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

NucPred

Fetching P70227 from www.uniprot.org...

The NucPred score for your sequence is 0.73 (see score help below)

   1  MNEMSSFLHIGDIVSLYAEGSVNGFISTLGLVDDRCVVEPAAGDLDNPPK    50
  51  KFRDCLFKVCPMNRYSAQKQYWKAKQTKQDKEKIADVVLLQKLQHAAQME   100
 101  QKQNDTENKKVHGDVVKYGSVIQLLHMKSNKYLTVNKRLPALLEKNAMRV   150
 151  TLDATGNEGSWLFIQPFWKLRSNGDNVVVGDKVILNPVNAGQPLHASNYE   200
 201  LSDNAGCKEVNSVNCNTSWKINLFMQFRDHLEEVLKGGDVVRLFHAEQEK   250
 251  FLTCDEYRGKLQVFLRTTLRQSATSATSSNALWEVEVVHHDPCRGGAGHW   300
 301  NGLYRFKHLATGNYLAAEENPSYKGDVSDPKAAGLGAQGRTGRRNAGEKI   350
 351  KYRLVAVPHGNDIASLFELDPTTLQKTDSFVPRNSYVRLRHLCTNTWIQS   400
 401  TNAPIDVEEERPIRLMLGTCPTKEDKEAFAIVSVPVSEIRDLDFANDASS   450
 451  MLASAVEKLNEGFISQNDRRFVIQLLEDLVFFVSDVPNNGQNVLDIMVTK   500
 501  PNRERQKLMREQNILKQIFGILKAPFRDKGGEGPLVRLEELSDQKNAPYQ   550
 551  YMFRLCYRVLRHSQEDYRKNQEHIAKQFGMMQSQIGYDILAEDTITALLH   600
 601  NNRKLLEKHITKTEVETFVSLVRKNREPRFLDYLSDLCVSNRIAIPVTQE   650
 651  LICKCVLDPKNSDILIQTELRPVKEMAQSHEYLSIEYSEEEVWLTWTDRN   700
 701  NEHHEKSVRQLAQEARAGNAHDENVLSYYRYQLKLFARMCLDRQYLAIDE   750
 751  ISKQLGVELLFLCMADEMLPFDLRASFCHLMLHVHVDRDPQELVTPVKFA   800
 801  RLWTEIPTAITIKDYDSNLNASRDDKKNKFASTMEFVEDYLNNVVSEAVP   850
 851  FANDEKNILTFEVVSLAHNLIYFGFYSFSELLRLTRTLLGIIDCIQAPAA   900
 901  MLQAYEEPGGKNVRRSIQGVGHMMSTMVLSRKQSVFGASSLPAGVGVPEQ   950
 951  LDRSKFEDNEHTVVMETKLKILEILQFILNVRLDYRISYLLSVFKKEFVE  1000
1001  VFPMQDSGADGTAPAFDSSTATMNLDRIGEQAEAMFGVGKTSSMLEVDDE  1050
1051  GGRMFLRVLLHLTMHDYPSLVSGALQLLFKHFSQRQEAMHTFKQVQLLIS  1100
1101  AQDVENYKVIKSELDRLRTMVEKSELWVDKKGSVKGEEVEAGATKDKKER  1150
1151  PSDEEGFLQPHGEKSSENYQIVKGILERLNKMCGVGEQMRKKQQRLLKNM  1200
1201  DAHKVMLDLLQIPYDKSDNKMLEILRYTHQFLQKFCAGNPGNQALLHKHL  1250
1251  QLFLTPGLLEAETMQHIFLNNYQLCSEISEPVLQHFVHLLATHGRHVQYL  1300
1301  DFLHTVIKAEGKYVKKCQDMIMTELTNAGDDVVVFYNDKASLAHLLDMMK  1350
1351  AARDGVEDHSPLMYHISLVDLLAACAEGKNVYTEIKCTSLLPLEDVVTVV  1400
1401  THEDCITEVKMAYVNFVNHCYVDTEVEMKEIYTSNHIWTLFENFTLDMAL  1450
1451  VCNKREKRLSDPTLEKYVLTVVLDTISAFFSSPFSENSTSLQTHQTIVVQ  1500
1501  LLQSTTRLLECPWLQQQHKGSVEACVRTLAMVAKSRAILLPMDLDAHMSA  1550
1551  LLSSGGSCSAAAQRSAANYKTATRTFPRVIPTANQWDYKNIIEKLQDIIM  1600
1601  ALEERLKPLVQAELSVLVDMLHWPELLFPEGSEAYQRCESGGFLSKLIRH  1650
1651  TKGLMESEEKLCVKVLRTLQQMLLKKSKFGDRGNQLRKMLLQNYLQNRKS  1700
1701  GARGELTDPTGSGLDQDWSAIAATQCRLDKEGATKLVCDLITSTKNEKIF  1750
1751  QESIGLAIRLLDGGNTEIQKSFYNLMTSDKKSERFFKVLHDRMKRAQQET  1800
1801  KSTVAVNMSDLGSQPREDREPADPATKGRVSSFSMPSSSRYLLGLGLHRG  1850
1851  HDMSERAQNNEMGTSVLIMRPILRFLQLLCENHNRDLQNFLRCQNNKTNY  1900
1901  NLVCETLQFLDIMCGSTTGGLGLLGLYINEDNVGLVIQTLETLTEYCQGP  1950
1951  CHENQTCIVTHESNGIDIITALILNDISPLCKYRMDLVLQLKDNASKLLL  2000
2001  ALMESRHDSENAERILISLRPQELVDVIKKAYLQEEERENSEVSPREVGH  2050
2051  NIYILALQLSRHNKQLQHLLKPVRRIQEEEAEGISSMLSLNNKQLSQMLK  2100
2101  SSAPAQEEEEDPLAYYENHTSQIEIVRQDRSMEQIVFPVPAICQFLTEET  2150
2151  KHRLFTTTEQDEQGSKVSDFFDQSSFLHNEMEWQRRLRSMPLIYWFSRRM  2200
2201  TLWGSISFNLAVFINIIIAFFYPYVEGASTGVLGSPLISLLFWILICFSI  2250
2251  AALFTKRYSVRPLIVALILRSIYYLGIGPTLNILGALNLTNKIVFVVSFV  2300
2301  GNRGTFIRGYKAMVMDMEFLYHVGYILTSVLGLFAHELFYSILLFDLIYR  2350
2351  EETLFNVIKSVTRNGRSILLTALLALILVYLFSIVGFLFLKDDFILEVDR  2400
2401  LPGNHSRASPLGMPHGAATFMGTCSGDKMDCVSEVSVPEILEEDEEPDST  2450
2451  ERACDTLLMCIVTVMNHGLRNGGGVGDILRKPSKDESLFPARVVYDLLFF  2500
2501  FIVIIIVLNLIFGVIIDTFADLRSEKQKKEEILKTTCFICGLERDKFDNK  2550
2551  TVSFEEHIKLEHNMWNYLYFIVLVRVKNKTDYTGPESYVAQMIKNKNLDW  2600
2601  FPRMRAMSLVSGEGEGEQNEIRILQEKLGSTMKLVSHLTSQLNELKEQMT  2650
2651  EQRKRRQRLGFVDVQNCMSR                                2670

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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