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

NucPred

Fetching Q9GL21 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MPSSLLLATRNQILSMMNCWFSCAPKNRHAADWNKYDDRLMKAAERGDVE    50
  51  KVSSILAKKGINPGKLDVEGRSAFHVVASKGNLECLNAILIHGVDITTSD   100
 101  TAGRNALHLAAKYGHALCLQKLLQYNCPTEHADLQGRTALHDAAMADCPS   150
 151  SIQLLCDHGASVNAKDVDGRTPLVLATQMCRPAICQLLIDRGAEINSRDK   200
 201  QNRTALMLGCEYGCKDAVEVLLKNGADVSLLDALGHDSSYYARIGDNLDI   250
 251  LTLLKTASENTNKGRELWKKGPSLQQRNLPYMLDEVNVKSSQREHRNIQE   300
 301  LEIENEDLKDRLRKIQQEQRILLDKVNGLQLQLNEEVMVADDLESEKEKL   350
 351  KSLLVAKEKQHEESLRTIESLKNRFKYFESDHLGSGSHFSNRKEDMLLKQ   400
 401  GQMYMTCTSPGVPAHMQSRSMLRPLELSLPNQTSYSENDLLKKELEAMRT   450
 451  FCESAKQDRLKLQNELAHKVAECKALGLECERIKEDSDEQIKQLEDALKD   500
 501  VQKRMYESEGKVKQMQTHFLALKEHLTSEAAIGNHRLMEELKDQLKDMKA   550
 551  KYEGASAEVGKLRNQIKQNELLVEQFRRDEGKLVEENKRLQKELSMCETE   600
 601  RDKKGRRVAEVEGQVKELLAKLTLSVPTEKFESMKSLLSSEVNEKVKKIG   650
 651  ETEREYEKSLTEIRQLRRELENCKAKLAQHVKPEEHEQLKSRLEQRAGEL   700
 701  AKKVTELTSKNQVLQRDVEKVYLDNKLLNQQVHNLTSEIKSHYVPLQVSE   750
 751  EMKKSHDVTVEELKKQLLDVTQKCADKQLEMEKLLLENDSLSKNVSRLET   800
 801  VFVPPEKHQKEVTALKSSVADLKRQLLELNKKCGEDREKINALVSENTSL   850
 851  KKTLSNQYVPAKTHEEVKTALSGTLDKTNRELLDAKKKWEDLNQEFVKTK   900
 901  DENEILKRNLENTQSQIKAEYISLREHEEKMSAINQNMKSVQDNSAEILA   950
 951  NYRKGQEEIVTLHAEIEAQKKELDTIQECIKLKYAPIISFEECERKFKAT  1000
1001  EKELKEQLSEQMQKYHVREEEAKKYKQENDKLKKEIFTLQKDLKDKNVLI  1050
1051  ENSHDMERALNRKAEELNKQLKDLLQKYSEIKTEKEKLVDDNARQTSELL  1100
1101  AAQTLLQKQHVPLEQVETLKKSLNSTIEHLKEELKNKQKCYEKEQQTVAK  1150
1151  LHQMLENQKNSSVPLGEHLRVKEAFEKEVGMIKASLREKEEESQNKTEEV  1200
1201  SKLQSEVQDTKQALQKLETREVVDLSKYKATKSDLETQISNLNEKLANLN  1250
1251  RKYEEACEEVLRAQRKQLSAKDEKELLHFSIEQEIKDQQERCDKSLTTIT  1300
1301  ELQKRIQESAKQIEAKDNKITELLNDVERLKQALSGLSQLTSPSGSPSKR  1350
1351  QSQLIDTLQHQVKSLQQQLADTDRQHQEVIAIYRTHLLSAAQGHMDEDVQ  1400
1401  AALLQIIQMRQGLVC                                     1415

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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