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

NucPred

Fetching Q4WP03 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MLRDELLRSKNDEIARCLLSRKRKLSELYFATVGFAGATENAPTNALYHQ    50
  51  KEQTFLDANDLTKGRYFNEATLPPFPDFAALIPRPEEQHSSLEITEPVVQ   100
 101  TDDVSSVIAPKAEGAVRGIAPSFQQQEGQTAQVIEQRLVEDSLKKDDARI   150
 151  HQQPALATTSEIPQVANSPTTPAQPDQLPQKASFAVPDTPPTSTSHESVD   200
 201  ASVSPALKGLPPSEVAPPRAVSNQLPSAQRKPESRPSLVLAQPSEDQPLS   250
 251  PASSAGPYSNNTPAPVAVSPDTSPAEEVTEGADEVALSPKRVGPVQLQPG   300
 301  LVPSTPDEQLQLEAAQSLQQNALASKSIGDVTTASSLSNEVIKEDVGPTP   350
 351  SAAADSSKETQDQTSTSVEAPEPKRPDGVVVAPEESQPPAQSIQEETQSQ   400
 401  VGAEVKVVASTTPAGKKPTAAAVLPAQPERMTTRVSSGAIRHKSVSEILG   450
 451  ETPKPSAVQPEKAHAIEKPADMVRAPASASPESAAKMRLKDRKAREKERS   500
 501  KLSTVVFPKQQQQQQQQQEKDDSLDIVRQYAGELARLNEEQDYLFTLFQN   550
 551  KAYAPPRGTNLSTLLASAHKTLTTSNHLLEYQEQMDCRTLRRIYALQNAN   600
 601  RWPLRQLKRSVEPPRQGTHWDVLLDHMKWMRTDYREERKWKIAAAKSCAD   650
 651  WCAEYVNSDPEHRALLRVPCRIPSKFEKKEAHASSMISPPEETTEEMLVV   700
 701  SQPTPDLIPSAEDESVSDGFNDEIRHDIRDTVAPAAIFSLGSDEFTFSLD   750
 751  MTPAAQKLLDELPIYTPVKIAPGANVPMFEQPPDSAWKTELLPVSKYASG   800
 801  RIKFHETESPRKRSRYDYSQYDSNPEHGMLDLPPEQTNVALFRPENKPIR   850
 851  DRIHPGHSFRPPTEYPMPSVGFFESRQSSQWTYAEDDELRRLVKEYSYNW   900
 901  SLISSCLTPSSQFTSGAERRTPWECFERWVGLEGLPADMSKTQYFRAYHQ   950
 951  RIETAQRTVLAQQQAAQQQQQQQQQQQQQGGNNSGQAQPPIRRRTTQPVR  1000
1001  VDRRRSSKHLALLDAMRKLAKKRETMLQKQQHASHLASLRKVNDANQPKP  1050
1051  PISSPAEFSRLKYDRELKLQERQEQYRQQMIAQQRANLAAQRAGQIPSQQ  1100
1101  PMMNAPPGRTPNGIPHNPGTPGIPGATPNGMHNGMPNALPNGIPPGMGVS  1150
1151  QGRPHMQGVPAGGPPMNGPIPPNPMAMKMMPQTGMPQGPGGRPGMPMQTS  1200
1201  PDNTRVMREANRLQEQQRILQSRQQQPQPPQHQQPQAQQAQQQFHNQQQF  1250
1251  GPQGSHSPNMNLPNVNGTPNNPAMMAAIQAGSGMQSPSLHNAMPQGVSTP  1300
1301  SPRMGQPNLLSGGVVPTISSIQSQIQRSNPNMPPEQVNKLATDRLHQYQQ  1350
1351  QRMSQVAMNAAAGNMASVQANYQVPHDGNFQSPQPGMNGTPGMQVPQSQG  1400
1401  FSPMMRVPQPAQQNRMGVGNSPAMNVALPQQSRSATPQTQRSGSAQAGPV  1450
1451  PGSSKSPHPPQAQIPSG                                   1467

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.)

Go back to the NucPred Home Page.