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

NucPred

Fetching P33892 from www.uniprot.org...

The NucPred score for your sequence is 0.59 (see score help below)

   1  MTAILNWEDISPVLEKGTRESHVSKRVPFLQDISQLVRQETLEKPQLSEI    50
  51  AFVLLNTFTIYEDNRSKSLVTSILLDILNLEPCLLENFIRFISDVVISNP   100
 101  ATKAVADYLNLLDWINSFLIFVSHNSNLFEEYIPKLLVAHSYATFGVETI   150
 151  LDNQEEGKKSQDKQNQHRKRIRYCIFQTTVKAFLKCLKDNDDSISFMKIS   200
 201  IKTVLESYSKLKITSVGVVMIMGALTQAALQLLSRQPALHSVLKENSAEK   250
 251  YCEYLGKEVFLGKNPPSSFCLEIGLKPFLKEFVSQELFIKFFIPNIEKAV   300
 301  LRSPEVGFSILSELYAGVSPEKVNLLNAFASSKLINQYFSSFKSSKEVVR   350
 351  SVSLQSMIILLRKISNTDTTLEDLTKLIDEIFKNIKSNLNADYKSLISKI   400
 401  LIEIPLTHYEVSEKICKGLSPYIGKEGNEAALTLMLNAFFVHYFSLGKPI   450
 451  EDLDKIISAGFADKKPALKKCWFAAFLNNSNAASEEVILNFIDGCLEFVK   500
 501  DSIIHYQTHGHACILASIEFTNKILALDNTELNDRVMQLIETLPENSSIG   550
 551  DAILTAALSTELSIENRIHAVNLLQELFYKKPEFIGFSVIDAIERRMRVQ   600
 601  ELIPQQNTSFKYVTSVLLAITSELPDKEASIKVLINALVIAQWNIFNIKN   650
 651  GWAGLVLRARLDPAEVVKEHASVIMEKILEITGSCEWIDTIYGACGLQAA   700
 701  AYAAFIQPNEFTPILCKTIEADLTADDFSRLSEEDFEIFAGEEGVLVVDV   750
 751  LEESMNKKLSNKNSKEYETLMWEQKIRKEQAKKNVKKLSKEEQELVNEQL   800
 801  AKESAVRSHVSEISTRLKRGIRLVSELSKAACLVQNGIATWFPLAVTKLL   850
 851  YLCSEPNISKLTEDVNNVFLQLSQNVSERLGNIRLFLGLATLRVHNANGI   900
 901  SQDYLQEPLVELLTRVLFRIKFVSNQAAIDSISLTYILPLLINVLEKGKA   950
 951  IALKNADKPVVKAEFVEEDEEEEHLLLAMEIISVHAEAFEDPSIPRISIV  1000
1001  EVLLSLLSLPSKAKIAKDCFNALCQSISVAPNQEDLDMILSNLLSPNQFV  1050
1051  RSTILETLDNEFELEPFMKYSPEVFICRFDSDPSNREIADFIWEFNKFVV  1100
1101  NDELLKSLFPLFNQDDSGLRLFAANAYAFGAVSLFTSEENSSKDYLNDLL  1150
1151  NFYKEKAKPLEPILDQFGLVLVSASEQKDPWQGRSTVAITLKIMAKAFSA  1200
1201  EDDTVVNIIKFLVDDGGLVDREPIVRQEMKEAGVELITLHGSQNSKDLIP  1250
1251  IFEEALSSSTDSALKENVIILYGTLARHLQQSDARIHTIIERLLSTLDTP  1300
1301  SADIQQAVSACIAPLVFQFKQKVGDYLGILMEKLLNPTVASSMRKGAAWG  1350
1351  IAGLVKGYGISALSEFDIIRNLIEAAEDKKEPKRRESVGFCFQYLSESLG  1400
1401  KFFEPYVIEILPNILKNLGDAVPEVRDATARATKAIMAHTTGYGVKKLIP  1450
1451  VAVSNLDEIAWRTKRGSVQLLGNMAYLDPTQLSASLSTIVPEIVGVLNDS  1500
1501  HKEVRKAADESLKRFGEVIRNPEIQKLVPVLLQAIGDPTKYTEEALDSLI  1550
1551  QTQFVHYIDGPSLALIIHIIHRGMHDRSANIKRKACKIVGNMAILVDTKD  1600
1601  LIPYLQQLIDEVEIAMVDPVPNTRATAARALGALVERLGEEQFPDLIPRL  1650
1651  LDTLSDESKSGDRLGSAQALAEVISGLGLTKLDEMLPTILAGVTNFRAYI  1700
1701  REGFMPLLLFLPVCFGSQFAPYINQIIQPILSGLADNDENIRDTALKAGK  1750
1751  LIVKNYATKAVDLLLPELERGMFDENDRIRLSSVQLTGELLFQVTGISSR  1800
1801  NEFSEEDGDHNGEFSGKLVDVLGQDRRDRILAALFVCRNDTSGIVRATTV  1850
1851  DIWKALVPNTPRAVKEILPTLTGMIVTHLASSSNVLRNIAAQTLGDLVRR  1900
1901  VGGNALSQLLPSLEESLIETSNSDSRQGVCIALYELIESASTETISQFQS  1950
1951  TIVNIIRTALIDESATVREAAALSFDVFQDVVGKTAVDEVLPYLLHMLES  2000
2001  SDNSDFALLGLQEIMSKKSDVIFPILIPTLLAPPIDAFRASALGSLAEVA  2050
2051  GSALYKRLSIIINALVDAIIGTSEDESTKGALELALDRVFLSVNDDEGLH  2100
2101  PLLQQIMSLLKSDNIEKRIAVLERLPNFFDKTVLDFDVYIPNFVSHAILS  2150
2151  LDDEDQRVVNGNFNALSTLLKKVDKPTLEKLVKPAKQSLALTGRQGQDVA  2200
2201  AFKLPRGPNCVLPIFLHGLMYGSNDEREESALAIADVVSKTPAANLKPFV  2250
2251  SVITGPLIRVVGERFSSDIKAAILFALNVLFIKIPMFLRPFIPQLQRTFV  2300
2301  KSLSDATNETLRLRAAKALGALIEHQPRVDPLVIELVTGAKQATDEGVKT  2350
2351  AMLKALLEVIMKAGSKLNENSKTNIVNLVEEEMLGSNDKLAVAYAKLIGS  2400
2401  LSEILSNDEAHKILQDKVLNADLDGETGKFAILTLNSFLKDAPTHIFNTG  2450
2451  LIDEFVSYILNAIRSPDVYFGENGTIAAGKLLLLEGEKRSPFVKKDAAEP  2500
2501  FKIGDENINLLINELSKAVLQPASNSTDVRRLALVVIRTLARFKFDECIK  2550
2551  QYFDVVGPSVFSCLRDPVIPIKLAAEKAYLALFKLVEEDDMHTFNEWFAK  2600
2601  ISDRGNSIETVTGTTIQLRSVGDYTKRVGKRLANVERERIAAGGDAETMF  2650
2651  SDRFEDEREIWAVGGVELTTDI                              2672

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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