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

NucPred

Fetching Q01970 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MAGAQPGVHALQLEPPTVVETLRRGSKFIKWDEETSSRNLVTLRVDPNGF    50
51 FLYWTGPNMEVDTLDISSIRDTRTGRYARLPKDPKIREVLGFGGPDARLE 100
101 EKLMTVVSGPDPVNTVFLNFMAVQDDTAKVWSEELFKLAMNILAQNASRN 150
151 TFLRKAYTKLKLQVNQDGRIPVKNILKMFSADKKRVETALESCGLKFNRS 200
201 ESIRPDEFSLEIFERFLNKLCLRPDIDKILLEIGAKGKPYLTLEQLMDFI 250
251 NQKQRDPRLNEVLYPPLRPSQARLLIEKYEPNQQFLERDQMSMEGFSRYL 300
301 GGEENGILPLEALDLSTDMTQPLSAYFINSSHNTYLTAGQLAGTSSVEMY 350
351 RQALLWGCRCVELDVWKGRPPEEEPFITHGFTMTTEVPLRDVLEAIAETA 400
401 FKTSPYPVILSFENHVDSAKQQAKMAEYCRSIFGDALLIEPLDKYPLAPG 450
451 VPLPSPQDLMGRILVKNKKRHRPSAGGPDSAGRKRPLEQSNSALSESSAA 500
501 TEPSSPQLGSPSSDSCPGLSNGEEVGLEKPSLEPQKSLGDEGLNRGPYVL 550
551 GPADREDEEEDEEEEEQTDPKKPTTDEGTASSEVNATEEMSTLVNYIEPV 600
601 KFKSFEAARKRNKCFEMSSFVETKAMEQLTKSPMEFVEYNKQQLSRIYPK 650
651 GTRVDSSNYMPQLFWNVGCQLVALNFQTLDVAMQLNAGVFEYNGRSGYLL 700
701 KPEFMRRPDKSFDPFTEVIVDGIVANALRVKVISGQFLSDRKVGIYVEVD 750
751 MFGLPVDTRRKYRTRTSQGNSFNPVWDEEPFDFPKVVLPTLASLRIAAFE 800
801 EGGKFVGHRILPVSAIRSGYHYVCLRNEANQPLCLPALLIYTEASDYIPD 850
851 DHQDYAEALINPIKHVSLMDQRARQLAALIGESEAQAGQETCQDTQSQQL 900
901 GSQPSSNPTPSPLDASPRRPPGPTTSPASTSLSSPGQRDDLIASILSEVA 950
951 PTPLDELRGHKALVKLRSRQERDLRELRKKHQRKAVTLTRRLLDGLAQAQ 1000
1001 AEGRCRLRPGALGGAADVEDTKEGEDEAKRYQEFQNRQVQSLLELREAQV 1050
1051 DAEAQRRLEHLRQALQRLREVVLDANTTQFKRLKEMNEREKKELQKILDR 1100
1101 KRHNSISEAKMRDKHKKEAELTEINRRHITESVNSIRRLEEAQKQRHDRL 1150
1151 VAGQQQVLQQLAEEEPKLLAQLAQECQEQRARLPQEIRRSLLGEMPEGLG 1200
1201 DGPLVACASNGHAPGSSGHLSGADSESQEENTQL 1234

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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