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

NucPred

Fetching Q8GU89 from www.uniprot.org...

The NucPred score for your sequence is 0.29 (see score help below)

   1  MDREVHRMASLRREGSMWRSGGDVFSRSSSRFQDEDDDEEALRWAALERL    50
  51  PTYDRVRRGILAVSSEDGGAGGEKVEVDVGRLGARESRALIERLVRAADD   100
 101  DHERFLLKLRERMDRVGIDYPTIEVRFENLEVEADVHVGNRGLPTLLNSV   150
 151  TNTVEAIGNALHILPNKKQPMTVLHDVSGIIKPRRMTLLLGPPGSGKTTL   200
 201  LLALAGKLDKDLKVSGKVTYNGHGMHEFVPERTAAYISQHDLHIGEMTVR   250
 251  ETLAFSARCQGVGTRYEMLTELARREKAANIKPDHDIDIYMKASAMGGQE   300
 301  SSVVTDYILKILGLDICADTVVGNEMLRGISGGQRKRVTTGEMLVGPARA   350
 351  LFMDEISTGLDSSTTYQIVNSLRQTIHILGGTAVISLLQPAPETYNLFDD   400
 401  IILLSDGQVVYQGPREHVLEFFEFMGFRCPARKGVADFLQEVTSRKDQGQ   450
 451  YWCRRDRPYRFVPVKQFADAFRSFHVGRSIQNELSEPFDRTRSHPAALAT   500
 501  SKYGVSRKELLKATIDRELLLMKRNAFMYIFKAVNLTLMALIVMTTFFRT   550
 551  SMRHDRDYGMIYLGALYFALDTVMFNGFAELAMTVMKLPVFFKQRDLLFF   600
 601  PAWAYTIPSWILQIPITFLEVGVYVFITYYVIGFDPSVSRFFKQYLLLLA   650
 651  LNQMSSALFRFIAGIGRDMVVSHTFGPLSLLAFAALGGFILARPDVKKWW   700
 701  IWGYWISPLSYAQNAISTNEFLGHSWSQILPGENVTLGVSVLKSRGIFTE   750
 751  AKWYWIGLGALLGYTLLFNLLYTVALSVLSPFTDSHASMSEDALKEKHAN   800
 801  LTGEVVEGQKDTKSRKQELELSHIADQNSGINSADSSASRKGMVLPFAPL   850
 851  SISFNDVRYSVDMPEAMKAQGITEDRLLLLKGVSGSFRPGVLTALMGVSG   900
 901  AGKTTLMDVLAGRKTGGYIEGDIRISGYPKKQETFARISGYCEQNDIHSP   950
 951  HVTVYESLVFSAWLRLPSEVDSEARKMFIEEVMDLVELTSLRGALVGLPG  1000
1001  VSGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTV  1050
1051  NTGRTVVCTIHQPSIDIFEAFDELFLMKRGGEEIYVGPVGQNSSKLIEYF  1100
1101  EGIDGVSRIKDGYNPATWMLEVTSSAQEEMLGVDFSEIYRQSELYQRNKE  1150
1151  LIEELSTPPPGSTDLNFPTQYSRSFITQCLACLWKQNWSYWRNPSYTAVR  1200
1201  LLFTIVIALMFGTMFWNLGTRTKKQQDLFNAMGSMYAAVLYIGVQNSGSV  1250
1251  QPVVVVERTVFYRERAAGMYSAFPYAFGQVAIELPYIMVQTLIYGVLVYS  1300
1301  MIGFEWTVAKFLWYLFFMYFTLLYFTFYGMMAVGLTPNESIAAIISSAFY  1350
1351  NVWNLFSGYLIPRPKIPVWWRWYCWICPVAWTLYGLVASQFGDIQHVLEG  1400
1401  DTRTVAQFVTDYFGFHHNFLWVVAVVHVVFAVTFAFLFSFAIMKFNFQRR  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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