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

NucPred

Fetching Q875Q8 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MSYEVGTRCWYPDKQQGWIGGEITKHTNLSNKHQLELTLEDNQIVEIESE    50
  51  TLDETKDDRLPLLRNPPILEATEDLTSLSYLNEPAVLHAIKARYAQLNIY   100
 101  TYSGIVLIATNPFDRVEQLYSQDMIQAYAGKRRGELEPHLFAIAEEAYRL   150
 151  MKNDKQNQTIVVSGESGAGKTVSAKYIMRYFASVEQNNEENAHHNLEMSE   200
 201  TEKKILATNPIMEAFGNAKTTRNDNSSRFGKYLEILFDKEISIIGARIRT   250
 251  YLLERSRLVFQPKSERNYHIFYQLLAGLTNEEKSQLKLTGVEDYHYMNQG   300
 301  GEAQIKGIDDAEEYQTTVEALSLVGISKDTQYQLFKILAALLHIGNVEIK   350
 351  KTRNDASLSSDEPNLAIACELLGIDSFNFAKWITKKQINTRSEKIVSNLN   400
 401  YNQALVARDSVAKFIYSALFEWLVDNINTVLCNPEVASEINSFIGVLDIY   450
 451  GFEHFEKNSFEQFCINYANEKLQQEFNQHVFKLEQEEYVKEEIEWSFIEF   500
 501  NDNQPCIDLIENKLGILSLLDEESRLPAGSDETWTQKLYQTLDKPPTNTV   550
 551  FSKPRFGQTKFVVSHYALDVSYDVEGFIEKNRDTVSDGHLEVLKASTNET   600
 601  LLSILETLDKHAAKLAEKEQVNKKPGPARMVNRKPTLGSIFKQSLIELMG   650
 651  TINSTNVHYIRCIKPNEVKEAWVFDNLMVLSQLRACGVLETIRISCAGFP   700
 701  SRWTYNEFVLRYHILIPSEHWSKMFSSDTTEEDIRDLCRTILGAIVEDKQ   750
 751  KYQLGNTKIFFKAGMLAYLEKLRSDRLHNSSVLIQKKVKAVYYRKKYLAI   800
 801  ISSIRNFHSRSEGFLTRQRVDLEFKTQAAILIQSMVRSTSTRNKTISLLS   850
 851  AITRLQSLVRKQLAQKELLQRRQRDAAVSIQKKIRAFEPRQSFNTTRRST   900
 901  VVVQSLVRKKFAQKKLKDLKTEAKSVNHLKEVSYKLENKVIQLTESLAEK   950
 951  VKENKGMTARIQELQQSLNESANIKELLNSQKDEHSKVLQQQKDAHDVQF  1000
1001  NEVQEKLVNAKKEVEEAKEEIEQLIAKQDELKAEVRTKIEELNKAKKTFT  1050
1051  EFQTQNSDLKNEVKSLKDEIARLQAAVRSGVTSSTITSTPTASRRFSAHS  1100
1101  SVADGTSPRQLNVISMNNGGIEDDARSTASALSQINDELYKLLEDTKSLN  1150
1151  TEIVEGLLKGFKIPETGVAVELTRKEVLYPARILIIVLSDMWRLGLTKQS  1200
1201  ESFLAEVLSTIQKLVTNLKGDDMILHGAFWLTNVRELYSFVVFAQESILN  1250
1251  DDSYNNGLNEDEYKEYVTLVTELKDDFESLSYNIYNIWLKKLQKDLERKA  1300
1301  ISAVVMSQSLPGFIAPESSPFLPKLFSQSSHYKMDDILTFFNNIYWSMKT  1350
1351  YHVETEVFREVIMTLLKYVDAICFNDLIMRRNFLSWKRGLQLNYNVTRLE  1400
1401  EWCKSHQLPEGTECLQHMLQASKLLQLKKANLEDINIIWEICSSLKPAQI  1450
1451  QKLISQYAVADYEVPIPQEILNFVADRVKKESSLSSDGKSQTHSSDIFLS  1500
1501  VDSGPFEDPFGQIETREFGKIEAYIPAWLNLPITRRVVELVTQHVTVQES  1550
1551  QRTE                                                1554

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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