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

NucPred

Fetching P24014 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MAAPSRTTLMPPPFRLQLRLLILPILLLLRHDAVHAEPYSGGFGSSAVSS    50
  51  GGLGSVGIHIPGGGVGVITEARCPRVCSCTGLNVDCSHRGLTSVPRKISA   100
 101  DVERLELQGNNLTVIYETDFQRLTKLRMLQLTDNQIHTIERNSFQDLVSL   150
 151  ERLRLNNNRLKAIPENFVTSSASLLRLDISNNVITTVGRRVFKGAQSLRS   200
 201  LQLDNNQITCLDEHAFKGLVELEILTLNNNNLTSLPHNIFGGLGRLRALR   250
 251  LSDNPFACDCHLSWLSRFLRSATRLAPYTRCQSPSQLKGQNVADLHDQEF   300
 301  KCSGLTEHAPMECGAENSCPHPCRCADGIVDCREKSLTSVPVTLPDDTTE   350
 351  LRLEQNFITELPPKSFSSFRRLRRIDLSNNNISRIAHDALSGLKQLTTLV   400
 401  LYGNKIKDLPSGVFKGLGSLQLLLLNANEISCIRKDAFRDLHSLSLLSLY   450
 451  DNNIQSLANGTFDAMKSIKTVHLAKNPFICDCNLRWLADYLHKNPIETSG   500
 501  ARCESPKRMHRRRIESLREEKFKCSWDELRMKLSGECRMDSDCPAMCHCE   550
 551  GTTVDCTGRGLKEIPRDIPLHTTELLLNDNELGRISSDGLFGRLPHLVKL   600
 601  ELKRNQLTGIEPNAFEGASHIQELQLGENKIKEISNKMFLGLHQLKTLNL   650
 651  YDNQISCVMPGSFEHLNSLTSLNLASNPFNCNCHLAWFAEWLRKKSLNGG   700
 701  AARCGAPSKVRDVQIKDLPHSEFKCSSENSEGCLGDGYCPPSCTCTGTVV   750
 751  RCSRNQLKEIPRGIPAETSELYLESNEIEQIHYERIRHLRSLTRLDLSNN   800
 801  QITILSNYTFANLTKLSTLIISYNKLQCLQRHALSGLNNLRVLSLHGNRI   850
 851  SMLPEGSFEDLKSLTHIALGSNPLYCDCGLKWFSDWIKLDYVEPGIARCA   900
 901  EPEQMKDKLILSTPSSSFVCRGRVRNDILAKCNACFEQPCQNQAQCVALP   950
 951  QREYQCLCQPGYHGKHCEFMIDACYGNPCRNNATCTVLEEGRFSCQCAPG  1000
1001  YTGARCETNIDDCLGEIKCQNNATCIDGVESYKCECQPGFSGEFCDTKIQ  1050
1051  FCSPEFNPCANGAKCMDHFTHYSCDCQAGFHGTNCTDNIDDCQNHMCQNG  1100
1101  GTCVDGINDYQCRCPDDYTGKYCEGHNMISMMYPQTSPCQNHECKHGVCF  1150
1151  QPNAQGSDYLCRCHPGYTGKWCEYLTSISFVHNNSFVELEPLRTRPEANV  1200
1201  TIVFSSAEQNGILMYDGQDAHLAVELFNGRIRVSYDVGNHPVSTMYSFEM  1250
1251  VADGKYHAVELLAIKKNFTLRVDRGLARSIINEGSNDYLKLTTPMFLGGL  1300
1301  PVDPAQQAYKNWQIRNLTSFKGCMKEVWINHKLVDFGNAQRQQKITPGCA  1350
1351  LLEGEQQEEEDDEQDFMDETPHIKEEPVDPCLENKCRRGSRCVPNSNARD  1400
1401  GYQCKCKHGQRGRYCDQGEGSTEPPTVTAASTCRKEQVREYYTENDCRSR  1450
1451  QPLKYAKCVGGCGNQCCAAKIVRRRKVRMVCSNNRKYIKNLDIVRKCGCT  1500
1501  KKCY                                                1504

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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