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

NucPred

Fetching Q10135 from www.uniprot.org...

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

   1  MPLGRSSWICCAKYFVNTKSRFNEILPPRFTLIVSFYSMNTSENDPDGHY    50
  51  DFPEMTEHHSDRASSYANANNVNSTQPQLVSSEQALLAILGGGLQSITPN   100
 101  SVNQNAYSRSTYRTDGGLNSQPVSSLNNQWGNYNPAFLPSRYDSSFHPYT   150
 151  ISQAANQPFPQHLLGNSNAGVAQQSGMRTIGLPPTVGSSFPQQKSSTYEN   200
 201  FFDANSPSSQQFPSTYPSRSQNPLSSSGDGSTAIHAGPIQHQNSNAFSNY   250
 251  PYPLDASHLSSQQLLSMYRDQVSHGVTPSTFRNHESFMPTQLVSATELSK   300
 301  SVDNAVLPIPPTTAPAVVSPPASSFPLMSSAATSGNISSPALFDSELGAR   350
 351  PEGSVAIEPSRVLLQWSSQSSSHTIPSAGASIPTSSLKSFFEHAAEAARK   400
 401  CNLDPRALESFEQHMLSDRLHDPVVLFHYFQIRNSICWLWIKNPTHAISR   450
 451  VEAQGVCVDRCLFQLASLAYEFLVRYGYINYGCLSFDSSFTNETNTGTTS   500
 501  SSASKQKTIAVVGAGLTGLICARQLTGLFSQYSSSFLSKNELPPKVIILE   550
 551  AKERTGGRIYSRALPVSHTSATQINHHTSNSNSISSNSTSLNPKDVTDPS   600
 601  HIPSAIDLGFQFLFSPMDDILLNLLNKQLGIEVTEMTGSDLVYDETDTKV   650
 651  LDMVEVKKLNILWEKLLEYVSVCFFINVEESVRISWISQFQLFIDEMFPD   700
 701  HLSKSLSLNASHEFSFKKTMLILIDEVSSYAKLGNSQKKFLIWCFKVAEL   750
 751  DDTLYPLNTVDTDFSKDILIPKVARRGLSQLPWALQSYPSPLNIHYEKFV   800
 801  SKVTIENDKCTLDCKDNSSYEVDQVVIACSPSHFSSNIEFSPGLPNFVTE   850
 851  NIKSIDFKPGKKVILRYAAAFWRKNIRSFGIIPKSLSQEMNNDENDGKSC   900
 901  FVLRIWNMLPETGVPILVADINPQMTSSSSNETSHLIQELHSLIVDHFQN   950
 951  DSNSSADLLDAWVTNWSRNGVYDGLNSYPNFANDKQQYEKRFRQSQLSYN  1000
1001  LGRLHIAGDYIFSCVGCRTLQRSFLSGLSVCTGIIDSLAPISLTIPIIGE  1050
1051  TSRKELDQFLRNSKVNNFDPNAEAQRHLSYQARYRLKKQERLDEHKEEQE  1100
1101  QLVTELLGYLPEPPSKPNANPFLLYQKMQWHVCRALADEDKRRLTGDSTA  1150
1151  KATINETRAKLGKTWRQLDDLGKKPWIDEIAAQREAYAGKILRYQRLTKE  1200
1201  YEMRAEQIRNDYAAKCQDEPIPDDEARLFMQAQREEEQRKQTQDDNISKS  1250
1251  REASDEEYHDDGSSDSGYNGTRY                             1273

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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