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

NucPred

Fetching Q5H9R4 from www.uniprot.org...

The NucPred score for your sequence is 0.39 (see score help below)

   1  MGRIQEVGWVTAGLVIWAGTCYYIYKFTKGRAQSVRTLARNGSTVKMETV    50
  51  VGVQSQTLAINEAEIKTKPQVEIGAETGARSGPRAEVETKATAIAIHRAN   100
 101  SQAKAMVGAEPETQSESKVVAGTLVMTEAVTLTEVKAKAREVAMKEAVTQ   150
 151  TDAEAGKIVKKEAVTQTKAKAWALVAKTEAKREAMTQTKAETHILAEKET   200
 201  EINRVMVTQSETLAVPREVAKMGATNKTGIVDETKTRALEETVSVAKTQS   250
 251  EARPGATVDARGNPNGMSREVAGVDMKSCAQSQAVTKIQGDDMPGTGVED   300
 301  MGNCKTMSRAESGADTRASAQPQIFAKTQTEAIPGAKIDAGGNTNAMCKV   350
 351  GAGADVRACIQPQTVAKKQAEVTSGARVDGRGNTNVISKAITGADMRAAA   400
 401  QPQAVASTHAEAMSDAKVKNRGNPNAMTKAGAKANLRANSQVEALPDARD   450
 451  KSRGNPNVMAKVGDGTDMLSCTQPQLVASVQADTLSDGKIKVRGNVNTMP   500
 501  KEGAGVDMKAQGMAQSQGEALPNTRGKARGKAKAKCKTGPGMDMKTCTQP   550
 551  QAGVKTPAEALLDSRVDGRGNPNATSKAGTKADQRVCGQPLVVANPQGEA   600
 601  LPGAKNKVKGNPHTVLKVGAGEGTTDSAQPEAVVSFQGEALLGTKNKVKG   650
 651  NPNVVLKAEVGEGAMGTAQLQIMASSKGEALLDSKNKVKGNSNAVSKAGA   700
 701  GTDTTGSVQPQIVANSQGEVLPGAKNKIRGNPTTVPNSGVGPYTTDSARL   750
 751  QAVANSQGEVLPGAKNKVKANLNAVSKAEAGMGATGSVQPQAVANSHCET   800
 801  LPGAKNKVRGNWNAVSKAGAGMDTRGSAQPQAVANSQGEVLPGAKNKVKG   850
 851  NPNVVSKAGAREDTVGSTQPQVLASSQRETLPGARNKVKGNSNVVSKAGA   900
 901  REDTMGSAQPQVVANSQRETLPGARNKVKGNSNAISKAEAGAGIMGSVQV   950
 951  QVVASFQGEVLPGAKNKVRGNSNAVPKAEAGADTVGSAQPQAVANSQSET  1000
1001  LLGARNKVKGNTIAVPKAGTGAGTRHSAQPQIVAGSQGETLPGARDKSMS  1050
1051  TSEAEATAEDEAYAKPEAEAMPTSESEGGSGTQACRKTQPNIHDYYWNGI  1100
1101  GVEDWIAAERWIKFRFQTMDGDWENSVSWADDENEASIGSWSGASDKAGI  1150
1151  IRSWAVACDETSVKSWAGARAENVVGIGTWARAGEQASGGLWAGGQTSEG  1200
1201  TWAGDKASGGAWTGAENQASGGSWALAGNQAIGELWAAGQASDGSWPGGQ  1250
1251  ASGVSWVGEEAIGGSWTGAENQASEGSWAGAGAGNMSSVSYWAGVVDQAG  1300
1301  GGSWAGTSDQSGGGSKPRFEDQASGEGSWAGAGGQASGGSMLGPEDQSSG  1350
1351  RSWADTADQASGGSRLGHVDQSSGGAWAGTLDQSGGGSKPRFENQTTEEG  1400
1401  SWAGAGGQAGGGSKVGPEDQSSGRSWANSGDQISGGFLVGIVDQANGGSW  1450
1451  TGAGHPASVGPKPIFEDQVSGRGSWADAREQVVGDSRLGLRDQSSGDSWA  1500
1501  GTGDQASGWFCVCPGSQTNGGSWGGASGQDVGGSRPGPTNQSSAGSWDSP  1550
1551  GSQVSGSCWTGAGAVDQAGGCSKPGFEDQAIGGGFWPGAGDQTGGGSRPG  1600
1601  SEDQSSGIGSWGVAGGQVLGGARPGPADQSSGGSWAGTGNQSSGRSWIGP  1650
1651  GDQAVDCSKPEFEDQACGGGSWAGAGSQASGESWAGSRPGNEAIGGSRMG  1700
1701  SEDQATGGSWARSEDQASGRFQVSFEVEANEGFWFGPGAEAVIGSWCWTE  1750
1751  EKADIVSRPDDKDEATTASRSGAGEEAMICSRIEAENKASSGSWIRSEEV  1800
1801  AYMGSCVGAEAGAGAEAGAGAEAGAGAGAEAGAEAGAGAGAGPGTESGAG  1850
1851  IWSWDGDATTVESRLGAGEEAGVESWTLARNVGEDELSRESSPDIEEISL  1900
1901  RSLFWAESENSNTFRSKSGKDASFESGAGDNTSIKDKFEAAGGVDIGSWF  1950
1951  CAGNENTSEDKSAPKAKAKKSSESRGIYPYMVPGAGMGSWDGAMIWSETK  2000
2001  FAHQSEASFPVEDESRKQTRTGEKTRPWSCRCKHEANMDPRDLEKLICMI  2050
2051  EMTEDPSVHEIANNALYNSADYSYSHEVVRNVGGISVIESLLNNPYPSVR  2100
2101  QKALNALNNISVAAENHRKVKTYLNQVCEDTVTYPLNSNVQLAGLRLIRH  2150
2151  LTITSEYQHMVTNYISEFLRLLTVGSGETKDHVLGMLLNFSKNPSMTKDL  2200
2201  LIANAPTSLINIFSKKETKENILNALSLFENINYHFKRRAKAFTQDKFSK  2250
2251  NSLYFLFQRPKACAKKLRALAAECNDPEVKERVELLISKL            2290

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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