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

NucPred

Fetching Q99M80 from www.uniprot.org...

The NucPred score for your sequence is 0.50 (see score help below)

   1  MGSLGGLALCLLRLLLLGLQRPPLPGAGAQSAAGGCSFDEHYSNCGYSVA    50
  51  LGTNGFTWEQINTWEKPMLDPAVPTGSFMMVNSSGRASGQKAHLLLPTLK   100
 101  ENDTHCIDFHYYFSSRDRSSPGALNVYVKVNGGPQGNPVWNVSGVVTEGW   150
 151  VKAELAISTFWPHFYQVIFESVSLKGHPGYIAVDEVRVLAHPCRKAPHFL   200
 201  RLQNVEVNVGQNATFQCIAGGKWSQHDKLWLQQWNGRDTALMVTRVVNHR   250
 251  RFSATVSVADTSQRSISKYRCVIRSDGGSGVSNYAELIVKEPPTPIAPPE   300
 301  LLAVGATYLWIKPNANSIIGDGPIILKEVEYRTTTGTWAETHIVDSPNYK   350
 351  LWHLDPDVEYEIRVLLTRPGEGGTGPPGPPLTTRTKCADPVHGPQNVEIV   400
 401  DIRARQLTLQWEPFGYAVTRCHSYNLTVQYQYVFNQQQYEAEEVIQTSSH   450
 451  YTLRGLRPFMTIRLRLLLSNPEGRMESEELVVQTEEDVPGAVPLESIQGG   500
 501  PFEEKIYIQWKPPNETNGVITLYEINYKAVGSLDPSADLSSQRGKVFKLR   550
 551  NETHHLFVGLYPGTTYSFTIKASTAKGFGPPVTTRIATKISAPSMPEYDA   600
 601  DTPLNETDTTITVMLKPAQSRGAPVSVYQLVVKEERLQKSRRAADIIECF   650
 651  SVPVSYRNASNLDSLHYFAAELKPSNLPVTQPFTVGDNKTYNGYWNPPLS   700
 701  PLKSYSIYFQALSKANGETKINCVRLATKGAPMGSAQVTPGTPLCLLTTA   750
 751  STQNSNTVEPEKQVDNTVKMAGVIAGLLMFIIILLGVMLTIKRRKLAKKQ   800
 801  KETQSGAQREMGPVASTDKPTAKLGTNRNDEGFSSSSQDVNGFTDGSRGE   850
 851  LSQPTLTIQTHPYRTCDPVEMSYPRDQFQPAIRVADLLQHITQMKRGQGY   900
 901  GFKEEYEALPEGQTASWDTAKEDENRNKNRYGNIISYDHSRVRLLVLDGD   950
 951  PHSDYINANYIDGYHRPRHYIATQGPMQETVKDFWRMIWQENSASIVMVT  1000
1001  NLVEVGRVKCVRYWPDDTEVYGDIKVTLIETEPLAEYVIRTFTVQKKGYH  1050
1051  EIRELRLFHFTSWPDHGVPCYATGLLGFVRQVKFLNPPEAGPIVVHCSAG  1100
1101  AGRTGCFIAIDTMLDMAENEGVVDIFNCVRELRAQRVNLVQTEEQYVFVH  1150
1151  DAILEACLCGNTAIPVCEFRSLYYNISRLDPQTNSSQIKDEFQTLNIVTP  1200
1201  RVRPEDCSIGLLPRNHDKNRSMDVLPLDRCLPFLISVDGESSNYINAALM  1250
1251  DSHKQPAAFVVTQHPLPNTVADFWRLVFDYNCSSVVMLNEMDTAQLCMQY  1300
1301  WPEKTSGCYGPIQVEFVSADIDEDIIHRIFRICNMARPQDGYRIVQHLQY  1350
1351  IGWPAYRDTPPSKRSLLKVVRRLEKWQEQYDGREGRTVVHCLNGGGRSGT  1400
1401  FCAICSVCEMIQQQNIIDVFHIVKTLRNNKSNMVETLEQYKFVYEVALEY  1450
1451  LSSF                                                1454

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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