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

NucPred

Fetching P25655 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MLSATYRDLNTASNLETSKEKQAAQIVIAQISLLFTTLNNDNFESVEREI    50
  51  RHILDRSSVDIYIKVWERLLTLSSRDILQAGKFLLQENLLHRLLLEFAKD   100
 101  LPKKSTDLIELLKERTFNNQEFQKQTGITLSLFIDLFDKSANKDIIESLD   150
 151  RSSQINDFKTIKMNHTNYLRNFFLQTTPETLESNLRDLLHSLEGESLNDL   200
 201  LALLLSEILSPGSQNLQNDPTRSWLTPPMVLDATNRGNVIARSISSLQAN   250
 251  QINWNRVFNLMSTKYFLSAPLMPTTASLSCLFAALHDGPVIDEFFSCDWK   300
 301  VIFKLDLAIQLHKWSVQNGCFDLLNAEGTRKVSETIPNTKQSLLYLLSIA   350
 351  SLNLELFLQREELSDGPMLAYFQECFFEDFNYAPEYLILALVKEMKRFVL   400
 401  LIENRTVIDEILITLLIQVHNKSPSSFKDVISTITDDSKIVDAAKIIINS   450
 451  DDAPIANFLKSLLDTGRLDTVINKLPFNEAFKILPCARQIGWEGFDTFLK   500
 501  TKVSPSNVDVVLESLEVQTKMTDTNTPFRSLKTFDLFAFHSLIEVLNKCP   550
 551  LDVLQLQRFESLEFSLLIAFPRLINFGFGHDEAILANGDIAGINNDIEKE   600
 601  MQNYLQKMYSGELAIKDVIELLRRLRDSDLPRDQEVFTCITHAVIAESTF   650
 651  FQDYPLDALATTSVLFGSMILFQLLRGFVLDVAFRIIMRFAKEPPESKMF   700
 701  KFAVQAIYAFRIRLAEYPQYCKDLLRDVPALKSQAQVYQSIVEAATLANA   750
 751  PKERSRPVQEMIPLKFFAVDEVSCQINQEGAPKDVVEKVLFVLNNVTLAN   800
 801  LNNKVDELKKSLTPNYFSWFSTYLVTQRAKTEPNYHDLYSKVIVAMGSGL   850
 851  LHQFMVNVTLRQLFVLLSTKDEQAIDKKHLKNLASWLGCITLALNKPIKH   900
 901  KNIAFREMLIEAYKENRLEIVVPFVTKILQRASESKIFKPPNPWTVGILK   950
 951  LLIELNEKANWKLSLTFEVEVLLKSFNLTTKSLKPSNFINTPEVIETLSG  1000
1001  ALGSITLEQQQTEQQRQIILMQQHQQQMLIYQQRQQQQQQRQQQQQHHIS  1050
1051  ANTIADQQAAFGGEGSISHDNPFNNLLGSTIFVTHPDLKRVFQMALAKSV  1100
1101  REILLEVVEKSSGIAVVTTTKIILKDFATEVDESKLKTAAIIMVRHLAQS  1150
1151  LARATSIEPLKEGIRSTMQSLAPNLMSLSSSPAEELDTAINENIGIALVL  1200
1201  IEKASMDKSTQDLADQLMQAIAIRRYHKERRADQPFITQNTNPYSLSLPE  1250
1251  PLGLKNTGVTPQQFRVYEEFGKNIPNLDVIPFAGLPAHAPPMTQNVGLTQ  1300
1301  PQQQQAQMPTQILTSEQIRAQQQQQQLQKSRLNQPSQSAQPPGVNVPNPQ  1350
1351  GGIAAVQSDLEQNQRVLVHLMDILVSQIKENATKNNLAELGDQNQIKTII  1400
1401  FQILTFIAKSAQKDQLALKVSQAVVNSLFATSESPLCREVLSLLLEKLCS  1450
1451  LSLVARKDVVWWLVYALDSRKFNVPVIRSLLEVNLIDATELDNVLVTAMK  1500
1501  NKMENSTEFAMKLIQNTVLSDDPILMRMDFIKTLEHLASSEDENVKKFIK  1550
1551  EFEDTKIMPVRKGTKTTRTEKLYLVFTEWVKLLQRVENNDVITTVFIKQL  1600
1601  VEKGVISDTDNLLTFVKSSLELSVSSFKESDPTDEVFIAIDALGSLIIKL  1650
1651  LILQGFKDDTRRDYINAIFSVIVLVFAKDHSQEGTTFNERPYFRLFSNIL  1700
1701  YEWATIRTHNFVRISDSSTRQELIEFDSVFYNTFSGYLHALQPFAFPGFS  1750
1751  FAWVTLLSHRMLLPIMLRLPNKIGWEKLMLLIIDLFKFLDQYTSKHAVSD  1800
1801  AVSVVYKGTLRVILGISNDMPSFLIENHYELMNNLPPTYFQLKNVILSAI  1850
1851  PKNMTVPNPYDVDLNMEDIPACKELPEVFFDPVIDLHSLKKPVDNYLRIP  1900
1901  SNSLLRTILSAIYKDTYDIKKGVGYDFLSVDSKLIRAIVLHVGIEAGIEY  1950
1951  KRTSSNAVFNTKSSYYTLLFNLIQNGSIEMKYQIILSIVEQLRYPNIHTY  2000
2001  WFSFVLMNMFKSDEWNDQKLEVQEIILRNFLKRIIVNKPHTWGVSVFFTQ  2050
2051  LINNNDINLLDLPFVQSVPEIKLILQQLVKYSKKYTTSEQDDQSATINRR  2100
2101  QTPLQSNA                                            2108

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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