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

NucPred

Fetching Q9U969 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MDVLEMLRASASGSYNTIFSDAWCQYVSKQITATVYMYFALVMMSLLFIA    50
  51  WFLYFKRMARLRLRDEIARSISTVTNSSGDMRGLRFRKRDKMLFYGRRML   100
 101  RKMKNVSGQMYSSGKGYKRRAVMRFARRILQLRRDNMPLEMRTVEPPAEY   150
 151  LEETIEGSDRVPPDALYMLQSIRIFGHFEKPVFLRLCKHTQLLELMAGDY   200
 201  LFKITDPDDSVYIVQSGMINVYISNADGSTLSLKTVRKGESVTSLLSFID   250
 251  VLSGNPSYYKTVTAKAIEKSVVIRLPMQAFEEVFQDNPDVMIRVIQVIMI   300
 301  RLQRVLFTALRNYLGLNAELVQNHMRYKSVSTMSGPINSQTSQSSRQAPN   350
 351  GPPMVISQMNLMQSAVSGTGSSGVSVTVTRPPSSPSRHSREEHTLSDPNP   400
 401  NPDGSFHGTTNLFTEVHGDAPNADLFHQQQQQHSVGNLSTRRSSITLMAP   450
 451  DGSHSCLQTPGVTTSIDMRLVQSSAVDSLRKELGLSEEDSHIIEPFVELR   500
 501  ELEPNVTLITEGNADDVCVWFVMTGTLAVYQSNQDATRAKQDKSDMLIHF   550
 551  VHPGEIVGGLAMLTGEASAYTIRSRSITRIAFIRRAAIYQIMRQRPRIVL   600
 601  DLGNGVVRRLSPLVRQCDYALDWIFLESGRAVYRQDESSDSTYIVLSGRM   650
 651  RSVITHPGGKKEIVGEYGKGDLVGIVEMITETSRTTTVMAVRDSELAKLP   700
 701  EGLFNAIKLRYPIVVTKLISFLSHRFLGSMQTRSGSGAPGAPVEANPVTH   750
 751  KYSTVALVPITDEVPMTPFTYELYHSLCAIGPVLRLTSDVVRKQLGSNIF   800
 801  EAANEYRLTSWLAQQEDRNIITLYQCDSSLSAWTQRCMRQADVILIVGLG   850
 851  DRSHLVGKFEREIDRLAMRTQKELVLLYPEASNAKPANTLSWLNARPWVT   900
 901  KHHHVLCVKRIFTRKSQYRINDLYSRVLLSEPNMHSDFSRLARWLTGNSI   950
 951  GLVLGGGGARGAAHIGMLKAIQEAGIPVDMVGGVSIGALMGALWCSERNI  1000
1001  TTVTQKAREWSKKMTKWFLQLLDLTYPITSMFSGREFNKTIHDTFGDVSI  1050
1051  EDLWIPYFTLTTDITASCHRIHTNGSLWRYVRSSMSLSGYMPPLCDPKDG  1100
1101  HLLLDGGYVNNLPADVMHNLGAAHIIAIDVGSQDDTDLTNYGDDLSGWWL  1150
1151  LYKKWNPFTSPVKVPDLPDIQSRLAYVSCVRQLEEVKNSDYCEYIRPPID  1200
1201  KYKTLAFGSFDEIRDVGYVFGKNYFESMAKAGRLGRFNQWFNKEPPKRVN  1250
1251  HASLNEYTFIDLAQIVCRLPETYAVNTAELFSEDEDCDGYISEPTTLNTD  1300
1301  RRRIQVSRAGNSLSFSETEMDSDVELDLKLERKTDKSTQSSPPSNSRSDM  1350
1351  RGKEEARHMSNWHWGVKHKDETGSGATEATKTQTGQEQELQQEQQDQGAT  1400
1401  AEQLVDKDKEENKENRSSPNNETKN                           1425

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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