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

NucPred

Fetching Q6Z351 from www.uniprot.org...

The NucPred score for your sequence is 0.36 (see score help below)

   1  MSDCNSGGGERRPNARATDAPPVRAPSGGAFRCRGCGACVILIAKYNPKT    50
  51  DEVTEFNASSCLTLLYSIHFCSIITTEGLGNTKDGFHAIQKRMSGFHASQ   100
 101  CGFCTPGMCMSIFSSLVNADKSKKPDPPKGFSKLSVSEAERSFSGNMCRC   150
 151  TGYRPIVDACKSFASDVDLEDLGLNIFWKKGDKHPDPTKLPSYTLGGGIC   200
 201  TFPDFLKSEIKSSIDFNDASISSPREGWYCPKNIKQYYKLVNSGLFSESS   250
 251  VKVVVGNTSTGVYKDQDLYDKYIDIAGIPELSAIVRKDKGIEIGAATSIS   300
 301  RTIEILNQESESTSSPNGSVVFRKLAEHMSKVASPFVRNTASIGGNIILA   350
 351  HKYPFRSDIATILLGAAATVNLQVSSKTLHVTLEQFLEQPPLGHNTLLLS   400
 401  IFIPHWASDCKKEHTLVFETYRAAPRPLGNAVSYVNSAFLGHVSLDKSSG   450
 451  DNILSNLHLAFGAYGTEHAIRARKVEEYLTGKILSASVVLEAIRLLRETI   500
 501  VPVEGTTHPEYRVSVAVGFLFSFLSPLCKGVIEPGKTLSISEDLVHTDNV   550
 551  HNMPLSSRRETLSGDEYKPVGDPIKKYKVELQASGEAIYVDDIPAPKNCL   600
 601  YGEFIYSTQPLANVKSIKFKPSLASKKILTVVSAKDIPTGGRNIGSTFLF   650
 651  GDEEPLFGDPIAEFAGQALGVVIAETQRYADMAAKQAVVEYTTDGLKAPI   700
 701  LTVEQAVQNNSYFQVPPERAPKQVGDFSKGMAEADHKIMSEEVKLASQYY   750
 751  FYMETQTALAIPDEDNTMTVYSSSQFPELAQNVISKCLGIPFNNVRVITR   800
 801  RAGGGFGGKAVRSLHIATAAALCAHTLRRPVRMYLNRNTDMIMVGGRHPM   850
 851  KARYSVGFKSDGKITALHLDLLINAGISADASPVIPGTIISGLKKYNWGA   900
 901  LSFDVKLCKTNNTSKSVMRAPGDTQGSFIAEAIIEHVAAILSLDANTVRQ   950
 951  KNFHTYDSLVLFYPDSAGESSTYTLHSIFDRLASTSRYLQRVESIKKFNS  1000
1001  TNKWRKRGISSVPLIFKVEPRPAPGRVSVLNDGSIVVEVGGVELGQGLWT  1050
1051  KVQQMTAFALGQLWPKGCEGLLDRIRVLQSDTLNLIQGGLTAGSTTSESS  1100
1101  CAATLQACNMLIERLKPVMERLQLQSDTVSWDTLISQASQENINLSASAY  1150
1151  WVPEQDSNFYLNYGAGTSEVEVDLLTGAITIIRSDLIYDCGKSLNPAVDL  1200
1201  GQIEGSFIQGIGFFIYEEHQTNSDGLVISNSTWDYKIPSVDTIPKQFNAE  1250
1251  VLNTGYHKHRVLSSKASGEPAVVLGASVHCAVREAIRAARIEFAGNNGSG  1300
1301  SSLLTFQLDVPAPMTVVKELCGLDIVEKYLEDLSNRGAASGN          1342

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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