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

NucPred

Fetching P13002 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MSTSTATTSVITSNELSLSGHAHGHGHAHQLHQHTHSRLGVGVGVGILSD    50
  51  ASLSPIQQGSGGHSGGGNTNSSPLAPNGVPLLTTMHRSPDSPQPELATMT   100
 101  NVNVLDLHTDNSKLYDKEAVFIYETPKVVMPADGGGGNNSDEGHAIDARI   150
 151  AAQMGNQAQQQQQQQQQTEHQPLAKIEFDENQIIRVVGPNGEQQQIISRE   200
 201  IINGEHHILSRNEAGEHILTRIVSDPSKLMPNDNAVATAMYNQAQKMNND   250
 251  HGQAVYQTSPLPLDASVLHYSGGNDSNVIKTEADIYEDHKKHAAAAAAAA   300
 301  GGGSIIYTTSDPNGVNVKQLPHLTVPQKLDPDLYQADKHIDLIYNDGSKT   350
 351  VIYSTTDQKSLEIYSGGDIGSLVSDGQVVVQAGLPYATTTGAGGQPVYIV   400
 401  ADGALPAGVEEHLQSGKLNGQTTPIDVSGLSQNEIQGFLLGSHPSSSATV   450
 451  STTGVVSTTTISHHQQQQQQQQQQQQQQQQQHQQQQQHPGDIVSAAGVGS   500
 501  TGSIVSSAAQQQQQQQLISIKREPEDLRKDPKNGNIAGAATANGPGSVIT   550
 551  QKILHVDAPTASEADRPSTPSSSINSTENTESDSQSVSGSESGSPGARTT   600
 601  ATLEMYATTGGTQIYLQTSHPSTASGAGGGAGPAGAAGGGGVSMQAQSPS   650
 651  PGPYITANDYGMYTASRLPPGPPPTSTTTFIAEPSYYREYFAPDGQGGYV   700
 701  PASTRSLYGDVDVSVSQPGGVVTYEGRFAGSVPPPATTTVLTSVHHHQQQ   750
 751  QQQQQQHQQQQQQQQHHQQQQHHSQDGKSNGGATPLYAKAITAAGLTVDL   800
 801  PSPDSGIGTDAITPRDQTNIQQSFDYTELCQPGTLIDANGSIPVSVNSIQ   850
 851  QRTAVHGSQNSPTTSLVDTSTNGSTRSRPWHDFGRQNDADKIQIPKIFTN   900
 901  VGFRYHLESPISSSQRREDDRITYINKGQFYGITLEYVHDAEKPIKNTTV   950
 951  KSVIMLMFREEKSPEDEIKAWQFWHSRQHSVKQRILDADTKNSVGLVGCI  1000
1001  EEVSHNAIAVYWNPLESSAKINIAVQCLSTDFSSQKGVKGLPLHVQIDTF  1050
1051  EDPRDTAVFHRGYCQIKVFCDKGAERKTRDEERRAAKRKMTATGRKKLDE  1100
1101  LYHPVTDRSEFYGMQDFAKPPVLFSPAEDMEKVGQLGIGAATGMTFNPLS  1150
1151  NGNSNSNSHSSLQSFYGHETDSPDLKGASPFLLHGQKVATPTLKFHNHFP  1200
1201  PDMQTDKKDHILDQNMLTSTPLTDFGPPMKRGRMTPPTSERVMLYVRQEN  1250
1251  EEVYTPLHVVPPTTIGLLNAIENKYKISTTSINNIYRTNKKGITAKIDDD  1300
1301  MISFYCNEDIFLLEVQQIEDDLYDVTLTELPNQ                   1333

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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