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

NucPred

Fetching Q9D952 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MFKGLSKGSQGKGSPKGSPAKGSPKGSPNKHNRAATQELALLISRMQANA    50
  51  DQVERDILETQKKLQQDRQNGEQNQALQHQQETGRNLKEAEVLLKDLFLD   100
 101  VDKARRLKHPQAEEIEKDIKQLHERVTQECSEYRALYEKMVLPPDVGPRV   150
 151  DWARVLEQKQNLVREGHYGPGMAELEQQVAEHNILQREIEAYGQQLRTLV   200
 201  GPDANTIRNQYRELLKAASWRRQSLGSLYTHLQGCTKQLSALADQQGRIL   250
 251  QQDWSDLMPDPAGVRREYEHFKQHELLAQERSINQLEDDADRMVELGHPA   300
 301  IGPIQVHQEALKMEWQNFLNLCICQESQLQRVEDYRRFQEEADSVSQTLA   350
 351  KLSSNLDTKYGFGTGDSSGSPTELLLQLEAEEKQLAIAERAVGDLQQRSQ   400
 401  EVAPLPQRRNPSKQPLHVDSICDWDSGEVQLLRGERYTLKDNADPYTWLV   450
 451  QGPGGETKSAPAACLCIPAPDPEAVAKASRLATELQTLKQKLSTEKNRLK   500
 501  AAAVEHLQPGQQAPAGSAPADPQGQTLLSQMTQLDGDLGQIERQVLSWAR   550
 551  SPLSQSSSLKDLEGRIHSCEGTAQRLQSLGAEKEAAQQECEAFLSTKPTG   600
 601  SAALQLPVVLNSVKNRYNDVQSLCHLYGEKAKAALGLEKQIQEADRVIQG   650
 651  FEAALALEGPVPEGSGALQERVSELQRQRKELLQQQACVLGLHRQLKATE   700
 701  HACSALQNNFQEFCQDLPRQQRQVRALTDRYHAVGDQLDLREKIVQDASL   750
 751  TYQQLRNSRDNLSSWLEQLPHHRVQPSDGPSQISYKLQAQKRLIQEILGR   800
 801  EQDQATVSRLTRDLQEALQDYELQADTYRCSLEPALAVSAPKRLRVISLQ   850
 851  ESIQAQEKNLAKAYTEVAAAEQQQLRQLEFAKKMLRKKELDEDIQAIHSA   900
 901  RQGSGSPAHARTAESEVLKTQLEEERKRVAEVQRDLEEQRQRLLQLRTQQ   950
 951  PVARLEEKEVVEFYRDPQLESNLSQAASRVEEEGKRRARLQAELEAVAQK  1000
1001  VVHLEGKRKTMQPHLLTKEVTQIERDPGLDSQVTQLHSEMQRLRGENGVL  1050
1051  TARLEELKDELLALEQKEMNVKEKVVVKEVVKVEKDLEMVKAAQTLRLQI  1100
1101  EEDAARRKGAKETVAKIQARIKDLEQAISSVEPKVIVKEVKKVEQDPGLL  1150
1151  KEASRLRSLLEEEKNNNVALARELQELQEKYRVVEKQKPKVQLQERVSEI  1200
1201  FQVLPETEQEIRRLRAQLQETGSKKSGVEQEVEKLLPELEVLRAQKPVVE  1250
1251  YKEVTQEVVRHEKNPEVLREIDRLKAQLNELVNTNGRSQEQLIRLQGERD  1300
1301  EWKRERSKVETKMVSKEVVRHEKDPVLEKEAERLRQEVREAVQRRRATED  1350
1351  AVYELQNKLLLLERRRPEEQIVVQEVVVTQKDPKLREEHSRLSRSLDEEV  1400
1401  GRRRQLELEVRQLGARVEEEEARLSFEEDRSKKLAAERELRQLTLKIQEL  1450
1451  EKRPPALQEKIIMEEVVKLEKDPDLERSTEALRRELDQEKNRVTELHREC  1500
1501  QGLQVQVDLLQKTKSQEKTIYKEVIRVEKDPVLEGERARVWEILNRERAA  1550
1551  RKGREEDVRSLQERIDRAEALRRSWSREEAELQRARDQASQDCGRLQRQL  1600
1601  RELEQQKQQKARQLQEEGRLLSQKTESERQKAAQRSQAVTQLEAAILQEK  1650
1651  DKIYEKERTLRDLHTKVSREELNQETQTRETNLSTKICILEPETGNDMSP  1700
1701  YEAYKRGVIDRGQYLQLQELECDWEEVTTSSPCGEESVLLDRKSGKQYSI  1750
1751  EAALRCRRISKEEYHRYKDGRLPISEFALLVAGETKPSSSLSIGSIISKS  1800
1801  PVCSPGPQSTGFFSPGLSFGLTEDSFPIAGIYDTTTDNKCSIKAAVAKNM  1850
1851  LDPITGQKLLEAQAATGGIVDLLSRERYSVHKAVERGLIENTSTQRLLNA  1900
1901  QKAFTGIEDPVTRKRLSVGEAIQKGWMPQESVLPHLLVQHLTGGLIDPKR  1950
1951  TGRIPVPQAVLCGMISEDLGQLLQDESGYEKDLTDPITKERLSYKEAMGR  2000
2001  CRKDPLSGLLLLPAMLEGYRCYRAASPTLPRSCVR                 2035

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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