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

NucPred

Fetching P83741 from www.uniprot.org...

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

   1  MSDGAAEKQSGTPGFLTPPAPVPKNGSSSDSSVGEKLGATVADSGVGRTE    50
  51  EYRRRRHTMDKDSRGAAATTTPTEHRFFRRSVICDSNATALELPGLPLSI   100
 101  PQPSVPAVVPQSAPPEPHREETLTATVASQVSQQPSAAASPGEQAVVGSA   150
 151  TTTVPSSTSKDRPVSQPSLVGSKEEPPPSRSGSGSGGASAKEAQEDRSQQ   200
 201  QDDIEELETKAVGMSNDGRFLKFDIEIGRGSFKTVYKGLDTETTVEVAWC   250
 251  ELQDRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWESTVKGKKCIVLV   300
 301  TELMTSGTLKTYLKRFKVMKIKVLRSWCRQILKGLQFLHTRTPPIIHRDL   350
 351  KCDNIFITGPTGSVKIGDLGLATLKRASFAKSVIGTPEFMAPEMYEEKYD   400
 401  ESVDVYAFGMCMLEMATSEYPYSECQNAAQIYRRVTSGVKPASFDKVAIP   450
 451  EVKEIIEGCIRQNKDERYSIKDLLNHAFFQEETGVRVELAEEDDGEKIAI   500
 501  KLWLRIEDIKKLKGKYKDNEAIEFSFDLERDVPEDVAQEMVESGYVCEGD   550
 551  HKTMAKAIKDRVSLIKRKREQRQLVREEQEKRKQEESSFKQQNEQQASVS   600
 601  QAGIQQLSAASTGIPTAPATSASVSTQVEPEEPEADQHQQLQYQQPSISV   650
 651  LSDGTIDSGQGSSVFTESRVSSQQTVSYGSQHEQAHSTGTAPGHTVSSIQ   700
 701  AQSQPHGVYPPSSMAQGQNQGQPSSSLAGVLSSQPIQHPQQQGIQPTVPS   750
 751  QQAVQYSLPQAASSSEGTTAQPVSQPQVSAGTQLPVSQTVATVQGEPHIP   800
 801  VSTQPSVVPVHSGAHFLPMGQPIPTSLLPQYPVSQIPISTPHVSTAQTGF   850
 851  SSVPITMAAGINQPLLTLASSATASSIPGGSPVVPNQLPTLLQPVNQLQS   900
 901  QVHPQLLQPTTVQSIGIPANLGQAAEGPLPSGDVLYQGFPSRLPPQYPGD   950
 951  SNIAPSSNVASVCIHSTVLAPPSMPTEALATQGYFPTVVQPYVESTPLVP  1000
1001  MGSVGGQVQVSQPAVSLTQQPPTTSSQQAVLESTQGVSQAAPPEQTPITQ  1050
1051  SQPTQPVPLVTSADSAHSDVASGMSDGNENAPSSSGRHEGRTTKRHYRKS  1100
1101  VRSRSRHEKTSRPKLRILNVSNKGDRVVECQLETHNRKMVTFKFDLDGDN  1150
1151  PEEIATIMVNNDFILAIERESFVAQVREIIEKADEMLSEDVSVEPEGDQG  1200
1201  LESLQGKDDYGFPGSQKLEGEFKQPIAVSSMPQQIGVPTSSLTQVVHSAG  1250
1251  RRFIVSPVPESRLRESKVFTSDISDPVVASTSQAPGMNLSHSASSLSLQQ  1300
1301  AFSELKHGQMTEGPNTAPPNFNHMAGPTFSPFLASIAGVQTVAASTPSVS  1350
1351  VPITSSPLNDISTSVMQSETALPTEKGIVGVTTTSTGVVASGGLTTMSVS  1400
1401  ESPTSSSAVSSSTVPAVVTVSTPSQPVQASTSGSIASSTGSFPPGTFSTT  1450
1451  TATTMGSVVAPDAKPPTVLLQQVASNTAGVAIVTSVSTTTPFPGMASQPS  1500
1501  LPLSSSTSAPTLAETMVVSAHSLDKASHSSTAGLGLSFCAPSSSSSSGTA  1550
1551  VSTSVSQPGMVHPLVISSAVVSTPGLPQPVVPTSTPLLPQVPNIPPLVQP  1600
1601  VVNVPAVQQTLIHSQPQPALLPNQPHTHCPEMDADTQSKAPGIDDIKTLE  1650
1651  EKLRSLFSEHSSSGTQHASVSLETPLVVETTVTPGITTTAVAPSKLMTST  1700
1701  TSTCLPPTSLPLGAAGMPVMPVGTPGQVSTPGTHASAPVGTATGVKPGTT  1750
1751  PPKPTKTVVPPVGTELSAGTVPCEQLPPFPGPSLIQSQQPLEDLDAQLRR  1800
1801  TLSPETITVAPAVGPLSTMSSTTVTEAGTRLQKDGTEGHVTATSSGAGVV  1850
1851  KMGRFQVSVTMDDAQKERKNRSEDTKSVHFESSTSESSVLSSSSPESTLV  1900
1901  KPEPNGISISGISLDVPDSTHKAPTPEAKSDAGQPTKVGRFQVTTTANKV  1950
1951  GRFSVSRTEDKVTELKKEGPVTSPPFRDSEQTVIPAVIPKKEKPELAEPS  2000
2001  HLNGPSSDLEAAFLSRGTEDGSGSPHSPPHLCSKSLPVQNLSQSLSNSFN  2050
2051  SSYMSSDNESDIEDEDLRLELRRLREKHLKEIQDLQSRQKHEIESLYTKL  2100
2101  GKVPPAVIIPPAAPLSGRRRRPTKSKGSKSSRSSSLGNKSPQLSGNLSGQ  2150
2151  SGTSVLHPQQTLHPAGNTPETGHNQLLQPLKPSPSSDNLYSAFTSDGAIS  2200
2201  VPSLSAPGQGTSSTNTVGGTVSSQAAQAQPPAMTSSRKGTFTDDLHKLVD  2250
2251  NWARDAMNLSGRRGSKGHMNYEGPGMARKFSAPGQLCVPMTSNLGGSTPI  2300
2301  SAASATSLGHFTKSMCPPQQYGFPPAPFGTQWSGTGGPAPQPLGQFQPVG  2350
2351  TASLQNFNISNLQKSISNPPGSNLRTT                         2377

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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