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

NucPred

Fetching Q91ZV8 from www.uniprot.org...

The NucPred score for your sequence is 0.54 (see score help below)

   1  MGAGGRRMPVPPARLLLLPLLPCLLLLAPGTRGAPGCPVPIRGCKCSGER    50
  51  PKGLSGGAHNPARRRVVCGGGDLPEPPDPGLLPNGTITLLLSNNKITGLR   100
 101  NGSFLGLSLLEKLDLRSNVISTVQPGAFLGLGELKRLDLSNNRIGCLTSE   150
 151  TFQGLPRLLRLNISGNIYSSLQPGVFDELPALKIVDFGTEFLTCDCRLRW   200
 201  LLPWARNHSLQLSERTLCAYPSALHAHALSSLQESQLRCEGALELHTHYL   250
 251  IPSLRQVVFQGDRLPFQCSASYLGNDTRIHWYHNGAPMESDEQAGIVLAE   300
 301  NLIHDCTFITSELTLSHIGVWASGEWECSVSTVQGNTSKKVEIVVLETSA   350
 351  SYCPAERVTNNRGDFRWPRTLAGITAYQSCLQYPFTSVPLSGGAPGTRAS   400
 401  RRCDRAGRWEPGDYSHCLYTNDITRVLYTFVLMPINASNALTLAHQLRVY   450
 451  TAEAASFSDMMDVVYVAQMIQKFLGYVDQIKELVEVMVDMASNLMLVDEH   500
 501  LLWLAQREDKACSGIVGALERIGGAALSPHAQHISVNSRNVALEAYLIKP   550
 551  HSYVGLTCTAFQRREVGVSGAQPSSVGQDAPVEPEPLADQQLRFRCTTGR   600
 601  PNISLSSFHIKNSVALASIQLPPSLFSTLPAALAPPVPPDCTLQLLVFRN   650
 651  GRLFRSHGNNTSRPGAAGPGKRRGVATPVIFAGTSGCGVGNLTEPVAVSL   700
 701  RHWAEGADPMAAWWNQDGPGGWSSEGCRLRYSQPNVSSLYCQHLGNVAVL   750
 751  MELNAFPREAGGSGAGLHPVVYPCTALLLLCLFSTIITYILNHSSIHVSR   800
 801  KGWHMLLNLCFHMAMTSAVFVGGVTLTNYQMVCQAVGITLHYSSLSSLLW   850
 851  MGVKARVLHKELSWRAPPLEEGEAAPPGPRPMLRFYLIAGGIPLIICGIT   900
 901  AAVNIHNYRDHSPYCWLVWRPSLGAFYIPVALILPITWIYFLCAGLHLRS   950
 951  HVAQNPKQGNRISLEPGEELRGSTRLRSSGVLLNDSGSLLATVSAGVGTP  1000
1001  APPEDGDGVYSPGVQLGALMTTHFLYLAMWACGALAVSQRWLPRVVCSCL  1050
1051  YGVAASALGLFVFTHHCARRRDVRASWRACCPPASPSASHVPARALPTAT  1100
1101  EDGSPVLGEGPASLKSSPSGSSGRAPPPPCKLTNLQVAQSQVCEASVAAR  1150
1151  GDGEPEPTGSRGSLAPRHHNNLHHGRRVHKSRAKGHRAGETGGKSRLKAL  1200
1201  RAGTSPGAPELLSSESGSLHNSPSDSYPGSSRNSPGDGLPLEGEPMLTPS  1250
1251  EGSDTSAAPIAETGRPGQRRSASRDNLKGSGSALERESKRRSYPLNTTSL  1300
1301  NGAPKGGKYEDASVTGAEAIAGGSMKTGLWKSETTV                1336

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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