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

NucPred

Fetching P61460 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MRTTKVYKLVIHKKGFGGSDDELVVNPKVFPHIKLGDIVEIAHPNDEYSP    50
  51  LLLQVKSLKEDLQKETISVDQTVTQVFRLRPYQDVYVNVVDPKDVTLDLV   100
 101  ELTFKDQYIGRGDMWRLKKSLVSTCAYITQKVEFAGIRAQAGELWVKNEK   150
 151  VMCGYISEETRVVFRSTSAMVYIFIQMSCEMWDFDIYGDLYFEKAVNGFL   200
 201  ADLFTKWKEKNCSHEVTVVLFSRTFYDAKSIDEFPEINRASIQEDHKGRF   250
 251  YEDFYKVVVQNERREEWTSLLVTIKKLFIQYPVLVRLEQAGGFPQGDNST   300
 301  SAQGNYLEAINLSFNVFDKHYINRNFDRTGQMSVVITPGVGVFEVDRLLM   350
 351  ILTKQRMIDNGIGVDLVCMGEQPLHAVPLFKLHNRSVPRDSRLGDDYNIP   400
 401  HWINHSFYTSKSQLFCNSFTPRIKLAGKKSASEKTKNGRDTSLGTPKESE   450
 451  NTLPIQVDYDAYDAQVFRLPGPSRAQRLATCRSVREQENHSRKSASSCDV   500
 501  SSSPSLPSRALPTEEVRSQASDDSSLGKSTNILMIPNPHLHQYEVSSSLG   550
 551  YTSTRDVLENMIEPPQRDSSAPGRFHVGSAESMLHVRPGGYTPQRALINP   600
 601  FAPSRMPMKLTSNRRRWMHTFPVGPSGEAIQIHHQTRQNMAELQGSRQRD   650
 651  PTHSSAELLELAYHEAAGRHSTSRQPGDSMSLNFSGTEELSVSLLSNSST   700
 701  GVNPRTQNKDSLEDSVSTSPDPMPGFCCTVGVDWKSLTTPACLPLTTDYF   750
 751  PDRQGLQNDYTEGCYDLLPEADMDRRDEEGVQMTAQQVFEEFICQRLMQG   800
 801  YQIIVQPKTQKPNTTVPPPLSSSPLYSRGLVSRNRPEEEGQYWLSMGRTF   850
 851  HKVTLKDKMITVTRYLPKYPYESAQIHYTYSLCPSHSDSEFVSCWVDFCH   900
 901  ERLEEYKWNYLDQYICSAGSEDFSLIESLKFWRTRFLLLPACVTATKRIT   950
 951  EGEVHCDIYGDKPRADEDEWQLLDGFIRFVEGLNRIRRRHRSDRMIRKGT  1000
1001  AMKGLQMTGPISAHSLEAAGPPVGKKGTSALSALLEMEASQKSLGEQQTT  1050
1051  VHGKSSTQPAENSSVAMTPTYVDSPRKDGAFFMEFVRSPRTASSAFYPQA  1100
1101  SVDQTAPLVLDSTSLGVSTGQPMDRGNNQTFGNSQNIEQAFPSANSGDYS  1150
1151  SQQHVASSLTSSSTLVEILEAMKHPSTGVQLLSEQKGLSPCCFISAEVVH  1200
1201  WLMNNVEGVQTQAMGIDIMQKMLEEQLITHASGEAWRTFIYGFYFYKIVM  1250
1251  DKEPERVAMQQPSAPWYTAGADDFASFQRKWFEVAFVAEELVHSEIPAFL  1300
1301  LPWLPSRPASYASRHSSFSRSFGGRSQAAALLAATVPEQRTVTLDVDVNN  1350
1351  RTDRLEWCSCYYHGNFSLNAAFEIKLHWMAVTATVLFEMVQGWHRKATSC  1400
1401  GFLLVPVLEGPFALPSYLYGDPLRAQLFIPLNLSCLLKEGSEHLFDSFEP  1450
1451  ETYWDRMHLFQEAIAHRFGFVQDKYSVSAFNFPAENKPQYIHVTGTVFLQ  1500
1501  LPYSKRKFSGQQRRRRNSTSSTNQNMFCEERVGYNWAYNTMLTKTWRSSA  1550
1551  TGDEKFADRLLKDFTDFCINRDNRLVTFWTNCLEKMHASAP           1591

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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