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

NucPred

Fetching P50533 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MHVKSIIIDGFKSYAQRTEINGFDPLFNAITGLNGSGKSNILDSICFLLG    50
  51  ISNLTQVRASNLQDLVYKNGQAGITKATVSITFDNYDKKQSPLGFEAHDE   100
 101  ITVTRQVVIGGRNKYLINGVNANNTRVQDLFCSVGLNVNNPHFLIMQGRI   150
 151  TKVLNMKPPEILAMIEEAAGTRMYECKKIAAQKTIEKKEAKLKEIQTILE   200
 201  EEITPTIHKLKEERSSYLEYQKIMREIEHLSRLYVAYQFVCAEETKVRSA   250
 251  EELKEMQDSILKLQDTMAENERKVKELGKEIAELEKMRDQEVGGALRSLE   300
 301  EALSEAQRADTKVQSALDLKKQNMKAEREKKRKELVKSMEEDAKVLTAKE   350
 351  KEVKKITDGLSSLQEASQKDVEAFTSAQQHFNAVSAGLSSNEDGEEATLA   400
 401  GQMMACKNETSKAETEAKQAQMKLKHAQQELKTKQAEVKKMDGGYKKDNE   450
 451  AFEAVKKSKEKLEVEMKKLNYEDGREEQLLEKRRGLSRDVNRLREAYESL   500
 501  MARFPNLQFEYKDPEKNWDSDRVKGLVASLISIKDVSTATALEVVAGGRL   550
 551  YNVVVDTEVTGKKLLEKGELKRRFTIIPLNKISARCLGKDTVNVAKNLVG   600
 601  ADNVNLALSLVGYESELQKAMEYVFGTTLVCDTMDNAKKVTFDKRIMTKT   650
 651  VTLGGDTFDPQGTLSGGARSQNASVLVRLQELKDVQDELKAKETELQEVE   700
 701  KELMTLKNTVERYRQLKQQWEMKSEEAELLQTKLQQSSYHKQQEELDSLK   750
 751  QTIEESEETLKNTKEVQKKAEEKFKVLEHKMKNAEAERERELKEAQQKLD   800
 801  TAKKKADASNKKMKEKQQEVDALVLELEELKREQTTYKQQIETVDEAMKA   850
 851  YQEQADSMASEVSKNKEAVKKAQDELAKQKEIIMGHDKEIKTKSSEAGKL   900
 901  RENNNDLQLKIKELEHNISKHKKDSADAAAKVAKMLNDYEWIASEKHLFG   950
 951  QANTAYDFKTNNPKEAGQRLHKLQEKKEKLGRNVNMRAMNMLTQAEERYN  1000
1001  DLMKRKRIVENDKSKILTTIEELDQKKNEALNIAWQKVNKDFGSIFSTLL  1050
1051  PGANAMLAPPEGQSVLDGLEFKVALGNTWKENLTELSGGQRSLVALSLIL  1100
1101  AMLLFKPAPIYILDEVDAALDLSHTQNIGQMLRTHFRHSQFIVVSLKDGM  1150
1151  FNNANVLFKTKFVDGVSTVARFAQNQNGGSSAGQQRSDKSKTKERRNRME  1200
1201  VDK                                                 1203

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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