 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q8R420 from www.uniprot.org...
The NucPred score for your sequence is 0.47 (see score help below)
1 MAVLRQLTLLLWKNYTLKKRKVLVTVLELFLPLLFSGILIWLRLKIQSEN 50
51 VPNATVYPDQSIQELPLFFSFPPPGGTWELAYVPSHSDAARTITETVKRE 100
101 FMIKMRVHGFSSEKDFEDYIRYDNHSSSVLAAVVFEHSFNHSQDPLPLAV 150
151 KYHLRFSYTRRNYMWTQTGNIFLKETEGWHTTSLFPLFPSPGPREPSSPD 200
201 GGEPGYIREGFLAMQHAVDKAIMRYHANTSAQQLFQKLMVITKRFPFPPY 250
251 ISDPFLIAIQYQLPLLLMLSFTYTSLTIIRAVVQEKEKKLKEYMRMMGLN 300
301 SWLHWSAWFLMFFLFFLIVVSFMTLLFCVKVKKDIAVLSNSDPSLVLAFL 350
351 LCFAISSISFSFMVSTFFSKANIAAAVGGFLYFFTYTPYFFVAPRYNWMT 400
401 LSQKLLSCLLSNVAMAMGAQLIGKFEAKGTGIQWRDLLNPVNVDDNFCFG 450
451 QVLGMLLLDSALYGLVTWYVEAVFPGQFGVPQPWHFFLMPSYWCGNPRTV 500
501 VGKEEEGSDPEKALRNEYFEAEPEDLVAGIKIKHLSKVFQVGNKDKMGIR 550
551 DLTLNLYEGQITVLLGHNGAGKTTTMSLLTGLFPPTSGHAYIHGYEISQD 600
601 MAQIRKSLGLCPQHDVLFDNLTVAEHLYFYAQLKGLSLQKCPEEVKQMLH 650
651 ILSLEDKRDLRSKFLSGGMKRKLSIGIALIAGSKVLMLDEPTSGMDAVSR 700
701 RAIWDLLQQQKSDRTVLLTTHFMDEADLLGDRIAILAKGELQCCGSSLFL 750
751 KQKYGAGYHMTLVKEPHCNPEGISQLVHHHVPNAMLESHAGAELSFILPK 800
801 ESTHRFESLFAKLEKKQKELGIASFGASVTTMEEVFLRVGKLVDTSMDIQ 850
851 AIQLPALQYQHERRASDWALDSNLCGVMDPTNGIGALIEEEEVLVKLNTG 900
901 LALHCQQFWAMFLKKAAYSWREWKMVAAQVLVPLTCLTLALLAIHYTSEI 950
951 FDDPLLKLSLNEYGRTVVPFSVPGTSRLAQQLSENLRDMLQAERQEPREV 1000
1001 LGDLEEFLVFRASVEGGGFNERCLVATSFKDRGELTVVTALFNNQAYHSP 1050
1051 ATALAIVDNLLFKLLCGPQASIEISNYPQPRNTLQVAKDHFNEGRKGFDI 1100
1101 ALNLLIAMAFLASTFSILAVSERAVQAKHVQFVSGVHVATFWFSALLWDL 1150
1151 ISFLVPSLLLLVVFQAFNVHAFTRDGHMADLLLLLMLYGWAIIPLMYLMS 1200
1201 FFFSAASTAYTRLTIFNILSGIATFIMVTIMRIPAVKLEELSRTLDHVFL 1250
1251 VLPNHCLGMAVSNFYENYETRRYCTSSELAAHYCKKYNIQYQESFYAWST 1300
1301 PGVGKFVTSMAASGGIYLTLLFLIETNLLWRLRTFICAFRRRWTLAELQN 1350
1351 RTSVLPEDQDVAEERSRILVPSLDSMLDTPLIINELSKVYDQRAPLLAVD 1400
1401 RISLAVQKGECFGLLGFNGAGKTTTFKMLTGEETITSGDAFVGGYSISSD 1450
1451 IGKVRQRMGYCPQFDALLDHMTGREMLVMYARLRGIPERLINACVENTLR 1500
1501 GLLLEPHANKLVKTYSGGNKRKLSTGIALIGEPAVIFLDEPSTGMDPVAR 1550
1551 RLLWDTVARARESGKAIVITSHSMEECEALCTRLAIMVQGQFKCLGSPQH 1600
1601 LKSKFGSGYSLQAKVRSEGKQDALEEFKAFVDLTFPGSILEDEHQDMVHY 1650
1651 HLPGCDLSWAKVFGILEKAKEKYGVDDYSVSQISLEQVFLSFAHLQPPTT 1700
1701 EDGR 1704
Positively and negatively influencing subsequences are coloured according to the following scale:
(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)
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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