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

NucPred

Fetching Q06698 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MAKKTKNNSKSSTPVNDVPTTAGKKKAKGKKGQEPEPEDDKRAKQQSNRA    50
  51  KVTSTASWTGKLPHTILHETCQKRKWNKVEYDMKKIGDKGFIAIAVLSFT   100
 101  DPKTKETLTARMNDPTYDKASGKGLVIPQETPIEARHMASTIALYRIAYN   150
 151  TNLHMMLPPNHRKTWYALDDFRKDNLKTDEKRINKLFDLDPFKTMVEDRK   200
 201  LKAQREKEQVAQNNQAQKEQVARTILSSHGGISSSGKDRQERKVASHKNS   250
 251  HNPSLVRFPKKVWENSIFVDLDESSRQLIETSLKEKIDWQAKKISHKNET   300
 301  IAENREDLKAKLLTLQFRPKHVEEAMLYKDPLSFLLFNLPEDDLPPFFHK   350
 351  KKGDTKNKVEITNLPLSTRMIVERLTEIGVSSDEALLALQQNDMNENEAA   400
 401  GFLTREILPTLNSNTNEPVSETESIECWNQELESLESIYEGCVMDAKEDS   450
 451  HYTLNLIEKLKIKLKVYRTKNYPASLPGIVVSTFDKNYKLPDYIKKQILT   500
 501  RLLHYLQEGNLIGDMLVYHIYEWLKENISKIIDNPGPLIPDSDSKGAINK   550
 551  RNISNGKRSINNSSSRKFTKTTISEDTLSVLREEYTKRIKSSEYKSMQLV   600
 601  REQLPAWKKQKVIIDIINKNEVVLITGETGSGKSTQVVQFILDFLQKEKG   650
 651  DFGKTKIVCTQPRRISAIGLAERVSDERCVTCGEEVGYVIRGVNKTKAST   700
 701  RIKFMTTGVLVRLLQNARTMLENTIVVIDEVHERSIDTDLIVTLMKNLLH   750
 751  RVRGMKIVLMSATVNVDLFKKFFPGLATCHIEGRTFPITDYFLEDILSDL   800
 801  DFKIKREKALSYDDDSVDERNNDDQYLKPRADSKFFTSGQINYDLLCQVV   850
 851  EYVHKRLKAANDNGSIIVFLPGVGEINKCCNLLANKSNEADFMVLPLHSA   900
 901  LTPEDQKRVFKKYHGKRKVVVSTNIAETSITIDDCVATIDTGRAKSMFYN   950
 951  PKDNTTKLIESFISKAEVKQRRGRAGRVREGLSYKLFSKNLYENDMISMP  1000
1001  IPEIKRIPLESLYLSVKAMGIKDVKAFLSTALDAPPLPALQKAERILTTI  1050
1051  GLVDESDKSLTQLGQFISLMPVMDSKHGKLLIYGILFGCTDISVLLVSIL  1100
1101  GIGVLPFIGGFENREKIKKLLCKYESRGDLFAVLEIVRDYFKIKDSSIKR  1150
1151  KYLRDNLLSYNKINEIKSSTAQYYSILKDVGFLPMDYKVGSISDLNRNER  1200
1201  NFDILRAILTGAFYPHIARVQLPDVKYLSTSSGAVEKDPEAKMIKYWIRS  1250
1251  EEYQDKLEEYKTKISQETQKVDLEDLPLPATRAFIHPSSVLFSTNSVNLE  1300
1301  DAKLLSEVDGPISRQSKIPTVVKYPFVLFTTSQVTNKLYLRDLTPTTTLS  1350
1351  LLLFGGAISYDIGGTIHSPGIVVDNWLPIRTWCKNGVLIKELRTQLDEAI  1400
1401  RKKLESPDYAKKSQIDNSGADKTLKIVEKIIASEQ                 1435

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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