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

NucPred

Fetching Q6FK48 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MSKNNKLNGKDNRQSKIEKLSELKLRHDQLTNELYHLHEYISLVEYDPFY    50
  51  IPNSENYERLLEEKDVTWGSIFQEKKQLHNESSGKKVRRSVRHLRDSGSS   100
 101  TINELDTMSENDINLLKEVDILAKQKLQDLKLQFSNSHIKKKGNTKRAKI   150
 151  VKQVPNHQDKSESPQISERDVKTVVKDLKPNHRGSEIKPEIMESSDVKNE   200
 201  IENCDFNEKQLKLYKDDDIASESDFYFTTSSEDELPNKRRGTIKRRKRIN   250
 251  LYVNPPKAVITNPDNIANSHYPTLHEYLDSFKILEDDMTNEEYNTFIKEQ   300
 301  QRFAKMIKKGIETGALKYDPVTETVQPSARKVPNMFSHAKVDPIQYMYKE   350
 351  QNLHIHQEHLINQGLFSSKLVQNRKKQRIAGAKKIAQMIEQHFKHIAGAE   400
 401  DRRLKENEKQRKAIARNIIQSVKKRWNLAEKAYRILKKDEEEQLKRIQGK   450
 451  EHLSKMLEKSSKLLGAQLKQHPNEDDIENSTSDDFSSTGDSDNLSSSSDE   500
 501  ESDDEINDLSEDQKNNINELKTSSTSAFSSPEISSPSKNPDLGLNSLLTN   550
 551  DFENESNSSDTNEEFIMGDSDTSHSDDENLTDDSEDSNDGEHDTTSDNEK   600
 601  SDLFPADTTNDPLAVQDVPTPSLLRGTLRTYQKQGLNWLASLYNNNTNGI   650
 651  LADEMGLGKTIQTISLLSYLACEKHNWGPHLIVVPTSVLLNWEMEFKRFA   700
 701  PGFKVLTYYGNPQQRKEKRKGWNKPDAFHVCIVSYQLIVQDQHSFKRKKW   750
 751  QYMVLDEAHNIKNFRSTRWQALLNFNTQRRILLTGTPLQNNIAELWSLLY   800
 801  FLMPQTVIDGQKVSGFADLDAFQQWFGRPVDKLIETGGTYEQDNETKRTV   850
 851  EKLHQVLRPYLLRRLKADVEKQIPGKYEHIVYCKLSKRQRFLYDDFMSRA   900
 901  QTKATLASGNFMSIVNCLMQLRKVCNHPDLFEVRPIKTSFLFGESVIARY   950
 951  SERANSITRRIHFHDKDTLVDLQNINLQFTNNDLEKTSYHTNTINKLACI  1000
1001  NEFVEEVQKLRKQNAEEERQKSRHLKINTQNISNFYEEFMQQKLDEQENK  1050
1051  INFIGYLNSQRCSRKTVYGMNLIRLLEMPHVSNNCIDDPNYDDLIKPLQT  1100
1101  RLLDGRTTIEKFAVLTPGAVTSNIGELTLGMDEFVTPNSKSGIIPYEELV  1150
1151  QLDNPFHQVQTKLTIAFPDKSLLQYDCGKLQKLAILLQQLKDGGHRALIF  1200
1201  TQMTKVLDILEQFLNYHGYLYMRLDGATKIEDRQILTERFNSDPKITVFI  1250
1251  LSSRSGGLGINLTGADTVIFYDSDWNPAMDKQCQDRCHRIGQTRDVHIYR  1300
1301  FVSEHTIESNILKKANQKRQLDDVIIQKGEFTTDYFSKLSVKDLFGSDVV  1350
1351  GDLPVIDTKPLLGSDSEAIKDPKKLEKLLAQAEDEDDVKAANSALREVNV  1400
1401  DDEDFDESSTNKTGGNILNGDDIDEDVDEYEGTNHVEEYMLRFIANGFYF  1450

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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