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

NucPred

Fetching Q96BY6 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MAGERTRRFTRSLLRPGQAAELRHSAASAAAVAVSSRQQQRQEKPRLLEP    50
  51  LDYETVIEELEKTYRNDPLQDLLFFPSDDFSAATVSWDIRTLYSTVPEDA   100
 101  EHKAENLLVKEACKFYSSQWHVVNYKYEQYSGDIRQLPRAEYKPEKLPSH   150
 151  SFEIDHEDADKDEDTTSHSSSKGGGGAGGTGVFKSGWLYKGNFNSTVNNT   200
 201  VTVRSFKKRYFQLTQLPDNSYIMNFYKDEKISKEPKGCIFLDSCTGVVQN   250
 251  NRLRKYAFELKMNDLTYFVLAAETESDMDEWIHTLNRILQISPEGPLQGR   300
 301  RSTELTDLGLDSLDNSVTCECTPEETDSSENNLHADFAKYLTETEDTVKT   350
 351  TRNMERLNLFSLDPDIDTLKLQKKDLLEPESVIKPFEEKAAKRIMIICKA   400
 401  LNSNLQGCVTENENDPITNIEPFFVSVALYDLRDSRKISADFHVDLNHAA   450
 451  VRQMLLGASVALENGNIDTITPRQSEEPHIKGLPEEWLKFPKQAVFSVSN   500
 501  PHSEIVLVAKIEKVLMGNIASGAEPYIKNPDSNKYAQKILKSNRQFCSKL   550
 551  GKYRMPFAWAVRSVFKDNQGNVDRDSRFSPLFRQESSKISTEDLVKLVSD   600
 601  YRRADRISKMQTIPGSLDIAVDNVPLEHPNCVTSSFIPVKPFNMMAQTEP   650
 651  TVEVEEFVYDSTKYCRPYRVYKNQIYIYPKHLKYDSQKCFNKARNITVCI   700
 701  EFKNSDEESAKPLKCIYGKPGGPLFTSAAYTAVLHHSQNPDFSDEVKIEL   750
 751  PTQLHEKHHILFSFYHVTCDINAKANAKKKEALETSVGYAWLPLMKHDQI   800
 801  ASQEYNIPIATSLPPNYLSFQDSASGKHGGSDIKWVDGGKPLFKVSTFVV   850
 851  STVNTQDPHVNAFFQECQKREKDMSQSPTSNFIRSCKNLLNVEKIHAIMS   900
 901  FLPIILNQLFKVLVQNEEDEITTTVTRVLTDIVAKCHEEQLDHSVQSYIK   950
 951  FVFKTRACKERTVHEELAKNVTGLLKSNDSTTVKHVLKHSWFFFAIILKS  1000
1001  MAQHLIDTNKIQLPRPQRFPESYQNELDNLVMVLSDHVIWKYKDALEETR  1050
1051  RANHSVARFLKRCFTFMDRGYVFKMVNNYISMFSSGDLKTLCQYKFDFLQ  1100
1101  EVCQHEHFIPLCLPIRSANIPDPLTPSESTQELHASDMPEYSVTNEFCRK  1150
1151  HFLIGILLREVGFALQEDQDVRHLALAVLKNLMAKHSFDDRYREPRKQAQ  1200
1201  IASLYMPLYGMLLDNMPRIYLKDLYPFTVNTSNQGSRDDLSTNGGFQSQT  1250
1251  AIKHANSVDTSFSKDVLNSIAAFSSIAISTVNHADSRASLASLDSNPSTN  1300
1301  EKSSEKTDNCEKIPRPLSLIGSTLRFDKLDQAETRSLLMCFLHIMKTISY  1350
1351  ETLIAYWQRAPSPEVSDFFSILDVCLQNFRYLGKRNIIRKIAAAFKFVQS  1400
1401  TQNNGTLKGSNPSCQTSGLLSQWMHSTSSHEGHKQHRSQTLPIIRGKNAL  1450
1451  SNPKLLQMLDNTMTSNSNEIDIVHHVDTEANIATEVCLTILDLLSLFTQT  1500
1501  HQRQLQQCDCQNSLMKRVFDTYMLFFQVNQSATALKHVFASLRLFVCKFP  1550
1551  SAFFQGPADLCGSFCYEVLKCCNHRSRSTQTEASALLYFFMRKNFEFNKQ  1600
1601  KSIVRSHLQLIKAVSQLIADAGIGGSRFQHSLAITNNFANGDKQMKNSNF  1650
1651  PAEVKDLTKRIRTVLMATAQMKEHEKDPEMLVDLQYSLANSYASTPELRR  1700
1701  TWLESMAKIHARNGDLSEAAMCYIHIAALIAEYLKRKGYWKVEKICTASL  1750
1751  LSEDTHPCDSNSLLTTPSGGSMFSMGWPAFLSITPNIKEEGAMKEDSGMQ  1800
1801  DTPYNENILVEQLYMCVEFLWKSERYELIADVNKPIIAVFEKQRDFKKLS  1850
1851  DLYYDIHRSYLKVAEVVNSEKRLFGRYYRVAFYGQGFFEEEEGKEYIYKE  1900
1901  PKLTGLSEISQRLLKLYADKFGADNVKIIQDSNKVNPKDLDPKYAYIQVT  1950
1951  YVTPFFEEKEIEDRKTDFEMHHNINRFVFETPFTLSGKKHGGVAEQCKRR  2000
2001  TILTTSHLFPYVKKRIQVISQSSTELNPIEVAIDEMSKKVSELNQLCTME  2050
2051  EVDMIRLQLKLQGSVSVKVNAGPMAYARAFLEETNAKKYPDNQVKLLKEI  2100
2101  FRQFADACGQALDVNERLIKEDQLEYQEELRSHYKDMLSELSTVMNEQIT  2150
2151  GRDDLSKRGVDQTCTRVISKATPALPTVSISSSAEV                2186

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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