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

NucPred

Fetching Q07889 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MQAQQLPYEFFSEENAPKWRGLLVPALKKVQGQVHPTLESNDDALQYVEE    50
  51  LILQLLNMLCQAQPRSASDVEERVQKSFPHPIDKWAIADAQSAIEKRKRR   100
 101  NPLSLPVEKIHPLLKEVLGYKIDHQVSVYIVAVLEYISADILKLVGNYVR   150
 151  NIRHYEITKQDIKVAMCADKVLMDMFHQDVEDINILSLTDEEPSTSGEQT   200
 201  YYDLVKAFMAEIRQYIRELNLIIKVFREPFVSNSKLFSANDVENIFSRIV   250
 251  DIHELSVKLLGHIEDTVEMTDEGSPHPLVGSCFEDLAEELAFDPYESYAR   300
 301  DILRPGFHDRFLSQLSKPGAALYLQSIGEGFKEAVQYVLPRLLLAPVYHC   350
 351  LHYFELLKQLEEKSEDQEDKECLKQAITALLNVQSGMEKICSKSLAKRRL   400
 401  SESACRFYSQQMKGKQLAIKKMNEIQKNIDGWEGKDIGQCCNEFIMEGTL   450
 451  TRVGAKHERHIFLFDGLMICCKSNHGQPRLPGASNAEYRLKEKFFMRKVQ   500
 501  INDKDDTNEYKHAFEIILKDENSVIFSAKSAEEKNNWMAALISLQYRSTL   550
 551  ERMLDVTMLQEEKEEQMRLPSADVYRFAEPDSEENIIFEENMQPKAGIPI   600
 601  IKAGTVIKLIERLTYHMYADPNFVRTFLTTYRSFCKPQELLSLIIERFEI   650
 651  PEPEPTEADRIAIENGDQPLSAELKRFRKEYIQPVQLRVLNVCRHWVEHH   700
 701  FYDFERDAYLLQRMEEFIGTVRGKAMKKWVESITKIIQRKKIARDNGPGH   750
 751  NITFQSSPPTVEWHISRPGHIETFDLLTLHPIEIARQLTLLESDLYRAVQ   800
 801  PSELVGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVETENLEERVA   850
 851  VVSRIIEILQVFQELNNFNGVLEVVSAMNSSPVYRLDHTFEQIPSRQKKI   900
 901  LEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKR   950
 951  HGKELINFSKRRKVAEITGEIQQYQNQPYCLRVESDIKRFFENLNPMGNS  1000
1001  MEKEFTDYLFNKSLEIEPRNPKPLPRFPKKYSYPLKSPGVRPSNPRPGTM  1050
1051  RHPTPLQQEPRKISYSRIPESETESTASAPNSPRTPLTPPPASGASSTTD  1100
1101  VCSVFDSDHSSPFHSSNDTVFIQVTLPHGPRSASVSSISLTKGTDEVPVP  1150
1151  PPVPPRRRPESAPAESSPSKIMSKHLDSPPAIPPRQPTSKAYSPRYSISD  1200
1201  RTSISDPPESPPLLPPREPVRTPDVFSSSPLHLQPPPLGKKSDHGNAFFP  1250
1251  NSPSPFTPPPPQTPSPHGTRRHLPSPPLTQEVDLHSIAGPPVPPRQSTSQ  1300
1301  HIPKLPPKTYKREHTHPSMHRDGPPLLENAHSS                   1333

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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