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

NucPred

Fetching Q5IS56 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MEAQSHSSTTTEKKKVENSIVKCSTRTDVSEKAVASSTTSNEDESPGQTY    50
  51  HRERRNAITMQPQNVQGLSKVSEEPSTSSDERASLIKKEIHGSLPHVAEP   100
 101  SVPYRGTVFAMDPRNGYMEPHYHPPHLFPAFHPPVPIDARHHEGRYHYDP   150
 151  SPIPPLHMTSALSSSPTYPDLPFIRISPHRNPAAASESPFSPPHPYINPY   200
 201  MDYIRSLHSSPSLSMISATRGLSPTDAPHAGVSPAEYYHQMALLTGQRSP   250
 251  YADIIPSAATAGTGAIHMEYLHAMDSTRFPSPRLSARPSRKRTLSISPLS   300
 301  DHSFDLQTMIRTSPNSLVTILNNSRSSSSASGSYGHLSASAISPALSFTY   350
 351  SSAPVSLHMHQQILSRQQSLGSAFGHSPPLIHPAPTFPTQRPIPGIPTVL   400
 401  NPVQVSSGPSESSQNKPTSESAVSSTGDPMHNKRSKIKPDEDLPSPGARG   450
 451  QQEQPEGTTLVKEEGDKDESKQEPEVIYETNCHWEGCAREFDTQEQLVHH   500
 501  INNDHIHGEKKEFVCRWLDCSREQKPFKAQYMLVVHMRRHTGEKPHKCTF   550
 551  EGCTKAYSRLENLKTHLRSHTGEKPYVCEHEGCNKAFSNASDRAKHQNRT   600
 601  HSNEKPYVCKIPGCTKRYTDPSSLRKHVKTVHGPEAHVTKKQRGDIHPRP   650
 651  PPPRDSGSHSQSRSPGRPTQGALGEQQDLSNTTSKREECLQVKTVKAEKP   700
 701  MTSQPSPGGQSSCSSQQSPISNYSNSGLELPLTDGGSIGDLSAIDETPIM   750
 751  DSTISTATTALALQARRNPAGTKWMEHVKLERLKQVNGMFPRLNPILPPK   800
 801  APAVSPLIGNGTQSNNTCSLGGPMTLLPGRSDLSGVDVTMLNMLNRRDSS   850
 851  ASTISSAYLSSRRSSGISPCFSSRRSSEASQAEGRPQNVSVADSYDPIST   900
 901  DASRRSSEASQSDGLPSLLSLTPAQQYRLKAKYAAATGGPPPTPLPNMER   950
 951  MSLKTRLALLGDALEPGVALPPVHAPRRCSDGGAHGYGRRHLQPHDAPGH  1000
1001  GVRRASDPVRTGSEGLALPRVPRFSSLSSCNPPAMATSAEKRSLVLQNYT  1050
1051  RPEGGQSRNFHSSPCPPSITENVTLESLTMDADANLNDEDFLPDDVVQYL  1100
1101  NSQNQAGYEQHFPSTLPDDSKVPHGPGDFDAPGLPDSHAGQQFHALEQPC  1150
1151  PEGSKTDLPIQWNEVSSGSADLSSSKLKCGPRPAVPQTRAFGFCNGMVVH  1200
1201  PQNPLRSGPAGGYQTLGENSNPYGGPEHLMLHNSPGSGTSGNAFHEQPCK  1250
1251  APQYGNCLNRQPVAPGALDGACGAGIQASKLKSTPMQGSGGQLNFGLPVA  1300
1301  PNESAGSMVNGMQNQDPVGQGYLAHQLLGDSMQHPGAGRPGQQMLGQISA  1350
1351  TSHINIYQGPESCLPGAHGMGSQPSSLAVVRGYQPCASFGGSRRQAMPRD  1400
1401  SLALQSGQLSDTSQTCRVNGIKMEMKGQPHPLCSNLQNYSGQFYDQTVGF  1450
1451  SQQDTKAGSFSISDASCLLQGTSAKNSELLSPGANQVTSTVDSLDSHDLE  1500
1501  GVQIDFDAIIDDGDHSSLMSGALSPSIIQNLSYSSSRLTTPRASLPFPAL  1550
1551  SMSTTNMAIGDMSSLLTSLAEESKFLAVMQ                      1580

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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