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

NucPred

Fetching P21440 from www.uniprot.org...

The NucPred score for your sequence is 0.24 (see score help below)

   1  MDLEAARNGTARRLDGDFELGSISNQGREKKKKVNLIGLLTLFRYSDWQD    50
  51  KLFMFLGTLMAIAHGSGLPLMMIVFGEMTDKFVDNTGNFSLPVNFSLSML   100
 101  NPGRILEEEMTRYAYYYSGLGGGVLVAAYIQVSFWTLAAGRQIKKIRQKF   150
 151  FHAILRQEMGWFDIKGTTELNTRLTDDVSKISEGIGDKVGMFFQAIATFF   200
 201  AGFIVGFIRGWKLTLVIMAISPILGLSTAVWAKILSTFSDKELAAYAKAG   250
 251  AVAEEALGAIRTVIAFGGQNKELERYQKHLENAKKIGIKKAISANISMGI   300
 301  AFLLIYASYALAFWYGSTLVISKEYTIGNAMTVFFSILIGAFSVGQAAPC   350
 351  IDAFANARGAAYVIFDIIDNNPKIDSFSERGHKPDNIKGNLEFSDVHFSY   400
 401  PSRANIKILKGLNLKVKSGQTVALVGNSGCGKSTTVQLLQRLYDPTEGKI   450
 451  SIDGQDIRNFNVRCLREIIGVVSQEPVLFSTTIAENIRYGRGNVTMDEIE   500
 501  KAVKEANAYDFIMKLPQKFDTLVGDRGAQLSGGQKQRIAIARALVRNPKI   550
 551  LLLDEATSALDTESEAEVQAALDKAREGRTTIVIAHRLSTIRNADVIAGF   600
 601  EDGVIVEQGSHSELMKKEGIYFRLVNMQTAGSQILSEEFEVELSDEKAAG   650
 651  DVAPNGWKARIFRNSTKKSLKSPHQNRLDEETNELDANVPPVSFLKVLKL   700
 701  NKTEWPYFVVGTVCAIANGALQPAFSIILSEMIAIFGPGDDAVKQQKCNM   750
 751  FSLVFLGLGVLSFFTFFLQGFTFGKAGEILTTRLRSMAFKAMLRQDMSWF   800
 801  DDHKNSTGALSTRLATDAAQVQGATGTRLALIAQNTANLGTGIIISFIYG   850
 851  WQLTLLLLSVVPFIAVAGIVEMKMLAGNAKRDKKEMEAAGKIATEAIENI   900
 901  RTVVSLTQERKFESMYVEKLHGPYRNSVRKAHIYGITFSISQAFMYFSYA   950
 951  GCFRFGSYLIVNGHMRFKDVILVFSAIVLGAVALGHASSFAPDYAKAKLS  1000
1001  AAYLFSLFERQPLIDSYSGEGLWPDKFEGSVTFNEVVFNYPTRANVPVLQ  1050
1051  GLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPMAGSVLLDGQEAKKL  1100
1101  NVQWLRAQLGIVSQEPILFDCSIAENIAYGDNSRVVPHDEIVRAAKEANI  1150
1151  HPFIETLPQKYNTRVGDKGTQLSGGQKQRIAIARALIRQPRVLLLDEATS  1200
1201  ALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVIENGKVKEH  1250
1251  GTHQQLLAQKGIYFSMVNIQAGTQNL                          1276

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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