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

NucPred

Fetching Q09575 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MNDLKRSIQKFQFNVAEPEAFKRWLARNKLTFVEDGKNLSERERTRLLLG    50
  51  CLEESTFHRYEDSQREISDIYSISFDDTVTALTKIFGSTKSLMMRRQQCL   100
 101  QICRANGLSQDYLDYTNSISDAVLDSKLSSMTSDEWSIFLFLRGLNSPGD   150
 151  EKAKLYLMQYVEASEKKNEKLKLSDVHDEWMKFIQMHQQSKIVSVKPSKS   200
 201  SQQVDVNKVDTNRSKKKKKPIPRKPEKSSQDSKKKGEIPTCFYCNKKGHY   250
 251  ATNCRSNPKTGNQGGNKGKSKGCDSVHVDGLDVKTEHQAKHRMSVEVCGK   300
 301  DVAFQLDTGSMITLISVKCWEKLGSPPLEKVPHRISCANGTPMAVKGRCL   350
 351  VKFKLKGIEYTEYVYVRDRQTNLLGTSWLNLCPQMRSALAQIVNQVSTSE   400
 401  TEASRLEVMLKNDFPEVFKDGLGLCTKEKAEFRTEENAVPVFKRARPVPY   450
 451  GSLEAVETELNRLQEMGVIVPITYAKWAAPIVVIKKKGTGKIRVCADFKC   500
 501  SGLNAALKDEFHPLPTSEDIFSRLKGTVYSQIDLKDAYLQVELDEEAQKL   550
 551  AVINTHRGIFKYLRMTFGLKPAPASFQKIMDKMVSGLTGVAVYWDDIIIS   600
 601  ASSIEEHEKILRELFERFKEYGFRVSAEKCAFAQKQVTFLGFVDEHGRRP   650
 651  DSKKTEAIRSMKAPTDQKQLASFLGAADWLSRMMQDHQQNADDVVIAEIY   700
 701  DDDDDEDDSIIQKLNPVTETDIRFESQKDHEVSSVVKLVRNDSWKPKPST   750
 751  EIEKHWIRYRDRLKLIHGCLLLDDRVIVPKSLQKIVLKQLHEGHPGIVQM   800
 801  KQKARSFVFWRGLDSDIENMVRHCNNCQENSKMPRVVPLNPWPVPEAPWK   850
 851  RIHIDFAGPLNGCYLLVVVDAKTKYAEVKLTRSISAVTTIDLLEEIFSIH   900
 901  GYPETIISDNGTQLTSHLFAQMCQSHGIEHKTSAVYYPRSNGAAERFVDT   950
 951  LKRGIAKIKGEGSVNQQILNKFLISYRNTPHSALNGSTPAECHFGRKIRT  1000
1001  TMSLLMPTDRVLKVPKLTQYQQNMKHHYELRNGARAKAFQVNQKVYVQVH  1050
1051  HGNKSQWKHGVIRRKFGGVLYEVQVGDRMQKSHVNQIRTRYGDYSRSSVN  1100
1101  PRLSSDPLGFVGESGGDEMSRNDDPVVTSNGSSTDVNRGSRITSELKKKE  1150
1151  SNAVRGQPCGSCSPTNNDVSAPGYASRSHPTTDPSHSVRRSSRIRRVLDR  1200
1201  YGSSVEHPSTSTGTPRGSTSTQLGQASTRNGSRYTASGRNPSCQGNRYSS  1250
1251  IRGEGVTARRERVRTTWR                                  1268

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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