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

NucPred

Fetching Q9VGG5 from www.uniprot.org...

The NucPred score for your sequence is 0.25 (see score help below)

   1  MKLPLGLLMICLGLTLAKGETNLPPVFTQTLNNIILYENVTVGTVVFRLE    50
  51  AYDPEGSPVTYGAIGADHFSVDPVSGNITLIKPLDREEKDTLKFLVSIRD   100
 101  RVDPEGESERDNVVEVPITFIILDLNDNPPEFQNTPYEADVNEDAAVGTT   150
 151  IFDKITVKDRDIVGESLDLKCLPQQQSPEACRKFRLHIIKRDATILEAAV   200
 201  VLNDTLNYNQRMVYHFQIEATDGPHKTQTTFEARVKDVQDKPPVFQGSLS   250
 251  TVIDEDSPINTLVLTVHARDGDTGEPRKIVYDLRTNPNDYFLLDAQTGEL   300
 301  RTAKPLDREALEDSTGIISLVIRARELVNGVPSDDPLTSATAKATVTIRD   350
 351  VNDSPPVFNHKEYSVSLLENTLPGTPLALDMSVSDADVGINSKFALRLDD   400
 401  VSGVFDVEPKLVTGYSQVNIRVANGTLDYENPNQRKFIVLVVAEETDTNP   450
 451  RLSSTATITVSVLDANDNKPVFEQESYSASVSEAALPGQYIATITARDVD   500
 501  SGSYGDSGIRYSLSGTGAELFHVNEQTGVISLANCHDNGESNRRERRDLN   550
 551  EDEHVEEDDGEGHLEMLSMEAATREIGTEPTVQYTLITQAPEEQASSVPL   600
 601  PAPVPHAAPSGVPAATANDDKAPQTCLDYESETTYFLSYKATDDNGRGSA   650
 651  SVVSLRISVTDANDSPPVCESPLYRASVDEGAVVFDSPLIVKARDADTMS   700
 701  RISYRIRGSEQVESIFDIDRETGQIIIRPNATLDVTNLNSDQLIFAVEAN   750
 751  DGLFTAHCGVNITVRDVNNHVPNFEQQSYSAVVEENSEIGTSVERVHATD   800
 801  LDTGKNAELRYRIQQGSFDDFGIVETTGEVFVSRKLDFDRRNTYQLQIQA   850
 851  SDQGTPSLTGTATLTINVQNSNDKDPYFVPATQHAEVRADAPPGQLVYTL   900
 901  IALDPDVANHNALEFAGTDDITAIDKEGKELPHYDQFKEYFKISRNGKVS   950
 951  VNKQLDRNLFAVMRINVLVTDSTAPNVQQGRGLLIIQIIDVNKNPPRFNA  1000
1001  PWSVEQPQIKLQMVEEQPVGTVLTTLQANDEDSSIGEFNISDNDYFAINQ  1050
1051  TSGMIYTIARLDYEVVKEVKFQVTVSDTGVPALTATADVVVDIINLNDND  1100
1101  PKFSQSDYYFNVTENSPRGTVAGKVEAHDGDVGVFGEITYTLIGENNKYF  1150
1151  SIDAYTGNVMVANSSILDREQIKELTLSVVAQDKAPAAVQKSATATIHIN  1200
1201  ILDVNDNAPVFTRDVYNSTVAENAAYQPPAALLQVQAIDQDEGLYGDVRY  1250
1251  IITAGNEMGLFKLDAQSGIVYPAQSLSGKHGAYELTISARDTQGSGTMES  1300
1301  TTKAIITVLRVNRHKPEFVIPALSNATIEIPGDIVQPDYLLLTVRAMDND  1350
1351  TEENGKVSYHLQVNNRNEQQTGEFKIDEVTGELRAKTQLNRKNRANYDII  1400
1401  LVARDAGNPPFESLRLLSVSIVDANENRPEFPDASNPYKVSINENSGRDV  1450
1451  KIGHIQAASRSKHNRDIFYYMLLGNEDGAFYVDKLTGDIYTNKSLDREET  1500
1501  DVYTLYILASIKADLHISEEERASFSIKTLNRDNTVAKVAITVLDVNDNP  1550
1551  PVFEKPIYYAGVNANAKMGAAITLVNATDADQGKNAKIEFMIVASNLYKF  1600
1601  GATKSTGSIVPSPFAISQDGRISANTIMAEYNQDRFELEIVARELEQPQS  1650
1651  SASTKVNIWVFDGTQLVRVILSRPPEEVYQEQEEIIAELRNATQHRIIVD  1700
1701  EIRFHLDSIGRIRMDWCDLYFHAVDPQTQQIAPVDEILKDIDRNYDYLKD  1750
1751  YYAGFAIENVVPAYIAIVQDEFDLAVAGLVALVIVLFVGVISFIVLCCCL  1800
1801  KHWNLSVPVETRRKEALIKKQIIEDLNTTENPLWIEQKLKLYEEQELTMQ  1850
1851  VFSEPDHISNSEAPGHLDHRSSLEQVHHVGQTVDNTYATIQPRNNQNRLT  1900
1901  GGGGAGGGSMRSGGGASAGGVGGAGLLLARVDPHMNEFADYATLRNNRAP  1950
1951  SLYEFTGSTFQAPIRDGDDAVAELI                           1975

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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