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

NucPred

Fetching Q13576 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MPHEELPSLQRPRYGSIVDDERLSAEEMDERRRQNIAYEYLCHLEEAKRW    50
  51  MEVCLVEELPPTTELEEGLRNGVYLAKLAKFFAPKMVSEKKIYDVEQTRY   100
 101  KKSGLHFRHTDNTVQWLRAMESIGLPKIFYPETTDVYDRKNIPRMIYCIH   150
 151  ALSLYLFKLGIAPQIQDLLGKVDFTEEEISNMRKELEKYGIQMPSFSKIG   200
 201  GILANELSVDEAALHAAVIAINEAVEKGIAEQTVVTLRNPNAVLTLVDDN   250
 251  LAPEYQKELWDAKKKKEENARLKNSCISEEERDAYEELLTQAEIQGNINK   300
 301  VNRQAAVDHINAVIPEGDPENTLLALKKPEAQLPAVYPFAAAMYQNELFN   350
 351  LQKQNTMNYLAHEELLIAVEMLSAVALLNQALESNDLVSVQNQLRSPAIG   400
 401  LNNLDKAYVERYANTLLSVKLEVLSQGQDNLSWNEIQNCIDMVNAQIQEE   450
 451  NDRVVAVGYINEAIDEGNPLRTLETLLLPTANISDVDPAHAQHYQDVLYH   500
 501  AKSQKLGDSESVSKVLWLDEIQQAVDDANVDKDRAKQWVTLVVDVNQCLE   550
 551  GKKSSDILSVLKSSTSNANDIIPECADKYYDALVKAKELKSERVSSDGSW   600
 601  LKLNLHKKYDYYYNTDSKESSWVTPESCLYKESWLTGKEIEDIIEEVTVG   650
 651  YIRENIWSASEELLLRFQATSSGPILREEFEARKSFLHEQEENVVKIQAF   700
 701  WKGYKQRKEYMHRRQTFIDNTDSIVKIQSWFRMATARKSYLSRLQYFRDH   750
 751  NNEIVKIQSLLRANKARDDYKTLVGSENPPLTVIRKFVYLLDQSDLDFQE   800
 801  ELEVARLREEVVTKIRANQQLEKDLNLMDIKIGLLVKNRITLEDVISHSK   850
 851  KLNKKKGGEMEILNNTDNQGIKSLSKERRKTLETYQQLFYLLQTNPLYLA   900
 901  KLIFQMPQNKSTKFMDTVIFTLYNYASNQREEYLLLKLFKTALEEEIKSK   950
 951  VDQVQDIVTGNPTVIKMVVSFNRGARGQNTLRQLLAPVVKEIIDDKSLII  1000
1001  NTNPVEVYKAWVNQLETQTGEASKLPYDVTTEQALTYPEVKNKLEASIEN  1050
1051  LRRVTDKVLNSIISSLDLLPYGLRYIAKVLKNSIHEKFPDATEDELLKIV  1100
1101  GNLLYYRYMNPAIVAPDGFDIIDMTAGGQINSDQRRNLGSVAKVLQHAAS  1150
1151  NKLFEGENEHLSSMNNYLSETYQEFRKYFKEACNVPEPEEKFNMDKYTDL  1200
1201  VTVSKPVIYISIEEIISTHSLLLEHQDAIAPEKNDLLSELLGSLGEVPTV  1250
1251  ESFLGEGAVDPNDPNKANTLSQLSKTEISLVLTSKYDIEDGEAIDSRSLM  1300
1301  IKTKKLIIDVIRNQPGNTLTEILETPATAQQEVDHATDMVSRAMIDSRTP  1350
1351  EEMKHSQSMIEDAQLPLEQKKRKIQRNLRTLEQTGHVSSENKYQDILNEI  1400
1401  AKDIRNQRIYRKLRKAELAKLQQTLNALNKKAAFYEEQINYYDTYIKTCL  1450
1451  DNLKRKNTRRSIKLDGKGEPKGAKRAKPVKYTAAKLHEKGVLLDIDDLQT  1500
1501  NQFKNVTFDIIATEDVGIFDVRSKFLGVEMEKVQLNIQDLLQMQYEGVAV  1550
1551  MKMFDKVKVNVNLLIYLLNKKFYGK                           1575

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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