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

NucPred

Fetching Q7S055 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MVTQVLIAHTGQRLEIDSRTITSLNGLKESVASQTSIPVECLIALTPQGR    50
  51  SLRWQPTQPETEIYIYDSRLTQRSQPGASSPPLSELPLPRYNAHTPPNSI   100
 101  EDTRSIPAWQKLFETRRAWAIDVVEDCARMDAATRERYAEMDVMLRCLDA   150
 151  AVANLENAVKGLENKYVELKEWSTSAQAEYSALATGFDRYLSLARGIAIS   200
 201  SSMARFMTSRDDGGWKGRPQRQSTLEDLVDLELARQAGKLAPSALRKFKD   250
 251  RITNLDKAATHLFQDADTLMHKFETTMSRSALSHDGESLHLLKDIEALAN   300
 301  KIDNDYNVTLEYTSSTRDTLLQVSKTAAHHTERLLPSIQKRALEMGDILC   350
 351  YATKARNSLAAESIEFMRSITEITSDSHSVKSQISETGQEDELATFDHLR   400
 401  LIQQIPYLYASFVAEAIRRREWLDKVKQDSTTLANEMAIFHEEEAKRRRR   450
 451  WHKSIGAVFGPAPTADSKVPNLEINLRGDDGEWPLMTRKDLDDFFNALRN   500
 501  QKADPELVVEIEKLIADMDKSTRQQSRRMKAFKNGSVHETALGRSGLLVR   550
 551  GDDDLLRSLQADKTRLESKLKTAESRVRRLEDLLHRQTQASRPNVGNLFQ   600
 601  NPSQQVLDRNDSISSLRNPRAVDDRSRSLDGLETLIHRTQQLETELNTER   650
 651  ERCVVLEREINALTTLHNDLKGQMDEANSTKKDLLQNMEALKREFTEERK   700
 701  SLEEEVKQLKARLEYTEDEIEHFGESRENEKASYDEKVHFLELEVERLTR   750
 751  ERRDDSLKADDQVVLLQNEARLQRERIAAQDIELRAAQDEIRVLSKRLEA   800
 801  VTEDKQKYRQALEDIWECLAPADDVPTELPDLLEGITGKAADILNTKQGV   850
 851  EGDMSLMKLNVDTLQNNIRTLRSEMDFTKDRLTEEESVSLRLREKFSEER   900
 901  AKVVAMEGELAHGREQLHEFRVKIADGETGSEYMRKRLEDEEQNLASMTE   950
 951  ELAAGQTQVQKMEEEVTRFKAKLHQTQMQLSELSIRLESRTECAKDLTQL  1000
1001  LWSQNDRLTRLLERLGFSISREEDGTMHIQRTPRSERSLATTANPNDSDP  1050
1051  SSSLRRSSTLNARPVTDNADLELLQWMSSATPEAEVEKYKIFMGLIGSLD  1100
1101  MDVFADAVYRRVKDVEHMARKLQREARAYREKAHSFQKEAHDKIAFKHFK  1150
1151  EGDLALFLPTRNQSTGAWAAFNVGFPHYFLREQDSHRLRNREWLVARIMR  1200
1201  IQERVVDLSKSLQHDQAGETRKDGARGETESLDDDENDNPFDLSDGLRWY  1250
1251  LIEAVEDKPGAPSTPGLAKSTVAANNVEAMADMRTQGHISKARGLTGRGG  1300
1301  TPLGIEGVSKTLSKSLESRRSSTGSRKTLPFVIGASSRGRESALASETNS  1350
1351  LRAVPADNNSSAPTNAAQQHMSPTDKLKDESLQETPQQTNSISAEGESMT  1400
1401  IAARNDQAILQPSQTHSEVRNEIESLIGP                       1429

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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