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

NucPred

Fetching Q8WN95 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MSEMSSFLHIGDIVSLYAEGSVNGFISTLGLVDDRCVVEPAAGDLDNPPK    50
  51  KFRDCLFKVCPMNRYSAQKQYWKAKQTKQDKEKIADVVLLQKLQHAAQME   100
 101  QKQNDTENKKVHGDVVKYGSVIQLLHMKSNKYLTVNKRLPALLEKNAMRV   150
 151  TLDATGNEGSWLFIQPFWKLRSNGDNVVVGDKVILNPVNAGQPLHASNYE   200
 201  LSDNAGCKEVNSVNCNTSWKINLFMQFRDHLEEVLKGGDVVRLFHAEQEK   250
 251  FLTCDEYRGKLQVFLRTTLRQSATSATSSNALWEVEVVHHDPCRGGAGHW   300
 301  NGLYRFKHLATGNYLAAEENPSYKGDASDPKAAGTGAQGRTGRRNAGEKI   350
 351  KYRLVAVPHGNDIASLFELDPTTLQKTDSFVPRNSYVRLRHLCTNTWIQS   400
 401  TNVPIDVEEERPIRLMLGTCPTKEDKEAFAIVSVPVSEIRDLDFANDASS   450
 451  MLASAVEKLHEGFISQNDRRFVIQLLEDLVFFVSDVPNNGQNVLDIMVTK   500
 501  PNRERQKLMREQNILKQIFGILKAPFRDKGGEGPLVRLEELSDQKNAPYQ   550
 551  HMFRLCYRVLRHSQEDYRKNQEHIAKQFGMMQSQIGYDILAEDTITALLH   600
 601  NNRKLLEKHITKTEVETFVSLVRKNREPRFLDYLSDLCVSNHIAIPVTQE   650
 651  LICKCVLDPKNSDILIQTELRPVKEMAQSHEYLSIEYSEEEVWLTWTDKN   700
 701  NEHHEKSVRQLAQEARAGNAHDENVLSYYRYQLKLFARMCLDRQYLAIDE   750
 751  ISQQLGVDLIFLCMADEMLPFDLRASFCHLMLHVHVDRDPQELVTPVKFA   800
 801  RLWTEIPTAITIKDYDSNLNASRDDKKNKFASTMEFVEDYLNNVVSEAVP   850
 851  FANEEKNKLTFEVVSLAHNLIYFGFYSFSELLRLTRTLLGIIDCVQAYED   900
 901  PGGKNVRRSTQGVGHMMSTMVLNRKQSVFGGPSLPAGAGAPEPLDGSKFE   950
 951  ENEDIVVMETKLKILEILQFILNVRLDYRISYLLSVFKKEFVEVFPMQDS  1000
1001  GADGTAPAFDSTTANMNLDRIGEQAEAMFGVGKTSSMLEVDDEGGRMLLR  1050
1051  VLIHLTMHDYAPLVSGALQLLFKHFSQRQEVMHTFKQVQLLISAQDVENY  1100
1101  KVIKSELDRLRTMVEKSELWVDKKGASKGEEGEAGPAKDKKERPTDEEGF  1150
1151  LHPPGEKSSENYQIVKGILERLNKMCGVGEQMRKKQQRLLKNMDAHKVML  1200
1201  DLLQIPYDKGDAKMMEILRYTHQFLQKFCAGNPGNQALLHKHLHLFLTPG  1250
1251  LLEAETMQHIFLNNYQLCSEIGEPVLQHFVHLLATHGHHVQYLDFLHTVI  1300
1301  KAEGKYVKKCQDMIMTEPANAGDDVVVFYNDKASLAHLLDMMKAARDGVE  1350
1351  DHSPLMYHISLVDLLAACAEGKNVYTEIKCTSLLPLEDVVSVVTHEDCIT  1400
1401  EVKMAYVNFVNHCYVDTEVEMKEIYTSNHIWTLFENFTLDMARVCSKREK  1450
1451  RLADPALEKYVLTVVLDTISAFFSSPFSENSTSLQTHQTIVVQLLQSTMR  1500
1501  LLECPWLQQQHKGSVEACIRTLAMVAKGRAISLPMDLDAHISSLLSSGAS  1550
1551  CVAAAQRNASNYKTATRAFPRVMPTANQWDYKNIIEKLQDIITALEERLR  1600
1601  PLVQAELSVLVDVLHWPELLFLEGSDAYQRCESGGFLSKLIQHTKDLMES  1650
1651  EEKLCVKVLRTLQQMLLKKTKYGDRGNQLRKMLLQNYLQNRKSSSRGDLP  1700
1701  DPMGTGLDQDWSAIAATQCRLDKEGATKLVCDLITSTKNEKIFQESIGLA  1750
1751  IRLLDGGNTEIQKSFYNLMTSDKKSERFFKVLHDRMKRAQQETKSTVAVN  1800
1801  MSDLGSQPREDREQADPTSKGRVASFSMPSSSSRYALGPSLRRGHEVGER  1850
1851  VQSNEMGTSVLIMQPILRFLQLLCENHNRDLQNFLRCQNNKTNYNLVCET  1900
1901  LQFLDIMCGSTTGGLGLLGLYINEDNVGLVIQTLETLTEYCQGPCHENQT  1950
1951  CIVTHESNGIDIITALILNDISPLCKYRMDLVLQLKDNASKLLLALMESR  2000
2001  HDSENAERILISLRPQELVDVIKKAYLQEEERENSDVSPREVGHNIYILA  2050
2051  LQLSRHNKQLQHLLKPVKRIQEEEAEGISSMLSLNNKQLTQMLKSSAPVQ  2100
2101  EQEEDPLAYYENHTSQIEIVRQDRSMEQIVFPVPGICQFLTEETKHRLFT  2150
2151  TTEQDEQGSKVSDLFDQPSFLHNEMEWQRKLRSMPLIYWFSRRMTLWGSI  2200
2201  SFNLAVFINIIIAFFYPYVEGASTGVLGSPLISLLFWILICFSIAALFTK  2250
2251  RYSVRPLIVALILRSIYYLGIGPTLNILGALNLTNKIVFVVSFVGNRGTF  2300
2301  IRGYKAMVMDMEFLYHVGYILTSVLGLFAHELFYSILLFDLIYREETLFN  2350
2351  VIKSVTRNGRSILLTALLALILVYLFSIVGFLFLKDDFILEVDRLPGNHS  2400
2401  RANPLGMPHGAATFVNTCSGDNVDCVSGVSVPEVLAEDEEPDSTERACDT  2450
2451  LLMCIVTVMNHGLRNGGGVGDILRKPSKDESLFPARVVYDLLFFFIVIII  2500
2501  VLNLIFGVIIDTFADLRSEKQKKEEILKTTCFICGLERDKFDNKTVSFEE  2550
2551  HIKFEHNMWNYLYFIVLVRVKNKTDYTGPESYVAQMIKNKNLDWFPRMRA  2600
2601  MSLVSSEGEGEQNEIRILQDKLSATMKLVSHLTAQLSELKEQMTEQRKRR  2650
2651  QRLGFVDVQNCMSR                                      2664

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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