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

NucPred

Fetching Q28969 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MGNLKSVGQEPGPPCGLGLGLGLGLCGKQGPATPAPEPSRAPAPATPHAP    50
  51  EHSPAPNSPTLTRPPEGPKFPRVKNWEVGSITYDTLCAQSQQDGPCTPRR   100
 101  CLGSLVLPRKLQSRPSPGPPPAEQLLSQARDFINQYYSSIKRSGSQAHEE   150
 151  RLQEVEAEVATTGTYHLGESELVFGAKQAWRNAPRCVGRIQWGKLQVFDA   200
 201  RDCSSAQEMFTYICNHIKYATNRGNLRSAITVFPQRTPGRGDFRIWNSQL   250
 251  VRYAGYRQQDGSVRGDPANVEITELCIQHGWTPGNGRFDVLPLLLQAPDE   300
 301  PPELFALPPELVLEVPLEHPTLEWFAALGLRWYALPAVSNMLLEIGGLEF   350
 351  PAAPFSGWYMSTEIGTRNLCDPHRYNILEDVAVCMDLDTRTTSSLWKDKA   400
 401  AVEINLAVLHSYQLAKVTIVDHHAATASFMKHLENEQKARGGCPADWAWI   450
 451  VPPISGSLTPVFHQEMVNYVLSPAFRYQPDPWKGSAAKGTGIARKKTFKE   500
 501  VANAVKISASLMATVMPKRVKASILYASETVRAQSYAQQLGRLFRKAFDP   550
 551  RVLCMDEYDVVSLEHETLVLVVTSTFGNGDPPENGESFAAALMEMSGPYN   600
 601  GSPRPEQHRSYKIRFNSVSCSDPLVSSWRRKRKESSNTDSAGALGTLRFC   650
 651  VFGLGSRAYPHFCAFARAVDTRLEELGGERLLQLGQGDELCGQEEAFRGW   700
 701  AQAAFQASCETFCVGEDAKAAARDIFSPKRSWKRQRYRLSAQVEGLQLLP   750
 751  GLVHVHRRKMFQATVLSVENLQSSKSTRATILVRLDTEGQEGLQYQPGDH   800
 801  IGICPPNRTGLVEALLSRVEDPTPPTESVGVEQLEKGSPGGPPPSWVRDP   850
 851  RLPPYTLRQALTFFLDITSPPSPRLLRVLSTLAEEPSEQQELETLSQDPR   900
 901  RYEEWKWFRCPTLLEVLEQFPSVALPTPLLLTQLALLQPRYYSVSSAPST   950
 951  YPGEIHPTVAVLAYRTQDGLGPLHYGVCSTWLGQLKPGDPVPCFIRAAPS  1000
1001  FRLPPDPSLPCILVGPGTGIAPFRGFWQERLHDIESKGLQPAPMTLVFGC  1050
1051  RCSQLDHLYRDEVQDAQQRGVFGRVLTAFSREPDSPKTYVQDILRTELAA  1100
1101  EVHRVLCLERGHMFVCGDVTMATSVLQTVQRILATEGNMELDEAGDVIGV  1150
1151  LRDQQRYHEDIFGLTLRTQEVTSRIRTQSFSLQERHLRGAVPWTFDPPGP  1200
1201  DTPGP                                               1205

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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