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

NucPred

Fetching Q61191 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MASAVSPANLPAVLLQPRWKRVVGWSGPVPRPRHGHRAVAIKELIVVFGG    50
  51  GNEGIVDELHVYNTATNQWFIPAVRGDIPPGCAAYGFVCDGTRLLVFGGM   100
 101  VEYGKYSNDLYELQASRWEWKRLKAKTPKNGPPPCPRLGHSFSLVGNKCY   150
 151  LFGGLANDSEDPKNNIPRYLNDLYILELRPGSGVVAWDIPITYGVLPPPR   200
 201  ESHTAVVYTEKDNKKSKLVIYGGMSGCRLGDLWTLDIETLTWNKPSLSGV   250
 251  APLPRSLHSATTIGNKMYVFGGWVPLVMDDVKVATHEKEWKCTNTLACLN   300
 301  LDTMAWETILMDTLEDNIPRARAGHCAVAINTRLYIWSGRDGYRKAWNNQ   350
 351  VCCKDLWYLETEKPPPPARVQLVRANTNSLEVSWGAVATADSYLLQLQKY   400
 401  DIPATAATATSPTPNPVPSVPANPPKSPAPAAAAPAVQPLTQVGITLVPQ   450
 451  AATAPPSTTTIQVLPTVPGSSISVPTAARTQGVPAVLKVTGPQATTGTPL   500
 501  VTMRPASQAGKAPVTVTSLPASVRMVVPTQSAQGTVIGSNPQMSGMAALA   550
 551  AAAAATQKIPPSSAPTVLSVPAGTTIVKTVAVTPGTTTLPATVKVASSPV   600
 601  MVSNPATRMLKTAAAQVGTSVSSAANTSTRPIITVHKSGTVTVAQQAQVV   650
 651  TTVVGGVTKTITLVKSPISVPGGSALISNLGKVMSVVQTKPVQTSAVTGQ   700
 701  ASTGPVTQIIQTKGPLPAGTILKLVTSADGKPTTIITTTQASGAGTKPTI   750
 751  LGISSVSPSTTKPGTTTIIKTIPMSAIITQAGATGVTSSPGIKSPITIIT   800
 801  TKVMTSGTGAPAKIITAVPKIATGHGQQGVTQVVLKGAPGQPGTILRTVP   850
 851  MGGVRLVTPVTVSAVKPAVTTLVVKGTTGVTTLGTVTGTVSTSLAGAGAH   900
 901  STSASLATPITTLGTIATLSSQVINPTAITVSAAQTTLTAAGGLTTPTIT   950
 951  MQPVSQPTQVTLITAPSGVEAQPVHDLPVSILASPTTEQPTATVTIADSG  1000
1001  QGDVQPGTVTLVCSNPPCETHETGTTNTATTTVVANLGGHPQPTQVQFVC  1050
1051  DRQETAASLVTSAVGQQNGNVVRVCSNPPCETHETGTTNTATTATSNMAG  1100
1101  QHGCSNPPCETHETGTTSTATTAMSSMGTGQQRDTRRTTNTPTVVRITVA  1150
1151  PGALERVQGTVKPQCQTQQTNMTTTTMTVQATGAPCSAGPLLRPSVALES  1200
1201  GSHSPAFVQLALPSVRVGLSGPSSKDMPTGRQPETYHTYTTNTPTTTRSI  1250
1251  MVAGELGAARVVPTSTYESLQASSPSSTMTMTALEALLCPSATVTQVCSN  1300
1301  PPCETHETGTTNTATTSNAGSAQRVCSNPPCETHETGTTHTATTATSNGG  1350
1351  AGQPEGGQQPASGHPCETHQTTSTGTTMSVSVGTLIPDATSSHGTLESGL  1400
1401  EVVAVPTVTSQAGSTLLASFPTQRVCSNPPCETHETGTTHTATTVTSNMS  1450
1451  SNQDPPPAASDQGEVASTQGDSTNITSASAITTSVSSTLPRAVTTVTQST  1500
1501  PVPGPSVPPPEELQVSPGPRQQLPPRQLLQSASTPLMGESTEVLSASQTP  1550
1551  ELQAAVDLSSTGDPSSGQEPTTSAVVATVVVQPPPPTQSEVDQLSLPQEL  1600
1601  MAEAQAGTTTLMVTGLTPEELAVTAAAEAAAQAAATEEAQALAIQAVLQA  1650
1651  AQQAVMGTGEPMDTSEAAAAVTQAELGHLSAEGQEGQATTIPIVLTQQEL  1700
1701  AALVQQQQQLQEAQAQAQQQHHLPTEALAPADSLNDPSIESNCLNELASA  1750
1751  VPSTVALLPSTATESLAPSNTFVAPQPVVASPAKMQAAATLTEVANGIES  1800
1801  LGVKPDLPPPPSKAPVKKENQWFDVGVIKGTSVMVTHYFLPPDDAVQSDD  1850
1851  DSGTVPDYNQLKKQELQPGTAYKFRVAGINACGRGPFSEISAFKTCLPGF  1900
1901  PGAPCAIKISKSPDGAHLTWEPPSVTSGKIIEYSVYLAIQSSQASGEPKS  1950
1951  STPAQLAFMRVYCGPSPSCLVQSSSLSNAHIDYTTKPAIIFRIAARNEKG  2000
2001  YGPATQVRWLQETSKDSSGTKPASKRPMSSPEMKSAPKKSKADGQ       2045

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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