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

NucPred

Fetching Q9QZ05 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MAGGRGASGRGRAEPQESYSQRQDHELQALEAIYGSDFQDLRPDARGRVR    50
  51  EPPEINLVLYPQGLAGEEVYVQVELQVKCPPTYPDVVPEIELKNAKGLSN   100
 101  ESVNLLKSHLEELAKKQCGEVMIFELAHHVQSFLSEHNKPPPKSFHEEML   150
 151  ERQAQEKQQRLLEARRKEEQEQREILHEIQRRKEEIKEEKKRKEMAKQER   200
 201  LEITSLTNQDYASKRDPAGHRAAAILHGGSPDFVGNGKARTYSSGRSRRE   250
 251  RQYSVCSGEPSPGSCDILHFSVGSPDQLMVHKGRCVGSDEQLGKVVYNAL   300
 301  ETATGSFVLLHEWVLQWQKMGPCLTSQEKEKIDKCKRQIQGAETEFSSLV   350
 351  KLSHPNIVRYFAMNSREEEDSIVIDILAEHVSGISLATHLSHSGPVPAHQ   400
 401  LRKYTAQLLAGLDYLHSNSVVHKVLSASSVLVDAEGTVKITDYSISKRLA   450
 451  DICKEDVFEQARVRFSDSALPYKTGKKGDVWRLGLLLLSLSQGQECGEYP   500
 501  VTIPSDLPADFQDFLKKCVCLDDKERWSPQQLLKHSFINPQPKLPLVEQS   550
 551  PEDSGGQDYIETVIPSNQLPSAAFFSETQKQFSRYFIEFEELQLLGKGAF   600
 601  GAVIKVQNKLDGCCYAVKRIPINPASRHFRRIKGEVTLLSRLHHENIVRY   650
 651  YNAWIERHERPAVPGTPPPDCTPQAQDSPATCGKTSGDTEELGSVEAAAP   700
 701  PPILSSSVEWSTSAERSTSTRFPVTGQDSSSDEEDEDERDGVFSQSFLPA   750
 751  SDSDSDIIFDNEDENSKSQNQDEDCNQKDGSHEIEPSVTAEAVHYLYIQM   800
 801  EYCEKSTLRDTIDQGLFRDTSRLWRLFREILDGLAYIHEKGMIHRDLKPV   850
 851  NIFLDSDDHVKIGDFGLATDHLAFTAEGKQDDQAGDGVIKSDPSGHLTGM   900
 901  VGTALYVSPEVQGSTKSAYNQKVDLFSLGIIFFEMSYHPMVTASERIFVL   950
 951  NQLRDPTSPKFPDDFDDGEHTKQKSVISWLLNHDPAKRPTAMELLKSELL  1000
1001  PPPQMEESELHEVLHHTLANIDGKAYRTMMSQIFCQHISPAIDYTYDSDI  1050
1051  LKGNFLIRTAKIQQLVCETIVRVFKRHGAVQLCTPLLLPRNRQIYEHNEA  1100
1101  ALFMDHSGMLVMLPFDLRVPFARYVARNNILNLKRYCIERVFRPRKLDRF  1150
1151  HPKELLECAFDIVTSTTNSSLPTAETIYTIYEIIQEFPALQERNYSIYLN  1200
1201  HTMLLKAILLHCGIPEDKLSQVYVILYDAVTEKLTRREVEAKFCNLSLSS  1250
1251  NSLCRLYKFIEQKGDLQDLTPTINSLIKQKTGVAQLVKYSLKDLEDVVGL  1300
1301  LKKLGVKLQVSINLGLVYKVQQHTGIIFQFLAFSKRRQRVVPEILAAGGR  1350
1351  YDLLIPKFRGPQTVGPVPTAVGVSIAIDKIFAAVLNMEEPVTVSSCDLLV  1400
1401  VSVGQMSMSRAINLTQKLWTAGITAEIMYDWSQSQEELQEYCRHHEITYV  1450
1451  ALVSDKEGSHVKVKSFEKERQTEKRVLESDLVDHVMQKLRTKVGDERNFR  1500
1501  DASDNLAVQTLKGSFSNASGLFEIHGTTVVPNVIVLAPEKLSASTRRRHE  1550
1551  IQVQTRLQTTLANLHQKSSEIEILAVDLPKETILQFLSLEWDADEQAFNT  1600
1601  TVKQLLSRLPKQRYLKLVCDEIYNIKVEKKVSVLFLYSYRDDYYRILF    1648

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.)

Go back to the NucPred Home Page.