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

NucPred

Fetching Q4P209 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MSTEPVSSLALPAPAILPTTPIPASTQQASSLVSDQIQEASTASQKSVTS    50
51 ITQPPIPSQQQPPQHITANHPASIAAAATVALSATLLNPNEWNALASTSM 100
101 VTLDDLRSAFLEQRQQQLKDLERSHRESLREMIFMSENYDKEDVAGSPWK 150
151 LGQSLQVAEDDAREHVKSFLDQHRLALDPKMSIKDHILEQPKLLRQRVSQ 200
201 ELKTGPIELAPPPTPTSATAPSAGEAQRDRDLKREIEQNNLHRSQAVARA 250
251 AAAVQAHAIAEGVAKIKPLTITAAESQGVRVAPLQPGQVPSFVIESTTPI 300
301 AHIVASSDSSTAVLVASDAQKVDSHTTMSAAEAVTPAIKVESTDNIDASP 350
351 SKASHALEKAVSPVPGLARNASTQSTSLRVPPSPMVVPTIPENITAPPLH 400
401 PTLQVLAPNPLSVTYAASLRPLPPDPTRRITGAGLSGGAIHHRSGRKITS 450
451 LSNHSNVNSYSSIAAAKIGPAGSGQADLYRWYVRARASPGAGMVGKADKC 500
501 LMTSDWRVAFNEQRFVRAMARIEKLKAQGEWSFRQPKKQKGPVVRKAHWD 550
551 HLLEEMKWLQTDFREERRWKMTVAFHLAHEVAAWHRARTPAERAQFCVHV 600
601 QRSYRHRTISDNVEQHNTDKLSAKEVVSSSQPFQAAAASLDDVEMTHSTS 650
651 SSHIQKDGEPATVKAESGQPVEDADVTMDGGADADEAVTQAVESALQTTN 700
701 EAASARAEEMDADGEDDADTDANDVEAATAALVSGEPSKPPKVEVVREPL 750
751 SQPQPMPTLADVSVPTTSSATPTVPASSTPTTAANDKLVHALRSQPKDAD 800
801 STLTAEMPPQLLATLRAPIFSTSVTTTVVSPAALLDSLNPEAAAALLGIE 850
851 VSDLANAADLLEPGSLSFSKMFPELPLYGGVSLPESNSKSDRRWDEGSLN 900
901 QPPRLTHVTKLLDSRPLLVSTLEPSKNRANGRWLADSDWVVAAEQSDPLR 950
951 GVTDGADTALPPMPGSLLFARKSNRAAKDASGPASTTPAEPASPDARAAL 1000
1001 FVWTPDEDNYLMTLAKQYHNNWALVADLFNSTRLNTATDKREAWDCYDRC 1050
1051 KRIEQAAAEGKPPPGPPPMPAPAADADKDSKKGDGKDADASSSKRDKLSK 1100
1101 KSGSKHDGSKRKQRRSNLMEVMRRSAKRREATKQAQQTQQTKKVNLNTHE 1150
1151 THAQIKAGPAITPQSLSALKTERDQAALRQYYEQQRAQLAYQQQQQQQQR 1200
1201 LLAQQAQAQRMAQQQGTAGTSAPAATAVTQAGKAGTAIVAGGTGGVGNVS 1250
1251 LLPAGTPAASAGPAGQAQQKAATGQGTNQAIAQQTQQQQQQPQSQQTAQM 1300
1301 QVQQPPAAAAAAQQQQQQQVQLQSQLQASQAAQMQNLYAQMQQQQQQQQR 1350
1351 QQQQQLGQAAAGLAQVRPGVGALTQQQLATLTPQQQQQYHAQLAAATAAA 1400
1401 QQQQLRSQMAAVAAAQGGQAGFQLPNAQAQAQAQAQAQFQLMQQQQQQQN 1450
1451 VMQNQGRPAMAQQAQQAALQMYQQQQRQAQMRPPQPTQPFAARPNARPGT 1500
1501 AASSQAKPQAAARSATPAPPMPATVQALQQQLAISLATSNLSAEQINGLA 1550
1551 IQLYKQAQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ 1600
1601 PQQPAPTQQRPPPQQLLNQAIQALAAQTQKNQQPAPTVHGVTGSPVRPPT 1650
1651 PRPS 1654

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.)

Go back to the NucPred Home Page.