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

NucPred

Fetching Q9LFH0 from www.uniprot.org...

The NucPred score for your sequence is 0.51 (see score help below)

   1  MAHMVGADDIESLRVELAEIGRSIRSSFRRHTSSFRSSSSIYEVENDGDV    50
  51  NDHDAEYALQWAEIERLPTVKRMRSTLLDDGDESMTEKGRRVVDVTKLGA   100
 101  VERHLMIEKLIKHIENDNLKLLKKIRRRIDRVGMELPTIEVRYESLKVVA   150
 151  ECEVVEGKALPTLWNTAKRVLSELVKLTGAKTHEAKINIINDVNGIIKPG   200
 201  RLTLLLGPPSCGKTTLLKALSGNLENNLKCSGEISYNGHRLDEFVPQKTS   250
 251  AYISQYDLHIAEMTVRETVDFSARCQGVGSRTDIMMEVSKREKEKGIIPD   300
 301  TEVDAYMKAISVEGLQRSLQTDYILKILGLDICAEILIGDVMRRGISGGQ   350
 351  KKRLTTAEMIVGPTKALFMDEITNGLDSSTAFQIVKSLQQFAHISSATVL   400
 401  VSLLQPAPESYDLFDDIMLMAKGRIVYHGPRGEVLNFFEDCGFRCPERKG   450
 451  VADFLQEVISKKDQAQYWWHEDLPYSFVSVEMLSKKFKDLSIGKKIEDTL   500
 501  SKPYDRSKSHKDALSFSVYSLPNWELFIACISREYLLMKRNYFVYIFKTA   550
 551  QLVMAAFITMTVFIRTRMGIDIIHGNSYMSALFFALIILLVDGFPELSMT   600
 601  AQRLAVFYKQKQLCFYPAWAYAIPATVLKVPLSFFESLVWTCLSYYVIGY   650
 651  TPEASRFFKQFILLFAVHFTSISMFRCLAAIFQTVVASITAGSFGILFTF   700
 701  VFAGFVIPPPSMPAWLKWGFWANPLSYGEIGLSVNEFLAPRWNQMQPNNF   750
 751  TLGRTILQTRGMDYNGYMYWVSLCALLGFTVLFNIIFTLALTFLKSPTSS   800
 801  RAMISQDKLSELQGTEKSTEDSSVRKKTTDSPVKTEEEDKMVLPFKPLTV   850
 851  TFQDLNYFVDMPVEMRDQGYDQKKLQLLSDITGAFRPGILTALMGVSGAG   900
 901  KTTLLDVLAGRKTSGYIEGDIRISGFPKVQETFARVSGYCEQTDIHSPNI   950
 951  TVEESVIYSAWLRLAPEIDATTKTKFVKQVLETIELDEIKDSLVGVTGVS  1000
1001  GLSTEQRKRLTIAVELVANPSIIFMDEPTTGLDARAAAIVMRAVKNVADT  1050
1051  GRTIVCTIHQPSIDIFEAFDELVLLKRGGRMIYTGPLGQHSRHIIEYFES  1100
1101  VPEIPKIKDNHNPATWMLDVSSQSVEIELGVDFAKIYHDSALYKRNSELV  1150
1151  KQLSQPDSGSSDIQFKRTFAQSWWGQFKSILWKMNLSYWRSPSYNLMRMM  1200
1201  HTLVSSLIFGALFWKQGQNLDTQQSMFTVFGAIYGLVLFLGINNCASALQ  1250
1251  YFETERNVMYRERFAGMYSATAYALGQVVTEIPYIFIQAAEFVIVTYPMI  1300
1301  GFYPSAYKVFWSLYSMFCSLLTFNYLAMFLVSITPNFMVAAILQSLFYVG  1350
1351  FNLFSGFLIPQTQVPGWWIWLYYLTPTSWTLNGFISSQYGDIHEEINVFG  1400
1401  QSTTVARFLKDYFGFHHDLLAVTAVVQIAFPIALASMFAFFVGKLNFQRR  1450

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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