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

NucPred

Fetching Q59U81 from www.uniprot.org...

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

   1  MPENGRLRRTSARLTQNGTSTSSSTIYQNGKRTSQHAQETSTASNKKRKV    50
  51  STQSKEDKLSDIIVDFNLAVNELYQLKEYKSIISWDPIENSSANDRGIKA   100
 101  EFEEFVKNNDYRLVWDKEIENNSNIDSLPLRFQKKKLAEQNKLLDDKFSI   150
 151  RQNVLASSKMLEESLVNKTRDEVKIESTFKAIQSQEKAGSKLKTPSQTSN   200
 201  AKTNIRKSGSTTPKRGNENGSRKQALEDQDEIIELSDDSSVVEIESDLSD   250
 251  AETHYRIKCIKKTVPPPLVTHPSHIPQWRPENLEDGNRSTGRLIQLKDSS   300
 301  SSSKIINFDPTPLEIIQLKDEVIAAPKLTEKLQNFLNNDFKTPIIDESNV   350
 351  PDYNFTRDEYNTIMSQQEKLLRKLYHKVNIENSLELNGDKIERRKVILPQ   400
 401  SNIKLTDPFRNTFSVKPKLHGAANNATHQDYLLAQGMAFSKVHQQMRKQH   450
 451  HLRTRKIAAMIDQHFKKKKGEKERLAKEREQNLKKMSRLTMQAVKKRWNQ   500
 501  AQKVYQIIQNEKEEELKKIKGRQHLSEMLEHSTQLLEAQLTSSREPTVEA   550
 551  ESDDNSTTFDDNTNDSDNFSSSEEEENEEDNTQQQINGNKKYDVNGKSND   600
 601  ENDMSLSVEELRKKYADLETSVEPLSSNVTSDKERESETSSEDAESSDDD   650
 651  DTDVTRGLASLYQNDEVADFATTTFEYSAEEKKLIEDLNQESDSRMNSLL   700
 701  DSDSVSSISDSESSEESSSDTEMDQSNVSEPPRSSETGSNTGLASLFTNG   750
 751  TIVSDEEDDASISSNFENESDESMNSSDRELEVNGNGKIDKIASTDEDDS   800
 801  NVEIVNGSKVKDVPIPSLLRGTLRPYQKQGLNWLASLYNNNTNGILADEM   850
 851  GLGKTIQTISLLAYLACEHHKWGPHLIIVPTSVMLNWEMEFKKFAPGFKV   900
 901  LTYYGSPQQRAQKRKGWNKPDAFHVCITSYQLVVQDQQSFKRRRWTYMIL   950
 951  DEAHNIKNFRSTRWRALLNFNTENRLLLTGTPLQNNLMELWSLLYFLMPS  1000
1001  SKVNQAMPEGFANLDDFQQWFGKPVDRILEQTSAGNSDLIDENERTTQKM  1050
1051  DEETRNTVARLHQVLRPYLLRRLKKDVEKQMPGKYEHIVYCRLSKRQRFL  1100
1101  YDDFMSRAKTKETLASGNFLSIINCLMQLRKVCNHPDLFEVRPIVTSFAM  1150
1151  PRSIPSYYQSTNELVKRQFNKDEKVSFQALNLDVTGCENMNYFVCQSTGK  1200
1201  LMTTEPFQDQINKLKILLVEFENSDPINYVSYYQRLRREEQAEIKEKLEH  1250
1251  VVYLNNLRCGRKPIYGESLLRLLTVNAHDFSDEPYNKYCLTLSGRVDKMN  1300
1301  DTIEKYSIITPAAVALDMKDQLIPISTKQRILHEVAENKIDNPFHKAQVK  1350
1351  LSIAFPDKTLLQYDCGKLQKLATLLQELTSQGHRALIFTQMTKVLDILEQ  1400
1401  FLNIHGYRYMRLDGATKIEDRQLLTEKFNRDPKIPVFILSTRSGGLGINL  1450
1451  TGADTVIFYDSDWNPAMDKQCQDRCHRIGQVRDVHIYRFVSEYTIESNII  1500
1501  KKANQKRQLDNVVIQEGEFTTDYFGKFSVRDLVSDSNIGKEITDRTIDFS  1550
1551  GDAKMGNVLAQAEDEEDRVAAGAALKEVAIDDDDFKEETRSATTGATPAP  1600
1601  TETNALSTTDGDAAFIDVDYEDGIGHIDEYMLRFISDGYYL           1641

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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