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

NucPred

Fetching Q9VQH2 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MSVPSAPHQRAESKNRVPRPGQKNRKLPKLRLHWPGATYGGALLLLLISY    50
  51  GLELGSVHCYEKMYSQTEKQRYDGWYNNLAHPDWGSVDSHLVRKAPPSYS   100
 101  DGVYAMAGANRPSTRRLSRLFMRGKDGLGSKFNRTALLAFFGQLVANEIV   150
 151  MASESGCPIEMHRIEIEKCDEMYDRECRGDKYIPFHRAAYDRDTGQSPNA   200
 201  PREQINQMTAWIDGSFIYSTSEAWLNAMRSFHNGTLLTEKDGKLPVRNTM   250
 251  RVPLFNNPVPSVMKMLSPERLFLLGDPRTNQNPAILSFAILFLRWHNTLA   300
 301  QRIKRVHPDWSDEDIYQRARHTVIASLQNVIVYEYLPAFLGTSLPPYEGY   350
 351  KQDIHPGIGHIFQAAAFRFGHTMIPPGIYRRDGQCNFKETPMGYPAVRLC   400
 401  STWWDSSGFFADTSVEEVLMGLASQISEREDPVLCSDVRDKLFGPMEFTR   450
 451  RDLGALNIMRGRDNGLPDYNTARESYGLKRHKTWTDINPPLFETQPELLD   500
 501  MLKEAYDNKLDDVDVYVGGMLESYGQPGEFFTAVIKEQFQRLRDADRFWF   550
 551  ENERNGIFTPEEIAELRKITLWDIIVNSTDVKEEEIQKDVFMWRTGDPCP   600
 601  QPMQLNATELEPCTYLEGYDYFSGSELMFIYVCVFLGFVPILCAGAGYCV   650
 651  VKLQNSKRRRLKIRQEALRAPQHKGSVDKMLAREWLHANHKRLVTVKFGP   700
 701  EAAIYTVDRKGEKLRTFSLKHIDVVSVEESATNHIKKKPYILLRVPSDHD   750
 751  LVLELESYGARRKFVKKLEDFLLLHKKEMTLMEVNRDIMLARAETRERRQ   800
 801  KRLEYFFREAYALTFGLRPGERRRRSDASSDGEVMTVMRTSLSKAEFAAA   850
 851  LGMKPNDMFVRKMFNIVDKDQDGRISFQEFLETVVLFSRGKTDDKLRIIF   900
 901  DMCDNDRNGVIDKGELSEMMRSLVEIARTTSLGDDQVTELIDGMFQDVGL   950
 951  EHKNHLTYQDFKLMMKEYKGDFVAIGLDCKGAKQNFLDTSTNVARMTSFN  1000
1001  IEPMQDKPRHWLLAKWDAYITFLEENRQNIFYLFLFYVVTIVLFVERFIH  1050
1051  YSFMAEHTDLRHIMGVGIAITRGSAASLSFCYSLLLLTMSRNLITKLKEF  1100
1101  PIQQYIPLDSHIQFHKIAACTALFFSVLHTVGHIVNFYHVSTQSHENLRC  1150
1151  LTREVHFASDYKPDITFWLFQTVTGTTGVMLFIIMCIIFVFAHPTIRKKA  1200
1201  YNFFWNMHTLYIGLYLLSLIHGLARLTGPPRFWMFFLGPGIVYTLDKIVS  1250
1251  LRTKYMALDVIDTDLLPSDVIKIKFYRPPNLKYLSGQWVRLSCTAFRPHE  1300
1301  MHSFTLTSAPHENFLSCHIKAQGPWTWKLRNYFDPCNYNPEDQPKIRIEG  1350
1351  PFGGGNQDWYKFEVAVMVGGGIGVTPYASILNDLVFGTSTNRYSGVACKK  1400
1401  VYFLWICPSHKHFEWFIDVLRDVEKKDVTNVLEIHIFITQFFHKFDLRTT  1450
1451  MLYICENHFQRLSKTSIFTGLKAVNHFGRPDMSSFLKFVQKKHSYVSKIG  1500
1501  VFSCGPRPLTKSVMSACDEVNKTRKLPYFIHHFENFG               1537

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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