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

NucPred

Fetching Q8R4H2 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MSGTQSTITDRFPLKKPIRHGSILNRESPTDKKQKVERSSSHDFDPTDSS    50
  51  SKKTKSSSEESRSEIYGLVQRCVIIQKDDNGFGLTVSGDNPVFVQSVKED   100
 101  GAAMRAGVQTGDRIIKVNGTLVTHSNHLEVVKLIRSGSYVALTVQGRPPG   150
 151  SPQIPLADSEVEPSVTGHMSPIMTSPHSPGAAGNMERITSPVLVGEENNV   200
 201  VHNQKVEILRKMLQKEQERLQLLQEDYNRTATQRLLKEIQEAKKHIPQLQ   250
 251  EQLSKATGSAQDGAVIAPSRPLGDALTLSEAEADPGDGLCRTDWSSGDAS   300
 301  RPSSDSADSPKSSLRERSYLEEAPERSEGVQDAEPQSLVGSPSTRGAPHI   350
 351  IGAEDDDFGTEHEQINGQCSCFQSIELLKSRPAHLAVFLHHVVSQFDPAT   400
 401  LLCYLYSDLYKQTNSKETRRVFLEFHQFFLDRSAHLKVPVPEEISVDLEK   450
 451  RRPELIPEDLHRLYIQTMQERVHPEVQRHLEDFRQKRSMGLTLAESELTK   500
 501  LDAERDKDRGTLEKERACAEQIVTKIEEVLMTAQAVEEERSSTMQYVILM   550
 551  YMKYLGVKVKEPRNLEHKRGRIGFLPKIKQSMKKDREGEEKGKRRGFPSI   600
 601  LGPPRRPSRHDNSAIGRAMEIQKSRHPKHLSTPSSVSPEPQDPAKLRQSG   650
 651  VANEGTDTGYLPASSMSSATSGTALSQEGGRENDTGTKQVGEASAPGDCL   700
 701  DSTPRVPTTVFDFPPPLLDQVQEEECEVERVAEHGTPKPFRKFDSIAFGE   750
 751  SQSEDEQFENDLETDPPNWQQLVSREVLLGLKPSEIKRQEVINELFYTER   800
 801  AHVRTLKVLDQVFYQRVSREGILSPSELRKIFSNLEDILQLHVGLNEQMK   850
 851  AVRKRNETSVIDHIGEDLLIWFSGPGEEKLKHAAATFCSNQPFALEMIKS   900
 901  RQKKDSRFHTFVQDAESNPLCRRLQLKDIIPTQMQRLTKYPLLLDNIAKY   950
 951  TEWPPEREKVKKAADHCRQILNYVNQAVREAENKQRLEDYQRRLDTSNLK  1000
1001  LSEYPNVDELRNLDLTKRKMIHEGPLVWKVNRDKSIDLYTLLLEDILVLL  1050
1051  QKQDDRLVLRCHSKILASTADSKHTFSPVIKLSTVLVRQVATDNKALFVI  1100
1101  SMSDNGAQIYELVAQTVSEKTVWQDLICRMAASVKEQSTKPIPLPQPPPC  1150
1151  EGDNDEEEPAKLKVEHHDLSVAGLQSPDRVLGLESPLISSKPQSHSLNTP  1200
1201  GKSAAEHLFVTATQFAKEQHANGALKEGDGGYPVTIPGPHLPVSEERWAL  1250
1251  DALRNLGLLKQLLVQQLGLTEKSTQEDWQSFSRYGPASEEVQADSGIRDL  1300
1301  ENVKACHAREGQMSFKTGTGDIATCDSPRTSTESCAAQDSVILASQDSQA  1350
1351  SNVLVMDHMILTPEMPPAEPEGGLDESGEHFFDAREAHSDDNPSEGDGAV  1400
1401  KKEEKDVNLRISGNCLILDGYDAVQESSTDEEVASSFPLQPVTGIPAVDS  1450
1451  SHQQQHSPQNVHPEGPVSPFTPEFLVQRHWRAMEDTCFEIQSPSCTDSQS  1500
1501  QILEYIHKIEADLEHLKKVEESYALLCQRLAGSALPDKLSDKS         1543

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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