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

NucPred

Fetching Q08470 from www.uniprot.org...

The NucPred score for your sequence is 0.41 (see score help below)

   1  MLKFIRGKGQQPTAERQRLQKDLFAYRKTAQHGFPHKPSALAYDPVAKLM    50
  51  AIGTQTGAIKVFGQPGVELYAQHTLVNNSAAELNVQLLEWVYGTGRILSL   100
 101  TAANQLILWEPVGTTLVPIKTLPFDGKLKKVSSLCCSLNKDLLWIGTEGG   150
 151  NIYQLDLKSFTIREPVIYHDVVLEQVPPTYKLNPGAIESIRQLPNSLNKL   200
 201  LIAYNRGLCVLWDMQTSAVERAYIAPGHGQSVGLSVNSTGTEFSWYHADG   250
 251  SYATWSIDNGEPPQNVNYVPYGPDPCKSINRLYKGQRGTNDVIVFSGGMP   300
 301  RSAYGDHNCVSVHVSDGHKVCLDFTSKVIDFFVTYKEGSDDVEVLIVLLE   350
 351  EELCAYDLTDPSILSIKAPYLHSVHASAVTCNYLASQVTQGVYERILRAG   400
 401  DEQDIDYSSIDWPITGGVLTDDSVESDEDEVVKDYEILLTGHEDGSVKFW   450
 451  DCTGVLLKPIYNFKTASIFGNEHEYREDGAADISAEQLDEGEPPFRKAGL   500
 501  FDPYSDDPRLAVKKIAFCPKTGQLVVGGTAGQIVIADFDTAAEDQSSLKY   550
 551  NSMNLVSDRDGFVWKGHDQLNVRANLLEDNAVPLTENGVNITGVLQVLPP   600
 601  ASITCMALEANWGLVSGGTAHGLVLFDFKNFVPVFHRCTLNPNDLTGAGE   650
 651  QLSRRKSFKKSLRESFRKLRKGRSTRNNPTNQVPTTLEARPVERQIEARC   700
 701  TDDGLGSMVRCLLFAKTYVTNVNITSPTLWSATNASTVSVFLLHLPPAQT   750
 751  AATTVPPASGNVPPQASRRISAQLAKEIQLKHRAPVVGISIFDQTGSPVD   800
 801  QFNAGENGSPPHRLLIASEEQFKVFSLPQLKPINKYKLTANEGARIRRIH   850
 851  FGSFSCRISPELLQSLHSGSPTKSVRSHGEGDGAGNVSATSAAGRGDLYH   900
 901  EMALICLTNMGDIMVLSVPELKRQLNAAAVRREDINGISSLCFTNDGEAL   950
 951  YMMSSSELQRIALSTSKVVQPTGIVEVEPLESEDNETASLVNDGNESDKD  1000
1001  GEANKELANTASDTQPPVATLRAKPLELNADRSSLHLTNGISNSNSPNRA  1050
1051  NETITSSIGDITVDSVRDHLNTTTTTLCSTTTEETVGRLSVLSTQTNQAT  1100
1101  TTVNMKDIPDINIPNLMDLASKSNTTETSTSSVVIKSVITSISHEKTNGE  1150
1151  SENVTTKTTAHEESQF                                    1166

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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