 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q5SX39 from www.uniprot.org...
The NucPred score for your sequence is 0.95 (see score help below)
1 MSSDAEMAVFGEAAPYLRKSEKERIEAQNKPFDAKSSVFVVDAKESYVKA 50
51 TVQSREGGKVTAKTEGGATVTVKDDQVFSMNPPKYDKIEDMAMMTHLHEP 100
101 AVLYNLKERYAAWMIYTYSGLFCVTVNPYKWLPVYNPEVVAAYRGKKRQE 150
151 APPHIFSISDNAYQFMLTDRENQSILITGESGAGKTVNTKRVIQYFATIA 200
201 VTGDKKKEEATSGKMQGTLEDQIISANPLLEAFGNAKTVRNDNSSRFGKF 250
251 IRIHFGATGKLASADIETYLLEKSRVTFQLKAERSYHIFYQIMSNKKPEL 300
301 IEMLLITTNPYDFAYVSQGEITVPSIDDQEELMATDTAVDILGFSADEKV 350
351 AIYKLTGAVMHYGNMKFKQKQREEQAEPDGTEVADKAAYLTSLNSADLLK 400
401 ALCYPRVKVGNEYVTKGQTVQQVYNSVGALAKSMYEKMFLWMVTRINQQL 450
451 DTKQPRQYFIGVLDIAGFEIFDFNTLEQLCINFTNEKLQQFFNHHMFVLE 500
501 QEEYKKEGIDWEFIDFGMDLAACIELIEKPMGIFSILEEECMFPKATDTS 550
551 FKNKLYEQHLGKSNNFQKPKPAKGKAEAHFSLVHYAGTVDYNIIGWLDKN 600
601 KDPLNETVVGLYQKSGLKTLAFLFSGGQAAEAEGGGGKKGGKKKGSSFQT 650
651 VSALFRENLNKLMTNLKSTHPHFVRCLIPNETKTPGAMEHELVLHQLRCN 700
701 GVLEGIRICRKGFPSRILYADFKQRYKVLNASAIPEGQFIDSKKASEKLL 750
751 GSIDIDHTQYKFGHTKVFFKAGLLGTLEEMRDEKLAQLITRTQAVCRGYL 800
801 MRVEFKKMMERRESIFCIQYNVRAFMNVKHWPWMKLYFKIKPLLKSAETE 850
851 KEMANMKEDFEKAKEDLAKSEAKRKELEEKMVALMQEKNDLQLQVQAEAD 900
901 GLADAEERCDQLIKTKIQLEAKIKELTERAEDEEEINAELTAKKRKLEDE 950
951 CSELKKDIDDLELTLAKVEKEKHATENKVKNLTEEMAGLDENIAKLTKEK 1000
1001 KALQEAHQQTLDDLQAEEDKVNTLTKAKTKLEQQVDDLEGSLEQEKKLRM 1050
1051 DLERAKRKLEGDLKLAQESTMDIENDKQQLDEKLKKKEFEMSNLQSKIED 1100
1101 EQALGMQLQKKIKELQARIEELEEEIEAERASRAKAEKQRSDLSRELEEI 1150
1151 SERLEEAGGATSAQIEMNKKREAEFQKMRRDLEEATLQHEATAAALRKKH 1200
1201 ADSVAELGEQIDNLQRVKQKLEKEKSELKMEIDDLASNMETVSKAKGNLE 1250
1251 KMCRTLEDQLSEVKTKEEEQQRLINELSTQKARLHTESGEFSRQLDEKDA 1300
1301 MVSQLSRGKQAFTQQIEELKRQLEEESKAKNALAHALQSARHDCDLLREQ 1350
1351 YEEEQEAKAELQRAMSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQR 1400
1401 LQDAEEHVEAVNSKCASLEKTKQRLQNEVEDLMIDVERSNAACAALDKKQ 1450
1451 RNFDKVLAEWKQKYEETQAELEASQKESRSLSTELFKVKNAYEESLDQLE 1500
1501 TLKRENKNLQQEISDLTEQIAEGGKHIHELEKIKKQIDQEKSELQASLEE 1550
1551 AEASLEHEEGKILRIQLELNQVKSEIDRKIAEKDEEIDQLKRNHLRVVES 1600
1601 MQSTLDAEIRSRNDALRIKKKMEGDLNEMEIQLNHANRQAAEAIRNLRNT 1650
1651 QGMLKDTQLHLDDALRGQDDLKEQLAMVERRANLMQAEIEELRASLEQTE 1700
1701 RSRRVAEQELLDASERVQLLHTQNTSLINTKKKLETDISQIQGEMEDIVQ 1750
1751 EARNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNMEQTVKDLQHR 1800
1801 LDEAEQLALKGGKKQIQKLEARVRELENEVENEQKRNIEAVKGLRKHERR 1850
1851 VKELTYQTEEDRKNVLRLQDLVDKLQTKVKAYKRQAEEAEEQSNVNLAKF 1900
1901 RKIQHELEEAEERADIAESQVNKLRVKSREVHTKVISEE 1939
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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