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

NucPred

Fetching P55937 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MDGASAKQDGLWESKSSSDVSSCPEASLETVGSLARLPDQQDTAQDASVE    50
  51  VNRGFKEEGSPDRSSQVAICQNGQIPDLQLSLDPTTSPVGPDASTGVDGF   100
 101  HDNLRNSQGTSAEGSVRKEALQSLRLSLPMQETQLCSTASSLPLEKEEQV   150
 151  RLQARKRLEEQLMQYRVKRHRERSSQPATKMKLFSTLDPELMLNPENLPR   200
 201  ASTVAVTKEYSFLRTSVPRGPKVGSLGLLAHSKEKKNSKSSKIRSLADYR   250
 251  TEDPSDSGGLGSTADAVGSSLKQSRSSTSVVSEVSPSSETDNRVESASMT   300
 301  GDSVSEADGNESDSSSHSSLSARGACGVLGNVGMPGTAYMVDGQEISAEA   350
 351  LGQFPSIKDVLQAAAAQHQDQNQEANGEVRSRRDSICSSVSMESSLAEPQ   400
 401  DELLQILKDKRRLEGQVEALSLEASQALQEKAELQAQLAALSTRLQAQVE   450
 451  HSHSSQQKQDSLSSEVDTLKQSCWDLGRAMTDLQSMLEAKNASLASSNND   500
 501  LQVAEEQYQRLMAKVEDMQRNILSKDNTVHDLRQQMTALQSQLQQVQLER   550
 551  TTLTSKLQASQAEITSLQHARQWYQQQLTLAQEARVRLQGEMAHIQVGQM   600
 601  TQAGLLEHLKLENVSLSHQLTETQHRSIKEKERIAVQLQSIEADMLDQEA   650
 651  AFVQIREAKTMVEEDLQRRLEEFEGEREQLQKVADAAASLEQQLEQVKLT   700
 701  LFQRDQQLAALQQEHLDVIKQLTSTQEALQAKGQSLDDLHTRYDELQARL   750
 751  EELQREADSREDAIHFLQNEKIVLEVALQSAKSDKEELDRGARRLEEDTE   800
 801  ETSGLLEQLRQDLAVKSNQVEHLQQETATLRKQMQKVKEQFVQQKVMVEA   850
 851  YRRDATSKDQLINELKATKKRLDSEMKELRQELIKLQGEKKTVEVEHSRL   900
 901  QKDMSLVHQQMAELEGHLQSVQKERDEMEIHLQSLKFDKEQMIALTEANE   950
 951  TLKKQIEELQQEAKKAITEQKQKMKRLGSDLTSAQKEMKTKHKAYENAVS  1000
1001  ILSRRLQEALASKEATDAELNQLRAQSTGGSSDPVLHEKIRALEVELQNV  1050
1051  GQSKILLEKELQEVITMTSQELEESREKVLELEDELQESRGFRRKIKRLE  1100
1101  ESNKKLALELEHERGKLTGLGQSNAALREHNSILETALAKREADLVQLNL  1150
1151  QVQAVLQRKEEEDRQMKQLVQALQVSLEKEKMEVNSLKEQMAAARIEAGH  1200
1201  NRRHFKAATLELSEVKKELQAKEHLVQTLQAEVDELQIQDGKHSQEIAQF  1250
1251  QTELAEARTQLQLLQKKLDEQMSQQPTGSQEMEDLKWELDQKEREIQSLK  1300
1301  QQLDLTEQQGKKELEGTQQTLQTIKSELEMVQEDLSETQKDKFMLQAKVS  1350
1351  ELKNNMKTLLQQNQQLKLDLRRGAAKKKEPKGESNSSSPATPIKIPDCPV  1400
1401  PASLLEELLRPPPAVSKEPLKNLNNCLQQLKQEMDSLQRQMEEHTITVHE  1450
1451  SLSSWAQVEAAPAEHAHPRGDTKLHNQNSVPRDGLGQ               1487

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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