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

NucPred

Fetching Q25410 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MHPGSISFNMIINKCIPICLFILFIMMMEFTVSKADSKNDIVSESHPSLQ    50
  51  KLGCGGSQSPTNGVCGSVDIRSSMDNFKLLENCTVIEGSLRISLFELKAL   100
 101  DFRHLSFPDLREITDYLLMYRVYGLETLSKLFPNLAIIRGRELFNSYAIV   150
 151  MYEMRDLQDLGLVNLRTISRGGVRLTKNFKLCYIETINWTQIGVSDPEAR   200
 201  RFINNKEQCPNSCKDECQSKRCWTYSDCQKGLNCQCKENTYCMENGSCCH   250
 251  DYCLGGCKVPMNPDECFSCKEVQFNNTCRPQCPPGTYKFLNRRCLTDKEC   300
 301  LALTNDPDGNTPKLLDGEKGEPSLCLYTCPQNYSVGDSKDNKNLSQCVKC   350
 351  RQLCPKECHGLEINNIQDAHKLKECSKISGPLKIQIMSGSNVAQELEKSL   400
 401  GNIREVTETIHIKRSYALVTLHFFKNLQIIGSKVPSSETQEGQSFSLFLM   450
 451  DNTNLQELFPEEQMKKMKILNGGIYVHDNGQLCPHTIKEFLSHLNLSEAQ   500
 501  SSISSISNGHQRPCEKHDLNVTVEKIAHNAAILAWNKYKADERQLLTYIL   550
 551  NYKEIKDESNDINIFQGRDLCSHDLWMTREYAPKEGPEADQIGMLYDLKP   600
 601  FTTYAVYIQAYTVSTATHAAMTNILTFTTYPFHPSEPTDLVAISEDPHEL   650
 651  RVSWKPPKYPNGNITHYKIVYHKLELNEKSYEQRNYCRDPLVHQKKKEKV   700
 701  KIEEEGKKINNSANSNCCKCPKSKEEMDTESRKREIEMYFEDYLHKHIYC   750
 751  KRYDKLPDEVDLNFDGMNLPQLVEMNYNSSETSDRIEVFPNYVIENTSDL   800
 801  ANLTEIVKEVVVYGTTEVTLPNLEHFSEYSIEVLACQDYNEKVLSKLCSI   850
 851  RAITFERTKDSYAADMINETTVDTEIETNFTGNVFIKWESPTSPNGLILK   900
 901  YLLWYKKANQENLVPQTICITRQEYLKNLGYKLTRLEPGNWTFKISAISL   950
 951  AENSSFTLERFFIVPRPPDPESSNTLLIVAIVLAFFGVLTVSLIVACVYY  1000
1001  KQKIRSDDMTVISRNMNYVPSEILYISDEWEVDRDKIKLIKELGQGSFGM  1050
1051  VYEGVAKGIRDDPNEEIPVAVKTVNDRASFSDRREFLKEATTMKEFHCHH  1100
1101  VVKLLGVVSTGQPALVIMELMALGDLKNYLRGHRPDEDHPGVMPPHLLDI  1150
1151  LQMAGEIADGMAYLADKKFVHRDLAARNCMVSEERTVKIGDFGMTRDIYE  1200
1201  TDYYRKGGKGMLPVRWMAPESLKDGVFTSLSDVWSYGVVMWEMVTLAAQP  1250
1251  YQGLSNEEVVKFISDGYIMELPENCPNEMAYLMQHCWAKKPNQRPTFKAI  1300
1301  IEYLLPKLKPSFEKVSYFFTSGGGHTDGAGEGTLAEPEGSDDSSSINSLS  1350
1351  CEGAAAPRQSLTPCGGGQFKSSTHFNGGSHTLYDEGVDRETILNGVDDGD  1400
1401  EDEAAGRYSLSEFGEDLDDSSRPFMSDDFIPPVMTRQPLLSHQSNGNDSN  1450
1451  VRNSGLIELKPLINKDKRPGLSSPRLNARSNPFSSEYIGHYPPTLTTELE  1500
1501  TLNGNQSSHNNNSFELMTPDPLKSGPASESSNGVSSSSWRPKPILKLPTL  1550
1551  NQARVGDSVGCLCLTLGTRINIVKPIETVRPETNTIRYLKPPHPMLIWST  1600
1601  LKMVLVL                                             1607

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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