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

NucPred

Fetching Q8TCU6 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MEAPSGSEPGGDGAGDCAHPDPRAPGAAAPSSGPGPCAAARESERQLRLR    50
  51  LCVLNEILGTERDYVGTLRFLQSAFLHRIRQNVADSVEKGLTEENVKVLF   100
 101  SNIEDILEVHKDFLAALEYCLHPEPQSQHELGNVFLKFKDKFCVYEEYCS   150
 151  NHEKALRLLVELNKIPTVRAFLLSCMLLGGRKTTDIPLEGYLLSPIQRIC   200
 201  KYPLLLKELAKRTPGKHPDHPAVQSALQAMKTVCSNINETKRQMEKLEAL   250
 251  EQLQSHIEGWEGSNLTDICTQLLLQGTLLKISAGNIQERAFFLFDNLLVY   300
 301  CKRKSRVTGSKKSTKRTKSINGSLYIFRGRINTEVMEVENVEDGTADYHS   350
 351  NGYTVTNGWKIHNTAKNKWFVCMAKTAEEKQKWLDAIIREREQRESLKLG   400
 401  MERDAYVMIAEKGEKLYHMMMNKKVNLIKDRRRKLSTVPKCFLGNEFVAW   450
 451  LLEIGEISKTEEGVNLGQALLENGIIHHVSDKHQFKNEQVMYRFRYDDGT   500
 501  YKARSELEDIMSKGVRLYCRLHSLYTPVIKDRDYHLKTYKSVLPGSKLVD   550
 551  WLLAQGDCQTREEAVALGVGLCNNGFMHHVLEKSEFRDESQYFRFHADEE   600
 601  MEGTSSKNKQLRNDFKLVENILAKRLLILPQEEDYGFDIEEKNKAVVVKS   650
 651  VQRGSLAEVAGLQVGRKIYSINEDLVFLRPFSEVESILNQSFCSRRPLRL   700
 701  LVATKAKEIIKIPDQPDTLCFQIRGAAPPYVYAVGRGSEAMAAGLCAGQC   750
 751  ILKVNGSNVMNDGAPEVLEHFQAFRSRREEALGLYQWIYHTHEDAQEARA   800
 801  SQEASTEDPSGEQAQEEDQADSAFPLLSLGPRLSLCEDSPMVTLTVDNVH   850
 851  LEHGVVYEYVSTAGVRCHVLEKIVEPRGCFGLTAKILEAFAANDSVFVEN   900
 901  CRRLMALSSAIVTMPHFEFRNICDTKLESIGQRIACYQEFAAQLKSRVSP   950
 951  PFKQAPLEPHPLCGLDFCPTNCHINLMEVSYPKTTPSVGRSFSIRFGRKP  1000
1001  SLIGLDPEQGHLNPMSYTQHCITTMAAPSWKCLPAAEGDPQGQGLHDGSF  1050
1051  GPASGTLGQEDRGLSFLLKQEDREIQDAYLQLFTKLDVALKEMKQYVTQI  1100
1101  NRLLSTITEPTSGGSCDASLAEEASSLPLVSEESEMDRSDHGGIKKVCFK  1150
1151  VAEEDQEDSGHDTMSYRDSYSECNSNRDSVLSYTSVRSNSSYLGSDEMGS  1200
1201  GDELPCDMRIPSDKQDKLHGCLEHLFNQVDSINALLKGPVMSRAFEETKH  1250
1251  FPMNHSLQEFKQKEECTIRGRSLIQISIQEDPWNLPNSIKTLVDNIQRYV  1300
1301  EDGKNQLLLALLKCTDTELQLRRDAIFCQALVAAVCTFSKQLLAALGYRY  1350
1351  NNNGEYEESSRDASRKWLEQVAATGVLLHCQSLLSPATVKEERTMLEDIW  1400
1401  VTLSELDNVTFSFKQLDENYVANTNVFYHIEGSRQALKVIFYLDSYHFSK  1450
1451  LPSRLEGGASLRLHTALFTKVLENVEGLPSPGSQAAEDLQQDINAQSLEK  1500
1501  VQQYYRKLRAFYLERSNLPTDASTTAVKIDQLIRPINALDELCRLMKSFV  1550
1551  HPKPGAAGSVGAGLIPISSELCYRLGACQMVMCGTGMQRSTLSVSLEQAA  1600
1601  ILARSHGLLPKCIMQATDIMRKQGPRVEILAKNLRVKDQMPQGAPRLYRL  1650
1651  CQPPVDGDL                                           1659

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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