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

NucPred

Fetching Q7SIH1 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MGKNKLLYPSLTLLLLLLLPTDASVSGKPQYMVLVPSLLHTETPEKGCLL    50
  51  LSHLNETVTVSASLESVRENRSLFTDVVAEKDLFHCVSFTLPRSPTSQEV   100
 101  MFLTIQVKGPTQEFKKRTTVLVKNEESLVFVQTDKPIYKPEQTVKFRIVL   150
 151  LDESFHPLNELVPLVYVEDPKGNRIAQWQNLEVENGLQQLTFPLSSEPFQ   200
 201  GSYKVVVQKGSGGTAEHPFTVEEFVLPKFEVQVRMPKIITILEEEVQVSV   250
 251  CGLYTYGKPVPGRVTMNMCRKYRNPSNCYGEESNAVCEKFSGELNNEGCF   300
 301  SQQVNTKIFQLKRQEFEMKIEVEAKIQEEGTEVELTGKGATEITTTITKL   350
 351  SFVTVDSNLRRGIPFTGKVLLVDGKGVPMPNKVIFITANEANHNSNTTTD   400
 401  EHGLAQFSITTTKIKGTSLSIRVKYKDHSPCYGYQWLSEEHQDAYHSANL   450
 451  VFSRSNSFVYLEPLPRELPCGKTQTVQAHYVLKGQVLKDLKELVFYYLIM   500
 501  AKGGIVRSGTHTLPVEQGDMQGHFSMSVPVESDIAPVARLLIYAILPDGE   550
 551  VVGDSARYEIEHCLANKVGLNFSPGQSFPASQAHLRVTASPQSLCALRAV   600
 601  DQSVLLMRPEAELSAATVYNLLPVKDLSSFPSSVNQQEEDNEDCISHDNV   650
 651  YINGIMYFPVSNTNEKDMYSFLQDMGLKAFTNSKIHKPKICPQPEEHRIQ   700
 701  HHTLLASPVRAEMGRNRDFVHFDDTSEPPTETVRKYFPETWIWDLVVVSS   750
 751  SGVHEVEVTVPDTITEWKAGALCLSRDTGLGLSPTASLRVFQPFFVELTM   800
 801  PYSVIRGEAFTLKATVLNYLPKCIRVSVQLEASPAFLAVPEKEQETYCIC   850
 851  GNGRQTVSWAVTPKSLGNVNFTVSAEAVESQELCGSEVPVVPEHGRKDTI   900
 901  IKPLLVEPEGLEKEVIFNSLLCPSVDFVFLGAEDGGQVLRHFPPAAATDT   950
 951  AADAHDPARPGAKVSESLSLKLPPNVVEESARASFSVLGDILGSAMRNTQ  1000
1001  NLLQMPYGCGEQNMARFAPNIYVLDYLNETQQLTAELKSKAILYLNTGYQ  1050
1051  RQLLYKHFDGSYSTFGEHRGNSEGNTWLTAFVLKSFAQARGYIFIDEAHI  1100
1101  TEALTWLAQKQKSNGCFRSTGTLLNNAIKGGVDDEVTLSAYITIALLEMP  1150
1151  LPVTHPVVRNALFCLDSAWKSAKEGSQGSHVYTKALLAYAFALAGNQERR  1200
1201  TEVLTSLYEEAVKEDNTIHWTRPQKPRLLTEDIYQPRAPSAEVEMTAYVI  1250
1251  LAHVTAQPAPNPEDLKRATSIVKWISKQQNCQGGFSSTQDTVVALHALSR  1300
1301  YGAATFTSARKAAQVTIQSSGTFSTKFQVENSNRLLLQQVSLPEVPGEYS  1350
1351  MSVTGEGCVYLQTSLKYNILPKKDEFPFALEVQTLPQTCDGPKAHTSFQI  1400
1401  SLSVSYIGSRPASNMAIVDVKMVSGFIPLKPTVKMLERSNVSRTEVSNNH  1450
1451  VLIYLDKVTNETLTLTFTVLQDIPVRDLKPAIVKVYDYYETDEFAVAEYS  1500
1501  APCSKDIGNA                                          1510

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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