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

NucPred

Fetching Q8CGM1 from www.uniprot.org...

The NucPred score for your sequence is 0.72 (see score help below)

   1  MTPACPLLLSVILSLRLATAFDPAPSACSALASGVLYGAFSLQDLFPTIA    50
  51  SGCSWTLENPDPTKYSLYLRFNRQEQVCTHFAPRLLPLDHYLVNFTCLRP   100
 101  GPEEATARAESEVGRPEEEEEEAAAAASGLELCGGSGPFTFLHFDKNFVQ   150
 151  LCLSAEPSEAPRLLAPAALAFRFVEVLLINNNNSSQFTCGVLCRWSEECG   200
 201  RAAGRACGFAQPGCSCPGEAGANPATTTSPGPPVAHTLSNALVPGGPAPP   250
 251  AEADLHSGSSNDLFTTEMRYGEEPEEEPKVKTQWPRSADEPGLYMAQTGD   300
 301  PAAEEWSPWSVCSLTCGQGLQVRTRSCVSSPYGTLCSGPLRETRPCNNSA   350
 351  TCPVHGVWEEWGSWSLCSRSCGRGSRSRMRTCVPPQHGGKACEGPELQTK   400
 401  LCSMAACPVEGQWLEWGPWGPCSSSCANGTQQRSRKCSVAGPAWATCAGA   450
 451  LTDTRECSNLDCPATDGKWGPWNAWSLCSKTCDTGWQRRFRMCQASGTQG   500
 501  YPCEGTGEEVKPCSEKRCPAFHEMCRDEYVMLMTWKRAAAGEIIYNKCPP   550
 551  NASGSASRRCLLSAQGVAYWGLPSFARCISHEYRYLYLSLREHLAKGQRM   600
 601  LAGEGMSQVVRSLQELLARRTYYSGDLLFSVDILRNVTDTFKRATYVPSA   650
 651  DDVQRFFQVVSFMVDSENKDKWDDAQQVSPGSVHLLRVVEDFIHLVGDAL   700
 701  KAFQSSLIVTDNLVISIQREPISAVSSDITFPMRGRRGMKDWVRHSEDRL   750
 751  FLPKEVLSLSSPGKPATPGAATAGSPGRGRGPGTVPPGPGHAHQRLLPAD   800
 801  PEESSSYFVIGAVLYRTLGLILPPPRPPLAVTSRVMTVTVRPPTQPPAEP   850
 851  LITVELSYIINGTTDPHCASWDYSRADTNSGDWNTESCQTLETQAAHTRC   900
 901  QCQHLSTFAVLAQPPKDLTLELAGAPSVPLVIGCAVSCMALLTLLAIYAA   950
 951  FWRFIKSERSIILLNFCLSILASNILILVGQSRVLSKGVCTMTAAFLHFF  1000
1001  FLSSFCWVLTEAWQSYLAVIGRMRTRLVRKRFLCLGWGLPALVVAVSVGF  1050
1051  TRTKGYGTSSYCWLSLEGGLLYAFVGPAAVIVLVNMLIGIIVFNKLMARD  1100
1101  GVSDKSKKQRAGSERCPWASLLLPCSACGAVPSPLLSSASARNAMASLWS  1150
1151  SCVVLPLLALTWMSAVLAMTDRRSVLFQALFAVFNSAQGFVITAVHCFLR  1200
1201  REVQDVVKCQMGVCRADESEDSPDSCKNGQLQILSDFEKDVDLACQTVLF  1250
1251  KEVNTCNPSTITGTLSRLSLDEDEEPKSCLVGPEGGLSFSPLPGNILVPM  1300
1301  AASPGLGEPPPPQETNPVYMCGEGGLRQLDLTWIRQSEPGSEGDYMVLPR  1350
1351  RTLSLQPGGGGTAGEEAPRARPEGTPRRAAKTVAHTEGYPSFLSVEHSGL  1400
1401  GLGPAYGSLQNPYGMTFQPPPPTPSARQVPEPGERSRTMPRTVPGSTMKL  1450
1451  GSLERKKLRYSDLDFEKVMHTRKRHSELYHELNQKFHTFDRYRSQSSAKE  1500
1501  KPSPPGGRPGLSQHRRHQSWSTFKSMTLGSLPPKPRERLALHRTAAWEPT  1550
1551  EPPDGDFQTEV                                         1561

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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