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

NucPred

Fetching P34545 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MDEPPSKKSRADSDYDSGLDALSALESLEAFPTSSKDTDVDNNPSTSAGG    50
  51  SGGPSGSTPHPQGTPQPAPSNNGGFNLQPGQSQPQQPPQNMGGGVNGSVL   100
 101  QELLMNPSQTSNNSPRPQAYPPGQQNAFNRSPMMPNGTPNMMSPPSMGRV   150
 151  PGPSPGGPQPPGPGQPQMRPGQPGMFQGDQQQQMMMGAQGQQFPGMMHRY   200
 201  PYAQGGPPPGAQGMPQGYPGVSRGGPTPGQPMGRGAMMNGAMPRSGPMPT   250
 251  QGRPGIPPNQQAMMQPMMTDRQFMQHGQYGQQRPEFMQQYGRPGGYPMMH   300
 301  QGMMMDSNGQPIRGPNQMMMMSNGHPGMSHGPPNGQPGPQAAAAQHAAQQ   350
 351  QAAAQAQAQAAAQQQQQQQREQEAAAAAQRNGAGRATTPGSSMLATHQDP   400
 401  EKRKLIQQQLVLLLHAHKCSQREKENRDFAAKNQPPPHAACTLPHCSTMK   450
 451  EVLTHMTSCNVGRLCHSDTTQTTKKCSVAHCASSRQIIAHWKNCSREDCP   500
 501  VCKPLKRIQDTPLQFSLPDLANLIGVNGNSNGSAEGDGLHQFGSPAMRTG   550
 551  NITNSLFEGFNGNPFQNGPNRGGPRPPGGNGEIPNLPPPDMPDCTKEWHH   600
 601  QVTKDLRNHLVGKLVKAIFPEPNQEAMNDNRLKDLIAYARKVEKEMFESA   650
 651  NDREEYYHLLAEKIYKIQKELQEKKNSRLNQGAAAHDQYAIPPSNELAQM   700
 701  LGVEGGRSDVHSEGSSMAVAPSQQNQPWGGAPNSNMHQQIPPNGQVPQVN   750
 751  NSSTFPSSGNSTPNIGASSTVSAMLQPKTEPMDDQNTDSLSSRPPTAIGF   800
 801  GGSSSSTPAPIMNGIVKKEEDPEESSNQAPPSVKDTKDGVAESKPKEQQA   850
 851  KREPTPPPTEDTVFSQEDLIKFLLPVWEKLDKSEDAAPFRVPVDAKLLNI   900
 901  PDYHEIIKRPMDLETVHKKLYAGQYQNAGQFCDDIWLMLDNAWLYNRKNS   950
 951  KVYKYGLKLSEMFVSEMDPVMKSMGYCCAKKLAFTPLSLFCYGAAMCTIA  1000
1001  REQQYWVFEQSSTQYNVTVTERYTYCQKCFDALPPEGISLSENPNDRNNM  1050
1051  APKTSFTEQKNSVIDYEPFERCKYCMRKWHRICALHDKKVYPEGFICECC  1100
1101  RTAKKYQKPDNKYLASKLPHNKLSTFLEDRVNGFIKKQLQAEAHKYPVII  1150
1151  RTLCVQDKEAEVKAQMKQKYVESNQFPEKFPYRTKAVFAFEIIDGVEVCF  1200
1201  FGLHVQEYGSACPAPNARRVYIAYLDSVHFFQPRELRTDVYHELLLGYLD  1250
1251  YAKMLGYTMAHIWACPPSEGDDYIFHCHPPEQKIPKPKRLQDWYKKMLEK  1300
1301  GVQEGSVVEFKDIYKQARDDNLTTPTQLPYFEGDFWPNVIEDCIREASNE  1350
1351  EAQRKVKEDDDDGEDADGGLGGGDSGKKKSSKNKKNNLKKNAKMNKKKAG  1400
1401  SITGNEVADKLYSQFEKHKEVFFTIRLVSLQNEPAVLAKPISDPDGLMQS  1450
1451  DMMDGRDTFLTKAREEHWEFSSLRRAKYSTLCLAYSLHETDSKGMEYTCN  1500
1501  KCSSPAVWHCQSCDDFDLCDGCKPTTQHPHEMEKIKSLIGGGEAGDSAAG  1550
1551  GTRYESIQRCIASLVHACQCRDANCRRMSCHKMKRVVQHTKMCKKRINGT  1600
1601  CPVCKQLIALCCYHAKHCTRDACTVPFCMNIRQKLAEQKRSQQRRADMMM  1650
1651  RRRMEGLQSHVGGAAPTPSTVSNGTPSNAPTPPVSAGPGPAVKGGGVGQV  1700
1701  QMQQHQGSHVGGSGPAGMGQPMNSFGGMPGMGLGPNAQNGPGLPGMNPQM  1750
1751  NANQSRYMPNGPGLGQSGAPGQQQQPMYSSGMPMQRPGGLGGMNPQQQPQ  1800
1801  QQQGHPGLQNPGGRPGGVHGMGQNQPVRNNQDMVMNMQMQNQHQQPPPFD  1850
1851  STLQPQIMKINSRLKAAKTEEERETVFSDLKKTPHLFHAWLRMRENQNLV  1900
1901  PNRMQGYSQMSMGSSNLQNLQQQQLQQQQAGAMRGGGGFAPGQNNSQPRA  1950
1951  PSGQFASMNPSMQQQYPQQQQGWPQQRQQNPGGMQQNANPYNQFQNRQNM  2000
2001  MMMPQQQQPHPSNAGGQ                                   2017

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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