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

NucPred

Fetching Q6ZNL6 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MFRGPKPPIAPKPRLTAPNEWRASVYLNDSLNKCSNGRLPCVDRGLDEGP    50
  51  RSIPKCSESETDEDYIVVPRVPLREDEPKDEGSVGNKALVSPESSAEEEE   100
 101  EREEGGEACGLEGTGAGEDSVAPAAPGAGALSREGEEGTDLALEDEGEGC   150
 151  ADEPGTLEQVSRSEEEEKLVQPHRECSLEDSGPWAGEGVFQSDLLLPHIH   200
 201  GEDQEPPDTPGEAEEDDEEGCASTDPAGADEGSGPDRPTEDMGQDAEDTS   250
 251  EEPPEKEELAGVQEAETATDCPEVLEEGCEEATGVTGGEQVDLSEPPDHE   300
 301  KKTNQEVAAATLEDHAQDESAEESCQIVPFENDCMEDFVTSLTGSPYEFF   350
 351  PTESTSFCSESCSPLSESAKGLESEQAPKLGLRAEENPMVGALCGQCGSL   400
 401  QGGAAEGPAAPDVVVVLEEEALDDALANPYVMGVGLPGQAAPGEGGQAAS   450
 451  DALGGYGSKEELNCEAEGGLVPADRKNTSTRVRPHSGKVAGYVPETVPEE   500
 501  TGPEAGSSAPGIGGAAEEVGKTLLSLEGKPLEASRALPAKPRAFTLYPRS   550
 551  FSVEGREIPVSVYQEPEGSGLDDHRIKRKEDNLSLSCVIGSSGSFSQRNH   600
 601  LPSSGTSTPSSMVDIPPPFDLACITKKPITKSSPSLLIESDSPDKYKKKK   650
 651  SSFKRFLALTFKKKTENKLHVDVNVSSSRSSSESSYHGPSRILEVDRRSL   700
 701  SNSPQLKSRTGKLRASESPSSLIFYRDGKRKGVPFSRTVSRVESFEDRSR   750
 751  PPFLPLPLTKPRSISFPSADTSDYENIPAMNSDYENIQIPPRRPARAGAF   800
 801  TKLFEDQSRALSTANENDGYVDMSSFNAFESKQQSADQDAESAYTEPYKV   850
 851  CPISSAAPKEDLTSDEEQRSSEEEDSASRDPSVTHKVEGQSRALVIAQEL   900
 901  LSSEKAYVEMLQHLNLDFHGAVMRALDDMDHEGRDTLAREELRQGLSELP   950
 951  AIHDLHQGILEELEERLSNWESQQKVADVFLAREQGFDHHATHILQFDRY  1000
1001  LGLLSENCLHSPRLAAAVREFEQSVQGGSQTAKHRLLRVVQRLFQYQVLL  1050
1051  TDYLNNLCPDSAEYDNTQGALSLISKVTDRANDSMEQGENLQKLVHIEHS  1100
1101  VRGQGDLLQPGREFLKEGTLMKVTGKNRRPRHLFLMNDVLLYTYPQKDGK  1150
1151  YRLKNTLAVANMKVSRPVMEKVPYALKIETSESCLMLSASSCAERDEWYG  1200
1201  CLSRALPEDYKAQALAAFHHSVEIRERLGVSLGERPPTLVPVTHVMMCMN  1250
1251  CGCDFSLTLRRHHCHACGKIVCRNCSRNKYPLKYLKDRMAKVCDGCFGEL  1300
1301  KKRGRAVPGLMRERPVSMSFPLSSPRFSGSAFSSVFQSINPSTFKKQKKV  1350
1351  PSALTEVAASGEGSAISGYLSRCKRGKRHWKKLWFVIKGKVLYTYMASED  1400
1401  KVALESMPLLGFTIAPEKEEGSSEVGPIFHLYHKKTLFYSFKAEDTNSAQ  1450
1451  RWIEAMEDASVL                                        1462

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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