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

NucPred

Fetching Q8IZD9 from www.uniprot.org...

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

   1  MWTPTEEEKYGVVICSFRGSVPQGLVLEIGETVQILEKCEGWYRGVSTKK    50
  51  PNVKGIFPANYIHLKKAIVSNRGQYETVVPLEDSIVTEVTATLQEWASLW   100
 101  KQLYVKHKVDLFYKLRHVMNELIDLRRQLLSGHLTQDQVREVKRHITVRL   150
 151  DWGNEHLGLDLVPRKDFEVVDSDQISVSDLYKMHLSSRQSVQQSTSQVDT   200
 201  MRPRHGETCRMPVPHHFFLSLKSFTYNTIGEDTDVFFSLYDMREGKQISE   250
 251  RFLVRLNKNGGPRNPEKIERMCALFTDLSSKDMKRDLYIVAHVIRIGRML   300
 301  LNDSKKGPPHLHYRRPYGCAVLSILDVLQSLTEVKEEKDFVLKVYTCNNE   350
 351  SEWSQIHENIIRKSSAKYSAPSASHGLIISLQLLRGDMEQIRRENPMIFN   400
 401  RGLAITRKLGFPDVIMPGDIRNDLYLTLEKGDFERGGKSVQKNIEVTMYV   450
 451  LYADGEILKDCISLGSGEPNRSSYHSFVLYHSNSPRWGEIIKLPIPIDRF   500
 501  RGSHLRFEFRHCSTKDKGEKKLFGFAFSTLMRDDGTTLSDDIHELYVYKC   550
 551  DENSTFNNHALYLGLPCCKEDYNGCPNIPSSLIFQRSTKESFFISTQLSS   600
 601  TKLTQNVDLLALLKWKAFPDRIMDVLGRLRHVSGEEIVKFLQDILDTLFV   650
 651  ILDDNTEKYGLLVFQSLVFIINLLRDIKYFHFRPVMDTYIQKHFAGALAY   700
 701  KELIRCLKWYMDCSAELIRQDHIQEAMRALEYLFKFIVQSRILYSRATCG   750
 751  MEEEQFRSSIQELFQSIRFVLSLDSRNSETLLFTQAALLNSFPTIFDELL   800
 801  QMFTVQEVAEFVRGTLGSMPSTVHIGQSMDVVKLQSIARTVDSRLFSFSE   850
 851  SRRILLPVVLHHIHLHLRQQKELLICSGILGSIFSIVKTSSLEADVMEEV   900
 901  EMMVESLLDVLLQTLLTIMSKSHAQEAVRGQRCPQCTAEITGEYVSCLLS   950
 951  LLRQMCDTHFQHLLDNFQSKDELKEFLLKIFCVFRNLMKMSVFPRDWMVM  1000
1001  RLLTSNIIVTTVQYLSSALHKNFTETDFDFKVWNSYFSLAVLFINQPSLQ  1050
1051  LEIITSAKRKKILDKYGDMRVMMAYELFSMWQNLGEHKIHFIPGMIGPFL  1100
1101  GVTLVPQPEVRNIMIPIFHDMMDWEQRKNGNFKQVEAELIDKLDSMVSEG  1150
1151  KGDESYRELFSLLTQLFGPYPSLLEKVEQETWRETGISFVTSVTRLMERL  1200
1201  LDYRDCMKGEETENKKIGCTVNLMNFYKSEINKEEMYIRYIHKLCDMHLQ  1250
1251  AENYTEAAFTLLLYCELLQWEDRPLREFLHYPSQTEWQRKEGLCRKIIHY  1300
1301  FNKGKSWEFGIPLCRELACQYESLYDYQSLSWIRKMEASYYDNIMEQQRL  1350
1351  EPEFFRVGFYGRKFPFFLRNKEYVCRGHDYERLEAFQQRMLSEFPQAVAM  1400
1401  QHPNHPDDAILQCDAQYLQIYAVTPIPDYVDVLQMDRVPDRVKSFYRVNN  1450
1451  VRKFRYDRPFHKGPKDKENEFKSLWIERTTLTLTHSLPGISRWFEVERRE  1500
1501  LVEVSPLENAIQVVENKNQELRSLISQYQHKQVHGNINLLSMCLNGVIDA  1550
1551  AVNGGIARYQEAFFDKDYINKHPGDAEKITQLKELMQEQVHVLGVGLAVH  1600
1601  EKFVHPEMRPLHKKLIDQFQMMRASLYHEFPGLDKLSPACSGTSTPRGNV  1650
1651  LASHSPMSPESIKMTHRHSPMNLMGTGRHSSSSLSSHASSEAGNMVMLGD  1700
1701  GSMGDAPEDLYHHMQLAYPNPRYQGSVTNVSVLSSSQASPSSSSLSSTHS  1750
1751  APSQMITSAPSSARGSPSLPDKYRHAREMMLLLPTYRDRPSSAMYPAAIL  1800
1801  ENGQPPNFQRALFQQVVGACKPCSDPNLSVAEKGHYSLHFDAFHHPLGDT  1850
1851  PPALPARTLRKSPLHPIPASPTSPQSGLDGSNSTLSGSASSGVSSLSESN  1900
1901  FGHSSEAPPRTDTMDSMPSQAWNADEDLEPPYLPVHYSLSESAVLDSIKA  1950
1951  QPCRSHSAPGCVIPQDPMDPPALPPKPYHPRLPALEHDEGVLLREETERP  2000
2001  RGLHRKAPLPPGSAKEEQARMAWEHGRGEQ                      2030

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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