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

NucPred

Fetching Q8R5G7 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MAAPQDLDIAVWLALVHLEQYADTFRRHGLATAGAAQHLGHEELRHLGIS    50
  51  ATGHRKRILRLLRAGSAEGFLDSHLDNTMEPTPSPAPDAQPPKPVPKPRT   100
 101  VFGLSNPATAQRPGLSPIFWDPEVSRNSECTQRSSPLLPSSSEQPSVPNT   150
 151  MEMMPNAIYFGLDLRGRAQAAQDVTPDSSQATVPTPAFRPTTGTVHIMDP   200
 201  GCLYYGVQPVGIPGASDRRDGRGVCQERAEHRQDLETREDAGYASLELPG   250
 251  DSILSLPTQDAETSDDLISPYASFSSTADRPVPLLSGWLDKLSPQGNYVF   300
 301  QRRFVQFNGRSLMYFGSDKDPFPKGVIPLTAIEMTRSSKDNKFQVITGQR   350
 351  VFVFRTESEAQRDLWCSTLQSCLKEQRLLGHPRPPHPPRPLRTGTLELRG   400
 401  HKAKVFAALIPGELALYKSEQAFSLGIGICFIELQGCSVRETKSRSFDLL   450
 451  TPHRCFSFTAESGGARQSWAAALQEAVTETLSDYEVAEKVWSNPANRHCA   500
 501  DCRASRPDWAAVNLGVVICKQCAGQHRALGSGISKVQSLKLDTSVWSNEI   550
 551  VQLFIVLGNDRANCFWAGALPPGEGLHPDSAPGPRGEFISRKYKLGLFRK   600
 601  PHPRHPDHSQLLQALCAAMAGPNLLKNMAQLLCVETSEGEEPLSPSALNG   650
 651  SLLSLLPSDSPGVYNEVVVPATYRGFLYCGSISNKAGAPPLRRGRDAPPR   700
 701  LWCVLGAALEMFASESSPEPLSLLQPQDIVCLGVSPPPADPGDLDRFPFS   750
 751  FELILTGGRIQHFATDGADSLEAWISAVGKWFSPLSCHQLLGPGLLRMGR   800
 801  LWLRSPSHAGLAPGLWLSGFGLLRGDHLFLCPAPGPGPPAPEDMVHLRRL   850
 851  QEISVVSAADTPDKKEHLVLVETGRTLYLQGEGRLDFAAWNTAIGGAAGG   900
 901  GGTGLQEQQMSRGDIPIIVDACISFVTQHGLRLEGVYRKGGARARSLRLL   950
 951  AEFRRDARSVKLRPREHFVEDVTDTLKRFFRELDDPVTSARLLPRWREAA  1000
1001  ELSQKNQRLEKYKEVISCLPRVNRRTLATLIGHLYRVQKCASLNQMCTRN  1050
1051  LALLFAPSVFQTDGRGEHEVRVLQELIDGYISVFDIDSDQAAQIDLEVSL  1100
1101  ITTWKDVQLSQAGDLIMEVYIEQQLPDNCVTLKVSPTLTAEELTNQVLEM  1150
1151  RGAASGTDLWVTFEILEHGELERPLHPKEKVLEQALQWCQLPEPCSASLL  1200
1201  LRKVSMAHAGCLFTGVRRESPRVGLLRCREEPPRLLGNRFQERFFLVRGR  1250
1251  CLLLLKEKKSSKPEREWSLEGAKVYLGIRKKLKPPTLWGFTLILEKMHLC  1300
1301  LSCMDEEEMWDWTTSILKAQHDDQQSVVLRRRSSSDLARQKFGTMPLLPI  1350
1351  RGDDSGATLLSANQTLRRLHNRRTLSMFFPMKSPQGSVEEQDELEEPVYE  1400
1401  EPVYEEVGAFPELTKDTTFSSTWEWSAKSDPSLTSQRSFDQPPLSKASML  1450
1451  GHEERIPDPPPGPPSKSSSQARGSLEEQLLQELNNLILRKGEPASCPESS  1500
1501  SQPTSPQAPSPTSLPTPTPSLPTQPPCTSNPPSSQPLT              1538

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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