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

NucPred

Fetching Q13796 from www.uniprot.org...

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

   1  MEGAEPRARPERLAEAETRAADGGRLVEVQLSGGAPWGFTLKGGREHGEP    50
  51  LVITKIEEGSKAAAVDKLLAGDEIVGINDIGLSGFRQEAICLVKGSHKTL   100
 101  KLVVKRRSELGWRPHSWHATKFSDSHPELAASPFTSTSGCPSWSGRHHAS   150
 151  SSSHDLSSSWEQTNLQRTLDHFSSLGSVDSLDHPSSRLSVAKSNSSIDHL   200
 201  GSHSKRDSAYGSFSTSSSTPDHTLSKADTSSAENILYTVGLWEAPRQGGR   250
 251  QAQAAGDPQGSEEKLSCFPPRVPGDSGKGPRPEYNAEPKLAAPGRSNFGP   300
 301  VWYVPDKKKAPSSPPPPPPPLRSDSFAATKSHEKAQGPVFSEAAAAQHFT   350
 351  ALAQAQPRGDRRPELTDRPWRSAHPGSLGKGSGGPGCPQEAHADGSWPPS   400
 401  KDGASSRLQASLSSSDVRFPQSPHSGRHPPLYSDHSPLCADSLGQEPGAA   450
 451  SFQNDSPPQVRGLSSCDQKLGSGWQGPRPCVQGDLQAAQLWAGCWPSDTA   500
 501  LGALESLPPPTVGQSPRHHLPQPEGPPDARETGRCYPLDKGAEGCSAGAQ   550
 551  EPPRASRAEKASQRLAASITWADGESSRICPQETPLLHSLTQEGKRRPES   600
 601  SPEDSATRPPPFDAHVGKPTRRSDRFATTLRNEIQMHRAKLQKSRSTVAL   650
 651  TAAGEAEDGTGRWRAGLGGGTQEGPLAGTYKDHLKEAQARVLRATSFKRR   700
 701  DLDPNPGDLYPESLEHRMGDPDTVPHFWEAGLAQPPSSTSGGPHPPRIGG   750
 751  RRRFTAEQKLKSYSEPEKMNEVGLTRGYSPHQHPRTSEDTVGTFADRWKF   800
 801  FEETSKPVPQRPAQKQALHGIPRDKPERPRTAGRTCEGTEPWSRTTSLGD   850
 851  SLNAHSAAEKAGTSDLPRRLGTFAEYQASWKEQRKPLEARSSGRCHSADD   900
 901  ILDVSLDPQERPQHVHGRSRSSPSTDHYKQEASVELRRQAGDPGEPREEL   950
 951  PSAVRAEEGQSTPRQADAQCREGSPGSQQHPPSQKAPNPPTFSELSHCRG  1000
1001  APELPREGRGRAGTLPRDYRYSEESTPADLGPRAQSPGSPLHARGQDSWP  1050
1051  VSSALLSKRPAPQRPPPPKREPRRYRATDGAPADAPVGVLGRPFPTPSPA  1100
1101  SLDVYVARLSLSHSPSVFSSAQPQDTPKATVCERGSQHVSGDASRPLPEA  1150
1151  LLPPKQQHLRLQTATMETSRSPSPQFAPQKLTDKPPLLIQDEDSTRIERV  1200
1201  MDNNTTVKMVPIKIVHSESQPEKESRQSLACPAEPPALPHGLEKDQIKTL  1250
1251  STSEQFYSRFCLYTRQGAEPEAPHRAQPAEPQPLGTQVPPEKDRCTSPPG  1300
1301  LSYMKAKEKTVEDLKSEELAREIVGKDKSLADILDPSVKIKTTMDLMEGI  1350
1351  FPKDEHLLEEAQQRRKLLPKIPSPRSTEERKEEPSVPAAVSLATNSTYYS  1400
1401  TSAPKAELLIKMKDLQEQQEHEEDSGSDLDHDLSVKKQELIESISRKLQV  1450
1451  LREARESLLEDVQANTVLGAEVEAIVKGVCKPSEFDKFRMFIGDLDKVVN  1500
1501  LLLSLSGRLARVENALNNLDDGASPGDRQSLLEKQRVLIQQHEDAKELKE  1550
1551  NLDRRERIVFDILANYLSEESLADYEHFVKMKSALIIEQRELEDKIHLGE  1600
1601  EQLKCLLDSLQPERGK                                    1616

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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