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

NucPred

Fetching Q27421 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MSTTTITTTVPAAPSKSAPPTPTTTGAAGATTNARTADCRKFTPNIFNKS    50
  51  KCSHCFRQREEHSAAALECNRRTSSNLAEPASRKVSKCGYLFVAPDWDFS   100
 101  NPLYRTKRWQRRWFVLYDDGELTYSVDDYPETIPQACVDMTKVLEVTSAV   150
 151  EVTGHPNSIAITAPERVTFVKGTSSEESQWWLNILAAFPKSKGRHKRSAT   200
 201  LPGGQVVGSLRPTSNGDLTLSTKLGNRHSSYHKDTLTSSQSAGNLLSSLD   250
 251  LGPSSTKTAGSPLTTTQSALADDEEDDGVETGEDVDEDEEDETSVPRKSK   300
 301  TVSMGGQDENNRNAGNEITNRVSQPTTCLLIEDIRRDEKTIKDIANTITN   350
 351  LSQQQNKRWSTAVNNALNNQHHFGHHSQYQVTSRDETDFQMSSNSSSTKS   400
 401  QNPASERPKSLPLASNSTPAIVSAIVKKIPTVMEQGDKTKPTARLQLHLK   450
 451  SPKHYQHERGDPDGGCNLDELCVNYMAKTDELRSVGKANSKSSSGQGKPP   500
 501  VKEESLNAKKGWLMKQDNRTCEWSKHWFTLSGAALFYYRDPLCEERGVLD   550
 551  GVLDVNSLTSVIPEPAASKQHAFQLTTWDKQRLVLASLSPSSRNSWLAVL   600
 601  RSAAGLPQLDTPPKQTDIEQDFIKAQLQQPSSSPVTPGTPAGPHFSSDEE   650
 651  YRTASEGGRRDSLDWGSPLSPSPPVLRSCLRNRSLASLHKRSRSSPPSSR   700
 701  RSTVDSVASDELPLLVVPEEMQPTESRELKQQCETLRAEASLREARMSEL   750
 751  LATLQRTEQQLTARLQEQQQQLNSELTQAKQSASDLMHNLGMQLTESQCQ   800
 801  IKQLEDRLAQGIEENEGLYKRLRELQAQDHSGGAALSNLQRHKIKRMDSL   850
 851  SDLTTISDIDPYCLQRDSLAEEYNELRSRFEKAVNEIRAMKRELKQSQNQ   900
 901  YDALELAQAALQQKLERRQHEDGAQLQLMAARIQDLTLKYSSSERQVRAL   950
 951  KQKLAKSERRRSLSLKGKEQLELKLSELQRETVERKEGTPPESSSSESSS  1000
1001  QSPLNAHLLQRLHSLEHVLLGSKERLEQSLTQLQQIRAGQRTRRSVSPMN  1050
1051  DRKDGLRQLERALAETCVMVSEQMELTCLQDSCHKCCDLRQRVEKLSALQ  1100
1101  QQTETDLQRSEQLLEQRETDLAQALEKCASQEQEQELLLQQRQELSEELG  1150
1151  RQQERCRRLEKRLELLEREHGKQLECLREVYHTEHANAADEQSFRKRYQT  1200
1201  EIEQLRTLCEKGLSAMETSHKRLTMDLEQKHKMEIERLLAEKETALAEET  1250
1251  QATLAALDAMRKAHQSEVQREVARFKQEFLRQVQRGEQMRGDGAKLKEED  1300
1301  LGELRMEILAFSEKYSIKCVENAALEEKLHMANSKLRHFQQMQQLELRNK  1350
1351  QFRAHLASDDPSNDVHFVQGLTSDAREDADCEDSEPAPQILGATATRTTA  1400
1401  TTTTTATATTTSAAPSETESNPDSDRETADSSRAPPEKMEQSLFVIPSHM  1450
1451  LNSSLVPAANASDQSQRSQLYRDLDGPEDGYEPCYRPFDIFAIYQNRLSY  1500
1501  QGLKGSSTFGKSLRKSAAQTSPASSEITTTTTAPTTDPKKPSHKQMFKTA  1550
1551  AVINIQQQVAQEEKAQ                                    1566

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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