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

NucPred

Fetching Q61043 from www.uniprot.org...

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

   1  MDEVEEDQHEARLKELFDSFDTLGTGSLGQEELTDLCHVLCLEDVGPVLQ    50
  51  QTLLQDNLLGRVHFDQFKEALILILSRTLSSEEHFEESDCSPEAQPKYVR   100
 101  GGKRYGRRSLPEFQESGEEIEEVTVLEPLEEEARSSPIPAGDCGEHWKTQ   150
 151  RSEEYEAEGQLRFWNPDDLNASHGGSCPPPDWIEEKLQEVCEDLGITRDG   200
 201  HLNRKKLVSICEQYGLQNVDGAMLEEVFLSLDPDGTMSVEDFFYGLFKTG   250
 251  KSLTPSASTPYRQLKRHLSMQSFDESGRRTATSSAMTSTIGFRVFSCLDD   300
 301  GMGQASVERILDTWQEEGIENSQEILKALDFSLDGNINLTELTLALENEL   350
 351  LVTKNGIHQAALASFKAEIRHLLERVDQVVREKEKLRSDLDKAEKLKSLM   400
 401  ASEVDDHHAAIERRNEYNLRKLDEEYKERIAALKNELRQEREQMLQQVGK   450
 451  QRVELEQEIQKAKTEENYIRDRLALSLKENNRLETELLENAEKLAEYESL   500
 501  TQKLQRSLENVLAEKFGDLDPSSAEFFLQEERLAQMRNEYEQQCRLLQDQ   550
 551  VDELQSELEEYQAQGRVLRLPLKNSLSEELDGHSGGIEPDQGPGSEECNP   600
 601  LNMSIEAELVIEQMKEQHHRDLCHLRLELEDKVRHYEKQLDDTRVASEQE   650
 651  QAAMKQKYEQGVHTLEKRVSELRSEIADLEGQAAVLREAHHKASCRHEEE   700
 701  KRQLQMAFDEEKAQLQEELRQEHERELQARLQQAAESFRQEREGLAQAAW   750
 751  TEEKVRGLEQSYQEQLLSLEEKHALEKEELREELSEHHRRELQEGREEME   800
 801  TECNRRVSQIEAQCQADCEKVTEHCEQTLQSLEVRHRQELRDLLDQHLEE   850
 851  RSQWEFEKDELTQECTDAQEQLKEALQRERATAAAMKQEQEILERTYKDR   900
 901  LNILSTERKQLLQDLKDLQNASESQHGLLSGQILELKRSQERELRDQGQA   950
 951  LCQTGVSEQLASQQLERLRVEHEQERREMTGKLAALESAHRASLERADQE  1000
1001  KAEMSTEICRLQNTVKDMQQAASLLMLQGGCQATAGEEAEGDGAMSLLQQ  1050
1051  GEQLLEENGDVLISLQRAHEHAVKENAKMATEISRLQQRLKKLEPGSVIS  1100
1101  SCLEEGTSEISGSSREQVEPIMKQGPATKHFLSDLGDHEARDLASTGTSS  1150
1151  VQRQECKTEASEASLDCFSELENSEDTRTESWDLKSQISQLREQLTVLRA  1200
1201  DCDRASERKQDLLFDISVLKKKLKMLERLPEASSRYKVLYEDAARENSCL  1250
1251  QEELRLVETRYEESLDSNKELTAEVYRLQDEMKKMEEVMETFLSLEKSYD  1300
1301  EVKVENEELRALVLRLQGKMEKVLGRAALQGDSYALWEAPSENLEVASDE  1350
1351  KMLELRQTPKECTPKVVSMHHIIEECTQETQCCEQGSTKLLARIKAHEIA  1400
1401  WFHRAIKTHPEKPSAQNRVIPEGSAALLGLQDKHLQQEATIAELELEKQK  1450
1451  LQELTRNLRERVTALVRQKDAPSQGQKEEELKAMMQDLQITCGEMQRKVE  1500
1501  LLRYESEKLQEENSILRNEITTLNEEDSISNLKLEELNGSQEELWQKIET  1550
1551  IEQEKASIQTMVEKLKKQVSDLKIKNQQLDSENIELSQKNSQNKEELKTL  1600
1601  NQRLAEMLCQREEPGACTSEKWEQENASLKEELDHYKVQTSTLVSSLEAE  1650
1651  LSEVKLQTHVMEQENLLLKDELERLKQLHRCPDLSDFQQKMSSILSYNEK  1700
1701  LLKEKEVLSEELKSCADKLAESSLLEHRIATMKQEQTAWEEQSESLKSQL  1750
1751  AVSQAKVQNLEDVLQNVNLQMAEIESDLQVTRQEKEALKQEVMSLHRQLQ  1800
1801  NAIDKDWVSETAPHLSGLRGQQRRLSWDKLDHLMNEEPQLLCQESKRLQT  1850
1851  VVQNTQADLTHSREKVRQLESNLLPTKHQKQLNQPCTVKSTEQEKLTLKR  1900
1901  ECEQSQKEQSPTSRKVGQMGSLERGLETIHLENEGLKKKQMQPLRSTVTR  1950
1951  SPSSHWDLQLLQQQACPMVPREQFLQLQQQLLQAEKRSQHLQEELENRTS  2000
2001  ETNTPQGNQEHLVNLMEERMIEVEQKLKLVKRLLQEKVNQLKEQLCKNTK  2050
2051  TDAVVKDLYVENAQLLKALEMTEQRQKTAEKRNFLLEEKIASLSTIVRNL  2100
2101  APAPLTSMPPLRS                                       2113

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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