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

NucPred

Fetching O14340 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MEHPSPDSVSSTSSSDHKKAELSDSLKQLQLLQAFQAGDIKQVDNLLHNK    50
  51  SKDECTHALFISIQCANVQMVKHILSVFDVDVNAYDKNKNTPLHLAAMAG   100
 101  RQDIVEALLLHPDINYNLVNANNKKAYQVATSPQLMDFMKGFYVTYTKET   150
 151  AREFKKAFKERNLESMDYLMRHNEFNDAIDLNEVDIKTGQTYLHVATKAK   200
 201  DAELVKWLLDNGADPYRRDKFGKLPTDYTKDENMRSLLRSYSGNRDSSSA   250
 251  PAVPQHMSGYLKKWTNYKSGYKLRWFTLNNGVLSYYKNQDDASSACRGSI   300
 301  NLKLARLVHDPKQPTVFQVIGKGSVRYSVKANSPVEAKKWIAAISSAIEN   350
 351  DEEANKPNVTADNASFGTHDLAPAAHKFTQSNASGNSGWDDNESDIDRAQ   400
 401  LPSRENFEFNVNIAKLQVETLHKLIDSAMQTEKVKKDPSLSQVFDGISNS   450
 451  FNTLHKTVLEMLDLQRQAEHYYKRKLDNAKAINALWAENLKTVVEEQDQI   500
 501  EERYHRSEAHRRRTKRAFRRLAASLKKRPSDKDNKLHIHYDDGAMSSTSY   550
 551  STDFTDDEEETNTKDEFFDVDAHDNNHANKAEPSQTANNVHEIREPSFSS   600
 601  EHKPQPSLKTTTDVSSPETKQNIADIRKTTLTDQTEEFTERRDNNGSIPS   650
 651  KQPSDEQHLGKESLPSQQSTVSNHHRKESIPSKQPTEGQHARQESLPSQQ   700
 701  TTETKHLRKESTPSKQPTEGQHTRQESLPSQQTTETKHLRKESIPSKQPT   750
 751  EGQHARQESLPSQQTTETKHLRKESIPSKQPSGGQQLRQESLPSQQSSES   800
 801  KQSTQHQQPVEVQKSIQSDVSAPKAKEVSEKPVSHQAKPSNASQLSRNTD   850
 851  DTQAKEAPKEASIPDNASTASTKVSNDSHLKPDADKKSVSSELTHASKPS   900
 901  LDEKTMQLAKQIAVSFHGYEAPTRENLDVNDDRPKISLWGILKGMIGKDM   950
 951  TKMTLPVSFNEPTSLLQRVAEDMEYTELLDQASHNKDPYQRILYVAAFAA  1000
1001  SEYASTLNRVAKPFNPLLGETYEFCHPQRGFRFIVEQVSHHPPVGAAYSE  1050
1051  SANWKYYGESSVKSKFYGKSFDISPLGTWFLELRHPSGEVELYTWKKVTS  1100
1101  SVVGIILGSPSVDNYGQMHIVNHSSGINCVLDFKPRGWRGTNAHEVKGSV  1150
1151  QSTDDTPKWMVNGHWNDKIFGQQPNGNKILLWQNHERPPRPFNLTPFAIS  1200
1201  LNALTPQLKPWLPPTDTRLRPDQRAMENGQYDLAASEKNRLEEKQRKKRR  1250
1251  MREQGEMPPWSPRWFSAAKHPVTGEDYWQFNNEYWKIREEAGEAHLAGKE  1300
1301  FEWPNVDDIF                                          1310

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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