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

NucPred

Fetching Q24298 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MSTSVQRMSRSYHCINMSATPQAGHLNPAQQQTHQQHKRKCRDLGRRLIP    50
  51  ARLLLGVIVAISLLSPALALHSPPDKNFSGDNRKPAFKNCAGYAPKVKEE   100
 101  QPENTYVLTVEAVDPDPDQVIRYSIVQSPFERPKFFINPSTGVIFTTHTF   150
 151  DRDEPIHEKFVFVTVQATDNGLPPLDDVCTFNVTIEDINDNAPAFNKARY   200
 201  DESMSENAQPDAVVMTISASDFDDGNNSLVEYEILRERDFQYFKIDKESG   250
 251  IIYLKRPIDKRPGQSYAIIVRAYNVVPDPPQDAQIEVRIRVVESSIKPPS   300
 301  FVNPIDTPIYLKENLKNFTHPIATLRAVSNMPDKPEVIFELNTGRTEQTN   350
 351  SKNTFVFNQIGNEVTISLGKTLDYEAITDYTLTMIVRNTHELGTEHQIKI   400
 401  QVEDVNDNIPYYTEVKSGTILENEPPGTPVMQVRAFDMDGTSANNIVSFE   450
 451  LADNREYFTIDPNTGNITALTTFDREERDFYNVKVIASDNSPSSLFDNGE   500
 501  PNRGHQVFRISIGDKNDHKPHFQQDKYLAERLLEDANTNTEVIEVKAEDE   550
 551  DNASQILYSIESGNVGDAFKIGLKTGKITVNQKLDYETITEYELKVRAFD   600
 601  GIYDDYTTVVIKIEDVNDNPPVFKQDYSVTILEETTYDDCILTVEAYDPD   650
 651  IKDRNADQHIVYSIHQNDGNRWTIDNSGCLRLVKTLDRDPPNGHKNWQVL   700
 701  IKANDEDGVGTTVSTVKEVTVTLKDINDNAPFLINEMPVYWQENRNPGHV   750
 751  VQLQANDYDDTPGAGNFTFGIDSEATPDIKTKFSMDGDYLHANVQFDREA   800
 801  QKEYFIPIRISDSGVPRQSAVSILHLVIGDVNDNAMSEGSSRIFIYNYKG   850
 851  EAPETDIGRVFVDDLDDWDLEDKYFEWKDLPHDQFRLNPSTGMITMLVHT   900
 901  AEGEYDLSFVVTEDSMFVPRHSVDAYVTVVVRELPEEAVDKSGSIRFINV   950
 951  TKEEFISVPRDFQSPDALSLKDRLQLSLAKLFNTSVSNVDVFTVLQNENH  1000
1001  TLDVRFSAHGSPYYAPEKLNGIVAQNQQRLENELDLQMLMVNIDECLIEK  1050
1051  FKCEESCTNELHKSSVPYMIYSNTTSFVGVNAFVQAQCVCEAPLMRRCLN  1100
1101  GGSPRYGENDVCDCIDGFTGPHCELVSVAFYGSGYAFYEPIAACNNTKIS  1150
1151  LEITPQIDQGLIMYLGPLNFNPLLAISDFLALELDNGYPVLTVDYGSGAI  1200
1201  RIRHQHIKMVADRTYQLDIILQRTSIEMTVDNCRLSTCQTLGAPIGPNEF  1250
1251  LNVNAPLQLGGTPVDLEQLGRQLNWTHVPNQKGFFGCIRNLTINEQTYNL  1300
1301  GMPSVFRNIDSGCQQSVAVAFSFGIDRNFIIAIIVCLALLLIILLAVVVQ  1350
1351  KKQKNGWHEKDIDDIRETIINYEDEGGGERDTDYDLNVLRTQPFYEEKLY  1400
1401  KDPHALQGNMRDPNDIPDIADFLGDKKENCDRDVGATTVDDVRHYAYEGD  1450
1451  GNSDGSLSSLASCTDDGDLNFDYLSNFGPRFRKLADMYGEEPSDTDSNVD  1500
1501  DDQGWRI                                             1507

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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