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

NucPred

Fetching Q9WUF3 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MAADDDNGDGTGLFDVCPASPLKNNDEGSLDIYAGLDSAVSDSTARSCVS    50
  51  FRNCLDLYEEILTEEGTAKEATYNDLQIEYGKCQQQMKDLMKRFKEIQTQ   100
 101  NLNLKNENQSLKKNISALIKTARVEINRKDEEINHLHQRLSEFPHFRNNH   150
 151  KTARTKDSQSTSPHLDDCSKTDHGVKSDVQKDVHPNTAQPNLEKEGKSHS   200
 201  EAQNPLHLSTGVEKHCANNVWSRSPYQVGEGNSNEDNRRGRSGTRHSQCS   250
 251  RGTDRTQKDLHSSCNDSEPRDKEANSRLQGHPEKHGNSEARTESKISESK   300
 301  SSTGMGYKSERSASSWEKETSRERPHTRVESQHDKNLEKQNERLQNMHRK   350
 351  ELPSQDKTERKVDVKFKPAGEEQGHRGRVDRALPPHPKNDVKHYGFNKYH   400
 401  PEERRGREDCKRDRGMNSHGFQDRRCSSFLSSNRNSKYPHSKEVSVAHQW   450
 451  ENTPFKAERHRTEDRRKRERENKEESRHVKSDKKSPPEHLQRTHKDTKKS   500
 501  TADGKRQTEPKHGKGAVSNSELSKGTDSKEGATKVESGPNEAKGKDLKLS   550
 551  FMEKLNLTLSPAKKQPACQDNPHQITGVPEPSGTCDSRSLETTGTVACLP   600
 601  SGSEHNREETKSELPEPKEALLATSQLRISIPENKMKEEKRLLFKSVENT   650
 651  VPCELLACGTEISLPAPVEIEQARCLLGSVEVEETCGGARTAASVVMHVL   700
 701  PEHASEDASQELDTKRHDGINACAISEGVKTKVILSPKAAAASESHLAPL   750
 751  VEEPSISLVNCSGDNNPKLEPSLEERPIVETKSCPLESCLPKETFVPSPQ   800
 801  KTELIDHKIETGESNSVYQDDDNSVLSIDFNNLRPIPDPISPLNSPVRPV   850
 851  CKVVSMESSCAIPLYDSSHKDEFPSNSTLSTFKSQSDLNKENEKPVPKFD   900
 901  KCSEADSCKHLSLDELEEGEIRSDDEESVAQKRLEKSARPRVSAEVQPGK   950
 951  SSPGSRRSTVHVHKDNGRTAVKLPRDRLTWSKRSSESRPSNTERKSKTMS  1000
1001  ISSLEKILPLILVPSSLWEVMHMLRLLGKHVRKNYMKFKIKFSLTQFHRI  1050
1051  IESAILSFTSLVKCLDLSKICKSVSTLQKSLCEVIESNLKQVKKNGIVDR  1100
1101  LFEQQQTDMKKKLWKFVDEQLDYLFEKLKKILLKFCDSVNFENENSEGKL  1150
1151  GKKYKERTQHSNCQKKKMDNKEIRREKVLKSENTVNFKSSLGCEKSEEKH  1200
1201  QDQNKTNASIVKHDVKRTFSTCSDNTKNAECKEQFLEKSCPSTPRPGKDE  1250
1251  GHTEEEAQAAQHASAKSERSFEILTEQQASSLTFNLVSDAQMGEIFKSLL  1300
1301  QGSDLLDTSGTEKAEWELKTPEKQLLESLKCESAPACATEELVSEGASLC  1350
1351  PKVISDDNWSLLSSEKGPSLSSGLSLPVHPDVLDENCMFEVSSNTALGKD  1400
1401  NVYSSEKSKPCISSILLEDLAVSLTVPSPLKSDGHLSFLKPEVLSTSTPE  1450
1451  EVISAHFSEDALLEEEDASEQDIHLALESDNSSSKSSCSSWTSRSVASGF  1500
1501  QYHPNLPMHAVIMEKSNDHFIVKIRRATPSTSPGLKHGVVAEESLTSLPR  1550
1551  TGKEAGVATEKEPNLFQSTVLKPVKDLENTDKNIDKSKLTHEEQNSIVQT  1600
1601  QVPDIYEFLKDASNKVVHCDQVVDDCFKLHQVWEPKVSENLQELPSMEKI  1650
1651  PHSLDNHLPDTHIDLTKDSATETKSLGELMEVTVLNVDHLECSQTNLDQD  1700
1701  AEITCSSLQPDTIDAFIDLTHDASSESKNEGSEPVLAVEGMGCQVICIDE  1750
1751  DTNKEGKMGRANSPLESIVEETCIDLTSESPGSCEIKRHNLKSEPPSKLD  1800
1801  CLELPETLGNGHKKRKNSPGVSHSSQKKQRKDIDLSSEKTQRLSPNSDRN  1850
1851  GDAHRKQASKKREPAVNETSLSSEASPEVKGSTAVLAASPASLSAKNVIK  1900
1901  KKGEIIVSWTRNDDREILLECQKRMPSLKTFTYLAVKLNKNPNQVSERFQ  1950
1951  QLKKLFEKSKCR                                        1962

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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