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

NucPred

Fetching Q810T2 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MPPPLLPKRSKLETEKAQSNKITPREEQQSEKIGKSNHAASSSSSSTQGA    50
  51  VKRRSVFEDVTNASHSQCVQSKEDNIELKSHVSKRTKKGVGEVTQKKIKS   100
 101  SKMGHVTSLSNMEKEFILDIPNKPKTLTTEEPSVFQKTLVLNEEPATKET   150
 151  CLMRKTLKSCAFHQETLLMEKPLTLLVETEDYNEFDTELMTSKKKDKPED   200
 201  PTIIEEMTDLKKSVIRKVTLTSSPLWLKNKHVVQEEKPVIQEKSSFKRIS   250
 251  LVSNVVTTKEKPPVKKPHFRKKKPTTEMKSLLQEPSLEEKYNTQEDASIL   300
 301  KKPQVLQENTNNKDATLTEPVTFKGKHSANEATHTKKPSSSKNNPDPQGK   350
 351  GTNLRPLRVHPVTYENEPMSSKKSTTKKKDSHFHGPSVLPDKHSPQMEVS   400
 401  TVKKSLALPNPTTEEKMLHFPVATVLEKQHNMGEAPCLKKPSPLRKQQQL   450
 451  PKRRRFFSNSAVQETVIRKPLFFKMSTTEKDPPSQWPSALPKKHISPGEL   500
 501  SKQKKQHVSPKHNMEEDSQCWLDSAFKKQLSREEPASTHTPLKLEMQQAI   550
 551  TKETGFHLRNPLVLPTVTSEAKSLTKEPPSFREQNTSLLKRKSTTHTITL   600
 601  QQAQSEWQEMTDEDRNLFSIKPGSHRKEPIPEFLQNPLPPNENCLISQKL   650
 651  SHSMPFASQKTTSQERAHRKESVASNDDKNFFSQDLFSPFSSADEDTLKF   700
 701  HKSLDFQEQVDRKNDSHKKMFDSQDSVSEEESFLRKLFCKDRCSSTEELS   750
 751  QERTVALEQEFLLIKILNENTSSDVDEPLSHQSPHIQNHSDTTKEALEAS   800
 801  EALEAPEALETLEALVASEDLEEPLNILEELSTENMVALMKMLVTEDEST   850
 851  KDSFSGNYTAAREAHAEKSLSLEETSINEAATLKESLSSQEKHRAELVTV   900
 901  LKELLVLMKNPSLKRVALAFQENPSNNVETLLREVLALVENSTADESTLQ   950
 951  EKPSTKTDVTPKELLALEENSSNKKANPMDSLSFDHKPDTEMGEIARMVL  1000
1001  TDEEYNIDTLYERVLALSQGLIAADQLSFTDLQNFEETKIVDEEEFFKSF  1050
1051  LVFENKNSPNMSSNAFESRTDNSSAIMPSSKAFNPVENSNPYVSSSKSFK  1100
1101  STLGAKETEITIQDDSDSLERIEKEGQDPLLNTIYAKDVFNYLKEREEKF  1150
1151  LVQKYMDGQMELTSDMRAILVDWLVEIQGSFQMTHETLYLAVKIMDLYLM  1200
1201  KAQCKKNHLQLLGSTTYMIAAKFEESYPPSLSEFLFICEDMYEKSDMVSL  1250
1251  ESSILQTLNFDINIPTAYNFLRRYASCIHASMKTLTLSRFICEMTLQEYE  1300
1301  YIEERPSKLAAASFILALYMRNLSNCVPTLEYFTGYKMAELHILVRKLNH  1350
1351  LLNFRSHSILKNVFEKYSEETYFEVAKIPPLSKQDLENLLNCALFH      1396

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.