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

NucPred

Fetching Q27152 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MFHLLLENEEIQFSNSFAQFYLQVDEAKKIFDEIDDDEYDKIQDQRKNDD    50
  51  FIVDDDGYGYRDHGGEIWERDDHPEDGGKKKKKSSMYVFSFSPKFIAQPL   100
 101  FLQPNEQSITAFMKPKSTINRPGAVTNSSAQIKQKPKVSAEQSKDIMNNL   150
 151  FQELDSKDVDELQDVNNSAVVTELNKPIAFNQNDMLTSKYAVTLETRQEV   200
 201  EQKRVTEQIQAQAQIGQNQQSSNPFSKKRKFEEISTNQNANASDSKRVSN   250
 251  QTNDNLNKVETQVISMLKVANPQIKVTSKLARMDDSMKIDQTSAQKNQIE   300
 301  QTVNHSKLQRYNQNQMMSGIKLDNRTSKPIRNLEIWNQVLANTQEFPLPL   350
 351  NENGTLSFYWIDAHEENNGTDLYIFGKIYQPQMRQFVSCSMKVNGMQREL   400
 401  YALPKMRGKARGALTVEEEKQQVRAVMMELDDIRKKRFPQISKWRCKPVN   450
 451  RKYAFEMPIQHGEHQFLKIKYDSTMPPLPSTIQGNTFECIFGSTQSMLEL   500
 501  FILKRKIRGPCWMTIKNPTKVTDFKKTWCRQGIVIDNPKNVEVTLEDLNK   550
 551  QELPPLTSLTFSFKTTRAQQNTNEIAMISCLINTNIAQEGPSQVERTQSF   600
 601  TLLRKLDGKPMPYDFDQKVKQRKENIIQKFENERQMIEAFIAKVFIVDPD   650
 651  LVVAHNLCGGMFDLLLARIQYLKVNHWSRIGRLKKTQIPNKKLDFGGSSY   700
 701  GGSQWIPRQVTCGRLLVDTFLSAKELVRETSYDLTYLAKVQLKKDRQDFD   750
 751  DELLPTLYITSERLFSLIDHTEKDAYLTIQLMNHLAIIPLTLQLTNIAGN   800
 801  LWFRSLQNARAERNEMLLLHEFKKKKFILPDKKAPFAKDFKRNMFADEFE   850
 851  ELKSGKGPKKGGKRKKAAYAGGLVIEPKAGFYDNIILLLDFNSLYPSIIQ   900
 901  EYNLCFTTVNRRPTKNFDGSEVKSQFKAAGTDANEGNEVEEADLPDKNVN   950
 951  VKDAVLPNVLRDLVQKRKAVKEKMKNEKDAVKLSQLEIRQKAIKLTANSM  1000
1001  YGCLGFGSSRFHAQAIAALITKTGRDTLLRTKDIAENKLGFNVVYGDTDS  1050
1051  IMINTGTNQLQQSLEMGKRPQGLKLIALYKCLEIEIDGVFKSLLLLKKKK  1100
1101  YAALKYEGFGTPDAKVVQEVKGLDMVRRDWCPLSKNVGNFVLNQILSGKQ  1150
1151  REDVVLNLNEYLSDIGEKMKNNGITLDQFIITKQLTKAISEYSDIKGQPH  1200
1201  VAVAQRLKNQGKSESDLVNNFIPYVIGAQPFDPSKTNPALAGKAYHPEEV  1250
1251  VSSKGKILLDIEWYITMQVLPPITRLIEHIDGIDVEFVAQCLGVDPKKYK  1300
1301  YHSSEKKTGETNNDDGTLIQNPILQTETERSLKGRTIAELTIKCPHCSES  1350
1351  YHFPGIFQDGKNNTLSGLLCIKCTQPIPEAYIQNRVTLFLKQLLTLYYQG  1400
1401  NKQCQEPACGAVSRQLLYNNKCINLACKLKNDTRYTEQKTNDTLRYLQGL  1450
1451  FNVKKYIQENQKNGCVHKTVEEVPNFDAFARMQGKVDDIMIRSKYNKVDL  1500
1501  SSIFNFMKLGKQQ                                       1513

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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