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

NucPred

Fetching Q9URV2 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MLELKTNVIQDPELKDSLDLQENDRVEIIGDAVHYIVNDHLNRVFNYTVD    50
  51  QQKIHAALITTFASGKKAIVVILDDIGYVYYVGDNNNDSYIINVPFSTES   100
 101  AWSSPSGLYLQRHRSSDENLNTDLPHIFCLNDPLDELTLIKFDGKKILSL   150
 151  FDSIVYVVGEIVVTHNKKEKKLSFWRSRFIDPESDQSIKSSRNRRRESSF   200
 201  SREKNPDLTRSDSIHYTANTRLSEKFEEQGLAYSTIFSHIESFPITGSTS   250
 251  FDSILGNGVLVITTLVKELEKGYMMLFRLVRDRSPYFLDSLQLHAINLSA   300
 301  IKSKHLQKIVVLSSKGKVSLESPMSPSLPIEGTFRSFRVHGATLYLEDTD   350
 351  GVQRYISLDNRASNSLVKWCLSVIRYVLPLREYEIFYTGHLYALFAFKLS   400
 401  HDEAFISSILACFTFFSRDKVHVEPIEDCNEAYSLSSKFHFKKEILIASQ   450
 451  LSSHLDYSTFKNYLMPLAITLHFISEELRLDSVVKPRKDQLVALLLQITT   500
 501  WLKWPRYCEYYNFDIAETFLSIPLSIQVDVEEPVGPTSILQWIIECLRSQ   550
 551  STVPFYGLESYGLPHSCSTMFPQTLSLMQLLDCLLNPNMTLQNLVEEMVR   600
 601  LGISRKRCERYPFGILCIIFTVLEIAAEEYSPNWESEELRLVNRLDVDSF   650
 651  LHPKTPKWVFNKQDQEVKEIKALTSTVTDSTLVDTQSFHPYKVVTDMIFR   700
 701  EDRRLAEVNKLLNYSSQITIMTEHFDVDLSSVPMQQKVAQCICVRTLSVP   750
 751  IGAGMLTYGSKNPLPTEKVTPRLFNFTLHLHPGTLIIQPNKEFVTQELTE   800
 801  WPEFNVGVALGLSISKFSKEINTSWIMFNRPETLTAYHAGFLFGLGLNGH   850
 851  LKALATWHSFIYLTSKHDTTSIGLLLGLASSYLGSMDAKVTKLLSVHISA   900
 901  LLPVGSNELNISPLTQTAGILGIGLLFHDSCHRRMSEVTMEEILASNESE   950
 951  LKNEGYKLAAGFSLGLINLGRGSNLPGMSDLKLVSRLQVGISSQATFQSL  1000
1001  EAGSPGAIMALTMIYMKTNDLEVAKKIDIPKSRYLLDFYRPDLILLRVAG  1050
1051  KNLIMWDEVKADYEWVKYQIPDIMLSQFDLQEKKVLSSDDLLLYNVLAGI  1100
1101  CFSLGLRFAGTGNPKAKEILINFLDSFIRLCHLPAKTHDERVTAVTVIRC  1150
1151  TQIVALSSSCVMAGYCDLDVLRRLRVLHGRMEPVNYGAQMATHMALGILS  1200
1201  LGGGRYSLSRSNLAIAALLISFYPQFPRTTQDNRAHLQAARNLWALAVEE  1250
1251  RCIIPRNQDTKQPCIVPLNVVQKSGAVQKLEAPILLPPYDSISSVSTLGD  1300
1301  KYWNLKIDLDNNSDYRELLRESQTLTLMPYDRTSSKEEPLNLFPKLKDTS  1350
1351  SPLWNLVKTSRLFQSSNSPLNVASLQESNNKTSLGVKLLLSMDFDNLTRD  1400
1401  RLLSLQILLQFFESCWTGVLLNKFHSRQYLFLSRDLVEDLSLRVWEYVYS  1450
1451  HNHNEESV                                            1458

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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