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

NucPred

Fetching Q6CQ43 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MSSWLPQNVQKRLLLYVLQQVSLFSNVDLTNLDVSLGSQSQFSFNDIDLN    50
  51  VKEIKLPNVDVLSGKIEKLNLQLAVAGNVDISGEGLTFVLKPIDRFFEDD   100
 101  LSDQWASSLTKSVIDMTKSIMESDVTDSSEHSVEALEEVSKSPTALDSMR   150
 151  NKVLQMALGKLSLKMKRIEFQFLLSTEVTLKFTIDTITLLTVDNKRTVDM   200
 201  GGIEVAFSKTQLSPTNSHQNTDSDVEENENTDSEDAMTASITYSKLEATS   250
 251  IYLSAMESLILESSDDAVQVVLTIDKVNIQFQGVTSINDLKVRDVIIRID   300
 301  EINIYLRKISPIRKHLLSILRASLDKTSSDGTRTENMRNYKRFQQEQNIK   350
 351  EEEVLTAILLKKVSLHLLDDLELNLIDISLKKSEGFTTSASVFDLKLLYM   400
 401  SNEYFFSSPSAQPLFSMQPDQTTAEKKMFLNRDITLNVDSVLLNELLKLV   450
 451  EEYGSAYNYIQKITRASANQKTAEVLHFKSQSINLKILMNNISLELSMDP   500
 501  IKSTLPHTLFDVEKISLLLIRGDKKVLIGTLSNLIISSKTNGCFHVESFD   550
 551  HKFGAIDINTRTKAVLESLHLFLSQAELELISSNLIAFCGSISSFTNPNT   600
 601  RNNGHENVTKKSVRLLHSSNVMNKRATLSNFVLQVHKAKMTITNTLENTF   650
 651  GDITIEAISCILSQDQNKTLCGIVKEARLQRLYMREKTDIICNVNHDRSK   700
 701  PQLILNMPNSGKPKLYLKGLGLFIDSKWRDLVPSSSKGDIKQERKLTFRT   750
 751  MEVRLYDCSLSLKPYRICTGMVISIPKSIINFSPLGITVSLRSLETLLID   800
 801  DMKVLKERNTKVLENISLSTWYQKQGYSPLIKVDVLSLHFSNTDSMAVSL   850
 851  KVQKVDVSVCSDSLNALMQTALDLKPAETYPDTLKYQIEPEAVDIFNELC   900
 901  EDFFVTKENPNDKTEDDYETPPVSQGSVNFEEEHFSTERRTVVENDSKSS   950
 951  VFSILTTIKIHIEEVKLKLYDGYEWRHTRKEIKSAVDRIQEDFNDGLELS  1000
1001  ETKVFDSIYIPAPKDTVENIKDNINRKIHNEETNEGKMKLRPTKKYKVLI  1050
1051  KGRDLCIEFKGGQDKIAERASSLSSINDYCILNNTFVKVSDLEIIDNLPT  1100
1101  STWNKFLTRSRSNDKMAQEPAMLVIECSLIRPVPHLYATELICNINIVPL  1150
1151  TLHVDQDTLEFLTLFFQFKDNRFELLDEYPDILYIQRLEINSVRLLLDYK  1200
1201  PKKVDYAGLKSGKTKEFMNFFILDEARIKLKHVILYGVNGFPQLETILSD  1250
1251  IWTPDITKTQIPGILSALTPLKPLAGLSYGARALISVPTEHYQQNGRFGG  1300
1301  SLQNGGMVFLKTTGGEVIKLAVRLTSGTQTILENTEKLLGGQGITGRNVP  1350
1351  ITLVEGDEKVDALIDESLLRSTALFNKEPDNKSNHLDVLLADGNHQKVLS  1400
1401  LYADQPKDFNSGLQDAYESMERNLYLTFDSMKKAKKELKTAKGAQEAVST  1450
1451  VAKAAPFVLIRPLIGVTEALSKTLQGLNNQYDEDRIAQIEEKYKSKKQNN  1500
1501  NQ                                                  1502

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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