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

NucPred

Fetching Q96RY7 from www.uniprot.org...

The NucPred score for your sequence is 0.46 (see score help below)

   1  MALYYDHQIEAPDAAGSPSFISWHPVHPFLAVAYISTTSTGSVDIYLEQG    50
  51  ECVPDTHVERPFRVASLCWHPTRLVLAVGWETGEVTVFNKQDKEQHTMPL   100
 101  THTADITVLRWSPSGNCLLSGDRLGVLLLWRLDQRGRVQGTPLLKHEYGK   150
 151  HLTHCIFRLPPPGEDLVQLAKAAVSGDEKALDMFNWKKSSSGSLLKMGSH   200
 201  EGLLFFVSLMDGTVHYVDEKGKTTQVVSADSTIQMLFYMEKREALVVVTE   250
 251  NLRLSLYTVPPEGKAEEVMKVKLSGKTGRRADIALIEGSLLVMAVGEAAL   300
 301  RFWDIERGENYILSPDEKFGFEKGENMNCVCYCKVKGLLAAGTDRGRVAM   350
 351  WRKVPDFLGSPGAEGKDRWALQTPTELQGNITQIQWGSRKNLLAVNSVIS   400
 401  VAILSERAMSSHFHQQVAAMQVSPSLLNVCFLSTGVAHSLRTDMHISGVF   450
 451  ATKDAVAVWNGRQVAIFELSGAAIRSAGTFLCETPVLAMHEENVYTVESN   500
 501  RVQVRTWQGTVKQLLLFSETEGNPCFLDICGNFLVVGTDLAHFKSFDLSR   550
 551  REAKAHCSCRSLAELVPGVGGIASLRCSSSGSTISILPSKADNSPDSKIC   600
 601  FYDVEMDTVTVFDFKTGQIDRRETLSFNEQETNKSHLFVDEGLKNYVPVN   650
 651  HFWDQSEPRLFVCEAVQETPRSQPQSANGQPQDGRAGPAADVLILSFFIS   700
 701  EEHGFLLHESFPRPATSHSLLGMEVPYYYFTRKPEEADREDEVEPGCHHI   750
 751  PQMVSRRPLRDFVGLEDCDKATRDAMLHFSFFVTIGDMDEAFKSIKLIKS   800
 801  EAVWENMARMCVKTQRLDVAKVCLGNMGHARGARALREAEQEPELEARVA   850
 851  VLATQLGMLEDAEQLYRKCKRHDLLNKFYQAAGRWQEALQVAEHHDRVHL   900
 901  RSTYHRYAGHLEASADCSRALSYYEKSDTHRFEVPRMLSEDLPSLELYVN   950
 951  KMKDKTLWRWWAQYLESQGEMDAALHYYELARDHFSLVRIHCFQGNVQKA  1000
1001  AQIANETGNLAASYHLARQYESQEEVGQAVHFYTRAQAFKNAIRLCKENG  1050
1051  LDDQLMNLALLSSPEDMIEAARYYEEKGVQMDRAVMLYHKAGHFSKALEL  1100
1101  AFATQQFVALQLIAEDLDETSDPALLARCSDFFIEHSQYERAVELLLAAR  1150
1151  KYQEALQLCLGQNMSITEEMAEKMTVAKDSSDLPEESRRELLEQIADCCM  1200
1201  RQGSYHLATKKYTQAGNKLKAMRALLKSGDTEKITFFASVSRQKEIYIMA  1250
1251  ANYLQSLDWRKEPEIMKNIIGFYTKGRALDLLAGFYDACAQVEIDEYQNY  1300
1301  DKAHGALTEAYKCLAKAKAKSPLDQETRLAQLQSRMALVKRFIQARRTYT  1350
1351  EDPKESIKQCELLLEEPDLDSTIRIGDVYGFLVEHYVRKEEYQTAYRFLE  1400
1401  EMRRRLPLANMSYYVSPQAVDAVHRGLGLPLPRTVPEQVRHNSMEDAREL  1450
1451  DEEVVEEADDDP                                        1462

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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