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

NucPred

Fetching P07589 from www.uniprot.org...

The NucPred score for your sequence is 0.39 (see score help below)

   1  MLGGPGPGLLLLLAVLSLGTAVPSAGASKSRRQAQQIVQPQSPLTVSQSK    50
  51  PGCYDNGKHYQINQQWERTYLGSALVCTCYGGSRGFNCESKPEPEETCFD   100
 101  KYTGNTYRVGDTYERPKDSMIWDCTCIGAGRGRISCTIANRCHEGGQSYK   150
 151  IGDTWRRPHETGGYMLECVCLGNGKGEWTCKPIAEKCFDQAAGTSYVVGE   200
 201  TWEKPYQGWMMVDCTCLGEGSGRITCTSRNRCNDQDTRTSYRIGDTWSKK   250
 251  DNRGNLLQCICTGNGRGEWKCERHTSLQTTSAGSGSFTDVRTAIYQPQPH   300
 301  PQPPPYGHCVTDSGVVYSVGMQWLKTQGNKQMLCTCLGNGVSCQETAVTQ   350
 351  TYGGNSNGEPCVLPFTYNGKTFYSCTTEGRQDGHLWCSTTSNYEQDQKYS   400
 401  FCTDHTVLVQTRGGNSNGALCHFPFLYNNHNYTDCTSEGRRDNMKWCGTT   450
 451  QNYDADQKFGFCPMAAHEEICTTNEGVMYRIGDQWDKQHDMGHMMRCTCV   500
 501  GNGRGEWTCVAYSQLRDQCIVDGITYNVNDTFHKRHEEGHMLNCTCFGQG   550
 551  RGRWKCDPVDQCQDSETRTFYQIGDSWEKYLQGVRYQCYCYGRGIGEWAC   600
 601  QPLQTYPDTSGPVQVIITETPSQPNSHPIQWSAPESSHISKYILRWKPKN   650
 651  SPDRWKEATIPGHLNSYTIKGLRPGVVYEGQLISVQHYGQREVTRFDFTT   700
 701  TSTSPAVTSNTVTGETTPLSPVVATSESVTEITASSFVVSWVSASDTVSG   750
 751  FRVEYELSEEGDEPQYLDLPSTATSVNIPDLLPGRKYTVNVYEISEEGEQ   800
 801  NLILSTSQTTAPDAPPDPTVDQVDDTSIVVRWSRPRAPITGYRIVYSPSV   850
 851  EGSSTELNLPETANSVTLSDLQPGVQYNITIYAVEENQESTPVFIQQETT   900
 901  GVPRSDKVPPPRDLQFVEVTDVKITIMWTPPESPVTGYRVDVIPVNLPGE   950
 951  HGQRLPVSRNTFAEVTGLSPGVTYHFKVFAVNQGRESKPLTAQQATKLDA  1000
1001  PTNLQFINETDTTVIVTWTPPRARIVGYRLTVGLTRGGQPKQYNVGPAAS  1050
1051  QYPLRNLQPGSEYAVSLVAVKGNQQSPRVTGVFTTLQPLGSIPHYNTEVT  1100
1101  ETTIVITWTPAPRIGFKLGVRPSQGGEAPREVTSESGSIVVSGLTPGVEY  1150
1151  VYTISVLRDGQERDAPIVKKVVTPLSPPTNLHLEANPDTGVLTVSWERST  1200
1201  TPDITGYRITTTPTNGQQGYSLEEVVHADQSSCTFENLSPGLEYNVSVYT  1250
1251  VKDDKESVPISDTIIPEVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYR  1300
1301  ITVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGIDYDISVITLINGGESAP  1350
1351  TTLTQQTAVPPPTDLRFTNVGPDTMRVTWAPPSSIELTNLLVRYSPVKNE  1400
1401  EDVAELSISPSDNAVVLTNLLPGTEYLVSVSSVYEQHESIPLRGRQKTAL  1450
1451  DSPSGIDFSDITANSFTVHWIAPRATITGYRIRHHPENMGGRPREDRVPP  1500
1501  SRNSITLTNLNPGTEYVVSIVALNSKEESLPLVGQQSTVSDVPRDLEVIA  1550
1551  ATPTSLLISWDAPAVTVRYYRITYGETGGSSPVQEFTVPGSKSTATISGL  1600
1601  KPGVDYTITVYAVTGRGDSPASSKPVSINYRTEIDKPSQMQVTDVQDNSI  1650
1651  SVRWLPSSSPVTGYRVTTAPKNGPGPSKTKTVGPDQTEMTIEGLQPTVEY  1700
1701  VVSVYAQNQNGESQPLVQTAVTNIDRPKGLAFTDVDVDSIKIAWESPQGQ  1750
1751  VSRYRVTYSSPEDGIHELFPAPDGEEETAELQGLRPGSEYTVSVVALHDD  1800
1801  MESQPLIGTQSTTIPAPTNLKFTQVTPTSLTAQWTAPNVQLTGYRVRVTP  1850
1851  KEKTGPMKEINLAPDSSSVVVSGLMVATKYEVSVYALKDTLTSRPAQGVV  1900
1901  TTLENVSPPRRARVTDATETTITISWRTKTETITGFQVDAIPANGQTPIQ  1950
1951  RTIRPDVRSYTITGLQPGTDYKIHLYTLNDNARSSPVVIDASTAIDAPSN  2000
2001  LRFLATTPNSLLVSWQPPRARITGYIIKYEKPGSPPREVVPRPRPGVTEA  2050
2051  TITGLEPGTEYTIQVIALKNNQKSEPLIGRKKTDELPQLVTLPHPNLHGP  2100
2101  EILDVPSTVQKTPFITNPGYDTGNGIQLPGTSGQQPSLGQQMIFEEHGFR  2150
2151  RTTPPTTATPVRHRPRPYPPNVNEEIQIGHVPRGDVDHHLYPHVVGLNPN  2200
2201  ASTGQEALSQTTISWTPFQESSEYIISCHPVGIDEEPLQFRVPGTSASAT  2250
2251  LTGLTRGATYNIIVEAVKDQQRQKVREEVVTVGNSVDQGLSQPTDDSCFD  2300
2301  PYTVSHYAIGEEWERLSDSGFKLSCQCLGFGSGHFRCDSSKWCHDNGVNY  2350
2351  KIGEKWDRQGENGQMMSCTCLGNGKGEFKCDPHEATCYDDGKTYHVGEQW  2400
2401  QKEYLGAICSCTCFGGQRGWRCDNCRRPGAEPGNEGSTAHSYNQYSQRYH  2450
2451  QRTNTNVNCPIECFMPLDVQADREDSRE                        2478

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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