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

NucPred

Fetching Q8CIQ7 from www.uniprot.org...

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

   1  MWTPTEEEKYGVVICSFRGSVPQGLVLEIGETVQILEKCEGWYRGVSTKK    50
  51  PNVKGLFPANYIHLKKAIVSNRGQYETVVPLEDSIVTEVTTTLQEWASLW   100
 101  KQLYVKHKVDLFYKLRHVMNELIDLRRQLLSGHLTQDQVREVKRHITVRL   150
 151  DWGNEHLGLDLVPRKDFEVVDSDQISVSDLYKMHLSSRQSVQQSTSQVDT   200
 201  MRPRHGETCRMPVPYHFFFSLKSFTYNTIGEDSDVFFSLYDMREGKQISE   250
 251  RFLVRLNKNGGPRNPEKIERMCALFTDLSSKDMKRDLYIVAHVIRIGRML   300
 301  LNDSKKGPAHLHYRRPYGCAVLSILDVLQSLTELKEEKDFVLKVYTCNNE   350
 351  SEWTQIHENIIRKSSTKYSAPSASHGLIISLQLFRGDMEQIRRENPMIFN   400
 401  RGLAITRKLGFPDVIMPGDIRNDLYLTLEKGDFERGGKSVQKNIEVTMYV   450
 451  LYADGEILKDCISLGSGEPNRSSYHSFVLYHSNSPRWGEIIKLPIPIDRF   500
 501  RGSHLRFEFRHCSTKDKGEKKLFGFAFSPLMRDDGTTLSDDIHELYVYKC   550
 551  DENSTFNNHALYLGLPCCKEDYNGCPNIPSSLIFQRSKESFFISTQLSST   600
 601  KLTQNVDLLALLKWKAFPDRIMDILGRLRHVSGEEIVKFLQDILDTLFVI   650
 651  LDDNTEKYGLLVFQSLVFIINLLRDIKYFHFRPVMDTYIQKHFAGALAYK   700
 701  ELIRCLKWYMDCSAELIRQDHIQEAMRALEYLFKFIVQSRILYSRATCGM   750
 751  EEEQFRSSIQELFQSIRFVLSLDSRNSETLLFTQAALLNSFPTIFDELLQ   800
 801  MFTVQEVAEFVRGTLGSMPSTVHIGQSMDVVKLQSIARTVDSRLFSFSES   850
 851  RRILLPVVLHHIHLHLRQQKELLICSGILGSIFSIVKTSSLEADVMEEVE   900
 901  MMVESLLDVLLQTLLTIMSKSHAQEAVRGHCPVTAEITGEYVSCLLSLLR   950
 951  QMCDTHFQHLLDNFQSKDELKEFLLKIFCVFRNLMKMSVFPRDWMVMRLL  1000
1001  TSNIIVTTVQYLSSALHKNFTETDFDFKVWNSYFSLAVLFINQPSLQLEI  1050
1051  ITSAKRKKILDKYGDMRVMMAYELFSMWQNLGEHKIHFIPGMIGPFLGVT  1100
1101  LVPQPEVRNIMIPIFHDMMDWEQRKNGNFKQVEAELIDKLDSMVSEGKGD  1150
1151  ESYRELFGLLTQLFGPYPSLLEKVEQETWRETGISFVTSVTRLMERLLDY  1200
1201  RDCMKGEETENKKVGCTVNLMNFYKSEINKEEMYIRYIHKLCDMHLQAEN  1250
1251  YTEAAFTLLLYCELLQWEDRPLREFLHYPSQTEWQRKEGLCRKIIHYFNK  1300
1301  GKSWEFGIPLCRELACQYESLYDYQSLSWIRKMEASYYDNIIEQQRLEPE  1350
1351  FFRVGFYGRKFPFFLRNKEYVCRGHDYERLEAFQQRMLSEFPQAVAMQHP  1400
1401  NHPDDAILQCDAQYLQIYAVTPIPDYVDVLQMDRVPDRVKSFYRVNNVRK  1450
1451  FRYDRPFHKGPKDKDNEFKSLWIERTTLTLTHSLPGISRWFEVERRELVE  1500
1501  VSPLENAIQVVENKNQELRALISQYQHKQVHGNINLLSMCLNGVIDAAVN  1550
1551  GGIARYQEAFFDKDYITKHPGDAEKISQLKELMQEQVHVLGVGLAVHEKF  1600
1601  VHPEMRPLHKKLIDQFQMMRASLYHEFPGLDKLSPACSGTSTPRGNVLAS  1650
1651  HSPMSPENIKMTHRHSPMNLMGTGRHSSSSLSSHASSEAGNMMMMGDNSM  1700
1701  GEAPEDLYHHMQLAYHNPRYQGSVTNVSVLSSSQASPSSSSLSSTHSAPS  1750
1751  QMITSAPSSTRGSPSLPDKYRHAREMMLLLPTHRDRPSSAMYPAAILENG  1800
1801  QPPNFQRALFQQVVGACKPCSDPNLSMAEKGHYSLHFDAFHHPLGDTPPA  1850
1851  LPARTLRKSPLHPIPASPTSPQSGLDGSNSTLSGSASSGVSSLSESNFGH  1900
1901  SSEAPPRTDTMDSMPSQAWNGDEGLEPPYLPVHYSLSESAVLDAIKSQPC  1950
1951  RSHSAPGCVLPQDPMDPPALPPKPYHPRLPALEHDEGMLLREEAERPRGL  2000
2001  HRKASLPPGSVKEEQARLAWEHGRGEQ                         2027

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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