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

NucPred

Fetching O13731 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MQLHDPPAPLSQPSASRLQKYLLESAEKHAYDSNEESKTHLLQEVFLSLL    50
  51  NYNEDNWKYFLKEKPGAITSDFRLSRLQHSEPECAQELQDKRSGSKVCGH   100
 101  VFRAGEVIYRCKNCGLDNTCVLCAPCFHATNHEGHETHVSISTSYSGICD   150
 151  CGDPEAWNVDLNCKIHNVPDDEEQKKPEEVIPLELQHSIRTTIHILLDFI   200
 201  LDVFSCSPVNLKAQSTVGSILADEEASRLSSAKYGVADRPCNVFRVMLWN   250
 251  DEVHTFDAVVGSVLEALDSSNTAFGLEVAQRVDSIGRFAVATSASVHEAI   300
 301  RIANAISKENLAVNVRTARDFFREDICGILLEWFDDLLESHVCYFADYLQ   350
 351  IIVCDEILKNWSPGLEKPAKPEVNFNNLPLEIVNDDDSEDDIYAAEELLD   400
 401  VIANLQDETGVTRIANLGGDEDFEADMTDPTIAGFDHPLDDDNDVNDLLD   450
 451  FETEREDIDDLTDEVMETEENEAAEADYPGVNRNTRQDDVQDISMETESQ   500
 501  NETDESQNTENVDYNPQTHTPVPIPTTATQDVVTIRPEFNSQLLNNLRQI   550
 551  INARRRPRPAAVCQVSLREDYWKSPHPIPPSSYSFVESPSSILRLDYFLL   600
 601  FDLKFWKRLRGLLSKLYVVPFNRNLLFKRLMGIRFVIHYRSLATAFLFAD   650
 651  REPDHSVMFLSVQFFTTPSLAEAVVKDYDFLTNLNATTLSLLTQSNRPST   700
 701  LFSSDIEYTPTIQLNRQVLKTRRTYNLFSDLGYLLQHPQVKKLVVDDTRY   750
 751  VHQYIDLLRVFQGVIPQQRAILSHVQWDFPHGKNILFVMQRVAMLSNTVS   800
 801  SCFTQAPYERLFYAIKCIITSITHPKLDIAESLEPLSCIPSSSLTNFTQP   850
 851  LVPFSVSRDPISFYHPLHWMLSNLFSYCRVDASSHWDKDTLLALLDHPLR   900
 901  VCVLLAQIDCNLWIRNGRSILLTDAFYRQLNNIEVSYDKDILAIQTILMF   950
 951  VDPNLVLNAVVQRFEFTDWLYNLTYNEHPNYDTERIPAMLCKMLELLIAL  1000
1001  ITEREQILHVDIQDIIRTRLAQQLCFGPLAYSALLSTISSNLVESLSFDK  1050
1051  IREEVTSYKAPDGLHDFGVYSLKDEYYDLVDPYYFHYNKNEREESDTILK  1100
1101  KRLAKKNNVSAESIIIEPKIRFLEKDGHDIFFAAVNASTFSLIIFRAIEY  1150
1151  ALVQAESFGSSDIGNTILGDALQLCLISMKIHEFSKSNDFCSRSCAERYP  1200
1201  TDSSIMREFGGSAYCLAELCFAILKSPKYKDVHVKVNAVLAGLQKNDPSA  1250
1251  YSNMLEATHFELSTTSSTSDSNEIEKTQEKKRLALEKQKKIMQQFRDQQA  1300
1301  SFLAQNTDFDIGEDQTEDEVTTEEPEEEVKYHEHIRGNCLLCQEECNDQA  1350
1351  PYGVIGIIQGSSLLRKTDVHSEIILDEIYSVPPNLDRESHSRPFGKKYDT  1400
1401  VVFNRSKDRLLSAYPPGNNIRGVFVSGCGHLMHLGCFKNYYVARSMYRND  1450
1451  VTAGLSEYYYKYSTAKFFMCPLCRSLSNVLLPMPQIPKMCLNIDTLNFPR  1500
1501  SMNGWLEEIGTMSSSSFEYQLVRSSLSDTKDTFRSCFLRPWINSKIISAM  1550
1551  LARLKIADGALIDQSNNRDVSDLYDRYCETTKLAMKLVKGSTFTNVSPHD  1600
1601  LLNSLAYTVSSLEVSQRCSPKQSGATRSVWFNELGPLTLSFLPTLSDTVL  1650
1651  KCVCDQIIKSDQQALLLMESQKLLVCKIFYRHSQLKSMLRNGRMSDHDQI  1700
1701  QPFLLSNTFDDFVKISSLMLIFGKQDNILYYVKLFYLSEICKTIISMIKV  1750
1751  VADSSVVPDLTINYSQQSKSQFYILCKNVLLWCGSSNNIEILDDESNLLR  1800
1801  LMSLVEKYSLPFLRRVALVLYCMFDISLEFNEFSNNEDDSELERLSKLIK  1850
1851  VPPLQELYSQMSSDENNQILELIAGWCEHLAQNTWGDSTISLEYPGIYEL  1900
1901  VKLPHRLENLIDSMQESVCCMCHKTPILPAICMLCGSVICFNARQNTVSS  1950
1951  RRLTGECNKHAATCTGSVGIFFITKACGILLLDSISNTGTIMPTPYLDIH  2000
2001  GETDLQLRRGCPQFLNQKRYDFVVREQWLRQTVLQKMARHMDMTEMQNWR  2050
2051  MA                                                  2052

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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