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

NucPred

Fetching Q03149 from www.uniprot.org...

The NucPred score for your sequence is 0.46 (see score help below)

   1  MEDPYRVYLFGDQTGDFEVGLRRLLQAKNHSLLSSFLQRSYHAVRQEISH    50
  51  LPPSERSTFPRFTSIGDLLARHCESPGNPAIESVLTCIYQLGCFINYYGD   100
 101  LGHTFPSHSQSQLVGLCTGLLSCAAVSCASNIGELLKPAVEVVVVALRLG   150
 151  LCVYRVRKLFGQDQAAPLSWSALVSGLSESEGTSLIDKFTRRNVIPPSSR   200
 201  PYISAVCANTLTISGPPVVLNQFLDTFISGKNKAVMVPIHGPFHASHLYE   250
 251  KRDVEWILKSCNVETIRNHKPRIPVLSSNTGELIVVENMEGFLKIALEEI   300
 301  LLRQMSWDKVTDSCISILKSVGDNKPKKLLPISSTATQSLFNSLKKSNLV   350
 351  NIEVDGGISDFAAETQLVNQTGRAELSKIAIIGMSGRFPEADSPQDFWNL   400
 401  LYKGLDVHRKVPEDRWDADAHVDLTGTATNTSKVPYGCWIREPGLFDPRF   450
 451  FNMSPREALQADPAQRLALLTAYEALEGAGFVPDSTPSTQRDRVGIFYGM   500
 501  TSDDYREVNSGQDIDTYFIPGGNRAFTPGRINYYFKFSGPSVSVDTACSS   550
 551  SLAAIHLACNSIWRNDCDTAITGGVNILTNPDNHAGLDRGHFLSRTGNCN   600
 601  TFDDGADGYCRADGVGTVVLKRLEDALADNDPILGVINGAYTNHSAEAVS   650
 651  ITRPHVGAQAFIFKKLLNEANVDPKNISYIEMHGTGTQAGDAVEMQSVLD   700
 701  VFAPDHRRGPGQSLHLGSAKSNIGHGESASGVTSLVKVLLMMKENMIPPH   750
 751  CGIKTKINHNFPTDLAQRNVHIALQPTAWNRPSFGKRQIFLNNFSAAGGN   800
 801  TALLLEDGPVSDPEGEDKRRTHVITLSARSQTALQNNIDALCQYISEQEK   850
 851  TFGVKDSNALPSLAYTTTARRIHHPFRVTAIGSSFQEMRDSLIASSRKEF   900
 901  VAVPAKTPGIGFLFTGQGAQYAAMGKQLYEDCSHFRSAIEHLDCISQGQD   950
 951  LPSILPLVDGSLPLSELSPVVVQLGTTCVQMALSSFWASLGITPSFVLGH  1000
1001  SLGDFAAMNAAGVLSTSDTIYACGRRAQLLTERCQPGTHAMLAIKAPLVE  1050
1051  VKQLLNEKVHDMACINSPSETVISGPKSSIDELSRACSEKGLKSTILTVP  1100
1101  YAFHSAQVEPILEDLEKALQGITFNKPSVPFVSALLGEVITEAGSNILNA  1150
1151  EYLVRHCRETVNFLSAFEAVRNAKLGGDQTLWLEVGPHTVCSGMVKATLG  1200
1201  PQTTTMASLRRDEDTWKVLSNSLSSLYLAGVDINWKQYHQDFSSSHRVLP  1250
1251  LPTYKWDLKNYWIPYRNNFCLTKGSSMSAASASLQPTFLTTSAQRVVESR  1300
1301  DDGLTATVVVHNDIADPDLNRVIQGHKVNGAALCPSSLYADSAQTLAEYL  1350
1351  IEKYKPELKGSGLDVCNVTVPKPLIAKTGKEQFRISATANWVDKHVSVQV  1400
1401  FSVTAEGKKLIDHAHCEVKLFDCMAADLEWKRGSYLVKRSIELLENSAVK  1450
1451  GDAHRLRRGMVYKLFSALVDYDENYQSIREVILDSEHHEATALVKFQAPQ  1500
1501  ANFHRNPYWIDSFGHLSGFIMNASDGTDSKSQVFVNHGWDSMRCLKKFSA  1550
1551  DVTYRTYVRMQPWRDSIWAGNVYIFEGDDIIAVFGGVKFQALSRKILDIA  1600
1601  LPPAGLSKAQTSPIQSSAPQKPIETAKPTSRPAPPVTMKSFVKKSAGPSV  1650
1651  VVRALNILASEVGLSESDMSDDLVFADYGVDSLLSLTVTGKYREELNLDM  1700
1701  DSSVFIEHPTVGDFKRFVTQLSPSVASDSSSTDRESEYSFNGDSCSGLSS  1750
1751  PASPGTVSPPNEKVIQIHENGTMKEIRAIIADEIGVSADEIKSDENLNEL  1800
1801  GMDSLLSLTVLGKIRESLDMDLPGEFFIENQTLDQIETALDLKPKAVPTA  1850
1851  VPQSQPITLPQSQSTKQLSTRPTSSSDNHPPATSILLQGNPRTASKTLFL  1900
1901  FPDGSGSATSYATIPGVSPNVAVYGLNCPYMKAPEKLTCSLDSLTTPYLA  1950
1951  EIRRRQPTGPYNLGGWSAGGICAYDAARKLVLQQGEIVETLLLLDTPFPI  2000
2001  GLEKLPPRLYSFFNSIGLFGEGKAAPPAWLLPHFLAFIDSLDAYKAVPLP  2050
2051  FNEQEWKGKLPKTYLVWAKDGVCPKPGDPWPEPAEDGSKDPREMVWLLSN  2100
2101  RTDLGPNGWDTLVGKENIGGITVIHDANHFTMTKGEKAKELATFMKNALG  2150
2151  VCERRLV                                             2157

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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