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

NucPred

Fetching O00555 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MARFGDEMPARYGGGGSGAAAGVVVGSGGGRGAGGSRQGGQPGAQRMYKQ    50
  51  SMAQRARTMALYNPIPVRQNCLTVNRSLFLFSEDNVVRKYAKKITEWPPF   100
 101  EYMILATIIANCIVLALEQHLPDDDKTPMSERLDDTEPYFIGIFCFEAGI   150
 151  KIIALGFAFHKGSYLRNGWNVMDFVVVLTGILATVGTEFDLRTLRAVRVL   200
 201  RPLKLVSGIPSLQVVLKSIMKAMIPLLQIGLLLFFAILIFAIIGLEFYMG   250
 251  KFHTTCFEEGTDDIQGESPAPCGTEEPARTCPNGTKCQPYWEGPNNGITQ   300
 301  FDNILFAVLTVFQCITMEGWTDLLYNSNDASGNTWNWLYFIPLIIIGSFF   350
 351  MLNLVLGVLSGEFAKERERVENRRAFLKLRRQQQIERELNGYMEWISKAE   400
 401  EVILAEDETDGEQRHPFDALRRTTIKKSKTDLLNPEEAEDQLADIASVGS   450
 451  PFARASIKSAKLENSTFFHKKERRMRFYIRRMVKTQAFYWTVLSLVALNT   500
 501  LCVAIVHYNQPEWLSDFLYYAEFIFLGLFMSEMFIKMYGLGTRPYFHSSF   550
 551  NCFDCGVIIGSIFEVIWAVIKPGTSFGISVLRALRLLRIFKVTKYWASLR   600
 601  NLVVSLLNSMKSIISLLFLLFLFIVVFALLGMQLFGGQFNFDEGTPPTNF   650
 651  DTFPAAIMTVFQILTGEDWNEVMYDGIKSQGGVQGGMVFSIYFIVLTLFG   700
 701  NYTLLNVFLAIAVDNLANAQELTKDEQEEEEAANQKLALQKAKEVAEVSP   750
 751  LSAANMSIAVKEQQKNQKPAKSVWEQRTSEMRKQNLLASREALYNEMDPD   800
 801  ERWKAAYTRHLRPDMKTHLDRPLVVDPQENRNNNTNKSRAAEPTVDQRLG   850
 851  QQRAEDFLRKQARYHDRARDPSGSAGLDARRPWAGSQEAELSREGPYGRE   900
 901  SDHHAREGSLEQPGFWEGEAERGKAGDPHRRHVHRQGGSRESRSGSPRTG   950
 951  ADGEHRRHRAHRRPGEEGPEDKAERRARHREGSRPARGGEGEGEGPDGGE  1000
1001  RRRRHRHGAPATYEGDARREDKERRHRRRKENQGSGVPVSGPNLSTTRPI  1050
1051  QQDLGRQDPPLAEDIDNMKNNKLATAESAAPHGSLGHAGLPQSPAKMGNS  1100
1101  TDPGPMLAIPAMATNPQNAASRRTPNNPGNPSNPGPPKTPENSLIVTNPS  1150
1151  GTQTNSAKTARKPDHTTVDIPPACPPPLNHTVVQVNKNANPDPLPKKEEE  1200
1201  KKEEEEDDRGEDGPKPMPPYSSMFILSTTNPLRRLCHYILNLRYFEMCIL  1250
1251  MVIAMSSIALAAEDPVQPNAPRNNVLRYFDYVFTGVFTFEMVIKMIDLGL  1300
1301  VLHQGAYFRDLWNILDFIVVSGALVAFAFTGNSKGKDINTIKSLRVLRVL  1350
1351  RPLKTIKRLPKLKAVFDCVVNSLKNVFNILIVYMLFMFIFAVVAVQLFKG  1400
1401  KFFHCTDESKEFEKDCRGKYLLYEKNEVKARDREWKKYEFHYDNVLWALL  1450
1451  TLFTVSTGEGWPQVLKHSVDATFENQGPSPGYRMEMSIFYVVYFVVFPFF  1500
1501  FVNIFVALIIITFQEQGDKMMEEYSLEKNERACIDFAISAKPLTRHMPQN  1550
1551  KQSFQYRMWQFVVSPPFEYTIMAMIALNTIVLMMKFYGASVAYENALRVF  1600
1601  NIVFTSLFSLECVLKVMAFGILNYFRDAWNIFDFVTVLGSITDILVTEFG  1650
1651  NNFINLSFLRLFRAARLIKLLRQGYTIRILLWTFVQSFKALPYVCLLIAM  1700
1701  LFFIYAIIGMQVFGNIGIDVEDEDSDEDEFQITEHNNFRTFFQALMLLFR  1750
1751  SATGEAWHNIMLSCLSGKPCDKNSGILTRECGNEFAYFYFVSFIFLCSFL  1800
1801  MLNLFVAVIMDNFEYLTRDSSILGPHHLDEYVRVWAEYDPAAWGRMPYLD  1850
1851  MYQMLRHMSPPLGLGKKCPARVAYKRLLRMDLPVADDNTVHFNSTLMALI  1900
1901  RTALDIKIAKGGADKQQMDAELRKEMMAIWPNLSQKTLDLLVTPHKSTDL  1950
1951  TVGKIYAAMMIMEYYRQSKAKKLQAMREEQDRTPLMFQRMEPPSPTQEGG  2000
2001  PGQNALPSTQLDPGGALMAHESGLKESPSWVTQRAQEMFQKTGTWSPEQG  2050
2051  PPTDMPNSQPNSQSVEMREMGRDGYSDSEHYLPMEGQGRAASMPRLPAEN  2100
2101  QRRRGRPRGNNLSTISDTSPMKRSASVLGPKARRLDDYSLERVPPEENQR  2150
2151  HHQRRRDRSHRASERSLGRYTDVDTGLGTDLSMTTQSGDLPSKERDQERG  2200
2201  RPKDRKHRQHHHHHHHHHHPPPPDKDRYAQERPDHGRARARDQRWSRSPS  2250
2251  EGREHMAHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTPSTPRPHVSYS  2300
2301  PVIRKAGGSGPPQQQQQQQQQQQQQAVARPGRAATSGPRRYPGPTAEPLA  2350
2351  GDRPPTGGHSSGRSPRMERRVPGPARSESPRACRHGGARWPASGPHVSEG  2400
2401  PPGPRHHGYYRGSDYDEADGPGSGGGEEAMAGAYDAPPPVRHASSGATGR  2450
2451  SPRTPRASGPACASPSRHGRRLPNGYYPAHGLARPRGPGSRKGLHEPYSE  2500
2501  SDDDWC                                              2506

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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