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

NucPred

Fetching Q6MG48 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MSDRSGPTAKGKDGKKYSSLNLFDTYKGKSLEIQKPAVAPRHGLQSLGKV    50
  51  AIARRMPPPANLPSLKAENKGNDPNVSLVPKDGTGWASKQEQSDPKSSDA   100
 101  STAQPPESQPLPASQTPASNQPKRPPTAPENTPSVPSGVKSWAQASVTHG   150
 151  AHGDGGRASSLLSRFSREEFPTLQAAGDQDKAAKERESAEQSSGPGPSLR   200
 201  PQNSTTWRDGGGRGPDELEGPDSKLHHGHDPRGGLQPSGPPQFPPYRGMM   250
 251  PPFMYPPYLPFPPPYGPQGPYRYPTPDGPSRFPRVAGPRGSGPPMRLVEP   300
 301  VGRPSILKEDNLKEFDQLDQENDDGWAGAHEEVDYTEKLKFSDEEDGRDS   350
 351  DEEGAEGHKDSQSAAGEEPETDGKKGTSPGSELPPPKTAWTENSRPSETE   400
 401  PAAPPIPKPPPPPPHRGPVGNWGPPGDYPDRGGPPCKPPAPEDEDEAWRQ   450
 451  RRKQSSSEISLAVERARRRREEEERRMQEERRAACAEKLKRLDEKFGAPD   500
 501  KRLKAEPAAPPVTPPAPALPPVVPKETPTPPALPPTPTPTPEKDPEEPAH   550
 551  APPVQSAPTQAGPPAPTPVSGGGTASSTSSGSFEASPAEPQLPSKEGPEP   600
 601  PEEVPAPTTPPAPKVEPKGDGVGPTRQPPSQGLGYPKYQKSLPPRFQRQQ   650
 651  QEQLLKQQQQQQWQQQQQQQGTAPPAPVPPSPPQPVTLGAVPAPQAPPPP   700
 701  PKALYPGALGRPPPMPPMNFDPRWMMIPPYVDPRLLQGRPPLDFYPPGVH   750
 751  PSGLVPRERSDSGGSSSEPFERHAPPLLRERGTPPVDPKLAWVGDVFTTT   800
 801  PTDPRPLTSPLRQAADEEEKSLRSETPPVPPPPPYLANYPGFPENGTPGP   850
 851  PISRFPLEESAPPGPRPLPWPPGNDEAAKMQAPPPKKEPPKEEPAQLSGP   900
 901  EAGRKPARGVGGGGQGPPPPRRENRTETRWGPRPGSCRRGIPPEDPGVPP   950
 951  RRAGPIKKPPPPVKADELPPKSLEPGDETPKAPKPDALKTAKGKVGPKET  1000
1001  PAGGNLSPAPRLRRDYSYERVGPTSCRGRGRGEYFARGRGFRGTYGGRGR  1050
1051  GARSREFRSYREFRGDDGRGGGSGGTNHPSAPRGRTASETRSEGSEYEEI  1100
1101  PKRRRQRGSETGSETHESDLAPSDKEAPPPKEGVLAQVPLAPPQPGAPPS  1150
1151  PAPARFSTARGGRVFTPRGVPSRRGRGGGRPPPVCSGWSPPAKSLVPKKP  1200
1201  PTGPLPPNKEPLKEKLISGPLSPMSRAGNMGVGMEDGERPRRRRHGRAQQ  1250
1251  QDKPPRFRRLKQDRENAARGTDGKPPPLTLPASTPAPTETLATVAAPPPP  1300
1301  RRTAAKSPDLSNQNSDQANEEWETASESSDFASERRGDKETPPAALITSK  1350
1351  AVGTPGGNSGGAGPGISTMSRGDLSQRAKDLSKRSFSSQRPGMDRQNRRP  1400
1401  GAGGKTGGGGSSGGGGAGPGGRTGPGRGDKRSWPSPKNRSRPPEERPPGL  1450
1451  PLPPPPPSSSAVFRLDQVIHSNPAGIQQALAQLSSRQGNVTAPGGHPRPK  1500
1501  PGPPQAPQGSSPRPPTHYDPPRASNAISSDPHFEEPGPMVRGVGGTPRDS  1550
1551  AGVNPFPPKRRERPPRKPELLQEETVPASHSSGFLGSKPEVPGPQEESRD  1600
1601  SGTEALTPHIWNRLHTATSRKSYQPGSIEPWMEPLSPFEDVAGTEMSQSD  1650
1651  SGVDLSGGSQVSSGPCSQRSSPDGGLKGSAEGPPRRPGGPSPLKAVPGES  1700
1701  SSASEPSEPHRRRPPASHEGERKELPREQPLPPGPIGTERSQRTDRGPEP  1750
1751  GPLRPAHRAGSQVEFGTTNKDSDLCLVVGDTLKGEKELAASATEAVPVSR  1800
1801  DWELLPSASASAEPQAKSLGSGQCGPEPSPSGQRLYPEVFYGSPGPPNSQ  1850
1851  VSGGAPIDSQLHPSSGGFRPGTPSVHQYRSQPLYLPPGPAPPSALLSGVA  1900
1901  LKGQFLDFSALQATELGKLPAGGVLYPPPSFLYSAAFCPSPLPDPPLLQV  1950
1951  RQDLPSPSDFYSTPLQPGGQSGFLPSGAPAQQMLLPVVDSQLPVVNFGSL  2000
2001  PPAPPPAPPPLSLLPVGPALQPPNLAVRPPPAPAARVLPSPARPFPASLG  2050
2051  RAELHPVELKPFQDYRKLSSNLGGPGSSRAPPSGRSFSGLNSRLKAPPST  2100
2101  YSGVFRTQRIDLYQQASPPDALRWMPKPWERTGPPSREGPPRRAEEPGPR  2150
2151  GEKEPGLPPPR                                         2161

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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