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

NucPred

Fetching Q9R1S7 from www.uniprot.org...

The NucPred score for your sequence is 0.30 (see score help below)

   1  MNRGRSMATPGEQCAGLRVWNQTEQEPAAYHLLSLCFVRAASSWVPPMYL    50
  51  WVLGPIYLLYIHRHGRCYLRMSHLFKTKMVLGLALILLYTFNVAVPLWRI   100
 101  HQGVPQAPELLIHPTVWLTTMSFATFLIHMERRKGVRSSGVLFGYWLLCC   150
 151  ILPGINTVQQASAGNFRQEPLHHLATYLCLSLVVAELVLSCLVDQPPFFS   200
 201  EDSQPLNPCPEAEASFPSKAMFWWASGLLWRGYKKLLGPKDLWSLGRENS   250
 251  SEELVSQLEREWRRSCNGLPGHKGHSSVGAPETEAFLQPERSQRGPLLRA   300
 301  IWRVFRSTFLLGTLSLVISDAFRFAVPKLLSLFLEFMGDRNSSAWTGWLL   350
 351  AVLMFAAACLQTLFEQQHMYRAKVLQMRLRTAITGLVYRKVLVLSSGSRK   400
 401  SSAAGDVVNLVSVDIQRLAESIIYLNGLWLLFLWIFVCFVYLWQLLGPSA   450
 451  LTAVAVFLSLLPLNFFITKKRGFHQEEQMRQKASRARLTSSMLRTVRTIK   500
 501  SHGWEHAFLERLLHIRGQELSALKTSTLLFSVSLVSFQVSTFLVALVVFA   550
 551  VHTLVAEDNAMDAEKAFVTLTVLSILNKAQAFLPFSVHCIVQARVSFDRL   600
 601  AAFLCLEEVDPNGMIASNSRRSSKDRISVHNGTFAWSQESPPCLHGINLT   650
 651  VPQGCLLAVVGPVGAGKSSLLSALLGELLKVEGSVSIEGSVAYVPQEAWV   700
 701  QNTSVVENVCFRQELDLPWLQKVLDACALGSDVASFPAGVHTPIGEQGMN   750
 751  LSGGQKQRLSLARAVYKKAAIYLLDDPLAALDAHVSQQVFKQVIGPSGLL   800
 801  QGTTRILVTHTLHVLPQADRILVLANGTIAEMGSYQDLLQRNGALVGLLD   850
 851  GARQPAGTHDAATSDDLGGFPGGGRPTCRPDRPRPTEAAPVKGRSTSEVQ   900
 901  MEASLDDPEATGLTAEEDSVRYGRVKTTIYLSYLRAVGTPLCTYTLFLFL   950
 951  CQQVASFSQGYWLSLWADDPVVDGRQMHAALRGWVFGLLGCLQAIGLFAS  1000
1001  MAAVFLGGARASGLLFRSLLWDVARSPIGFFERTPVGNLLNRFSKETDTV  1050
1051  DVDIPDKLRSLLTYAFGLLEVGLAVTMATPLAIVAILPLMVLYAGFQSLY  1100
1101  VATSCQLRRLESARYSSVCSHMAETFQGSLVVRAFRAQASFTAQHDALMD  1150
1151  ENQRVSFPKLVADRWLATNLELLGNGLVFVAATCAVLSKAHLSAGLVGFS  1200
1201  VSAALQVTQTLQWVVRSWTDLENSMVAVERVQDYARIPKEAPWRLPTCAA  1250
1251  QPLWPCGGQIEFRDFGLRHRPELPLAVQGVSLKIHAGEKVGIVGRTGAGK  1300
1301  SSLAWGLLRLQEAAEGNIWIDGVPITHVGLHTLRSRITIIPQDPVLFPGS  1350
1351  LRMNLDLLQEHTDEGIWAALETVQLKAFVTSLPGQLQYECAGQGDDLSVG  1400
1401  QKQLLCLARALLRKTQILILDEATASVDPGTEMQMQAALERWFTQCTVLL  1450
1451  IAHRLRSVMDCARVLVMDEGQVAESGSPAQLLAQKGLFYRLAHESGLA    1498

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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