPPMPNFPSKTDQTQETAKPNQTNPQEPQPQKQPLKEPPNE   150
 151  AARAKDDAQPPQPFPPFGNGLYPYPQPPWPIPQRGPPTAFGRPKFSNEEG   200
 201  NPYYAFFGYHGFGGRPYYSEEMFEDYEKPKEKDPPKPEDPPPDDPPPEAS   250
 251  TNSTVPDANATQSIPEGGNDTSPIGNTGPGPNAGNNPTVQNGVFPPPKVN   300
 301  VSGQGVPKSQIPWRPSQPNIYENYPYPNYPSERQWQTTGTQGPRQNGPGY   350
 351  RNPQVERGPQWNSFAWEGKQATRPGNPTYGKPPSPTSGVNYAGNPVHFGR   400
 401  NLPGPNKPFVGANPASNKPFVGANPASNKPFVGANPASNKPFVGANPASN   450
 451  KPFVGANPASNKPYVGANPASNKPFIGANPAANKPSIGTNPAANKPSIGT   500
 501  NPAANKPFVRNNVGANKPFVGTNPSSNQPFLRSNQASNKPFMRSNQASNK   550
 551  PFVGTNVASVGPKQVTVSHNMKTQNPKEKSLGQKERTVTPTKDASNPWRS   600
 601  AKQYGINNPNYNLPRSEGSMVGPNFNSFDQQENSYFSKGASKRVPSPNIQ   650
 651  IQSQNLPKGIALEPRRTPFQSETKKPELKHGTHQPAYPKKIPSPTRKHFP   700
 701  AERNTWNRQKILPPLKEDYGRQDENLRHPSYGSRGNIFYHEYTNPYHNEK   750
 751  SQYIKSNPWDKSSPSTMMRPENPQYTMTSLDQKETEQYNEEDPIDPNEDE   800
 801  SFPGQSRWGDEEMNFKGNPTVRQYEGEHYASTLAKEYLPYSLSNPPKPSE   850
 851  DFPYSEFYPWNPQETFPIYNPGPTIAPPVDPRSYYVNNAIGQEESTLFPS   900
 901  WTSWDHRNQAERQKESEPYFNRNVWDQSINLHKSNIPNHPYSTTSPARFP   950
 951  KDPTWFEGENLNYDLQITSLSPPEREQLAFPDFLPQSYPTGQNEAHLFHQ  1000
1001  SQRGSCCIGGSTGHKDNVLALQDYTSSYGLPPRKNQETSPVHTESSYIKY  1050
1051  ARPNVSPASILPSQRNISENKLTAESPNPSPFGDGVPTVRKNTPYSGKNQ  1100
1101  LETGIVAFSEASSSQPKNTPCLKSDLGGDRRDVLKQFFEGSQLSERTAGL  1150
1151  TPEQLVIGIPDKGSGPDSIQSEVQGKEGEMQQQRPPTIMKLPCFGSNSKF  1200
1201  HSSTTGPPINNRRPTLLNGALSTPTESPNTLVGLATREQLKSINVDKLNA  1250
1251  DEHTTLESFQGTSPQDQGCLLLQA                            1274

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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