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

NucPred

Fetching O60469 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MWILALSLFQSFANVFSEDLHSSLYFVNASLQEVVFASTTGTLVPCPAAG    50
  51  IPPVTLRWYLATGEEIYDVPGIRHVHPNGTLQIFPFPPSSFSTLIHDNTY   100
 101  YCTAENPSGKIRSQDVHIKAVLREPYTVRVEDQKTMRGNVAVFKCIIPSS   150
 151  VEAYITVVSWEKDTVSLVSGSRFLITSTGALYIKDVQNEDGLYNYRCITR   200
 201  HRYTGETRQSNSARLFVSDPANSAPSILDGFDHRKAMAGQRVELPCKALG   250
 251  HPEPDYRWLKDNMPLELSGRFQKTVTGLLIENIRPSDSGSYVCEVSNRYG   300
 301  TAKVIGRLYVKQPLKATISPRKVKSSVGSQVSLSCSVTGTEDQELSWYRN   350
 351  GEILNPGKNVRITGINHENLIMDHMVKSDGGAYQCFVRKDKLSAQDYVQV   400
 401  VLEDGTPKIISAFSEKVVSPAEPVSLMCNVKGTPLPTITWTLDDDPILKG   450
 451  GSHRISQMITSEGNVVSYLNISSSQVRDGGVYRCTANNSAGVVLYQARIN   500
 501  VRGPASIRPMKNITAIAGRDTYIHCRVIGYPYYSIKWYKNSNLLPFNHRQ   550
 551  VAFENNGTLKLSDVQKEVDEGEYTCNVLVQPQLSTSQSVHVTVKVPPFIQ   600
 601  PFEFPRFSIGQRVFIPCVVVSGDLPITITWQKDGRPIPGSLGVTIDNIDF   650
 651  TSSLRISNLSLMHNGNYTCIARNEAAAVEHQSQLIVRVPPKFVVQPRDQD   700
 701  GIYGKAVILNCSAEGYPVPTIVWKFSKGAGVPQFQPIALNGRIQVLSNGS   750
 751  LLIKHVVEEDSGYYLCKVSNDVGADVSKSMYLTVKIPAMITSYPNTTLAT   800
 801  QGQKKEMSCTAHGEKPIIVRWEKEDRIINPEMARYLVSTKEVGEEVISTL   850
 851  QILPTVREDSGFFSCHAINSYGEDRGIIQLTVQEPPDPPEIEIKDVKART   900
 901  ITLRWTMGFDGNSPITGYDIECKNKSDSWDSAQRTKDVSPQLNSATIIDI   950
 951  HPSSTYSIRMYAKNRIGKSEPSNELTITADEAAPDGPPQEVHLEPISSQS  1000
1001  IRVTWKAPKKHLQNGIIRGYQIGYREYSTGGNFQFNIISVDTSGDSEVYT  1050
1051  LDNLNKFTQYGLVVQACNRAGTGPSSQEIITTTLEDVPSYPPENVQAIAT  1100
1101  SPESISISWSTLSKEALNGILQGFRVIYWANLMDGELGEIKNITTTQPSL  1150
1151  ELDGLEKYTNYSIQVLAFTRAGDGVRSEQIFTRTKEDVPGPPAGVKAAAA  1200
1201  SASMVFVSWLPPLKLNGIIRKYTVFCSHPYPTVISEFEASPDSFSYRIPN  1250
1251  LSRNRQYSVWVVAVTSAGRGNSSEIITVEPLAKAPARILTFSGTVTTPWM  1300
1301  KDIVLPCKAVGDPSPAVKWMKDSNGTPSLVTIDGRRSIFSNGSFIIRTVK  1350
1351  AEDSGYYSCIANNNWGSDEIILNLQVQVPPDQPRLTVSKTTSSSITLSWL  1400
1401  PGDNGGSSIRGYILQYSEDNSEQWGSFPISPSERSYRLENLKCGTWYKFT  1450
1451  LTAQNGVGPGRISEIIEAKTLGKEPQFSKEQELFASINTTRVRLNLIGWN  1500
1501  DGGCPITSFTLEYRPFGTTVWTTAQRTSLSKSYILYDLQEATWYELQMRV  1550
1551  CNSAGCAEKQANFATLNYDGSTIPPLIKSVVQNEEGLTTNEGLKMLVTIS  1600
1601  CILVGVLLLFVLLLVVRRRRREQRLKRLRDAKSLAEMLMSKNTRTSDTLS  1650
1651  KQQQTLRMHIDIPRAQLLIEERDTMETIDDRSTVLLTDADFGEAAKQKSL  1700
1701  TVTHTVHYQSVSQATGPLVDVSDARPGTNPTTRRNAKAGPTARNRYASQW  1750
1751  TLNRPHPTISAHTLTTDWRLPTPRAAGSVDKESDSYSVSPSQDTDRARSS  1800
1801  MVSTESASSTYEELARAYEHAKMEEQLRHAKFTITECFISDTSSEQLTAG  1850
1851  TNEYTDSLTSSTPSESGICRFTASPPKPQDGGRVMNMAVPKAHRPGDLIH  1900
1901  LPPYLRMDFLLNRGGPGTSRDLSLGQACLEPQKSRTLKRPTVLEPIPMEA  1950
1951  ASSASSTREGQSWQPGAVATLPQREGAELGQAAKMSSSQESLLDSRGHLK  2000
2001  GNNPYAKSYTLV                                        2012

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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