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

NucPred

Fetching Q14573 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MSEMSSFLHIGDIVSLYAEGSVNGFISTLGLVDDRCVVEPAAGDLDNPPK    50
  51  KFRDCLFKVCPMNRYSAQKQYWKAKQTKQDKEKIADVVLLQKLQHAAQME   100
 101  QKQNDTENKKVHGDVVKYGSVIQLLHMKSNKYLTVNKRLPALLEKNAMRV   150
 151  TLDATGNEGSWLFIQPFWKLRSNGDNVVVGDKVILNPVNAGQPLHASNYE   200
 201  LSDNAGCKEVNSVNCNTSWKINLFMQFRDHLEEVLKGGDVVRLFHAEQEK   250
 251  FLTCDEYKGKLQVFLRTTLRQSATSATSSNALWEVEVVHHDPCRGGAGHW   300
 301  NGLYRFKHLATGNYLAAEENPSYKGDASDPKAAGMGAQGRTGRRNAGEKI   350
 351  KYCLVAVPHGNDIASLFELDPTTLQKTDSFVPRNSYVRLRHLCTNTWIQS   400
 401  TNVPIDIEEERPIRLMLGTCPTKEDKEAFAIVSVPVSEIRDLDFANDASS   450
 451  MLASAVEKLNEGFISQNDRRFVIQLLEDLVFFVSDVPNNGQNVLDIMVTK   500
 501  PNRERQKLMREQNILKQVFGILKAPFREKGGEGPLVRLEELSDQKNAPYQ   550
 551  HMFRLCYRVLRHSQEDYRKNQEHIAKQFGMMQSQIGYDILAEDTITALLH   600
 601  NNRKLLEKHITKTEVETFVSLVRKNREPRFLDYLSDLCVSNHIAIPVTQE   650
 651  LICKCVLDPKNSDILIRTELRPVKEMAQSHEYLSIEYSEEEVWLTWTDKN   700
 701  NEHHEKSVRQLAQEARAGNAHDENVLSYYRYQLKLFARMCLDRQYLAIDE   750
 751  ISQQLGVDLIFLCMADEMLPFDLRASFCHLMLHVHVDRDPQELVTPVKFA   800
 801  RLWTEIPTAITIKDYDSNLNASRDDKKNKFANTMEFVEDYLNNVVSEAVP   850
 851  FANEEKNKLTFEVVSLAHNLIYFGFYSFSELLRLTRTLLGIIDCVQGPPA   900
 901  MLQAYEDPGGKNVRRSIQGVGHMMSTMVLSRKQSVFSAPSLSAGASAAEP   950
 951  LDRSKFEENEDIVVMETKLKILEILQFILNVRLDYRISYLLSVFKKEFVE  1000
1001  VFPMQDSGADGTAPAFDSTTANMNLDRIGEQAEAMFGVGKTSSMLEVDDE  1050
1051  GGRMFLRVLIHLTMHDYAPLVSGALQLLFKHFSQRQEAMHTFKQVQLLIS  1100
1101  AQDVENYKVIKSELDRLRTMVEKSELWVDKKGSGKGEEVEAGAAKDKKER  1150
1151  PTDEEGFLHPPGEKSSENYQIVKGILERLNKMCGVGEQMRKKQQRLLKNM  1200
1201  DAHKVMLDLLQIPYDKGDAKMMEILRYTHQFLQKFCAGNPGNQALLHKHL  1250
1251  HLFLTPGLLEAETMQHIFLNNYQLCSEISEPVLQHFVHLLATHGRHVQYL  1300
1301  DFLHTVIKAEGKYVKKCQDMIMTELTNAGDDVVVFYNDKASLAHLLDMMK  1350
1351  AARDGVEDHSPLMYHISLVDLLAACAEGKNVYTEIKCTSLLPLEDVVSVV  1400
1401  THEDCITEVKMAYVNFVNHCYVDTEVEMKEIYTSNHIWTLFENFTLDMAR  1450
1451  VCSKREKRVADPTLEKYVLSVVLDTINAFFSSPFSENSTSLQTHQTIVVQ  1500
1501  LLQSTTRLLECPWLQQQHKGSVEACIRTLAMVAKGRAILLPMDLDAHISS  1550
1551  MLSSGASCAAAAQRNASSYKATTRAFPRVTPTANQWDYKNIIEKLQDIIT  1600
1601  ALEERLKPLVQAELSVLVDVLHWPELLFLEGSEAYQRCESGGFLSKLIQH  1650
1651  TKDLMESEEKLCIKVLRTLQQMLLKKTKYGDRGNQLRKMLLQNYLQNRKS  1700
1701  TSRGDLPDPIGTGLDPDWSAIAATQCRLDKEGATKLVCDLITSTKNEKIF  1750
1751  QESIGLAIHLLDGGNTEIQKSFHNLMMSDKKSERFFKVLHDRMKRAQQET  1800
1801  KSTVAVNMNDLGSQPHEDREPVDPTTKGRVASFSIPGSSSRYSLGPSLRR  1850
1851  GHEVSERVQSSEMGTSVLIMQPILRFLQLLCENHNRDLQNFLRCQNNKTN  1900
1901  YNLVCETLQFLDIMCGSTTGGLGLLGLYINEDNVGLVIQTLETLTEYCQG  1950
1951  PCHENQTCIVTHESNGIDIITALILNDISPLCKYRMDLVLQLKDNASKLL  2000
2001  LALMESRHDSENAERILISLRPQELVDVIKKAYLQEEERENSEVSPREVG  2050
2051  HNIYILALQLSRHNKQLQHLLKPVKRIQEEEAEGISSMLSLNNKQLSQML  2100
2101  KSSAPAQEEEEDPLAYYENHTSQIEIVRQDRSMEQIVFPVPGICQFLTEE  2150
2151  TKHRLFTTTEQDEQGSKVSDFFDQSSFLHNEMEWQRKLRSMPLIYWFSRR  2200
2201  MTLWGSISFNLAVFINIIIAFFYPYMEGASTGVLDSPLISLLFWILICFS  2250
2251  IAALFTKRYSIRPLIVALILRSIYYLGIGPTLNILGALNLTNKIVFVVSF  2300
2301  VGNRGTFIRGYKAMVMDMEFLYHVGYILTSVLGLFAHELFYSILLFDLIY  2350
2351  REETLFNVIKSVTRNGRSILLTALLALILVYLFSIVGFLFLKDDFILEVD  2400
2401  RLPNNHSTASPLGMPHGAAAFVDTCSGDKMDCVSGLSVPEVLEEDRELDS  2450
2451  TERACDTLLMCIVTVMNHGLRNGGGVGDILRKPSKDESLFPARVVYDLLF  2500
2501  FFIVIIIVLNLIFGVIIDTFADLRSEKQKKEEILKTTCFICGLERDKFDN  2550
2551  KTVSFEEHIKLEHNMWNYLYFIVLVRVKNKTDYTGPESYVAQMIKNKNLD  2600
2601  WFPRMRAMSLVSNEGEGEQNEIRILQDKLNSTMKLVSHLTAQLNELKEQM  2650
2651  TEQRKRRQRLGFVDVQNCISR                               2671

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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