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

NucPred

Fetching Q93008 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MTATTRGSPVGGNDNQGQAPDGQSQPPLQQNQTSSPDSSNENSPATPPDE    50
  51  QGQGDAPPQLEDEEPAFPHTDLAKLDDMINRPRWVVPVLPKGELEVLLEA   100
 101  AIDLSKKGLDVKSEACQRFFRDGLTISFTKILTDEAVSGWKFEIHRCIIN   150
 151  NTHRLVELCVAKLSQDWFPLLELLAMALNPHCKFHIYNGTRPCESVSSSV   200
 201  QLPEDELFARSPDPRSPKGWLVDLLNKFGTLNGFQILHDRFINGSALNVQ   250
 251  IIAALIKPFGQCYEFLTLHTVKKYFLPIIEMVPQFLENLTDEELKKEAKN   300
 301  EAKNDALSMIIKSLKNLASRVPGQEETVKNLEIFRLKMILRLLQISSFNG   350
 351  KMNALNEVNKVISSVSYYTHRHGNPEEEEWLTAERMAEWIQQNNILSIVL   400
 401  RDSLHQPQYVEKLEKILRFVIKEKALTLQDLDNIWAAQAGKHEAIVKNVH   450
 451  DLLAKLAWDFSPEQLDHLFDCFKASWTNASKKQREKLLELIRRLAEDDKD   500
 501  GVMAHKVLNLLWNLAHSDDVPVDIMDLALSAHIKILDYSCSQDRDTQKIQ   550
 551  WIDRFIEELRTNDKWVIPALKQIREICSLFGEAPQNLSQTQRSPHVFYRH   600
 601  DLINQLQHNHALVTLVAENLATYMESMRLYARDHEDYDPQTVRLGSRYSH   650
 651  VQEVQERLNFLRFLLKDGQLWLCAPQAKQIWKCLAENAVYLCDREACFKW   700
 701  YSKLMGDEPDLDPDINKDFFESNVLQLDPSLLTENGMKCFERFFKAVNCR   750
 751  EGKLVAKRRAYMMDDLELIGLDYLWRVVIQSNDDIASRAIDLLKEIYTNL   800
 801  GPRLQVNQVVIHEDFIQSCFDRLKASYDTLCVLDGDKDSVNCARQEAVRM   850
 851  VRVLTVLREYINECDSDYHEERTILPMSRAFRGKHLSFVVRFPNQGRQVD   900
 901  DLEVWSHTNDTIGSVRRCILNRIKANVAHTKIELFVGGELIDPADDRKLI   950
 951  GQLNLKDKSLITAKLTQISSNMPSSPDSSSDSSTGSPGNHGNHYSDGPNP  1000
1001  EVESCLPGVIMSLHPRYISFLWQVADLGSSLNMPPLRDGARVLMKLMPPD  1050
1051  STTIEKLRAICLDHAKLGESSLSPSLDSLFFGPSASQVLYLTEVVYALLM  1100
1101  PAGAPLADDSSDFQFHFLKSGGLPLVLSMLTRNNFLPNADMETRRGAYLN  1150
1151  ALKIAKLLLTAIGYGHVRAVAEACQPGVEGVNPMTQINQVTHDQAVVLQS  1200
1201  ALQSIPNPSSECMLRNVSVRLAQQISDEASRYMPDICVIRAIQKIIWASG  1250
1251  CGSLQLVFSPNEEITKIYEKTNAGNEPDLEDEQVCCEALEVMTLCFALIP  1300
1301  TALDALSKEKAWQTFIIDLLLHCHSKTVRQVAQEQFFLMCTRCCMGHRPL  1350
1351  LFFITLLFTVLGSTARERAKHSGDYFTLLRHLLNYAYNSNINVPNAEVLL  1400
1401  NNEIDWLKRIRDDVKRTGETGIEETILEGHLGVTKELLAFQTSEKKFHIG  1450
1451  CEKGGANLIKELIDDFIFPASNVYLQYMRNGELPAEQAIPVCGSPPTINA  1500
1501  GFELLVALAVGCVRNLKQIVDSLTEMYYIGTAITTCEALTEWEYLPPVGP  1550
1551  RPPKGFVGLKNAGATCYMNSVIQQLYMIPSIRNGILAIEGTGSDVDDDMS  1600
1601  GDEKQDNESNVDPRDDVFGYPQQFEDKPALSKTEDRKEYNIGVLRHLQVI  1650
1651  FGHLAASRLQYYVPRGFWKQFRLWGEPVNLREQHDALEFFNSLVDSLDEA  1700
1701  LKALGHPAMLSKVLGGSFADQKICQGCPHRYECEESFTTLNVDIRNHQNL  1750
1751  LDSLEQYVKGDLLEGANAYHCEKCNKKVDTVKRLLIKKLPPVLAIQLKRF  1800
1801  DYDWERECAIKFNDYFEFPRELDMEPYTVAGVAKLEGDNVNPESQLIQQS  1850
1851  EQSESETAGSTKYRLVGVLVHSGQASGGHYYSYIIQRNGGDGERNRWYKF  1900
1901  DDGDVTECKMDDDEEMKNQCFGGEYMGEVFDHMMKRMSYRRQKRWWNAYI  1950
1951  LFYERMDTIDQDDELIRYISELAITTRPHQIIMPSAIERSVRKQNVQFMH  2000
2001  NRMQYSMEYFQFMKKLLTCNGVYLNPPPGQDHLLPEAEEITMISIQLAAR  2050
2051  FLFTTGFHTKKVVRGSASDWYDALCILLRHSKNVRFWFAHNVLFNVSNRF  2100
2101  SEYLLECPSAEVRGAFAKLIVFIAHFSLQDGPCPSPFASPGPSSQAYDNL  2150
2151  SLSDHLLRAVLNLLRREVSEHGRHLQQYFNLFVMYANLGVAEKTQLLKLS  2200
2201  VPATFMLVSLDEGPGPPIKYQYAELGKLYSVVSQLIRCCNVSSRMQSSIN  2250
2251  GNPPLPNPFGDPNLSQPIMPIQQNVADILFVRTSYVKKIIEDCSNSEETV  2300
2301  KLLRFCCWENPQFSSTVLSELLWQVAYSYTYELRPYLDLLLQILLIEDSW  2350
2351  QTHRIHNALKGIPDDRDGLFDTIQRSKNHYQKRAYQCIKCMVALFSNCPV  2400
2401  AYQILQGNGDLKRKWTWAVEWLGDELERRPYTGNPQYTYNNWSPPVQSNE  2450
2451  TSNGYFLERSHSARMTLAKACELCPEEEPDDQDAPDEHESPPPEDAPLYP  2500
2501  HSPGSQYQQNNHVHGQPYTGPAAHHMNNPQRTGQRAQENYEGSEEVSPPQ  2550
2551  TKDQ                                                2554

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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