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

NucPred

Fetching Q8VDD5 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MAQQAADKYLYVDKNFINNPLAQADWAAKKLVWVPSSKNGFEPASLKEEV    50
  51  GEEAIVELVENGKKVKVNKDDIQKMNPPKFSKVEDMAELTCLNEASVLHN   100
 101  LKERYYSGLIYTYSGLFCVVINPYKNLPIYSEEIVEMYKGKKRHEMPPHI   150
 151  YAITDTAYRSMMQDREDQSILCTGESGAGKTENTKKVIQYLAHVASSHKS   200
 201  KKDQGELERQLLQANPILEAFGNAKTVKNDNSSRFGKFIRINFDVNGYIV   250
 251  GANIETYLLEKSRAIRQAKEERTFHIFYYLLSGAGEHLKTDLLLEPYNKY   300
 301  RFLSNGHVTIPGQQDKDMFQETMEAMRIMGIPEDEQMGLLRVISGVLQLG   350
 351  NIAFKKERNTDQASMPDNTAAQKVSHLLGINVTDFTRGILTPRIKVGRDY   400
 401  VQKAQTKEQADFAIEALAKATYERMFRWLVLRINKALDKTKRQGASFIGI   450
 451  LDIAGFEIFDLNSFEQLCINYTNEKLQQLFNHTMFILEQEEYQREGIEWN   500
 501  FIDFGLDLQPCIDLIEKPAGPPGILALLDEECWFPKATDKSFVEKVVQEQ   550
 551  GTHPKFQKPKQLKDKADFCIIHYAGKVDYKADEWLMKNMDPLNDNIATLL   600
 601  HQSSDKFVSELWKDVDRIIGLDQVAGMSETALPGAFKTRKGMFRTVGQLY   650
 651  KEQLAKLMATLRNTNPNFVRCIIPNHEKKAGKLDPHLVLDQLRCNGVLEG   700
 701  IRICRQGFPNRVVFQEFRQRYEILTPNSIPKGFMDGKQACVLMIKALELD   750
 751  SNLYRIGQSKVFFRAGVLAHLEEERDLKITDVIIGFQACCRGYLARKAFA   800
 801  KRQQQLTAMKVLQRNCAAYLRLRNWQWWRLFTKVKPLLNSIRHEDELLAK   850
 851  EAELTKVREKHLAAENRLTEMETMQSQLMAEKLQLQEQLQAETELCAEAE   900
 901  ELRARLTAKKQELEEICHDLEARVEEEEERCQYLQAEKKKMQQNIQELEE   950
 951  QLEEEESARQKLQLEKVTTEAKLKKLEEDQIIMEDQNCKLAKEKKLLEDR  1000
1001  VAEFTTNLMEEEEKSKSLAKLKNKHEAMITDLEERLRREEKQRQELEKTR  1050
1051  RKLEGDSTDLSDQIAELQAQIAELKMQLAKKEEELQAALARVEEEAAQKN  1100
1101  MALKKIRELETQISELQEDLESERASRNKAEKQKRDLGEELEALKTELED  1150
1151  TLDSTAAQQELRSKREQEVSILKKTLEDEAKTHEAQIQEMRQKHSQAVEE  1200
1201  LADQLEQTKRVKATLEKAKQTLENERGELANEVKALLQGKGDSEHKRKKV  1250
1251  EAQLQELQVKFSEGERVRTELADKVTKLQVELDSVTGLLSQSDSKSSKLT  1300
1301  KDFSALESQLQDTQELLQEENRQKLSLSTKLKQMEDEKNSFREQLEEEEE  1350
1351  AKRNLEKQIATLHAQVTDMKKKMEDGVGCLETAEEAKRRLQKDLEGLSQR  1400
1401  LEEKVAAYDKLEKTKTRLQQELDDLLVDLDHQRQSVSNLEKKQKKFDQLL  1450
1451  AEEKTISAKYAEERDRAEAEAREKETKALSLARALEEAMEQKAELERLNK  1500
1501  QFRTEMEDLMSSKDDVGKSVHELEKSKRALEQQVEEMKTQLEELEDELQA  1550
1551  TEDAKLRLEVNLQAMKAQFERDLQGRDEQSEEKKKQLVRQVREMEAELED  1600
1601  ERKQRSMAMAARKKLEMDLKDLEAHIDTANKNREEAIKQLRKLQAQMKDC  1650
1651  MRELDDTRASREEILAQAKENEKKLKSMEAEMIQLQEELAAAERAKRQAQ  1700
1701  QERDELADEIANSSGKGALALEEKRRLEARIAQLEEELEEEQGNTELIND  1750
1751  RLKKANLQIDQINTDLNLERSHAQKNENARQQLERQNKELKAKLQEMESA  1800
1801  VKSKYKASIAALEAKIAQLEEQLDNETKERQAASKQVRRTEKKLKDVLLQ  1850
1851  VEDERRNAEQFKDQADKASTRLKQLKRQLEEAEEEAQRANASRRKLQREL  1900
1901  EDATETADAMNREVSSLKNKLRRGDLPFVVTRRIVRKGTGDCSDEEVDGK  1950
1951  ADGADAKAAE                                          1960

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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