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

NucPred

Fetching Q5R7Y0 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MTPACPLLLSVILSLRLAAAFDPAPSACSALASGVLYGAFSLQDLFPTIA    50
  51  SGCSWTLENPDPTKYSLYLRFNRQEQVCAHFAPRLLPLDHYLVNFTCLRP   100
 101  SPEEAVTQAESEVGRPEEEEAEAAAGLELCSGAGPFTFLHFDKNFVQLCL   150
 151  SAEPSEAPRLLAPAALAFRFVEVLLINNNNSSQFTCGVLCRWSEECGRAA   200
 201  GRACGFAQPGCSCPGEAGAGSATTTSPGPPAAHTLSNALVPGGPAPPAEA   250
 251  DLHSGSSNDLFTTEMRYGEEPEEEPKVKTQWPRSADEPGLYMAQTVHGVW   300
 301  EEWGSWSLCSRSCGRGSRSRMRTCVPPQHGGKACEGPELQTKLCSMAACP   350
 351  VEGQWLEWGPWGPCSTSCANGTQQRSRKCSVAGPAWATCTGALTDTRECS   400
 401  NLECPATDSKWGPWNAWSLCSKTCDTGWQRRFRMCQATGTQGYPCEGTGE   450
 451  EVKPCSEKRCPAFHEMCRDEYVMLMTWKKAAAGEIIYNKCPPNASGSASR   500
 501  RCLLSAQGVAYWGLPSFARCISHEYRYLYLSLREHLAKGQRMLAGEGMSQ   550
 551  VVRSLQELLARRTYYSGDLLFSVDILRNVTDTFKRATYVPSADDVQRFFQ   600
 601  VVSFMVDAENKEKWDDAQQVSPGSVHLLRVVEDFIHLVGDALKAFQSSLI   650
 651  VTDNLVISIQREPVSAVSSDITFPMRGRRGMKDWVRHSEDRLFLPKEVLS   700
 701  LSSPGKPATSGAAGSPGRGRGPGTVPPGPGHSHQRLLPADPDESSYFVIG   750
 751  AVLYRTLGLILPPPRPPLAVASRVMTVTVRPPTQPPAEPLITVELSYIIN   800
 801  GTTDPHCASWDYSRADASSGDWDTENCQTLETQAAHTRCQCQHLSTFAVL   850
 851  AQPPKDLTLELAGSPSVPLVIGCAVSCMALLTLLAIYAAFWRFVKSERSI   900
 901  ILLNFCLSILASNILILVGQSRVLSKGVCTMTAAFLHFFFLSSFCWVLTE   950
 951  AWQSYLAVIGRMRTRLVRKRFLCLGWGLPALVVAVSVGFTRTKGYGTSSY  1000
1001  CWLSLEGGLLYAFVGPAAVIVLVNMLIGIIVFNKLMARDGISDKSKKQRA  1050
1051  GASLWSSCVVLPLLALTWMSAVLAMTDRRSVLFQALFAVFNSAQGFVITA  1100
1101  VHCFLRREVQDVVKCQMGVCRADESEDSPDSCKNGQLQILSDFEKDVDLA  1150
1151  CQTVLFKEVNTCNPSTITGTLSRLSLDEDEEPKSCLVGPEGSLSFSPLPG  1200
1201  NILVPMAASPGLGEPPPPQEANPVYMCGEGGLRQLDLTWLRPTEPGSEGD  1250
1251  YMVLPRRTLSLQPGGGGGGGEDAPRARPEGTPRRAAKTVAHTEGYPSFLS  1300
1301  VDHSGLGLGPAYGSLQNPYGMTFQPPPPTPSARQVPEPGERSRTMPRTVP  1350
1351  GSTMKMGSLERKKLRYSDLDFEKVMHTRKRHSELYHELNQKFHTFDRYRS  1400
1401  QSTAKREKRWSVSSGGAAERSVCADKPSPGERPSLSQHRRHQSWSTFKSM  1450
1451  TLGSLPPKPRERLTLHRAAAWEPTEPPDGDFQTEV                 1485

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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