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

NucPred

Fetching P56698 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MARLGNDVPACYGGSPAGGGRGANRHAGPQAGQRGMYGSKSLAQRARTMA    50
  51  LYNPIPVRQNCLTVNRSLFIFSEDNIIRKYAKRITEWPPFEYMILATIIA   100
 101  NCIVLALEQHLPDGDKTPMSERLDDTEPYFIGIFCFEAGIKIIALGFAFH   150
 151  KGSYLRNGWNVMDFVVVLTGILTTIGTDFDLRTLRAVRVLRPLKLVSGIP   200
 201  SLQVVLKSIMKAMVPLLQIGLLLFFAILMFAIIGLEFYMGKFHKTCFSEE   250
 251  TNEPVEEFPCGTKYPSRLCPNGTVCKGYWNGPNFGITNFDNILFAVLTVF   300
 301  QCITMEGWTDMLYTANDALGNTWNWLYFIPLIVIGSFFMLNLVLGVLSGE   350
 351  FAKERERVENRRAFLKLRRQQQVEQEFNRYLRWIHIAEEVMLAEEDKNAE   400
 401  DKCALDVLKRATTKKSKNDLINAEEGEDHFTDISSVGFNRPSLKSVKNER   450
 451  SSYFRRKEKRFRFFIRRMVKSQSFYWIVLCLVGLNTLCVAIVHYDQPPLL   500
 501  TDALYFAEFVFLGLFLTEMSLKMYGLGPRNYFHSSFNCFDFGVIVGSIFE   550
 551  VVWTAVKPDTSFGISVLRALRLLRIFKVTKYWNSLRNLVVSLLNSMKSII   600
 601  SLLFLLFLFIVVFALLGMQLFGGQFNFEDGTPPTNFDTFPAAILTVFQIL   650
 651  TGEDWNEVMYYGIEAHGGVKKGMFSSVYFIILTLFGNYTLLNVFLAIAVD   700
 701  NLANAQELTKDEEEMEEANIQKNTIQKAMEVADVSPISATNLSIAAKDQQ   750
 751  KSFKSMSIWEQRTSQLRRQHILTSQEALFNELDDEQRRMYVSSHQIRPDM   800
 801  KTHLDRPLVVEPRNSTRKSADKVCPSDCQEGEQERLVQPESCEAPRRSHR   850
 851  HRDKLGEQDKGDGALDTGEPRANSKDDKRCSHRSHSKETEKERDEKGRKG   900
 901  ERSRSHEGGRRHHHAQSSLDDAPEREHRRHRSHRHGTEQQHREANGTKGE   950
 951  RHSRAKDGSRSGGREGEAVSRSHHAEGAERRRKHRQKVASTNESEEKREI  1000
1001  GEKERETVLRERRVHRVKETQPSQDSGTQGNVSLPPIGLQHLPQQPEDAD  1050
1051  NQKNIKLVTLPTGDAQNPATVNIPVTVTTPAAEMTLLPINNVAVDLENVM  1100
1101  KPEEKKAENGDDLNEDGPRQIPPFNSMFLFSTTNPVRRACHYIVNLRYFE  1150
1151  MCILLVITMSSIALAAEDPVQGDAPRNNVLKYLDYVFTGVFTFEMVIKMI  1200
1201  NLGLILHPGSYFRDLWNILDFIVVSGALVAFAFTGSRGKDLNTIKSLRVL  1250
1251  RVLRPLKTIKRLPKLKAVFDCVVNSLKNVLNILIVYMLFMFIFAVIAVQL  1300
1301  FKGKFFYCTDESKDLEKDCRGQYLVYDNDEIEAEPREWKKCDFHYDNVLW  1350
1351  ALLTLFTVSTGEGWPTVLKNSIDATEEDQGPSPSYRMEMSIFYVVYFVVF  1400
1401  PFFFVNIFVALIIITFQEQGDKVMSDCSLEKNERACIDFAISAKPLTRYM  1450
1451  PQNKQTFQYKMWKFVVSPPFEYLIMALIALNTIVLMMKFYNAPDPYDRML  1500
1501  QYLNILFTFLFSMECVLKLIGFGVLNYFRDAWNVFDFVTVLGSITDILVT  1550
1551  ELADSFINLSFLRLFRAARLIKLLRQGYTIRILLWTFVQSFKALPYVCLL  1600
1601  IAMLFFIYAIIGMQVFGNIELDDDGAINRHNNFRTFLQAVMLLLRSATGE  1650
1651  GWQEIMLACLNQSPCDARSGIDGDECGSNFAYFYFVSFIFFSSFLMLNLF  1700
1701  VAVIMDNFEYLTRDSSILGPHHLDEFIRVWAEYDPGARGRITYNDMYEML  1750
1751  RHMCPPLGLGKKCPARVAYKRLVRMNMPIAEDGSVHFTSTLMALIRTALD  1800
1801  VKISPGGAYQQQCDAELRKEITAVWPNLSQKFLDILVPPQRASELTVGKV  1850
1851  YAALMIYDYYKQNKSKKVQQQQQLSGLSQTRKSFFQRVVGVLAATQEEPS  1900
1901  SYSTSHKNSVNPLYQGGRQKEPFSWLRSRDTCAEGKKEVPESHPEEAGVT  1950
1951  KSSSQAVEMREMGSDLNHADQSSLENYGRAASMPRLTAETQKISRPSGRV  2000
2001  RAPIADTSPMKRSVSTLTPQRSHVMPDYSLERVIPVQMPHHHHHHHRCHH  2050
2051  RREKKQRSLERATNRHADEEAGQLDAQLRDQSSKERERGRSQERRPPSSA  2100
2101  EKQRYYSCDRYGSREPPQPRSTDHSRSASPSTGTEQGFHRQGSGSVNDSP  2150
2151  LQSASGSSTPSRGRRQLPRTPLTPRPSVTYKTANSSPAHFGNLHDALPPS  2200
2201  SPGRLSRGQSEHNHLLSGESQNRPYAGGDSRQPMGTRISSDPYLGFRSSC  2250
2251  GSEDLELLEETLTFEVAVAATTATGRSPRTSSFTTQPPQSRRVPNGYHCN  2300
2301  LGRSTGPSTAASKRKYYRETDEDDWC                          2326

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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