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

NucPred

Fetching Q8IRI6 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MAFLCAPGLTFFLTYSIFSAVLGMLQFGYNTGVINAPEKNIENFMKDVYK    50
  51  DRYGEDISEEFIQQLYSVAVSIFAIGGMLGGFSGGWMANRFGRKGGLLLN   100
 101  NVLGIAGACLMGFTKVSHSYEMLFLGRFIIGVNCGLNTSLVPMYISEIAP   150
 151  LNLRGGLGTVNQLAVTVGLLLSQVLGIEQILGTNEGWPILLGLAICPAIL   200
 201  QLILLPVCPESPRYLLITKQWEEEARKALRRLRASGSVEEDIEEMRAEER   250
 251  AQQSESHISTMELICSPTLRPPLIIGIVMQLSQQFSGINAVFYYSTSLFM   300
 301  SSGLTEESAKFATIGIGAIMVVMTLVSIPLMDRTGRRTLHLYGLGGMFIF   350
 351  SIFITISFLIKEMIDWMSYLSVVATLGFVVFFAVGPGSIPWMITAELFSQ   400
 401  GPRPSAMAIAVLVNWMANFVVGIGFPSMKTALENYTFLPFSVFLAIFWIF   450
 451  TYKKVPETKNKTFEEILALFRHNNGRSMLNCTNSLEPQSMNSGIEHAALM   500
 501  VSEEKTQHDSLFGTTSFSLTVEGMGPYPLSDSTNLLGPGSSSYGPGGVLG   550
 551  LAGSGSGLGGQCYTNYGTNLQTPQAARKCHYDEVDDYSFRRHSAHGRITQ   600
 601  MKGKPLILGPTIKKDKKKERTDWLTASERFLEGGRSTHQGRSAASAPHHP   650
 651  RQPPPVCPSSGPXLRSASPPDSASVRSTSRAEEPHQPQQVHHQQQQVHHQ   700
 701  QQHQSRYATHEYVHCSYEKEVVCDQANPSQAPPQQPAPPVQQHQQQPPPP   750
 751  LHHCQQRKHSHSPHHSRHTSPHSHHHHSHHSRHSRRSRRQGSGSLPGAHQ   800
 801  GSANHSVMRPSICTSRRHRSVTDISTTNVCQDPACSDREVQEIMVRRTCC   850
 851  NTTATNSSSRTELAQCFAEDLYGSSRRPSSCCTSSDYCYQTDSTSLYGSR   900
 901  SSLSRNNSIKSASALVRKHHRSQRSLLPEHRHPSYTSISLRGLNASRPNS   950
 951  QLGSLTSIFDRAKNMAPEGSTLERQSSKGALGSSELPEYACSPSPIRWSF  1000
1001  LADGRSPSEMEGAVGGGPEREQEEEDKLDAWQVPEPEPEKKPCRKITTSS  1050
1051  SVYDEGPSTSAAAARKRRGSKGSRGSKGSGSYHCEFEDEATTTVMFHQDA  1100
1101  GEAYNNCCSNNYNYIQCNTYLDQDLQITSEDIHQYLSKGDATASDILNNS  1150
1151  KNYPFQPSNALEFQYKNNFQQGQANANNNNTNTTNTASSDAAECFQNYRA  1200
1201  ISKETNLNQTSTEQLSPTNINLSTSSNNINIVFSSSLERNANEVKFINNR  1250
1251  SGASGGSEMGCEVGHHAGYLPYTYPSYDYTNMSGNSHFEKPLGIDELPKE  1300
1301  FCGLEGAGGGGASTTSEHSSSLPSPQPLTHHQQLHHFESFDAASEHNLLA  1350
1351  AQPMSPGSPLSGSVNPAGDDFVQMHHYHHANSPHSQSHHSHAHTHTHGHH  1400
1401  VHHLLNHPAYDLTDDQFRLGSALKRVRKRARKYTDFLRKK            1440

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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