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

NucPred

Fetching Q96AY4 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MEQSPPPAPEPTQGPTPARSRRRREPESPPASAPIPLFGADTIGQRSPDG    50
  51  PVLSKAEFVEKVRQSNQACHDGDFHTAIVLYNEALAVDPQNCILYSNRSA   100
 101  AYMKIQQYDKALDDAIKARLLNPKWPKAYFRQGVALQYLGRHADALAAFA   150
 151  SGLAQDPKSLQLLVGMVEAAMKSPMRDSLEPTYQQLQKMKLDKSPFVVVS   200
 201  VVGQELLTAGHHGASVVVLEAALKIGTCSLKLRGSVFSALSSAYWSLGNT   250
 251  EKSTGYMQQDLDVAKTLGDQTGECRAHGNLGSAFFSKGNYREALTNHRHQ   300
 301  LVLAMKLKDREAASSALSSLGHVYTAIGDYPNALASHKQCVLLAKQSKDE   350
 351  LSEARELGNMGAVYIAMGDFENAVQCHEQHLKIAKDLGNKREEARAYSNL   400
 401  GSAYHYRRNFDKAMSYHNYVLELAQELMEKAIEMRAYAGLGHAARCMQDL   450
 451  ERAKQYHEQQLGIAEDLKDRAAEGRASSNLGIIHQMKGDYDTALKLHKTH   500
 501  LCIAQELSDYAAQGRAYGNMGNAYNALGMYDQAVKYHRQELQISMEVNDR   550
 551  ASQASTHGNLAVAYQALGAHDRALQHYQNHLNIARELRDIQSEARALSNL   600
 601  GNFHCSRGEYVQAAPYYEQYLRLAPDLQDMEGEGKVCHNLGYAHYCLGNY   650
 651  QEAVKYYEQDLALAKDLHDKLSQAKAYCNLGLAFKALLNFSKAEECQKYL   700
 701  LSLAQSLNNSQAKFRALGNLGDIFICKKDINGAIKFYEQQLGLAHQVKDR   750
 751  RLEASAYAALGTAYRMIQKYDKALGYHTQELEVYQELSDLPGECRAHGHL   800
 801  AAVYMALGKYTMAFKCYEEQLDLGQKLKDPSLEAQVYGNMGITKMNMNVM   850
 851  EEAIGYFEQQLAMLQQLSGNESVLDRGRAYGNLGDCYEALGDYEEAIKYY   900
 901  EQYLSVAQSLNRMQDQAKAYRGLGNGHRAMGSLQQALVCFEKRLVVAHEL   950
 951  GEAFNKAQAYGELGSLHSQLGNYEQAISCLERQLNIARDMKDRALESDAA  1000
1001  CGLGGVYQQMGEYDTALQYHQLDLQIAEETNNPTCQGRAYGNLGLTYESL  1050
1051  GTFERAVVYQEQHLSIAAQMNDLAAKTVSYSSLGRTHHALQNYSQAVMYL  1100
1101  QEGLRLAEQLGRREDEAKIRHGLGLSLWASGNLEEAQHQLYRASALFETI  1150
1151  RHEAQLSTDYKLSLFDLQTSSYQALQRVLVSLGHHDEALAVAERGRTRAF  1200
1201  ADLLVERQTGQQDSDPYSPVTIDQILEMVNGQRGLVLYYSLAAGYLYSWL  1250
1251  LAPGAGIVKFHEHYLGENTVENSSDFQASSSVTLPTATGSALEQHIASVR  1300
1301  EALGVESHYSRACASSETESEAGDIMDQQFEEMNNKLNSVTDPTGFLRMV  1350
1351  RRNNLFNRSCQSMTSLFSNTVSPTQDGTSSLPRRQSSFAKPPLRALYDLL  1400
1401  IAPMEGGLMHSSGPVGRHRQLILVLEGELYLIPFALLKGSSSNEYLYERF  1450
1451  GLLAVPSIRSLSVQSKSHLRKNPPTYSSSTSMAAVIGNPKLPSAVMDRWL  1500
1501  WGPMPSAEEEAYMVSELLGCQPLVGSVATKERVMSALTQAECVHFATHIS  1550
1551  WKLSALVLTPSMDGNPASSKSSFGHPYTIPESLRVQDDASDGESISDCPP  1600
1601  LQELLLTAADVLDLQLPVKLVVLGSSQESNSKVTADGVIALTRAFLAAGA  1650
1651  QCVLVSLWPVPVAASKMFIHAFYSSLLNGLKASAALGEAMKVVQSSKAFS  1700
1701  HPSNWAGFMLIGSDVKLNSPSSLIGQALTEILQHPERARDALRVLLHLVE  1750
1751  KSLQRIQNGQRNAMYTSQQSVENKVGGIPGWQALLTAVGFRLDPPTSGLP  1800
1801  AAVFFPTSDPGDRLQQCSSTLQSLLGLPNPALQALCKLITASETGEQLIS  1850
1851  RAVKNMVGMLHQVLVQLQAGEKEQDLASAPIQVSISVQLWRLPGCHEFLA  1900
1901  ALGFDLCEVGQEEVILKTGKQANRRTVHFALQSLLSLFDSTELPKRLSLD  1950
1951  SSSSLESLASAQSVSNALPLGYQQPPFSPTGADSIASDAISVYSLSSIAS  2000
2001  SMSFVSKPEGGSEGGGPGGRQDHDRSKNAYLQRSTLPRSQLPPQTRPAGN  2050
2051  KDEEEYEGFSIISNEPLATYQENRNTCFSPDHKQPQPGTAGGMRVSVSSK  2100
2101  GSISTPNSPVKMTLIPSPNSPFQKVGKLASSDTGESDQSSTETDSTVKSQ  2150
2151  EESNPKLDPQELAQKILEETQSHLIAVERLQRSGGQVSKSNNPEDGVQAP  2200
2201  SSTAVFRASETSAFSRPVLSHQKSQPSPVTVKPKPPARSSSLPKVSSGYS  2250
2251  SPTTSEMSIKDSPSQHSGRPSPGCDSQTSQLDQPLFKLKYPSSPYSAHIS  2300
2301  KSPRNMSPSSGHQSPAGSAPSPALSYSSAGSARSSPADAPDIDKLKMAAI  2350
2351  DEKVQAVHNLKMFWQSTPQHSTGPMKIFRGAPGTMTSKRDVLSLLNLSPR  2400
2401  HNKKEEGVDKLELKELSLQQHDGAPPKAPPNGHWRTETTSLGSLPLPAGP  2450
2451  PATAPARPLRLPSGNGYKFLSPGRFFPSSKC                     2481

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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