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

NucPred

Fetching Q6BKC2 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MARGGSRRRNTSVISTQKIEPSNESTKAPEGPQKRKPKTEIPNSNGNGVI    50
  51  KKEIKKRKLDNELDESQEHLAQLITDFNLSVNELFQLKEYKTIAYWNPDD   100
 101  FSRASSTSQVPEIFDLFSKEPEYQISWGADSNEQDLSNIPLRLQKKIINE   150
 151  REQKLLEKFPFKEKVLKRSRDLEIELLQNIRQSKKTLEKSHIKPSPPVKP   200
 201  SKTSKGNQKIIKKKQVVKQEEEEAQENHQNEEYESDMDEGTHYKLKAVKY   250
 251  SIPPPIVTHPSHIPSWVPDPNHTESSFNSKDSEIIDYHPDAIQFVSNSKT   300
 301  TYTTPNIQAKIQNFLASYKSAIIDETSSGDFNNTLEEYEKIMTQQEQFIK   350
 351  KLYEKTSIEKRLELNGEKIERRKTVLPHSSNTKQAVDPFRSHGAIIPKTQ   400
 401  GVTIHSTHHDYFLSHGMAFSRLHQQMRRQHQLRTKKITQMIEQHFKKKKG   450
 451  EKERLAKEKEQNLKRISKMAVQAVKKRWIQASKVYRFLQLQKEEELKKIK   500
 501  GREHLSQMLEHSTQLLEAQFNKSSRDISEVDTENENETDDHLSSSSDEDS   550
 551  GSPQNARDDSNVNMDENDMQLTVEELRAKYADIDQSIEPSSKTISSDSSN   600
 601  HESDSDDEDIDANKGLVALYGNNAVSVEPVSSLAATEYTDEQKTLIEKFS   650
 651  KEDEGISSESVSDDSLNDSSSSESDDDSEVDESNHKQVDSTKPTGLAALL   700
 701  GNGPTEDEEDSNDDVSADSDGNVSDDENMSTTDEEDEPKTPKSSEDPKMD   750
 751  EKENESDVLEEEVNGSKVRDVPLPPLLRGTLRPYQKQGLNWLASLYNNGT   800
 801  NGILADEMGLGKTIQTISLLAYLAAEHHIWGPHLIVVPTSVMLNWEMEFK   850
 851  KFAPGFKVLTYYGSPQQRAQKRKGWNKPNAFHVCITSYQLVVHDHQSFKR   900
 901  RRWRYMILDEAHNIKNFRSARWRALLNFNTENRLLLTGTPLQNNLMELWS   950
 951  LLYFLMPSSKVNQAMPDGFANLEDFQTWFGRPVDKILEKTSNGTSSDVID  1000
1001  ENDKTTQRMDEETRNTVSRLHQVLRPYLLRRLKKDVEKQMPGKYEHIIYC  1050
1051  RLSKRQRYLYDDFMSRAQTKETLASGNFLSIINCLMQLRKVCNHPDLFEV  1100
1101  RPIVTSLAMPRCVANSFASTDSVVRKYLNDDSFKGQVSLKALNLDITSLD  1150
1151  QLNYFTSQTTSKLKSSSELDKQADKLNELISASEYDQPNLDNFLEYYKFI  1200
1201  KSNEQVGIRDNLKHASYLNSLRCDRIPLLGESVIKFLQTATQPRQPFTDA  1250
1251  YNDIILSIPKRVEKMDDVIEKYSVLTPSVVTLDLKDQLIPLSTQRTIMNE  1300
1301  VANKNIDNPFHKSQVKLSIAFPDKSLLQFDCGKLQKLATLLQDLTANGHR  1350
1351  ALIFTQMTKVLDILEQFLNIHGYRYMRLDGATKIEDRQLLTEKFNRDSKI  1400
1401  PVFILSTRSGGLGINLTGADTVIFYDSDWNPAMDKQCQDRCHRIGQSRDV  1450
1451  HIYRFVSEYTIESNILRKANQKRQLDNVVIQEGEFTTDYFGKFSVKDLVN  1500
1501  DAEVADIPDKPLEPAYGNVENVLAQAEDEDDRVAANAAMKEVAIDDEDFD  1550
1551  EESKAATNTATPSQTPGPDTAGSGIVDSTVKINNKTDSLEDVDYEDGVSH  1600
1601  VDEYMLRFIANGYYWD                                    1616

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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