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

NucPred

Fetching Q8TD84 from www.uniprot.org...

The NucPred score for your sequence is 0.69 (see score help below)

   1  MWLVTFLLLLDSLHKARPEDVGTSLYFVNDSLQQVTFSSSVGVVVPCPAA    50
  51  GSPSAALRWYLATGDDIYDVPHIRHVHANGTLQLYPFSPSAFNSFIHDND   100
 101  YFCTAENAAGKIRSPNIRVKAVFREPYTVRVEDQRSMRGNVAVFKCLIPS   150
 151  SVQEYVSVVSWEKDTVSIIPEHRFFITYHGGLYISDVQKEDALSTYRCIT   200
 201  KHKYSGETRQSNGARLSVTDPAESIPTILDGFHSQEVWAGHTVELPCTAS   250
 251  GYPIPAIRWLKDGRPLPADSRWTKRITGLTISDLRTEDSGTYICEVTNTF   300
 301  GSAEATGILMVIDPLHVTLTPKKLKTGIGSTVILSCALTGSPEFTIRWYR   350
 351  NTELVLPDEAISIRGLSNETLLITSAQKSHSGAYQCFATRKAQTAQDFAI   400
 401  IALEDGTPRIVSSFSEKVVNPGEQFSLMCAAKGAPPPTVTWALDDEPIVR   450
 451  DGSHRTNQYTMSDGTTISHMNVTGPQIRDGGVYRCTARNLVGSAEYQARI   500
 501  NVRGPPSIRAMRNITAVAGRDTLINCRVIGYPYYSIKWYKDALLLPDNHR   550
 551  QVVFENGTLKLTDVQKGMDEGEYLCSVLIQPQLSISQSVHVAVKVPPLIQ   600
 601  PFEFPPASIGQLLYIPCVVSSGDMPIRITWRKDGQVIISGSGVTIESKEF   650
 651  MSSLQISSVSLKHNGNYTCIASNAAATVSRERQLIVRVPPRFVVQPNNQD   700
 701  GIYGKAGVLNCSVDGYPPPKVMWKHAKGSGNPQQYHPVPLTGRIQILPNS   750
 751  SLLIRHVLEEDIGYYLCQASNGVGTDISKSMFLTVKIPAMITSHPNTTIA   800
 801  IKGHAKELNCTARGERPIIIRWEKGDTVIDPDRVMRYAIATKDNGDEVVS   850
 851  TLKLKPADRGDSVFFSCHAINSYGEDRGLIQLTVQEPPDPPELEIREVKA   900
 901  RSMNLRWTQRFDGNSIITGFDIEYKNKSDSWDFKQSTRNISPTINQANIV   950
 951  DLHPASVYSIRMYSFNKIGRSEPSKELTISTEEAAPDGPPMDVTLQPVTS  1000
1001  QSIQVTWKAPKKELQNGVIRGYQIGYRENSPGSNGQYSIVEMKATGDSEV  1050
1051  YTLDNLKKFAQYGVVVQAFNRAGTGPSSSEINATTLEDVPSQPPENVRAL  1100
1101  SITSDVAVISWSEPPRSTLNGVLKGYRVIFWSLYVDGEWGEMQNITTTRE  1150
1151  RVELRGMEKFTNYSVQVLAYTQAGDGVRSSVLYIQTKEDVPGPPAGIKAV  1200
1201  PSSASSVVVSWLPPTKPNGVIRKYTIFCSSPGSGQPAPSEYETSPEQLFY  1250
1251  RIAHLNRGQQYLLWVAAVTSAGRGNSSEKVTIEPAGKAPAKIISFGGTVT  1300
1301  TPWMKDVRLPCNSVGDPAPAVKWTKDSEDSAIPVSMDGHRLIHTNGTLLL  1350
1351  RAVKAEDSGYYTCTATNTGGFDTIIVNLLVQVPPDQPRLTVSKTSASSIT  1400
1401  LTWIPGDNGGSSIRGFVLQYSVDNSEEWKDVFISSSERSFKLDSLKCGTW  1450
1451  YKVKLAAKNSVGSGRISEIIEAKTHGREPSFSKDQHLFTHINSTHARLNL  1500
1501  QGWNNGGCPITAIVLEYRPKGTWAWQGLRANSSGEVFLTELREATWYELR  1550
1551  MRACNSAGCGNETAQFATLDYDGSTIPPIKSAQGEGDDVKKLFTIGCPVI  1600
1601  LATLGVALLFIVRKKRKEKRLKRLRDAKSLAEMLISKNNRSFDTPVKGPP  1650
1651  QGPRLHIDIPRVQLLIEDKEGIKQLGDDKATIPVTDAEFSQAVNPQSFCT  1700
1701  GVSLHHPTLIQSTGPLIDMSDIRPGTNPVSRKNVKSAHSTRNRYSSQWTL  1750
1751  TKCQASTPARTLTSDWRTVGSQHGVTVTESDSYSASLSQDTDKGRNSMVS  1800
1801  TESASSTYEELARAYEHAKLEEQLQHAKFEITECFISDSSSDQMTTGTNE  1850
1851  NADSMTSMSTPSEPGICRFTASPPKPQDADRGKNVAVPIPHRANKSDYCN  1900
1901  LPLYAKSEAFFRKADGREPCPVVPPREASIRNLARTYHTQARHLTLDPAS  1950
1951  KSLGLPHPGAPAAASTATLPQRTLAMPAPPAGTAPPAPGPTPAEPPTAPS  2000
2001  AAPPAPSTEPPRAGGPHTKMGGSRDSLLEMSTSGVGRSQKQGAGAYSKSY  2050
2051  TLV                                                 2053

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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