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

NucPred

Fetching Q8BGE5 from www.uniprot.org...

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

   1  MSGRQRTLFQTWGPSLVRGSGDSGCGQPRSPAMAEALPEEDDEVLLVAAY    50
  51  EAERQLDPGDGGFCAAAGALWIYPTNCPVRDYQLDISRSALFCNTLVCLP   100
 101  TGLGKTFIAAVVMYNFYRWFPSGKVVFMAPTKPLVTQQMEACFHVMGIPQ   150
 151  SHMAEMTGSTQAVNRKEIWSSRRVLFLTPQVMVNDLTRGAVPATHVKCLV   200
 201  VDEAHKALGNYAYCQVVRELVKYTTHFRILALSATPGSDIKAVQQVITNL   250
 251  LIGKIELRSEESPDILPYSHERRVEKLVVPLGEELGAIQKTYIQILETFA   300
 301  SSLIHRNVLMKRDIPNLTKYQIILARDQFRKNPSPNIVGIQQGIIEGEFA   350
 351  LCISLYHGYELLQQMGMRSLYFFLSGIMDGTKGMTRARNELSRNEDFMKL   400
 401  YTHLQSAFAPASTSDASAFQRGNKEKKFVYSHPKLKKLEEVILEHFKSWN   450
 451  AKATTEKKCHESRVMIFSSFRDSVEEIAEMLLQHRPVIRVMTFVGHASGK   500
 501  NTKGFTQKEQLQVVRQFRDGGYNTLVSTCVGEEGLDIGEVDLIICFDAQK   550
 551  SPIRLIQRMGRTGRKRQGRIVVILAEGREERTYNQSQSNKKNIYKAISGN   600
 601  RQVLRLYQGSPRMVPDKINPELHKMYITHGVYEPEKARSVQRRPFSSRGG   650
 651  IKASKSNKDGLLSEEEFNLWSRLYRLGDSDQVKGVALPQSHFPSLQEDRV   700
 701  IQDPTTRIHQLSLSEWSLWQDRPLPTHQVDHSDRCHHFISIMKMIEGMRH   750
 751  EEGECSYELKIRPFLQMEDVCSKYHAPRNGYNNVASVASSAHQKSSFRPS   800
 801  VDAGGSLTVIESEEEHADTVKQRDSKWTKITSLREKPCRAGRKGQTCEHS   850
 851  EGEGEDGDAGSSDADGQSPAEADSQVDPPSGERMADVGGISILGAVTEED   900
 901  NHPGTLQMECQVTNKSCARYSLDSGYSSFSDEKSVSSNLFLPLEEELFTD   950
 951  RAAEQFYNCRPMTEDVLANVERFLSRSPPSLSGLSDLVYDVTQGCEFDNA  1000
1001  SCSPYPEHEHSPRPVSPASHSAGNSQQNLESNSAKRISHPTEKYCLPGTT  1050
1051  HNKVSDRPSFCESDSEGHNIKYQNSGSNSCAQIQADLENNFVDKNSHDDS  1100
1101  EPPVLFTDEDESLLLFEDDFKNIEDGPEELNGASLPPFNSISQPLRVSGK  1150
1151  TLTSEMPPVSHFLISDELLLDDDSEPEDQIVCGAKSWKCQEGVEDGQEEL  1200
1201  RTDGQTFDCSVDLFSVTFDLGFRCSSGSDDEMLAGASDRTRTLGAADVSG  1250
1251  RHSDKEIKDAGGASGPLGRAISPIPTETAQWSPWAQNKEYASFHVASSSP  1300
1301  VKQRVRSTPLSKSHASSKTGAHMLKTLDSTKEKAGGQGFKMALNPRLGHL  1350
1351  GFSVEETKSSDQVFVHQSPRRTEVEHLTSESEDDVFLRKTKKPKRNVLKS  1400
1401  PEDQKNNEVDSPIHAVKKPRVLRSELASSDDESENFGRTCPRLEHFKGRN  1450
1451  RNIRKGSAAQKNRSQVKTMARRFLDDEAEVSGEDVDCVSADEEDESENEQ  1500
1501  DSSLLDFVNDRTQLSQAINDSEMRAIYMKSVRSPLMSTKYRMVREKRPNM  1550
1551  NIFSQIPEQDENYLEDSFCVDEEESCKSQSSEEEISVDFNLTKDSFTDED  1600
1601  IRYKTRYAVKIKQMNKKQNYTRPRKKLSRIILPDDDSSEEENIPKDREHS  1650
1651  VAGGHAAAEHTQQGQLWASGPSGSSVPPQVLSDPSWNQSSRQRLQVQPSI  1700
1701  TDAVPRTLNVKAQSHNKIKSASPPCTGVESRKEYGNHPVQLKADSQEHSD  1750
1751  TSAAPCSTSLLHVAEGHTAPRHLQEGNRACILVDSREITTGLEVISSLRT  1800
1801  VHGLQVEICPLNGCDYIVSSRMVVVRRSQSEMLSNTSKNKFIEQMQRLQS  1850
1851  MFQRICVIVEKDREKAGDTSKKFRRTKCYDSLLTALVGAGIRILFSSGQE  1900
1901  ETADLLKELSLVEQRKNAGIHIPAVLNTSKLEALPFYLSIPGISYITALN  1950
1951  MCHQFSSVKKMANSSPEEISTCAQVNHQKAEEIYKYIHYIFDMQMLPNDL  2000
2001  NQERQKPDTCLTLGVAMKELS                               2021

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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