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

NucPred

Fetching Q6R2V0 from www.uniprot.org...

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

   1  MSGGGADQQSSPPGSLFLSPPAPAPKNGSSSDSSVGEKLGAAAADAGAGR    50
  51  TEEYRRRRHTMDKDSRGAAATTTTEHRFFRRSVICDSNATALELPGLPLP   100
 101  LPQPGAAAVAQQRSPPEPHREETLTPAVAHVAQQPPAAATPGEPAAAVPA   150
 151  AASAPGSASRDRQVAQPSQAGSKEEPPSARSGSGGGSAKEPQEERSQQQD   200
 201  DIEELETKAVGMSNDGRFLKFDIEIGRGSFKTVYKGLDTETTVEVAWCEL   250
 251  QDRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWESTVKGKKCIVLVTE   300
 301  LMTSGTLKTYLKRFKVMKIKVLRSWCRQILKGLQFLHTRTPPIIHRDLKC   350
 351  DNIFITGPTGSVKIGDLGLATLKRASFAKSVIGTPEFMAPEMYEEKYDES   400
 401  VDVYAFGMCMLEMATSEYPYSECQNAAQIYRRVTSGVKPASFDKVAIPEV   450
 451  KEIIEGCIRQNKDERYSIKDLLNHAFFQEETGVRVELAEEDDGEKIAIKL   500
 501  WLRIEDIKKLKGKYKDNEAIEFSFDLERDVPEDVAQEMVESGYVCEGDHK   550
 551  TMAKAIKDRVSLIKRKREQRQLVREEQEKRKQEESSLKQQGEQQSSASQA   600
 601  GILQPSSASTGLPAAATTSASVSTQVEPEEPEADQHQQLQYQQPSISVLS   650
 651  DGTVDSGQGSSVFTESRVSSQQTVSYGSQHEQAHSTCTLPGHTASVVQAQ   700
 701  AQPHGGYPPSSMAQGQSQGQPSSSSLTGIPSSQPVQHSQQQQGVQQTAPS   750
 751  QQTVQYSLPQTSAPSEPTTAQPASQPQPPQVLPPVSAGKQLPVSQPVPTI   800
 801  QGEPQISVATQPSVVPVHSGAHFLPVGQPLPPSLLPQYPVSQVPSAPHVS   850
 851  AAQPGFSPLPVTAAAGVNQPLLTLASSAAAAAVPGGSTVVPSQLPTLLQP   900
 901  VTQLPSQAHPQLLQTAVQSMGIPANLGQTAEAPLPSGDVLYQGFPPRLPP   950
 951  QYPGDSNIAPSSSVASVCIPSTVLSPPRPTEALAAPGYFPTVVQSYAESN  1000
1001  LLVPVGSIGGQIQVSQPAVSLAQAPTTSSQQAALESTQGVSQVAPPEPVP  1050
1051  AAPPQPTQPTTLVSSIDRSAHSDVASGMSDGNENVPSSSGRHEGRTIKRH  1100
1101  YRKSVRSRSRHEKTSRPKLRILNVSNKGDRVVECQLETHNRKMVTFKFDL  1150
1151  DGDNPEEIATIMVNNDFILAIEREAFVDQVREIIEKADEMLSEDVSVEPE  1200
1201  GDQGLENLQGKDDYGFSGSQKLEGEFKQPIPASSMPQQIAGLPTSSLTQV  1250
1251  VHSAGRRFIVSPVPESRLRESKVFTSEISDTVAASTSPGTGMNLSHSASS  1300
1301  LSLQQAFSELRRAQMTEGPSTAPPHFSHTGPTFPVVPPSMSSIAGAAATP  1350
1351  SVSVPATSCPFSDISTSVTPSEVTASTEKGIAGVATCTGVISSSGLTVPP  1400
1401  ASDSPILSSVVSSITVPVAVSVSTTSLSVQAPTPGSIVSNTGTFPSISVA  1450
1451  MTSASAVSSTAAPGAKPPPVSSQQVSGSTAGITTLASVPTTAPAPSVASQ  1500
1501  PSLSLSSSTSAPTLAETIVVSAHSLDKASHSSTAGLALSLPASSSSASPA  1550
1551  AGVSSSVSQPGVAHPLVIPSAVASIPVLSQAGPTCAPLLPQVPGIPPLVQ  1600
1601  PAASVPAVQQTLVHSQPQPALLPNQPHTHCPEMDADAQPRAPGIDDIKTL  1650
1651  EEKLRSLFSEHSSSGTQHASVSLETSLVVETTVTPGIPTTAVAPGKLMTS  1700
1701  TTSTCLPPTSLPLGTTGLSILPVVTPGQVSTPVSTIPAVKPGTAPSKPPS  1750
1751  TKPPVLPLGTELPAGTPPSEQLPPFPGPSLMQAQQPLEDLDAQLRRTLSP  1800
1801  ETVVLTSTVGPVSVVAPTAAVEAGAQLQKDVSQVTEGPIPAPTSGTGVFQ  1850
1851  MGRFQVSVAMDDTQKEGKNKSEDVKSVHFESSTSESSVLSSSSPESTLVK  1900
1901  PEPNGTAIRGISSDMPDSAHKTSASEAKSEAGQPTKVGRFQVTTTADKVG  1950
1951  RFSVSRTEDAIAEAKKEGPVASPPFMDLEHSILPAVIPKKEKPELSEPSH  2000
2001  LNGPSSDLEAAFLSRDGDDGSGSPHSPPQLCSKSLPIQSLSQSLSNSFNS  2050
2051  SYMSSDNESDIEDEDLKLELRRLREKHLKEIQDLQSRQKHEIESLYTRLG  2100
2101  KAPPAVIIPAAAPLAGRRRRPTKSKGSKSSRSSSLGNKSPGPAGNLSGQS  2150
2151  TATVLHPQQTLPAPGNIPETGQNQLLQPLKPSPSSDNLYSAFTSDGAISV  2200
2201  PSLSAPGQGTSSTNTVGGTVSSQAAQAQPPTMTSSRKGTFTDDLHKLVDN  2250
2251  WARDAMNLSGRRGSKGHMSYEGPGMARKFSAPGQLCISMTSNLGGSAPIS  2300
2301  AASATSLGHFTKSMCPPQQYGFPAPPFGTQWSGTGGPAPQPLSQFQPVGT  2350
2351  ASLQNFNISNLQKSISNPPGSNLRTT                          2376

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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