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

NucPred

Fetching Q92072 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MPARSAPPPPALPPALRRRLRDLERDEDSLSEKETLQEKLRLTRGFLRAE    50
  51  VQRRLSALDADVRCRELSEERYLAKVKALLRRELAAENGDAAKLFSRASN   100
 101  GCAGNGEEEWERGGRGEDGAMEVEEAAASSSSSSSSSSSSSSSSSSSSSL   150
 151  LPAPRARKARRSRSNGESKKSPASSRVTRSSGRQPTILSVFSKGSTKRKS   200
 201  EEVNGAVKPEVSAEKDEEEEEELEEKEQDEKRIKIETKEGSEIKDEITQV   250
 251  KTSTPAKTTPPKCVDCRQYLDDPDLKFFQGDPDDALEEPEMLTDERLSIF   300
 301  DANEDGFESYEDLPQHKVTSFSVYDKRGHLCPFDTGLIERNIELYFSGAV   350
 351  KPIYDDNPCLDGGVRAKKLGPINAWWITGFDGGEKALIGFTTAFADYILM   400
 401  EPSEEYAPIFALMQEKIYMSKIVVEFLQNNRDVSYEDLLNKIETTVPPVG   450
 451  LNFNRFTEDSLLRHAQFVVEQVESYDEAGDSDEPPVLITPCMRDLIKLAG   500
 501  VTLGKRRAVRRQAIRHPTRIDKDKGPTKATTTKLVYLIFDTFFSEQIEKD   550
 551  EREDDKENAMKRRRCGVCEVCQQPECGKCKACQNMVKFGGSGRSKQACLQ   600
 601  RRCPNLAVREADEDEEVDDNIPEMPSPKKMLQGRKKKQNKSRISWVGEPI   650
 651  KSDGKKDFYQRVCIDSETLEVGDCVSVSPDDPTKPLYLARVTAMWEDSSG   700
 701  QMFHAHWFCPGSDTVLGATSDPLELFLVDECEDMQLSYIHGKVNVIYKPP   750
 751  SENWAMEGGLDMEIKMVEDDGRTYFYQMWYDQEYARFETPPRAQPMEDNK   800
 801  YKFCLSCARLDEVRHKEIPKVAEPLDEGDGKMFYAMATKNGVQYRVGDSV   850
 851  YLLPEAFSFSMKPASPAKRPKKEAVDEDLYPEHYRKYSEYIKGSNLDAPD   900
 901  PYRVGRIKEIFCHIRTNGKPNEADIKLRIWKFYRPENTHKSMKATYHADI   950
 951  NLLYWSDEETTVDFCAVQGRCTVVYGEDLTESIQDYSAGGLDRFYFLEAY  1000
1001  NAKTKSFEDPPNHARSSGNKGKGKGKGKGKGKGKSSTTCEQSEPEPTELK  1050
1051  LPKLRTLDVFSGCGGLSEGFHQAGVSETLWAIEMWEPAAQAFRLNNPGTT  1100
1101  VFTEDCNVLLKLVMSGEKTNSLGQKLPQKGDVEMLCGGPPCQGFSGMNRF  1150
1151  NSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLR  1200
1201  CLVRMGYQCTFGVLQAGQYGVAQTRRRAIVLAAAPGEKLPMFPEPLHVFA  1250
1251  PRACQLSVVVDDKKFVSNITRTYSGPFRTITVRDTMSDLPEIRNGASALE  1300
1301  ISYNGEPQSWFQRQIRGSQYQPILRDHICKDMSALVAARMRHIPLAPGSD  1350
1351  WRDLPNIEVRLSDGTSTRKLRYTHHEKKNGRSSSGALRGVCSCAEGKPCD  1400
1401  PADRQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQ  1450
1451  GRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAK  1500
1501  AIGLEIRACVGARMREESGAAVAPPAPEKMEMTAAAD               1537

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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