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

NucPred

Fetching Q9C102 from www.uniprot.org...

The NucPred score for your sequence is 0.29 (see score help below)

   1  MAVLSSVQPINHNSALVEARDEQVNTTACSDDLLNAPPYEYDTEGNPSWA    50
  51  GALPKAQALYDPAYEKDSCGVGFTCHIKGQVSHKIVTDARLLLCNMTHRG   100
 101  ATGADTRDGDGAGVMTGMPYTFMQKEFGQIGCTLPKSGEYAIGNVFFSPE   150
 151  ADVCREAMTAFTQVAEKLGLAILAWRSVPCDNSILGPAALSREPTILQPC   200
 201  VVLKAAYDGEAEFDTDLFERQLYVLRKQSSHLIGKEKWFYICSLHRETIV   250
 251  YKGQLAPVQVYNYFLDLNNAEYVSHFALVHSRFSTNTFPSWDRAQPMRLA   300
 301  AHNGEINTLRGNKNWMHAREGLMKSSRFGEEFASLLPIIERGGSDSAAFD   350
 351  NVIELLCASGVVSLPEAVMLLIPEAWQNDKNISDEKAAFYEWAACQMEPW   400
 401  DGPALFTFADGRYCGANLDRNGLRPCRFYLTSDDMMICASEVGTVGIEPD   450
 451  RIVQKGRLYPGRMLLVDTKEGRIVDDKELKHNIASRYDFRSWLDQELIDM   500
 501  NSIVDSLIESTSVDLTPIVDDVPLADDKTMLAFGYTLEQINMIMAPMANG   550
 551  GKETLGSMGNDAAIACLSDQPRLLYDYFRQLFAQVTNPPIDPIREAIVMS   600
 601  LQCYIGPSGNLLEINQSQCRRLRMPTPILTVEEFNALKNVDRIYPDWKVA   650
 651  SIDITFFKSEGVAGYAAAIERICSEADTAVNEGYKAIVLSDRNVNSERVP   700
 701  LASIAACGAVHHYLVQNKLRSRVALVCESGDAREVHHMCTLLGYGADAVC   750
 751  PYLAMEALTKLVRQNAMKPGITEETAIKNFKHAINGGILKVMSKMGISTL   800
 801  QSYKGAQIFEALGIDNEVINKCFLGTASRIRGVTFEHIALDAFALHERGY   850
 851  PTDQSIRSLQIPDMGDFYYRDGGEQHVNHPKAIASLQDAVRNKNEAAYAE   900
 901  FSRTHYEQTRRCTLRGMLDFDFDSSQAIPIEQVEPWTEIVRRFCTGAMSY   950
 951  GSISMESHSSLAIAMNRLGGKSNTGEGGEDPARSQRLANGDTMRSAIKQI  1000
1001  ASGRFGVTSWYLSDADELQIKMAQGAKPGEGGELPGNKVSESIAKTRHST  1050
1051  AGVGLISPPPHHDIYSIEDLKQLIYDMKSANPRARVSVKLVSEVGVGIVA  1100
1101  SGVAKAKADHILVSGHDGGTGASRWTGIKYAGLPWELGVAETHQTLVLND  1150
1151  LRGRVVIQTDGQIRTGRDVAIACLLGAEEWGFATTPLIALGCIMMRKCHL  1200
1201  NTCPVGIATQDPELRKKFEGQPEHVVNFFYYVAEELRGIMAKLGFRTINE  1250
1251  MVGRSDKLKVAEPINNKSKLLDLTPLLTPAFTLRPGAATYNVRKQDHRLY  1300
1301  TRLDNKLIDEAEVTLEEGIPSVVECEIINTDRTLGATLSNKISKRYGEEG  1350
1351  LPTDSIRVNVFGSAGQSFGAFLAPGVTLQLEGDCNDYVGKGLSGGRLIIY  1400
1401  PPRVSPFKPEENMIIGNVCLYGATSGHAFISGVAAERFAVRNSGAIAVVE  1450
1451  GVGDHGCEYMTGGRVVILGSTGRNFAAGMSGGIAYVYDMQMDFAGKINTE  1500
1501  MVDISSVTDAAEIAFLRGLIQDHRHYTGSQVADRILSDFPRHLSRFVKVL  1550
1551  PREYKAVLEREAAKKEEAKRLQYPKAFMPGNPIRQQIEETNAQIADVEDT  1600
1601  LGATVKKSAPLDKLRGFMKYQRRSEHYRNPLKRTNDWKELSVRLREDELR  1650
1651  VQTARCMDCGTPFCQSDYGCPISNKIFTWNDLVFKQQWKEALTQLLLTNN  1700
1701  FPEFTGRVCPAPCEGACTLGIIESPVGIKSVERAIIDKAWEEGWIVPRPP  1750
1751  AERTGRRVAIIGSGPAGLAAADQLNRAGHHVVIYERADRPGGLLQYGIPN  1800
1801  MKLDKKVVERRIQLMIDEGIEVLTNVEVGKNGDVSLDELHKVYDAVVLAS  1850
1851  GSTVPRDLPIPNRDSKGIHFAMEFLHKNTKSLLDSELKDGNYISAKGKDV  1900
1901  IVIGGGDTGNDCLGTSVRHGAKSVRNLELLPIPPRERAFDNPWPQYPRVF  1950
1951  RVDYGHAEVQAHYGQDFREYSILTKSFEKDEDGNVKGINTVRIEWTKNSK  2000
2001  GRWIMKEIRNSEEFFPADLVILALGFLGPEEQATAGMNVDRDARSNISTP  2050
2051  TKSYETSVPGIYAAGDCRRGQSLVVWGIQEGRQCAREIDLKFQGKTFLPG  2100
2101  DGGLVKRTVNC                                         2111

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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