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

NucPred

Fetching Q5TM26 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MSDRSGPTAKGKDGKKYSSLNLFDTYKGKSLEIQKPAVAPRHGLQSLGKV    50
  51  AIARRMPPPANLPSLKAENKGNDPNVSLVPKDGTGWASKQEQSDPKSSDA   100
 101  STAQPPESQPLPASQTPASNQPKRPPAAPENTPLVPSGVKSWAQASVTHG   150
 151  AHGDGGRASSLLSRFSREEFPTLQAAGDQDKAAKERESAEQSSGPGPSLR   200
 201  PQNSTTWRDGGGRGPDELEGPDSKLHHGHDPRGALQPSGPPQFPPYRGMM   250
 251  PPFMYPPYLPFPPPYGPQGPYRYPTPDGPSRFPRVAGPRGSGPPMRLVEP   300
 301  VGRPSILKEDNLKEFDQLDQENDDGWAGAHEEVDYTEKLKFSDEEDGRDS   350
 351  DEEGAEGHKDSQSASGEERPTEADGKKGNSPNSELPPPKTAWAETSRPPE   400
 401  TEPGPPAPKPPLPPPHRGPAGNWGPPGDYPDRGGPPCKPPAPEDEDEAWR   450
 451  QRRKQSSSEISLAVERARRRREEEERRMQEERRAACAEKLKRLDEKFGAP   500
 501  DKRLKAEPAAPPAAPSTPAPPPAVPKELPAPLAPSPASAPTPEKEPEESA   550
 551  QAPPAQCTPTPGVAAAPTLVSGGGSTSSTSSGSFEASPVEPQLPSKEGPE   600
 601  PPEEVPPPTTPPAPKVEPKGDGIGPTRQPPSQGLGYPKYQKSLPPRFQRQ   650
 651  QQEQLLKQQQQQQWQQHQQGSAPPTPVPPSPPQPVTLGAVPAPQAPPPPP   700
 701  KALYPGALGRPPPMPPMNFDPRWMMIPPYVDPRLLQGRPPLDFYPPGVHP   750
 751  SGLVPRERSDSGGSSSEPFDRHAPAMLRERGTPPVDPKLAWVGDVFTATP   800
 801  TDPRPLTSPLRQAADEDDKGMRSETPPVPPPPPYLASYPGFPENGAPGPP   850
 851  VSRFPLEEPAPPGPRPLPWPPGSDEGAKIQTQPPKKEPPKEETAQLTGPE   900
 901  AGRKPARGVGSGGQGPPPPRRESRTETRWGPRPGSSRRGIPPEEPGAPPR   950
 951  RAGPIKKPPPPTKVEELPPKPLEQGDETPKAPKPDPLKIAKGKLAGPKET  1000
1001  PPNGNLSPAPRLRRDYSYERVGPTSCRGRGRGEYFARGRGFRGTYGGRGR  1050
1051  GARSREFRSYREFRGDDGRGGGTGGPNHPPAPRGRTASETRSEGSEYEEI  1100
1101  PKRRRQRGSETGSETHESDLAPSDKEAPPPKEGTLTQVPLAPPPPGAPPS  1150
1151  PAPARFTARGGRVFTPRGVPSRRGRGGGRPPPQVCPGWSPPAKSLAPKKP  1200
1201  PTGPLPPSKEPLKEKLIPGPLSPVARGGSSGGSNVGMEDGERPRRRRHGR  1250
1251  AQQQDKPPRFRRLKQERENAARGSEGKPSLTLPASTPGPEEALTTVTVAP  1300
1301  PPRRAAAKSPDLSNQNSDQANEEWETASESSDFASERRGDKEAPPPALLT  1350
1351  PKAVGTPGGGGGGAVPGISAMSRGDLSQRAKDLSKRSFSSQRPGMERQNR  1400
1401  RPGPGGKAGSSGSSSGGGGAGPGGRTGPGRGDKRSWPSPKNRSRPPEERP  1450
1451  PGLPLPPPPPSSSAVFRLDQVIHSNPAGIQQALAQLSSRQGSVTAPGGHP  1500
1501  RHKPGPPQTPQGPSPRPPTRYEPQRVNNGLSSDPHFEEPGPMVRGVGGTP  1550
1551  RDSARVSPFPAKRRERPPRKPELLQEESLPPPHSSGFLGSKPEGPGPQAE  1600
1601  SRDTGTEALTPHIWNRLHTATSRKSYRPSSMEPWMEPLSPFEDVAGTEMS  1650
1651  QSDSGVDLSGDSQVSSGPCSQRSSPDGGLKGAAEGPPKRPGGPSPLNAVP  1700
1701  CEGPPGSEPPRRPPPAPHDGDRKELPREQPLPPGPIGTERSQRTDRGTEP  1750
1751  GPIRPSHLPGPPVQFDTSDKDSDLRLVVGDSLKAEKELTASVTEAIPVSR  1800
1801  DWELLPSAAASAEPQSKNLGSGHCGPEPPSSGQRLYPEVFYGSAGPSSSQ  1850
1851  ISGGAMDSQLHPNSGGFRPGTPSLHPYRSQPLYLPPGPAPPSALLSGVAL  1900
1901  KGQFLDFSTLQAAELGKLPAGGVLYPPPSFLYSPAFCPSPLPDTSLLQVR  1950
1951  QDLPSPSDFYSTPLQPGGQSGFLPSGAPAQQMLLPMVDSQLPVVNFGSLP  2000
2001  PAPPPAPPPLSLLPVGPALQPPSLAVRPPPAPATRVLPSPARPFPASLGR  2050
2051  AELHPVELKPFQDYQKLSSNLGGPGSSRTPPTGRSFSGLNSRLKAPPSTY  2100
2101  SGVFRTQRIDLYQQASPPDALRWIPKPWERTGPPSREGPSRRAEEPGSRG  2150
2151  DKEPGLPPPR                                          2160

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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