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

NucPred

Fetching Q03570 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MSSNVLPMYASTPSRAFAHSKLSSQLRAALADNSPAAPISPAPSGSALSL    50
  51  DESSGISDRDVHSSQEQTAHLSEVDVKSIHSSDSEDEPAQNPLPEVPANC   100
 101  GPPTIPLNVLLDFAIQHVYHEITVLAELMQRKTNDQGEQERKMSLVHFAH   150
 151  ATRSQFLKLVALVKWIRISKRMDVCYSIDYLLDLQSQYFIDTADRLVAMT   200
 201  RGDLELARLPEYHIAPAIDVLVLGTYNRMPSKIKEAFIPPAKITPREQKL   250
 251  VTSRLNQLIESRLSRLSSGIPPNIKEIHINNGLATLLVPGEFEIKITLLG   300
 301  ETEMTKWTLLNIKILVEDYELGMGLPLVHPLQLNQLHGVLQSRMNVSLNP   350
 351  IKEAFSFLHSFCVSLQLDVLFCQTSRLAAGRLRDNITIEKYDPKERVLVV   400
 401  GYWVKRSKSRRLTVGQVKCDAQYRVQIYEDPNDKLGGLKVRHFPHAPQLG   450
 451  RLDSGAGMLSIDRLLSETYVVRCKERLMRLRRILEAAEPRLEVKMTGISA   500
 501  PSLSLALLPDTSSKDEMMTVSVNSFCGKVLCNVHILSAEHEDVLAFGKAL   550
 551  YSSQCSAHTIQMYLRKLRVALVIERYRRSVKALPVREVQEAELLPFAKEC   600
 601  LGDAPAQRIILQFLRSEDYYLLVTFSPDEKAVVKTHIQLLEVVGDRAQFI   650
 651  QLEDDEMNGMHVKEAINQGTMRFSPSHKTSLQEECSREQRLAFAVATVED   700
 701  RITYMYLAAELMKKGIGVDVRKDSAHVPGGLALHITDVKNVVPFEASEFF   750
 751  ECCIRCCLRLDNRNRYTFQFEMCFENIPLVRDVPHGLPHRRDGEPKDRTS   800
 801  KDATWLQELNHINQSSPEKLVELIIHRLMRYLYMYKVVHQFSLAYEKHFK   850
 851  NYCNIEAYTFHKLVVSYGDNRDMLMILAFNVKSQAPGSSEDFFFLNFGQS   900
 901  MPHRQFNSTEIDWHQKPRWNPHSMMSQLMRDDLKETNDLVFTMHFLCETI   950
 951  RPLVAIGNFSRIRFQSQKSLSQLIGPDVHFPFRLKYHLYALDQTTLRLMQ  1000
1001  GNVILEIKLLEGCKIAVRDVSRYRPRCAGLFQLFSNIDSETTAIMNDEIA  1050
1051  IPQSDNPQTAGPTMWTPEQFMDSLDERPEEIDPRMAITSQPILMSHDTII  1100
1101  KACDFKDTEGRITCPLDEYLCSISYLQRALLTLERMSPRATLNKNSSSNL  1150
1151  SCGFVTIIDAKPDFIRFRASQMNGDGVNATSMVHYKIYLCPVAMTLKIRI  1200
1201  EFEEGTNSAATADNLKTLTTYFEKVVFPCGDEYALQSYICLTRLTSFEAT  1250
1251  QSIANLMNVQMEHPPTSKCCVQLSLTYNNTSTKKLAPATKVDQPLQNIIF  1300
1301  NVIVSQSRTSESFSVLRFIYRIKENFVVVPSANEKNKQMADEVNAETKTS  1350
1351  GGNPIWNLVRLVMDRFNSGDWNPGNRDEPIISSVAPPTYVNPGSVAGPSS  1400
1401  VAAPGSVSIQQPGSVLQPGSMMGPQSVNALQYGMHRQPMGGPQSMQMNPS  1450
1451  SVGQPGSVGGPGSHQQHMMNPGSVGPGSVGGPGSVNPGSVGYPQWNPPSV  1500
1501  GQSYHHPLHHQQYPPQ                                    1516

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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