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

NucPred

Fetching Q8R1A4 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MAERRAFAQKISRTVAAEVRKQISGQYSGSPQLLKNLNIVGNISHHTTVP    50
  51  LTEAVDPVDLEDYLVTHPLSGDSGPLRDLVEFPPDDIEVVYSPRDCRTLV   100
 101  SAVPEESEMDPHVRDCIRSYTEDWAVVVRKYHKLGTGFNPNTLDKQKERQ   150
 151  KGLPRQVFESDEAPDGSSYQDEQDDLKRRSMSIDDTPRGSWACSIFDLKN   200
 201  SLPDALLPNLLDRTPNEEIDHQNDDQRKSNRHKELFALHPSPDEEEPIER   250
 251  LSVPDVPKEHFGQRLLVKCLSLKFEIEIEPIFASLALYDVKEKKKISENF   300
 301  YFDLNSEQMKGLLRPHVPPAAITTLARSAIFSITYPSQDVFLVIKLEKVL   350
 351  QQGDIGECAEPYMIFKEADATKNKEKLEKLKSQADQFCQRLGKYRMPFAW   400
 401  TAIHLMNIVSSAGSLERDSTEVEISTGERKGSWSERRNSSLVGRRSLERT   450
 451  TSGDDACNLTSFRPATLTVANFFKQEGDRLSDEDLYKFLADMRRPSSVLR   500
 501  RLRPITAQLKIDISPAPENPHYCLTPELLQVKLYPDSRVRPTREILEFPA   550
 551  RDVYVPNTTYRNLLYIYPQSLNFANRQGSARNITVKVQFMYGEDPSNAMP   600
 601  VIFGKSSCSEFSKEAYTAVVYHNRSPDFHEEIKVKLPATLTDHHHLLFTF   650
 651  YHVSCQQKQNTPLETPVGYTWIPMLQNGRLKTGQFCLPVSLEKPPQAYSV   700
 701  LSPEVPLPGMKWVDNHKGVFNVEVVAVSSIHTQDPYLDKFFALVNALDEH   750
 751  MFPVRIGDMRIMENNLESELKSSISALNSSQLEPVVRFLHLLLDKLILLV   800
 801  VRPPVIAGQIVNLGQASFEAMASIINRLHKNLEGNHDQHGRNNLLASYIY   850
 851  YVFRLPNTYPNSPSPGPGGLGGSVHYATMARSAVRPASLNLNRSRSLSNS   900
 901  NPDISGTPTSPDDEVRSIIGSKGLDRSNSWVNTGPKAAPWGSNPSPSAES   950
 951  TQAMDRSCNRMSSHTETSSFLQTLTGRLPTKKLFHEELALQWVVCSGSVR  1000
1001  ESALQQAWFFFELMVKSMVHHLYFNDKLDAPRESRFPERFMDDIAALVST  1050
1051  IAGDVVSRFQKDTEMVERLNTSLAFFLNDLLSVMDRGFVFSLIKSCYKQV  1100
1101  SAKLYSLPNPSVLVSLRLDFLRIICSHEHYVTLNLPCSLLTPPASPSPSV  1150
1151  SSATSQSSGFSTSVQDQKIANMFELSLPFRQQHYLAGLVLTELALILDPD  1200
1201  AEGLFGLHKKVINMVHNLLSTHDSDPRYSDPQIKARVAMLYLPLIGIIME  1250
1251  TVPQLYDFTESHNQRGRPICIAPDDYDSESGSMISQTVAMAIAGTSVPQL  1300
1301  TRPGSFLLTSTSGRQHTTFSAESSRSLLICLLWVLKNADETVLQKWFTDL  1350
1351  SVLQLNRLLDLLYLCVSCFEYKGKKVFERMNSLTFKKSKDMRAKLEEAIL  1400
1401  GSIGARQEMVRRSRGQLERSPSGSAFGSQENLRWRKDMTHWRQNSEKLDK  1450
1451  SRAEIEHEALIDGNLATEANLIILDTLEIIVQTVSVTESKESILGGVLKV  1500
1501  LLQSMACNQSAVYLQHCFATQRALVSKFPELLFEEETEQCADLCLRLLRH  1550
1551  CSSSISTIRSHASASLYLLMRQNFEIGNNFARVKMQVTMSLSSLVGTSQN  1600
1601  FNEEFLRRSLKTILTYAEEDLELRETTFPDQVQDLVFNLHMILSDTVKMK  1650
1651  EHQEDPEMLIDLMYRIAKGYQTSPDLRLTWLQNMAGKHSERSNHAEAAQC  1700
1701  LVHSAALVAEYLSMLEDRKYLPVGCVTFQNISSNVLEESAVSDDVVSPDE  1750
1751  EGICSGKYFTESGLVGLLEQAAASFSMAGMYEAVNEVYKVLIPIHEANRD  1800
1801  AKKLSTIHGKLQEAFSKIVHQSTGWERMFGTYFRVGFYGTKFGDLDEQEF  1850
1851  VYKEPAITKLAEISHRLEGFYGERFGEDVLEVIKDSNPVDKCKLDPNKAY  1900
1901  IQITYVEPFFDTYEMKDRITYFDKNYNLRRFMYCTPFTLDGRAHGELHEQ  1950
1951  FKRKTILTTSHAFPYIKTRVNVTHKEEIILTPIEVAIEDMQKKTQELAFA  2000
2001  THQDPADPKMLQMVLQGSVGTTVNQGPLEVAQVFLSEIPGDPKLFRHHNK  2050
2051  LRLCFKDFTKRCEDALRKNKSLIGPDQKEYQRELERNYHRLKEALQPLIN  2100
2101  RKIPQLYKAVLPVTCHRDSFSRMSLRKMEL                      2130

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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