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

NucPred

Fetching Q64512 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MHVSLAEALEVRGGPLQEEEIWAVLNQSAESLQEVFRRVSIADPAALGFI    50
  51  ISPWSLLLLPSGSVSFTDENVSNQDLRASTAPEVLQSHSLTSLADVEKIH   100
 101  IYSLGMTLYWGADHEVPQSQPIKLGDHLNSILLGMCEDVIYARVSVRTVL   150
 151  DACSAHIRNSNCAPSFSNVKQLVKLVLGNISGTDPLSRSSEQKPDRSQAI   200
 201  RDRLRGKGLPTGRSSTSDALDTHEAPLSQQTFVNKGLSKSMGFLSIRDTR   250
 251  DEEDYLKDTPSDNNSRHEDSETFSSPYQFKTSTPQMDALSKKKTWASSMD   300
 301  LLCAANRDISGETGRYQRCDPKTVTGRTSITPRKKEGRYSDGSIALDIFG   350
 351  PQKVEPVIHTRELPTSTAVSSALDRIRERQQKLQVLREAMNVEEPVRRYK   400
 401  TYHSDIFSISSESPSVISSESDFRQVRKSEASKRFESSSGLPGVDETGQT   450
 451  RPSRQYETSLEGNLINQDIMLRRQEEEMMQLQARMALRQSRLSLYPGDTV   500
 501  KASMLDISRDPLREMALETAMTQRKLRNFFGPEFVKMTVEPFVSLDLPRS   550
 551  ILSQTKKGKSEDQRRKVNIRLLSGQRLELTCDTKTICKDVFDMVVAHIGL   600
 601  VEHHLFALATRKENEYFFVDPDLKLTKVAPEGWKEEPKRKGKAAVDFTLF   650
 651  FRIKFFMDDVSLIQHDLTCHQYYLQLRKDLLDERVHCDDEAALLLASLAL   700
 701  QAEYGDYQPEVHGVSYFRLEHYLPARVMEKLDVSYIKEELPKLHNTYAGA   750
 751  SEKETELEFLKVCQRLTEYGVHFHRVHPEKKSQTGILLGVCSKGVLVFEV   800
 801  HNGVRALVLRFPWRETKKISFSKKKITLQNTSDGIKHAFQTDSSKACQYL   850
 851  LHLCSSQHKFQLQMRARQSNQDAQDIERASFRSLNLQAESVRGFNMGRAI   900
 901  STGSLASSTINKLAVRPLSVQAEILKRLSSSEWSLYQPLQNSSKEKTDKA   950
 951  SWEEKPRGMSKSYHDLSQASLCPHRKQVINMEALPQAFAELVGKPLYPMA  1000
1001  RSDTESLAGLPKLDNSKSVASLNRSPERRNHESDSSTEDPGQAYVVGMSL  1050
1051  PSSGKSSSQVPFKDNDTLHKRWSIVSSPEREITLVNLKKDPKHGLGFQII  1100
1101  GGEKMGRLDLGVFISAVTPGGPADLDGCLKPGDRLISVNSVSLEGVSHHA  1150
1151  AVDILQNAPEDVTLVISQPKEKPSKVPSTPVHFANGMKSYTKKPAYMQDS  1200
1201  AMDPSEDQPWPRGTLRHIPESPFGLSGGLREGSLSSQDSRTESASLSQSQ  1250
1251  VNGFFASHLGDRGWQEPQHSSPSPSVTTKVNEKTFSDSNRSKAKRRGISD  1300
1301  LIEHLDCADSDKDDSTYTSSQDHQTSKQEPSSSLSTSNKTSFPTSSASPP  1350
1351  KPGDTFEVELAKTDGSLGISVTGGVNTSVRHGGIYVKAIIPKGAAESDGR  1400
1401  IHKGDRVLAVNGVSLEGATHKQAVETLRNTGQVVHLLLEKGQVPTSRERD  1450
1451  PAGPQSPPPDQDAQRQAPEKVAKQTPHVKDYSFVTEDNTFEVKLFKNSSG  1500
1501  LGFSFSREDNLIPEQINGSIVRVKKLFPGQPAAESGKIDVGDVILKVNGA  1550
1551  PLKGLSQQDVISALRGTAPEVSLLLCRPAPGVLPEIDTTFLNPLYSPANS  1600
1601  FLNSSKETSQPSSSVEQGASSDDNGVSGKTKNHCRAPSRRESYSDHSESG  1650
1651  EDDSVRAPAKMPNVTRVAAFPHEAPRSQEESICAMFYLPRKIPGKLESES  1700
1701  SHPPPLDVSPGQTCQPPAECAPSDATGKHFTHLASQLSKEENITTLKNDL  1750
1751  GNHLEDSELEVELLITLVKSEKGSLGFTVTKGSQSIGCYVHDVIQDPAKG  1800
1801  DGRLKAGDRLIKVNDTDVTNMTHTDAVNLLRAAPKTVRLVLGRILELPRM  1850
1851  PVFPHLLPDITVTCHGEELGFSLSGGQGSPHGVVYISDINPRSAAAVDGS  1900
1901  LQLLDIIHYVNGVSTQGMTLEDANRALDLSLPSVVLKVTRDGCPVVPTTR  1950
1951  AAISAPRFTKANGLTSMEPSGQPALMPKNSFSKVNGEGVHEAVCPAGEGS  2000
2001  SSQMKESAGLTETKESNSRDDDIYDDPQEAEVIQSLLDVVDEEAQNLLNQ  2050
2051  RHATRRACSPDPLRTNGEAPEEGDTDYDGSPLPEDVPESVSSGEGKVDLA  2100
2101  SLTAASQEEKPIEEDATQESRNSTTETTDGEDSSKDPPFLTNEELAALPV  2150
2151  VRVPPSGKYTGTQLQATIRTLQGLLDQGIPSKELENLQELKPLDQCLIGQ  2200
2201  TKENRRKNRYKNILPYDTTRVPLGDEGGYINASFIRIPVGTQEFVYIACQ  2250
2251  GPLPTTVGDFWQMVWEQNSTVIAMMTQEVEGEKIKCQRYWPSILGTTTMA  2300
2301  NERLRLALLRMQQLKGFIVRVMALEDIQTGEVRHISHLNFTAWPDHDTPS  2350
2351  QPDDLLTFISYMRHIRRSGPVITHCSAGIGRSGTLICIDVVLGLISQDLE  2400
2401  FDISDLVRCMRLQRHGMVQTEGQYVFCYQVILYVLTHLQAEEQKAQQPGL  2450
2451  PQP                                                 2453

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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