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

NucPred

Fetching P10978 from www.uniprot.org...

The NucPred score for your sequence is 0.56 (see score help below)

   1  MSGVKYEVAKFNGDNGFSTWQRRMRDLLIQQGLHKVLDVDSKKPDTMKAE    50
  51  DWADLDERAASAIRLHLSDDVVNNIIDEDTARGIWTRLESLYMSKTLTNK   100
 101  LYLKKQLYALHMSEGTNFLSHLNVFNGLITQLANLGVKIEEEDKAILLLN   150
 151  SLPSSYDNLATTILHGKTTIELKDVTSALLLNEKMRKKPENQGQALITEG   200
 201  RGRSYQRSSNNYGRSGARGKSKNRSKSRVRNCYNCNQPGHFKRDCPNPRK   250
 251  GKGETSGQKNDDNTAAMVQNNDNVVLFINEEEECMHLSGPESEWVVDTAA   300
 301  SHHATPVRDLFCRYVAGDFGTVKMGNTSYSKIAGIGDICIKTNVGCTLVL   350
 351  KDVRHVPDLRMNLISGIALDRDGYESYFANQKWRLTKGSLVIAKGVARGT   400
 401  LYRTNAEICQGELNAAQDEISVDLWHKRMGHMSEKGLQILAKKSLISYAK   450
 451  GTTVKPCDYCLFGKQHRVSFQTSSERKLNILDLVYSDVCGPMEIESMGGN   500
 501  KYFVTFIDDASRKLWVYILKTKDQVFQVFQKFHALVERETGRKLKRLRSD   550
 551  NGGEYTSREFEEYCSSHGIRHEKTVPGTPQHNGVAERMNRTIVEKVRSML   600
 601  RMAKLPKSFWGEAVQTACYLINRSPSVPLAFEIPERVWTNKEVSYSHLKV   650
 651  FGCRAFAHVPKEQRTKLDDKSIPCIFIGYGDEEFGYRLWDPVKKKVIRSR   700
 701  DVVFRESEVRTAADMSEKVKNGIIPNFVTIPSTSNNPTSAESTTDEVSEQ   750
 751  GEQPGEVIEQGEQLDEGVEEVEHPTQGEEQHQPLRRSERPRVESRRYPST   800
 801  EYVLISDDREPESLKEVLSHPEKNQLMKAMQEEMESLQKNGTYKLVELPK   850
 851  GKRPLKCKWVFKLKKDGDCKLVRYKARLVVKGFEQKKGIDFDEIFSPVVK   900
 901  MTSIRTILSLAASLDLEVEQLDVKTAFLHGDLEEEIYMEQPEGFEVAGKK   950
 951  HMVCKLNKSLYGLKQAPRQWYMKFDSFMKSQTYLKTYSDPCVYFKRFSEN  1000
1001  NFIILLLYVDDMLIVGKDKGLIAKLKGDLSKSFDMKDLGPAQQILGMKIV  1050
1051  RERTSRKLWLSQEKYIERVLERFNMKNAKPVSTPLAGHLKLSKKMCPTTV  1100
1101  EEKGNMAKVPYSSAVGSLMYAMVCTRPDIAHAVGVVSRFLENPGKEHWEA  1150
1151  VKWILRYLRGTTGDCLCFGGSDPILKGYTDADMAGDIDNRKSSTGYLFTF  1200
1201  SGGAISWQSKLQKCVALSTTEAEYIAATETGKEMIWLKRFLQELGLHQKE  1250
1251  YVVYCDSQSAIDLSKNSMYHARTKHIDVRYHWIREMVDDESLKVLKISTN  1300
1301  ENPADMLTKVVPRNKFELCKELVGMHSN                        1328

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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