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

NucPred

Fetching Q8BWT5 from www.uniprot.org...

The NucPred score for your sequence is 0.37 (see score help below)

   1  MADRGCPLEAAPLPAEVLESLAELELELSEGDITQKGYEKKRAKLLARYI    50
  51  PLIQDVHTEAVQAALAKYKERKMPMPSKRRSALVHSSVETYTPPDTSSAS   100
 101  EDEGSLRRPGRLTSTLLQSHSGIEPWLDRVIQGSSTSSSASSTSSHPGGR   150
 151  PAAAPSASTALAGLTAHAHIDLHSAPPDVTTGLVEHSSYERPQMASVRGI   200
 201  PRGHGRNVLETADGVPVNSRVSSKIQQLLNTLKRPKRPPLKEFFVDDFEE   250
 251  LLEVQQPDPNQPKPEGDQMAVLKGEPLSVGTNGPLSLLAALQLWGTTQPK   300
 301  APCLTALDTAGKATCTLTYGKLWSRSLKLAYTLLNKLTSKNEPLLNPGDR   350
 351  VALVFPNSDPVMFMVAFYGCLLAELVPVPIEVPLTRKDAGSQQVGFLLGS   400
 401  CGVTLALTTDACQKGLPKAPTGEVATFKGWPPLAWLVIDGKHLTRPPKDW   450
 451  YPLAQDTGSRTAYIEYKTSKEGSTVGVTVSHSSLLAQCQALTQACGYTEA   500
 501  ETLTNVLDFKRDAGLWHGVLTSVMNRMHVITIPYALMKVNPLSWIQKVCS   550
 551  YKARAALVKSRDMHWSLLAQRGQRDVCLSSLRMLIVADGANPWSISSCDA   600
 601  FLNVFQSRGLRPEVICPCASSPEALTVAIRRPPDLGGPPPRKAVLSMNGL   650
 651  SYGVIRVDTEEKLSVLTVQDVGQVMPGASVCVVKVDGAPYLCKTDEIGEI   700
 701  CVNSVATGTAYYGLLGITKNTFETVPVTADGVPVSDRPFTRTGLLGFIGP   750
 751  DNLVFVVGKLDGLMVVGVRRHNADDIVATALAVEPMKFVYRGRIAVFSVT   800
 801  VLHDDRIVLVAEQRPDASEEDSFQWMSRVLQAIDSIHQVGVYCLALVPAN   850
 851  TLPKAPLGGIHISETKQRFLEGTLHPCNVLMCPHTCVTNLPKPRQKQPEV   900
 901  GPASMIVGNLVAGKRIAQASGRELAHLEDSDQARKFLFLADVLQWRAHTT   950
 951  PDHPLFLLLNAKGTVTSTATCIQLHKRAERVAAALMEKGRLDAGDHVALV  1000
1001  YPPGVDLIAAFYGCLYCGCVPVTVRPPHPQNLGTTLPTVKMIVEVSKSAC  1050
1051  VLSTQAITRLLKSKEAAAAVDVRTWPTILDTDDIPKKKVASIFRPPSPDV  1100
1101  LAYLDFSVSTTGILAGVKMSHAATSALCRSIKLQCELYPSRQIAICLDPY  1150
1151  CGLGFALWCLCSVYSGHQSVLVPPLELESNVSLWLSAVSQYKARVTFCSY  1200
1201  SVMEMCTKGLGAQTGALRMKGVNLSCVRTCMVVAEERPRISLTQSFSKLF  1250
1251  KDLGLPARAVSTTFGCRVNVAICLQGTTGPDPTTVYVDMRALRHDRVRLV  1300
1301  ERGSPHSLPLMESGKILPGVKVIIAHTETKGPLGDSHLGEIWVSSPHNAT  1350
1351  GYYTVYGEETLHADHFSARLSFGDTQTIWARTGYLGFLRRTELTDASGER  1400
1401  HDALYVVGSLDETLELRGMRYHPIDIETSVIRAHRSIAECAVFTWTNLLV  1450
1451  VVVELDGLEQDALDLVALVTNVVLEEHYLVVGVVVIVDPGVIPINSRGEK  1500
1501  QRMHLRDGFLADQLDPIYVAYNM                             1523

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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