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

NucPred

Fetching P36495 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MITFTFMSLVTSVKDYVEITHKLIEIEPLKNYTEFGAVFTYFIFSIGEFF    50
  51  KNFFSFSFLNNIWSIPIIIPDIASAMISEVSVLDGYFHNAFTFLETSVNT   100
 101  TTNPSLVIFEKFVIGIINSLFLILPTSTSHLITLRRFVMQGLEAGYMAGL   150
 151  GTLAGNFLWLASIILGWRFFVIPWLSLDIFRYLLGFVLLVKYIWDSSKER   200
 201  RMALEDLSKWKIFLLNFLLALTEQSCIYPFISNLSFGPDASILEGFPVDN   250
 251  YPQFLLIHGAYLLGILFGSFSLLQFTCWFWENPAFSIYLWITTKSSLKIS   300
 301  TSSYYKILNFTFLYATMLCAIASIPYYGLDYTITNPIGLVPQDRILNQKK   350
 351  SQSDPDKLITETAFLNLNPTDKNSRIRDGVHARRERWKQRLIKYQAFDAS   400
 401  TYDQGVYDFLTIEDLNYGFDRFWLRRKMRNHQIRFRLFPGPWMRSLKKQL   450
 451  NNPANPSLETSTKAASGPRVEFFRILFEQFYHPNFHDRAAMQTNPAEARN   500
 501  KFISTSPLASTESKKALNSTFSLGNINNSSTGIEGLVLTNTQATLLPTDL   550
 551  QTKRTIKPGLIYTNSALRKFVRNVNTRLNLKLLNSKETNLTTKYKSQFIY   600
 601  SKRWKSIFSKIQPLQNGTTRKSYQLFRNVAKQILVTPDAKSLKLITINQK   650
 651  LSLKERKLLELRTQYNNNSTLTTTAPLTLVRPLNVYLQKEEAFKRKLRYY   700
 701  GTMPMRKLTVGNQAPYFKALMKRGFYYYKPTLRWRKTLYVASLRRGFRKK   750
 751  SRKQRILVMPSNQQNFNNTLDNTKTNINQNNLANPLGGNEVPMYGADGEN   800
 801  SLITKPTHSYTVLGKRASRYRHQIYKDVLQHWYYTPFNRLLMKFDVDAFI   850
 851  NRQPKSHFLTKNEERALHIRRFLLSEHYDTLRWYTYMQHYKTMKTNIGGT   900
 901  KSFANRAYNQQFQGTFKKIRHLFAITPKQGDFYTLKFDQPLYNDNKLKDN   950
 951  LYFHEELLTDYYNGTNLQTNQTSNISVNSTTTFIDNSLRTTQLPVPSSSF  1000
1001  DIVNQSSTLIGLTTMQNALRKNVVESTLTSLNSDGEAATSQPKLNFVYSE  1050
1051  LFVKLIKECKKRIHDQTFLKNYITHRIEKREQLNQEQTKELNKRLEKLKV  1100
1101  WLNSDKGSISKLQNTPVQDPNISSPDKVLTTAMQKAVNESISLSGIMPSD  1150
1151  KIKTTYGNLTNAYTIKTENAILTKLNVINQLTNNETTTQKNTLIKSIGVN  1200
1201  KIQTVLQTIITNFKSSLYNQTQLLRVKTDKDLQWWRTKQRVITKRKSARK  1250
1251  RDRFKKQIAVVNKKLAALSKKVETEKSNLYQTLYGNYEISDYLLRNVPTG  1300
1301  SSAVIDSTVLRKKQDNQAYLPKETNNVQFNSFVDSNNNVWQTFFAKKLRK  1350
1351  KISSKGRRYRSLSLARYLTATRKPRLVGLDNLTKIDNITTLQGAFITKEE  1400
1401  KQDSLNLTIQRKQELTNSLKKSQIKKRSRHSWKKRSRHQFSRNHYKYRKR  1450
1451  HTHGNGKLRVMNKKLKKFKATNELRQWWWNSFLPRYLSNLQVNNSTLTNK  1500
1501  NVSFKPLSNTNSVPSTNMASPTTSRNLLDNLNSSNQISTSASMNQNIVTE  1550
1551  SVKVETNQVYLPEGEKSFDITSMTTTLPFYAGWDESLKKFVVTNRLLSRR  1600
1601  DAGLSVNNNPQEINFTNPPIQGLNEGSFLYWQTEMPFNSYNIDQFITTNQ  1650
1651  SFYAPLGWRRFEFRHSILKTWVNNTKAGNNNIKKKTLIISLKNLQPLKSS  1700
1701  QQKQNQIKTKKLVARRIKKRYKLLKQMPNQLMYSPTGPLLTEVLPSHYIS  1750
1751  VFDQQYRLPRNRYLKRNPLKTLKKTTLLALMDSSKQTNGVNKEFTLRKRV  1800
1801  KPRRKYHRKRFIKKDGLIFPRRTKFNTNTTLTGNALITNNVNSIEEDDLR  1850
1851  WRPSSRTKQKRKDNTRSSAASKTKSNKRVKTNPLRLRQLRRREFQQVLKP  1900
1901  LQRYIPQNGGFTWPGDYLRLEIVEMPKLKSINIKKTSLKQKINVQPVGIM  1950
1951  PRKYLIEKHNIKVLKKKLSQAYSTQQLTKVVQEYKNLIQNSPPAI       1995

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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