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

NucPred

Fetching Q12923 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MHVSLAEALEVRGGPLQEEEIWAVLNQSAESLQELFRKVSLADPAALGFI    50
  51  ISPWSLLLLPSGSVSFTDENISNQDLRAFTAPEVLQNQSLTSLSDVEKIH   100
 101  IYSLGMTLYWGADYEVPQSQPIKLGDHLNSILLGMCEDVIYARVSVRTVL   150
 151  DACSAHIRNSNCAPSFSYVKHLVKLVLGNLSGTDQLSCNSEQKPDRSQAI   200
 201  RDRLRGKGLPTGRSSTSDVLDIQKPPLSHQTFLNKGLSKSMGFLSIKDTQ   250
 251  DENYFKDILSDNSGREDSENTFSPYQFKTSGPEKKPIPGIDVLSKKKIWA   300
 301  SSMDLLCTADRDFSSGETATYRRCHPEAVTVRTSTTPRKKEARYSDGSIA   350
 351  LDIFGPQKMDPIYHTRELPTSSAISSALDRIRERQKKLQVLREAMNVEEP   400
 401  VRRYKTYHGDVFSTSSESPSIISSESDFRQVRRSEASKRFESSSGLPGVD   450
 451  ETLSQGQSQRPSRQYETPFEGNLINQEIMLKRQEEELMQLQAKMALRQSR   500
 501  LSLYPGDTIKASMLDITRDPLREIALETAMTQRKLRNFFGPEFVKMTIEP   550
 551  FISLDLPRSILTKKGKNEDNRRKVNIMLLNGQRLELTCDTKTICKDVFDM   600
 601  VVAHIGLVEHHLFALATLKDNEYFFVDPDLKLTKVAPEGWKEEPKKKTKA   650
 651  TVNFTLFFRIKFFMDDVSLIQHTLTCHQYYLQLRKDILEERMHCDDETSL   700
 701  LLASLALQAEYGDYQPEVHGVSYFRMEHYLPARVMEKLDLSYIKEELPKL   750
 751  HNTYVGASEKETELEFLKVCQRLTEYGVHFHRVHPEKKSQTGILLGVCSK   800
 801  GVLVFEVHNGVRTLVLRFPWRETKKISFSKKKITLQNTSDGIKHGFQTDN   850
 851  SKICQYLLHLCSYQHKFQLQMRARQSNQDAQDIERASFRSLNLQAESVRG   900
 901  FNMGRAISTGSLASSTLNKLAVRPLSVQAEILKRLSCSELSLYQPLQNSS   950
 951  KEKNDKASWEEKPREMSKSYHDLSQASLYPHRKNVIVNMEPPPQTVAELV  1000
1001  GKPSHQMSRSDAESLAGVTKLNNSKSVASLNRSPERRKHESDSSSIEDPG  1050
1051  QAYVLGMTMHSSGNSSSQVPLKENDVLHKRWSIVSSPEREITLVNLKKDA  1100
1101  KYGLGFQIIGGEKMGRLDLGIFISSVAPGGPADLDGCLKPGDRLISVNSV  1150
1151  SLEGVSHHAAIEILQNAPEDVTLVISQPKEKISKVPSTPVHLTNEMKNYM  1200
1201  KKSSYMQDSAIDSSSKDHHWSRGTLRHISENSFGPSGGLREGSLSSQDSR  1250
1251  TESASLSQSQVNGFFASHLGDQTWQESQHGSPSPSVISKATEKETFTDSN  1300
1301  QSKTKKPGISDVTDYSDRGDSDMDEATYSSSQDHQTPKQESSSSVNTSNK  1350
1351  MNFKTFSSSPPKPGDIFEVELAKNDNSLGISVTGGVNTSVRHGGIYVKAV  1400
1401  IPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVETLRNTGQVVHLLLE  1450
1451  KGQSPTSKEHVPVTPQCTLSDQNAQGQGPEKVKKTTQVKDYSFVTEENTF  1500
1501  EVKLFKNSSGLGFSFSREDNLIPEQINASIVRVKKLFPGQPAAESGKIDV  1550
1551  GDVILKVNGASLKGLSQQEVISALRGTAPEVFLLLCRPPPGVLPEIDTAL  1600
1601  LTPLQSPAQVLPNSSKDSSQPSCVEQSTSSDENEMSDKSKKQCKSPSRRD  1650
1651  SYSDSSGSGEDDLVTAPANISNSTWSSALHQTLSNMVSQAQSHHEAPKSQ  1700
1701  EDTICTMFYYPQKIPNKPEFEDSNPSPLPPDMAPGQSYQPQSESASSSSM  1750
1751  DKYHIHHISEPTRQENWTPLKNDLENHLEDFELEVELLITLIKSEKGSLG  1800
1801  FTVTKGNQRIGCYVHDVIQDPAKSDGRLKPGDRLIKVNDTDVTNMTHTDA  1850
1851  VNLLRAASKTVRLVIGRVLELPRIPMLPHLLPDITLTCNKEELGFSLCGG  1900
1901  HDSLYQVVYISDINPRSVAAIEGNLQLLDVIHYVNGVSTQGMTLEEVNRA  1950
1951  LDMSLPSLVLKATRNDLPVVPSSKRSAVSAPKSTKGNGSYSVGSCSQPAL  2000
2001  TPNDSFSTVAGEEINEISYPKGKCSTYQIKGSPNLTLPKESYIQEDDIYD  2050
2051  DSQEAEVIQSLLDVVDEEAQNLLNENNAAGYSCGPGTLKMNGKLSEERTE  2100
2101  DTDCDGSPLPEYFTEATKMNGCEEYCEEKVKSESLIQKPQEKKTDDDEIT  2150
2151  WGNDELPIERTNHEDSDKDHSFLTNDELAVLPVVKVLPSGKYTGANLKSV  2200
2201  IRVLRGLLDQGIPSKELENLQELKPLDQCLIGQTKENRRKNRYKNILPYD  2250
2251  ATRVPLGDEGGYINASFIKIPVGKEEFVYIACQGPLPTTVGDFWQMIWEQ  2300
2301  KSTVIAMMTQEVEGEKIKCQRYWPNILGKTTMVSNRLRLALVRMQQLKGF  2350
2351  VVRAMTLEDIQTREVRHISHLNFTAWPDHDTPSQPDDLLTFISYMRHIHR  2400
2401  SGPIITHCSAGIGRSGTLICIDVVLGLISQDLDFDISDLVRCMRLQRHGM  2450
2451  VQTEDQYIFCYQVILYVLTRLQAEEEQKQQPQLLK                 2485

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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