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

NucPred

Fetching Q59LR2 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MTSNQSISTTELLQFLTDIETNIDDHETDFRKLLLYLLRFTNEKLIVIAQ    50
  51  EENKTPTELQLLSKLIDTIELVLSKKTPLLSTLLTIEDVNIIHTTGSGSL   100
 101  VYEVPLHEWCISFALSHIPNFVSHTAGLNQLKRLVFLIVNLVSTQLHSFK   150
 151  VIKSTRIHLLKTLDDNLNFCLQNLLSANTFLFKSKLTTAVNLFSIVHDYD   200
 201  ISQKLSLNLNNYQLKFESCSRKIWFILNEISLVSELDNLNLLDCLKSVFI   250
 251  LDQSSALVLNVSVGWNQIGFLLSCIVEYLQQDFRTLDSNTNNFEFVNLNR   300
 301  SISLSLLNVYIVCFDKDLLENFMSFSNIKGILSKLIYDDSIPSVIRKTLN   350
 351  IVQYTYQLMSNPDGDDIKLYSTSVYNDYVWTPFVDSELESLRARLLDLQG   400
 401  NHEDSRKEELLSFSIDETHKLAKSTNSLNYTDEKAWIRTVKKLIGIDKNV   450
 451  LEDETTLYTLVTALSHYPCILKGDYDYTINECTKCGFGPLTKNNYSSIDP   500
 501  NRFPLNYSTEATTLQDIIQQFLIPKLETQQDPLLCCNTLLLIFNFYASFS   550
 551  PMADMQDHNILDFLLRLLATNDNRDVRMLVARILPLYLIQSKDDKLLDET   600
 601  FKYIFQKVTSIDFSSQHRLHFGESTIRAVVELATVSTGERLCAIYFKLVD   650
 651  WLGEQNEQHSNYVYCGILNLASAKSLPPHKLLSPYLPSVAEIIIKKPQVF   700
 701  ERIIKVSMVTKNYFLNRTKEYTVPRILEYYKDPTLLTQIANAAGLEVGKL   750
 751  LANCLPRILATYLTKESVNERYIMKVLSSVCPDYKMIHTEELFTRIGDIT   800
 801  WYILLEIQMDEFGNIRNLANITRALECVCKNVSLRKNGSELTKNNSINDL   850
 851  IEDQVLLLVQKFSDVTHSSRGAKPYLELKNSFYAIEFLIKGHIDAITSAL   900
 901  GQLSTCLQATLEEPNFHVLSLRCWNELIKKVPPSHLISLIDIIISIILQK   950
 951  FESFGSEAKSIAIEILRKIYEEIKDKYNRYSLYFLSLPFLSYMEDYQMVK  1000
1001  EFRNMKSPSRAMIFSEFTRRLQTSNMYVVKHALFDLSNYFEKYQINCQKD  1050
1051  LFKDPGLTPAITSLVRTILDTAAKFKNKDTTVSTACAKALAIIGALDSNK  1100
1101  FQFKTVKSLIIISSDFEDIEENSTFLVDLIENHLLKIFWASNDPHKQLFA  1150
1151  AYVMQSFLAVMGLDERVLNTKDNRVWNKFTDVAKSTLTPFLKSKYAAPKP  1200
1201  KLDNLKFPFFKLGMKYETWLVDVTLFLLKRASIDNGKGNQKAKTRKLIFQ  1250
1251  SYAVLIQREHDIPLCEHLLRYVALSHVINEGVPEDLHKEFLHILKMDSKS  1300
1301  TSPDRAEQLKLCYQTIFSVLDYFNQWVSNMRVVTSNSGSELTSSDIRHKM  1350
1351  DAVAKFSSFPQDLLTTRSAECDAYERTIMYLENCYRDSQSEKSFKLSNLN  1400
1401  GAATLQDMYAHIDDYDALNGTLKMFSTNNLNEKLTTFQYSDSWSLAHESF  1450
1451  EALGSTKNSVSNNTKLLQSLNEHGLYNEVLSTLSARTDSNDLKSIPLDWS  1500
1501  LMGLHAAVYKGDSKQLEKWLQVINSIGKPHDMETMINYELAKALSFLFQS  1550
1551  RIDMFKGSMDKLYNIIGCSLVPSVSSNFTRNITLMNQLHAIYDVSLIVLS  1600
1601  KDSEDTLDLRIGNVDQDFDTQRNILTLHNVANTVMKNPAMISKNLLRESS  1650
1651  LARKYNRLDISTRSIVQAMSLEDDQANIEFAELQWAQGKQSEAIKCLFDI  1700
1701  LKDNKFHDDKSKAKVQLQYANWLDESNHLSAHQIITEYNKAFHLNMVDEK  1750
1751  CNFDIGKYYNKLMESSNDESGEYEHLTVRNYIRAVSVGTTYIFEALPKVL  1800
1801  TIWLDFADKSNKSNAAENRLKQIIDDLYNAIANVPNYSWYTVLTQILSRI  1850
1851  VHEHEPSFKVLKRIVQNVTLEYPKHCVWYIFSHARSSDKVRKRRVRELLN  1900
1901  QVCTQDGNDTLPKSTMAAGNLFAKLIKIAELKIPKTNRKRQMSLLQDFEV  1950
1951  DLSEPIDDLVIPIQSNLQIQIPSHLNSKHKGFSRSSSISFDGFDDNVNIF  2000
2001  FSLQMPRQLTVRGSDGNAYRLMVKSDDTRKDAKVVEFTTMVNRILSTSTE  2050
2051  ARKRGLQIANYSVVPLSDHFGIIEFVMNVQTMKGVISEQRKRQGIPINER  2100
2101  KVFMHIDSLQKAKKKDSKQLDKLVAGFRAIMDRCPPVLHTWFVEQFSDPS  2150
2151  AWYMARNAFTRSSAVMSMVGYIMGLGDRHCENILIFKNTGAVLHIDFDCL  2200
2201  FEKGTTLPTPEIVPFRLTQNMVDAMGITGVDGIYRITCEVTGTLLRENEQ  2250
2251  ILMNILETLIYDPLIDWRNHNPREDLSKVRKKIRGLINEDEGLPMNIHGQ  2300
2301  VDVLIQEATSLERLSQMYAGWAAYM                           2325

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.)

Go back to the NucPred Home Page.