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

NucPred

Fetching P21439 from www.uniprot.org...

The NucPred score for your sequence is 0.32 (see score help below)

   1  MDLEAAKNGTAWRPTSAEGDFELGISSKQKRKKTKTVKMIGVLTLFRYSD    50
  51  WQDKLFMSLGTIMAIAHGSGLPLMMIVFGEMTDKFVDTAGNFSFPVNFSL   100
 101  SLLNPGKILEEEMTRYAYYYSGLGAGVLVAAYIQVSFWTLAAGRQIRKIR   150
 151  QKFFHAILRQEIGWFDINDTTELNTRLTDDISKISEGIGDKVGMFFQAVA   200
 201  TFFAGFIVGFIRGWKLTLVIMAISPILGLSAAVWAKILSAFSDKELAAYA   250
 251  KAGAVAEEALGAIRTVIAFGGQNKELERYQKHLENAKEIGIKKAISANIS   300
 301  MGIAFLLIYASYALAFWYGSTLVISKEYTIGNAMTVFFSILIGAFSVGQA   350
 351  APCIDAFANARGAAYVIFDIIDNNPKIDSFSERGHKPDSIKGNLEFNDVH   400
 401  FSYPSRANVKILKGLNLKVQSGQTVALVGSSGCGKSTTVQLIQRLYDPDE   450
 451  GTINIDGQDIRNFNVNYLREIIGVVSQEPVLFSTTIAENICYGRGNVTMD   500
 501  EIKKAVKEANAYEFIMKLPQKFDTLVGERGAQLSGGQKQRIAIARALVRN   550
 551  PKILLLDEATSALDTESEAEVQAALDKAREGRTTIVIAHRLSTVRNADVI   600
 601  AGFEDGVIVEQGSHSELMKKEGVYFKLVNMQTSGSQIQSEEFELNDEKAA   650
 651  TRMAPNGWKSRLFRHSTQKNLKNSQMCQKSLDVETDGLEANVPPVSFLKV   700
 701  LKLNKTEWPYFVVGTVCAIANGGLQPAFSVIFSEIIAIFGPGDDAVKQQK   750
 751  CNIFSLIFLFLGIISFFTFFLQGFTFGKAGEILTRRLRSMAFKAMLRQDM   800
 801  SWFDDHKNSTGALSTRLATDAAQVQGATGTRLALIAQNIANLGTGIIISF   850
 851  IYGWQLTLLLLAVVPIIAVSGIVEMKLLAGNAKRDKKELEAAGKIATEAI   900
 901  ENIRTVVSLTQERKFESMYVEKLYGPYRNSVQKAHIYGITFSISQAFMYF   950
 951  SYAGCFRFGAYLIVNGHMRFRDVILVFSAIVFGAVALGHASSFAPDYAKA  1000
1001  KLSAAHLFMLFERQPLIDSYSEEGLKPDKFEGNITFNEVVFNYPTRANVP  1050
1051  VLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPLAGTVFVDFGFQ  1100
1101  LLDGQEAKKLNVQWLRAQLGIVSQEPILFDCSIAENIAYGDNSRVVSQDE  1150
1151  IVSAAKAANIHPFIETLPHKYETRVGDKGTQLSGGQKQRIAIARALIRQP  1200
1201  QILLLDEATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIV  1250
1251  VFQNGRVKEHGTHQQLLAQKGIYFSMVSVQAGTQNL                1286

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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