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

NucPred

Fetching Q14315 from www.uniprot.org...

The NucPred score for your sequence is 0.27 (see score help below)

   1  MMNNSGYSDAGLGLGDETDEMPSTEKDLAEDAPWKKIQQNTFTRWCNEHL    50
  51  KCVGKRLTDLQRDLSDGLRLIALLEVLSQKRMYRKFHPRPNFRQMKLENV   100
 101  SVALEFLEREHIKLVSIDSKAIVDGNLKLILGLIWTLILHYSISMPMWED   150
 151  EDDEDARKQTPKQRLLGWIQNKVPQLPITNFNRDWQDGKALGALVDNCAP   200
 201  GLCPDWEAWDPNQPVENAREAMQQADDWLGVPQVIAPEEIVDPNVDEHSV   250
 251  MTYLSQFPKAKLKPGAPVRSKQLNPKKAIAYGPGIEPQGNTVLQPAHFTV   300
 301  QTVDAGVGEVLVYIEDPEGHTEEAKVVPNNDKDRTYAVSYVPKVAGLHKV   350
 351  TVLFAGQNIERSPFEVNVGMALGDANKVSARGPGLEPVGNVANKPTYFDI   400
 401  YTAGAGTGDVAVVIVDPQGRRDTVEVALEDKGDSTFRCTYRPAMEGPHTV   450
 451  HVAFAGAPITRSPFPVHVSEACNPNACRASGRGLQPKGVRVKEVADFKVF   500
 501  TKGAGSGELKVTVKGPKGTEEPVKVREAGDGVFECEYYPVVPGKYVVTIT   550
 551  WGGYAIPRSPFEVQVSPEAGVQKVRAWGPGLETGQVGKSADFVVEAIGTE   600
 601  VGTLGFSIEGPSQAKIECDDKGDGSCDVRYWPTEPGEYAVHVICDDEDIR   650
 651  DSPFIAHILPAPPDCFPDKVKAFGPGLEPTGCIVDKPAEFTIDARAAGKG   700
 701  DLKLYAQDADGCPIDIKVIPNGDGTFRCSYVPTKPIKHTIIISWGGVNVP   750
 751  KSPFRVNVGEGSHPERVKVYGPGVEKTGLKANEPTYFTVDCSEAGQGDVS   800
 801  IGIKCAPGVVGPAEADIDFDIIKNDNDTFTVKYTPPGAGRYTIMVLFANQ   850
 851  EIPASPFHIKVDPSHDASKVKAEGPGLNRTGVEVGKPTHFTVLTKGAGKA   900
 901  KLDVQFAGTAKGEVVRDFEIIDNHDYSYTVKYTAVQQGNMAVTVTYGGDP   950
 951  VPKSPFVVNVAPPLDLSKIKVQGLNSKVAVGQEQAFSVNTRGAGGQGQLD  1000
1001  VRMTSPSRRPIPCKLEPGGGAEAQAVRYMPPEEGPYKVDITYDGHPVPGS  1050
1051  PFAVEGVLPPDPSKVCAYGPGLKGGLVGTPAPFSIDTKGAGTGGLGLTVE  1100
1101  GPCEAKIECQDNGDGSCAVSYLPTEPGEYTINILFAEAHIPGSPFKATIR  1150
1151  PVFDPSKVRASGPGLERGKVGEAATFTVDCSEAGEAELTIEILSDAGVKA  1200
1201  EVLIHNNADGTYHITYSPAFPGTYTITIKYGGHPVPKFPTRVHVQPAVDT  1250
1251  SGVKVSGPGVEPHGVLREVTTEFTVDARSLTATGGNHVTARVLNPSGAKT  1300
1301  DTYVTDNGDGTYRVQYTAYEEGVHLVEVLYDEVAVPKSPFRVGVTEGCDP  1350
1351  TRVRAFGPGLEGGLVNKANRFTVETRGAGTGGLGLAIEGPSEAKMSCKDN  1400
1401  KDGSCTVEYIPFTPGDYDVNITFGGRPIPGSPFRVPVKDVVDPGKVKCSG  1450
1451  PGLGAGVRARVPQTFTVDCSQAGRAPLQVAVLGPTGVAEPVEVRDNGDGT  1500
1501  HTVHYTPATDGPYTVAVKYADQEVPRSPFKIKVLPAHDASKVRASGPGLN  1550
1551  ASGIPASLPVEFTIDARDAGEGLLTVQILDPEGKPKKANIRDNGDGTYTV  1600
1601  SYLPDMSGRYTITIKYGGDEIPYSPFRIHALPTGDASKCLVTVSIGGHGL  1650
1651  GACLGPRIQIGQETVITVDAKAAGEGKVTCTVSTPDGAELDVDVVENHDG  1700
1701  TFDIYYTAPEPGKYVITIRFGGEHIPNSPFHVLACDPLPHEEEPSEVPQL  1750
1751  RQPYAPPRPGARPTHWATEEPVVPVEPMESMLRPFNLVIPFAVQKGELTG  1800
1801  EVRMPSGKTARPNITDNKDGTITVRYAPTEKGLHQMGIKYDGNHIPGSPL  1850
1851  QFYVDAINSRHVSAYGPGLSHGMVNKPATFTIVTKDAGEGGLSLAVEGPS  1900
1901  KAEITCKDNKDGTCTVSYLPTAPGDYSIIVRFDDKHIPGSPFTAKITGDD  1950
1951  SMRTSQLNVGTSTDVSLKITESDLSQLTASIRAPSGNEEPCLLKRLPNRH  2000
2001  IGISFTPKEVGEHVVSVRKSGKHVTNSPFKILVGPSEIGDASKVRVWGKG  2050
2051  LSEGHTFQVAEFIVDTRNAGYGGLGLSIEGPSKVDINCEDMEDGTCKVTY  2100
2101  CPTEPGTYIINIKFADKHVPGSPFTVKVTGEGRMKESITRRRQAPSIATI  2150
2151  GSTCDLNLKIPGNWFQMVSAQERLTRTFTRSSHTYTRTERTEISKTRGGE  2200
2201  TKREVRVEESTQVGGDPFPAVFGDFLGRERLGSFGSITRQQEGEASSQDM  2250
2251  TAQVTSPSGKVEAAEIVEGEDSAYSVRFVPQEMGPHTVAVKYRGQHVPGS  2300
2301  PFQFTVGPLGEGGAHKVRAGGTGLERGVAGVPAEFSIWTREAGAGGLSIA  2350
2351  VEGPSKAEIAFEDRKDGSCGVSYVVQEPGDYEVSIKFNDEHIPDSPFVVP  2400
2401  VASLSDDARRLTVTSLQETGLKVNQPASFAVQLNGARGVIDARVHTPSGA  2450
2451  VEECYVSELDSDKHTIRFIPHENGVHSIDVKFNGAHIPGSPFKIRVGEQS  2500
2501  QAGDPGLVSAYGPGLEGGTTGVSSEFIVNTLNAGSGALSVTIDGPSKVQL  2550
2551  DCRECPEGHVVTYTPMAPGNYLIAIKYGGPQHIVGSPFKAKVTGPRLSGG  2600
2601  HSLHETSTVLVETVTKSSSSRGSSYSSIPKFSSDASKVVTRGPGLSQAFV  2650
2651  GQKNSFTVDCSKAGTNMMMVGVHGPKTPCEEVYVKHMGNRVYNVTYTVKE  2700
2701  KGDYILIVKWGDESVPGSPFKVKVP                           2725

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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