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

NucPred

Fetching Q9YH85 from www.uniprot.org...

The NucPred score for your sequence is 0.39 (see score help below)

   1  MNTRSLLSAWAALLVVTVRHRAHAMASLYPFWPNDTKTPKVDDGSSSEIK    50
  51  LSVPFIFFRSPYRTVYVNNNGVISFNSLVSQFTPEAFPLADGRAFVAPFC   100
 101  GDVANGIRGEIYYRESTNPELLGESSKDIRKYFKDMASFSASWVFIVTWE   150
 151  EVQFYGGSSTTPVNTFQAVLITDGVSSFAIFNYQEISWTTGTASGGDPLT   200
 201  GLGGVMAQAGFNGGNISNFFSIPGSRTPDIVNIEQTTNVNIPGRWAFKID   250
 251  GREIDPANLSLRGQFLHQGEIFWENSNCSTKCRCLDFNNEIFCQEMLAPF   300
 301  ETVEPKIKFFQCVPVETACVVFGDPHYHTFDGFLFHFQGSCSYLLARQCW   350
 351  PGSQLPYFNVEAKNERGGSSVSWAEDIFVEVYRHKIVLPKGGFGKAKVDD   400
 401  LVVSLGAIKVYQSGLSTALETDFGLLVTYDGQHYASVSVPGTYINGTCGL   450
 451  CGNYNKDPEDDALRSDGRLASSVPELGESWRVPHPERKCSPGCVENCSVC   500
 501  DASRILYSPICGFSQECGAWSVLVATAFVHSCVYDLCSARRTHRLCQAIQ   550
 551  VTLRCCQGLGIRWENGVPDGMRGGLAVPGHSHYSGCASGCPATCSDLTAP   600
 601  LRCTAPCPEGCECDDGHVLSARPLHSLCRSGCVVDGRSRCREVFWATADC   650
 651  TAECQCEDGGEAKCFNTSCPEGEVCTIEDGYRGCYPKREGLCSVGQNQVL   700
 701  RTFDGVTFPYPLEHSYTLLKTCMEKPDFIEVDISQKKPDTLPMAGRVVRI   750
 751  QVVGQEVKVGGASLSEVKVNGYDVDLPYFHPSGHLEIYRTDNGTVTESEG   800
 801  LLSIGYYDSGLLEIRLSTAYFNCTGGLCGFFNGNDSDEFCTPKAKCTDNL   850
 851  ELFLESWTTFDEICNGECGDLLKACNNDSELLKTYRSRSNCAIINDPTNS   900
 901  SFLECHNVSIVSAYYRTCLFRLCQSGGNQSELCSAVARYASACKNSEVDV   950
 951  GQWRSHSFCPLACPENSHFEECMSCVETCETLATGCCMDTCTEGCQCDEG  1000
1001  FALRSPCVPRGECGCNFEGHELATNQTFWMDISCHLLCYCNGSDNSVYCE  1050
1051  NVLQDDEYYCHVRTDASCIVSGYGHYLTFDGFSFDFQSSCALVLCTTIHG  1100
1101  ACERSDTFPTFTVTVTAKNEDRDTSLACVVKQVEVEVFNYYIVIHRAYKY  1150
1151  TVMINNERLYLPLKLGQGKVNIFAFGFHIVVETDFGLKVVYDWKTFLSVT  1200
1201  IPRSFQNLTYGLCGRYNGNPDDDLVAAGGTPRFGVTDFVQSWAKRDTFCR  1250
1251  VGSGDRCPACGKVEGFWKPQQLCSLIPSQSGVFAKCHSKINPSYFYKNCL  1300
1301  FDTVVDGGAMARRVADWLQNYASTCQTQGIAIIGWRNFTSCSVSCPPNSH  1350
1351  YESCVSLCQPRCAAIRLKSDCGHYCVEGCQCDPGYVLNGKSCILPQNCGC  1400
1401  YSDGKYYEPKQLFWNGDCTRRCARFRRNLIQCDPRHCKSDEECASRNGVR  1450
1451  GCFSTRSSFCLAAGGGVFRTFDGAFLRFPANCAFVLSTICQRLADFSFQL  1500
1501  IINFDKWSSPNLTIISVYIYINEEQILISDRSTVKVNGSLVSIPFVTGLS  1550
1551  TKIYSQEGFLVIDSGPDIHIRYNGFNVIKITIGDRLQNKVCGLCGNFNGD  1600
1601  PADDYATLRGKPVVSSVVLAQSWKTNGMQKSCNELQYSQYAASCDNVQIQ  1650
1651  KLQSDSYCLKLTDMKGFFQPCYGLLDPLPFYESCFLDGCYNRKQVQLCGS  1700
1701  LAAYGEACRTFGILGTEWIEKENCSGVVEDPCAGADCPNRTCELDDGGEL  1750
1751  CGCIEPPPYGNTTHDIIDAEVTCKAAQMEVSISKCKLFQLGFEREGVRVN  1800
1801  DRHCPGIEGEDFISFQINNTKGNCGNLVQSNSTHIVYKNTVWIESANNTG  1850
1851  NIITRDRTINVEVFCAYELDIKISLDSVVRPMLSVINLTVPTQEGSFTTK  1900
1901  MALYKNSSYKHPYRQGEVVLTTRDVLYVGVFVVGADSNHLILMLNKCYAT  1950
1951  PSRDSNDKLRYFIIEGGCQNLKDNTIGIEENGVSLTCRFHVTVFKFIGDY  2000
2001  DEVHLHCAVSLCDSEKYSCKINCPQHRRSASAFAQEAHEQILSVGPIRRK  2050
2051  RSDWCEDNGGCEQICTSQADGPLCSCVTGTLQGDGKSCMASSSSADIRAQ  2100
2101  ASLLVAAQLWLWAALHDPTS                                2120

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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