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

NucPred

Fetching Q9UBG0 from www.uniprot.org...

The NucPred score for your sequence is 0.72 (see score help below)

   1  MGPGRPAPAPWPRHLLRCVLLLGCLHLGRPGAPGDAALPEPNVFLIFSHG    50
  51  LQGCLEAQGGQVRVTPACNTSLPAQRWKWVSRNRLFNLGTMQCLGTGWPG   100
 101  TNTTASLGMYECDREALNLRWHCRTLGDQLSLLLGARTSNISKPGTLERG   150
 151  DQTRSGQWRIYGSEEDLCALPYHEVYTIQGNSHGKPCTIPFKYDNQWFHG   200
 201  CTSTGREDGHLWCATTQDYGKDERWGFCPIKSNDCETFWDKDQLTDSCYQ   250
 251  FNFQSTLSWREAWASCEQQGADLLSITEIHEQTYINGLLTGYSSTLWIGL   300
 301  NDLDTSGGWQWSDNSPLKYLNWESDQPDNPSEENCGVIRTESSGGWQNRD   350
 351  CSIALPYVCKKKPNATAEPTPPDRWANVKVECEPSWQPFQGHCYRLQAEK   400
 401  RSWQESKKACLRGGGDLVSIHSMAELEFITKQIKQEVEELWIGLNDLKLQ   450
 451  MNFEWSDGSLVSFTHWHPFEPNNFRDSLEDCVTIWGPEGRWNDSPCNQSL   500
 501  PSICKKAGQLSQGAAEEDHGCRKGWTWHSPSCYWLGEDQVTYSEARRLCT   550
 551  DHGSQLVTITNRFEQAFVSSLIYNWEGEYFWTALQDLNSTGSFFWLSGDE   600
 601  VMYTHWNRDQPGYSRGGCVALATGSAMGLWEVKNCTSFRARYICRQSLGT   650
 651  PVTPELPGPDPTPSLTGSCPQGWASDTKLRYCYKVFSSERLQDKKSWVQA   700
 701  QGACQELGAQLLSLASYEEEHFVANMLNKIFGESEPEIHEQHWFWIGLNR   750
 751  RDPRGGQSWRWSDGVGFSYHNFDRSRHDDDDIRGCAVLDLASLQWVAMQC   800
 801  DTQLDWICKIPRGTDVREPDDSPQGRREWLRFQEAEYKFFEHHSTWAQAQ   850
 851  RICTWFQAELTSVHSQAELDFLSHNLQKFSRAQEQHWWIGLHTSESDGRF   900
 901  RWTDGSIINFISWAPGKPRPVGKDKKCVYMTASREDWGDQRCLTALPYIC   950
 951  KRSNVTKETQPPDLPTTALGGCPSDWIQFLNKCFQVQGQEPQSRVKWSEA  1000
1001  QFSCEQQEAQLVTITNPLEQAFITASLPNVTFDLWIGLHASQRDFQWVEQ  1050
1051  EPLMYANWAPGEPSGPSPAPSGNKPTSCAVVLHSPSAHFTGRWDDRSCTE  1100
1101  ETHGFICQKGTDPSLSPSPAALPPAPGTELSYLNGTFRLLQKPLRWHDAL  1150
1151  LLCESRNASLAYVPDPYTQAFLTQAARGLRTPLWIGLAGEEGSRRYSWVS  1200
1201  EEPLNYVGWQDGEPQQPGGCTYVDVDGAWRTTSCDTKLQGAVCGVSSGPP  1250
1251  PPRRISYHGSCPQGLADSAWIPFREHCYSFHMELLLGHKEARQRCQRAGG  1300
1301  AVLSILDEMENVFVWEHLQSYEGQSRGAWLGMNFNPKGGTLVWQDNTAVN  1350
1351  YSNWGPPGLGPSMLSHNSCYWIQSNSGLWRPGACTNITMGVVCKLPRAEQ  1400
1401  SSFSPSALPENPAALVVVLMAVLLLLALLTAALILYRRRQSIERGAFEGA  1450
1451  RYSRSSSSPTEATEKNILVSDMEMNEQQE                       1479

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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