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

NucPred

Fetching Q8BTM8 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MSSSHSRCGQSAAVASPGGSIDSRDAEMPATEKDLAEDAPWKKIQQNTFT    50
  51  RWCNEHLKCVSKRIANLQTDLSDGLRLIALLEVLSQKKMHRKHNQRPTFR   100
 101  QMQLENVSVALEFLDRESIKLVSIDSKAIVDGNLKLILGLIWTLILHYSI   150
 151  SMPMWDEEEDEEAKKQTPKQRLLGWIQNKLPQLPITNFSRDWQSGRALGA   200
 201  LVDSCAPGLCPDWDSWDASKPVNNAREAMQQADDWLGIPQVITPEEIVDP   250
 251  NVDEHSVMTYLSQFPKAKLKPGAPLRPKLNPKKARAYGPGIEPTGNMVKK   300
 301  RAEFTVETRSAGQGEVLVYVEDPAGHQEEAKVTANNDKNRTFSVWYVPEV   350
 351  TGTHKVTVLFAGQHIAKSPFEVYVDKSQGDASKVTAQGPGLEPSGNIANK   400
 401  TTYFEIFTAGAGMGEVEVVIQDPTGQKGTVEPQLEARGDSTYRCSYQPTM   450
 451  EGVHTVHVTFAGVPIPRSPYTVTVGQACNPAACRAIGRGLQPKGVRVKET   500
 501  ADFKVYTKGAGSGELKVTVKGPKGEERVKQKDLGDGVYGFEYYPTIPGTY   550
 551  TVTITWGGQNIGRSPFEVKVGTECGNQKVRAWGPGLEGGIVGKSADFVVE   600
 601  AIGDDVGTLGFSVEGPSQAKIECDDKGDGSCDVRYWPQEAGEYAVHVLCN   650
 651  SEDIRLSPFMADIREAPQDFHPDRVKARGPGLEKTGVAVNKPAEFTVDAK   700
 701  HAGKAPLRVQVQDNEGCSVEATVKDNGNGTYSCSYVPRKPVKHTAMVSWG   750
 751  GVSIPNSPFRVNVGAGSHPNKVKVYGPGVAKTGLKAHEPTYFTVDCTEAG   800
 801  QGDVSIGIKCAPGVVGPTEADIDFDIIRNDNDTFTVKYTPCGAGSYTIMV   850
 851  LFADQATPTSPIRVKVEPSHDASKVKAEGPGLNRTGVELGKPTHFTVNAK   900
 901  TAGKGKLDVQFSGLAKGDAVRDVDIIDHHDNTYTVKYIPVQQGPVGVNVT   950
 951  YGGDHIPKSPFSVGVSPSLDLSKIKVSGLGDKVDVGKDQEFTVKSKGAGG  1000
1001  QGKVASKIVSPSGAAVPCKVEPGLGADNSVVRFVPREEGPYEVEVTYDGV  1050
1051  PVPGSPFPLEAVAPTKPSKVKAFGPGLQGGNAGSPARFTIDTKGAGTGGL  1100
1101  GLTVEGPCEAQLECLDNGDGTCSVSYVPTEPGDYNINILFADTHIPGSPF  1150
1151  KAHVAPCFDASKVKCSGPGLERATAGEVGQFQVDCSSAGSAELTIEICSE  1200
1201  AGLPAEVYIQDHGDGTHTITYIPLCPGAYTVTIKYGGQPVPNFPSKLQVE  1250
1251  PAVDTSGVQCYGPGIEGQGVFREATTEFSVDARALTQTGGPHVKARVANP  1300
1301  SGNLTDTYVQDCGDGTYKVEYTPYEEGVHSVDVTYDGSPVPSSPFQVPVT  1350
1351  EGCDPSRVRVHGPGIQSGTTNKPNKFTVETRGAGTGGLGLAVEGPSEAKM  1400
1401  SCMDNKDGSCSVEYIPYEAGTYSLNVTYGGHQVPGSPFKVPVHDVTDASK  1450
1451  VKCSGPGLSPGMVRANLPQSFQVDTSKAGVAPLQVKVQGPKGLVEPVDVV  1500
1501  DNADGTQTVNYVPSREGSYSISVLYGEEEVPRSPFKVKVLPTHDASKVKA  1550
1551  SGPGLNTTGVPASLPVEFTIDAKDAGEGLLAVQITDPEGKPKKTHIQDNH  1600
1601  DGTYTVAYVPDVPGRYTILIKYGGDEIPFSPYRVRAVPTGDASKCTVTVS  1650
1651  IGGHGLGAGIGPTIQIGEETVITVDTKAAGKGKVTCTVCTPDGSEVDVDV  1700
1701  VENEDGTFDIFYTAPQPGKYVICVRFGGEHVPNSPFQVTALAGDQPTVQT  1750
1751  PLRSQQLAPQYNYPQGSQQTWIPERPMVGVNGLDVTSLRPFDLVIPFTIK  1800
1801  KGEITGEVRMPSGKVAQPSITDNKDGTVTVRYSPSEAGLHEMDIRYDNMH  1850
1851  IPGSPLQFYVDYVNCGHITAYGPGLTHGVVNKPATFTVNTKDAGEGGLSL  1900
1901  AIEGPSKAEISCTDNQDGTCSVSYLPVLPGDYSILVKYNDQHIPGSPFTA  1950
1951  RVTGDDSMRMSHLKVGSAADIPINISETDLSLLTATVVPPSGREEPCLLK  2000
2001  RLRNGHVGISFVPKETGEHLVHVKKNGQHVASSPIPVVISQSEIGDASRV  2050
2051  RVSGQGLHEGHTFEPAEFIIDTRDAGYGGLSLSIEGPSKVDINTEDLEDG  2100
2101  TCRVTYCPTEPGNYIINIKFADQHVPGSPFSVKVTGEGRVKESITRRRRA  2150
2151  PSVANIGSHCDLSLKIPEISIQDMTAQVTSPSGKTHEAEIVEGENHTYCI  2200
2201  RFVPAEMGMHTVSVKYKGQHVPGSPFQFTVGPLGEGGAHKVRAGGPGLER  2250
2251  AEVGVPAEFGIWTREAGAGGLAIAVEGPSKAEISFEDRKDGSCGVAYVVQ  2300
2301  EPGDYEVSVKFNEEHIPDSPFVVPVASPSGDARRLTVSSLQESGLKVNQP  2350
2351  ASFAVSLNGAKGAIDAKVHSPSGALEECYVTEIDQDKYAVRFIPRENGIY  2400
2401  LIDVKFNGTHIPGSPFKIRVGEPGHGGDPGLVSAYGAGLEGGVTGSPAEF  2450
2451  IVNTSNAGAGALSVTIDGPSKVKMDCQECPEGYRVTYTPMAPGSYLISIK  2500
2501  YGGPYHIGGSPFKAKVTGPRLVSNHSLHETSSVFVDSLTKVATVPQHATS  2550
2551  GPGPADVSKVVAKGLGLSKAYVGQKSNFTVDCSKAGNNMLLVGVHGPRTP  2600
2601  CEEILVKHMGSRLYSVSYLLKDKGEYTLVVKWGDEHIPGSPYRIMVP     2647

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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