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

NucPred

Fetching Q5SW75 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MALVTVQRSPTPSTTSSPCASEADSGEEECRSQPRSISESFLTVKGAALF    50
  51  LPRGNGSSTPRVSHRRNKHAGDLQQHLQAMFILLRPEDNIRLAVRLESTY   100
 101  QNRTRYMVVVSTNGRQDTEESIVLGMDFSSNDSSTCTMGLVLPLWSDTLI   150
 151  HLDGDGGFSVSTDNRVHIFKPVSVQAMWSALQSLHKACEVARMHNYYPGS   200
 201  LFLTWVSYYESHINSDQSSVNEWNAMQDVQSHRPDSPALFTDIPTERERT   250
 251  ERLIKTKLREIMMQKDLENITSKEIRTELEMQMVCNLREFKEFIDNEMIV   300
 301  ILGQMDSPTQIFEHVFLGSEWNASNLEDLQNRGVRYILNVTREIDNFFPG   350
 351  VFEYHNIRVYDEEATDLLAYWNDTYKFISKAKKHGSKCLVHCKMGVSRSA   400
 401  STVIAYAMKEYGWNLDRAYDYVKERRTVTKPNPSFMRQLEEYQGILLASK   450
 451  QRHNKLWRSHSDSDLSDHHEPICKPGLELNKKEMTTSADQIAEVKTVENL   500
 501  AAMPTVFMEHVVPQDANQKGLHTKERVICLEFSSQEFRAGQIEDELNLND   550
 551  INGCSSGCCLSESKLPLDNCHASKALLQPGQAPDIANKFPDLAVEDLETD   600
 601  ALKADMNVHLLPMEELTSRLKDLPMSPDLESPSPQASCQAAISDFSTDRI   650
 651  DFFSALEKFVELSQETRSRSFSHSRIEELGGGRSEGCRLSVIEVAASEMA   700
 701  ADDQRSSSLSNTPHASEESSVDEDQSKAITELVSPDIIMQSHSENAISVK   750
 751  EIVTEIESISQGVGQVQLKGDILSNPCHTPKKSTIHELPLERVPAPESKP   800
 801  GHWEQDESFCSVQPELARDSGKCAPEEGCLTTHSSTADLEEEEPVEGEHD   850
 851  WGPGMHSGAKWCPGSVRRATLEFEERLRQEQENHGTASAGPTLSNRKNSK   900
 901  NDSSVADLMPKWKSDETTPEHSFFLKEAEPSKGKGKCSGSEAGSLSHCER   950
 951  NPTMPDCELLEHHSLPAPQDCLGSDSRSKKQEGDLKKQRAVVPNQECDTQ  1000
1001  AILLPLPKKIEIIEYTPTVTSLGHTEPGGEATPSKEGEKQGLRKVKMEQS  1050
1051  ITMFCALDENLNRTLEPSQVSLHPQVLPLPHSSSECDRPADPNPMLSSPQ  1100
1101  DKGDCPSTPFKTAAPFVSCSTQGASFSLDYLLPHSVVHLEGCTEQSSATD  1150
1151  NELSPEQASWEDSRGHFLSSGSGMAHTSSPLTNEDLSLINKLGDSVGVLQ  1200
1201  KKLDPSPEACRIPHSSSSENIRDLSHSRGVVKEHAKEIESRVIFQAGFSK  1250
1251  TSQMKRSASLAKLGYLDLCKDYLPDRELVSSESPHLKLLQPFLRTDSGMH  1300
1301  ALMAHEPSESAGAQQNPQPTKYSVEQLKTSECIVQSKPVERPSVQYAKEF  1350
1351  GYSQQCLLPKARPELTSSEGGLPLLQTQGLQYTGPSPGLAVAPRQQHGRT  1400
1401  HPLRRLKRANDKKRTTNPFYNTM                             1423

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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