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

NucPred

Fetching Q28275 from www.uniprot.org...

The NucPred score for your sequence is 0.36 (see score help below)

   1  LGAALRSAGAARGRRQAQQIVQPPGPPGCYDNGKHYQINQQWERTYLGNA    50
  51  LVCTCYGGSRGFNCESKPEPEETCFDKYTGNTYRVGDTYERPKDSMIWDC   100
 101  TCIGAGRGRISCTIANRCHEGGQSYKIGDTWRRPHETGGYMLECVCLGNG   150
 151  KGEWTCKPIAEKCFDHAAGTSYVVGETWEKPYQGWMMVDCTCLGEGSGRI   200
 201  TCTSRNRCNDQDTRTSYRIGDTWSKKDNRGNLLQCICTGNGRGEWKCERH   250
 251  ASLQTTSTGSGPFTDVRTAIYQPQPHPQPAPYGHCVTDSGVVYSVGMQWL   300
 301  KTQGNKQMLCTCLGNGVSCQETAVTQTYGGNSNGEPCVLPFTYNGRTFYS   350
 351  CTTEGRQDGHLWCSTTSNYEQDQKYSFCTDHTVLVQTRGGNSNGALCHFP   400
 401  FLYNNHNYTDCTSEGRRDNMKWCGTTPNYDADQKFGFCPHAHEEICTTNE   450
 451  GHDMGHMMRCTCVGNGRGEWTCVAYSQLRDQCIVDDITYNVNDTFHKRHE   500
 501  EGHMLNCTCFGQGRGRWKCDPIDQCQDSETRTFYQIGDSWEKYVHGVRYQ   550
 551  CYCYGRGIGEWHCQPLQTYPGTTGPVQVIITETPSQPNSHPIQWNAPEPS   600
 601  HISKYILRWKPKNSPGRWKEATIPGHLNSYTIKGLTPGVVYEGQLISVQH   650
 651  YGHREVTRFDFTTTSTSPPVTSNTVTGETTPLSPVVATSESVTEITASSF   700
 701  VVSWVSASDTVSGFRVEYELSEEGDEPQYLDLPSTATSVNIPDLLPGRKY   750
 751  IVNVYQISEEGEQSLILSTSQTTAPDAPPDPAVDRVDDTSIVVRWSRPQA   800
 801  PITGYRIVYSPSVEGSSTELNLPETANSVTLSDLQPGVQYNITIYAVEEN   850
 851  QESTPVFIQQETTGVPRSDKVPPPRDLQFVEVTDVKITIMWTPPESTVTG   900
 901  YRVDVIPVNLPGEHGQRLPINRNTFAEVTGLSPGVTYHFKVFAVNQGRES   950
 951  RPLTAEQTTKLDAPTNLRFANETDSTVLVIWTPPRARIAGYRLTVGPTRG  1000
1001  GHPKQYNVGPSASQYPLRNLQPATEYTVSLVAVKGNQQSPKATGVFTTLQ  1050
1051  PLSSIPPYNTEVTETTIVITWTPAPRIGFKLGVRPSQGGEAPREVTSDSG  1100
1101  SIVVSGLTPGVEYVYTISVLRDGQERDTPIVKKVVTPLSPPTNLHLEANP  1150
1151  DTGVLTVSWERSTTPDITGYRITTTPTNGQQGYSLEEVVHADQSSCTFEN  1200
1201  LSPGLEYNVSVYTVKDDKESVPISDTIIPEVPQLTDLSFVDITDSSIGLR  1250
1251  WTPLNSSTIIGYRITVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGIDYDI  1300
1301  SVITLINGGESAPTTLTQQTAVPPPTDLRFTNIGPDTMRVTWAPPPSIEL  1350
1351  TNFLVRYSPVKNEEDVAELSISPSDNVVVLTNLLPGTEYLVSVSSVYEQH  1400
1401  ESTPLRGRQKTGLDSPSGIDFSDITANSFTVHWIAPRATITGYRIRHHPE  1450
1451  HTSGRPREDRVPPSRNSITLTNLNPGTEYVVSIIALNGREESPPLIGQQS  1500
1501  SLQPPTSLLISWDAPAVTVRYYRITYGENSPVQEFTVPGSKSTATISGLK  1550
1551  PGADYTITVYAVTGRGDSPASSKPVSIDYRTGTDSSMQVTDVQDNSISVR  1600
1601  WLPSSSPVTGYRVTTTPKNGPGPSKTKTAGPDQTEMTIEGLQPTVEYVVS  1650
1651  VYAQNRNGESQPLVQTAVTTIPAPADLKFTQVTPTSLTAQWTAPNVQLTG  1700
1701  YRVRVTPKEKTGPMKEINLAPDSSSVVVSGLMVATKYEVSVYALKDTLTS  1750
1751  RPAQGVVTTLENVSPPRRARVTDATETTITISWRTKTETITGFQVDAIPA  1800
1801  NGQNPIQRTIRPDVRSYTITGLQPGTDYKIYLYTLNDNARSSPVVIDRLT  1850
1851  FVFFQPLMHHPTCVFLATTPNSLLVSWQPPRARITGYIIKYEKPGSPPRE  1900
1901  VVPRPRPGVTEATITGLEPGTEYTIQVIALKNNQKSEPLIGRKKTGQEAL  1950
1951  SQTTISWTPFQESSEYIISCHPVGIDEEPLQFRVPGTSASATLTGLTRGA  2000
2001  TYNIIVEALKDQKRHKVREEVVTVGNSVDQGLNQPTDDSCFDPYTRLSES  2050
2051  GFKLSCQCLGFGSGHFRCDSSKWCHDNGVNYKIGEKWDRQGENGQMMSCT  2100
2101  CLGNGKGEFKCDPHEATCYDDGKTYHVGEQWQKEYLGAICSCTCFGGQRG  2150
2151  WRCDNCRRPGAEPGHEGSTGHYNQYSQRYHQRTNTNVNCPIECFMPLDVQ  2200
2201  ADREDSRE                                            2208

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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