 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q5SX40 from www.uniprot.org...
The NucPred score for your sequence is 0.96 (see score help below)
1 MSSDAEMAVFGEAAPYLRKSEKERIEAQNKPFDAKSSVFVVDAKESFVKA 50
51 TVQSREGGKVTAKTEGGTTVTVKDDQVYPMNPPKYDKIEDMAMMTHLHEP 100
101 AVLYNLKERYAAWMIYTYSGLFCVTVNPYKWLPVYNAEVVAAYRGKKRQE 150
151 APPHIFSISDNAYQFMLTDRENQSILITGESGAGKTVNTKRVIQYFATIA 200
201 VTGEKKKEEATSGKMQGTLEDQIISANPLLEAFGNAKTVRNDNSSRFGKF 250
251 IRIHFGTTGKLASADIETYLLEKSRVTFQLKAERSYHIFYQIMSNKKPDL 300
301 IEMLLITTNPYDYAFVSQGEITVPSIDDQEELMATDSAIDILGFTSDERV 350
351 SIYKLTGAVMHYGNMKFKQKQREEQAEPDGTEVADKAAYLQNLNSADLLK 400
401 ALCYPRVKVGNEYVTKGQTVQQVYNSVGALAKAVYEKMFLWMVTRINQQL 450
451 DTKQPRQYFIGVLDIAGFEIFDFNSLEQLCINFTNEKLQQFFNHHMFVLE 500
501 QEEYKKEGIEWEFIDFGMDLAACIELIEKPMGIFSILEEECMFPKATDTS 550
551 FKNKLYEQHLGKSNNFQKPKPAKGKVEAHFSLVHYAGTVDYNIAGWLDKN 600
601 KDPLNETVVGLYQKSSMKTLAYLFSGAAAAAEAESGGGGGKKGAKKKGSS 650
651 FQTVSALFRENLNKLMTNLRSTHPHFVRCIIPNETKTPGAMEHELVLHQL 700
701 RCNGVLEGIRICRKGFPSRILYADFKQRYKVLNASAIPEGQFIDSKKASE 750
751 KLLGSIDIDHTQYKFGHTKVFFKAGLLGLLEEMRDDKLAQLITRTQAMCR 800
801 GYLARVEYQKMVERRESIFCIQYNVRAFMNVKHWPWMKLYFKIKPLLKSA 850
851 ETEKEMANMKEEFEKAKENLAKAEAKRKELEEKMVALMQEKNDLQLQVQS 900
901 EADSLADAEERCDQLIKTKIQLEAKIKEVTERAEDEEEINAELTAKKRKL 950
951 EDECSELKKDIDDLELTLAKVEKEKHATENKVKNLTEEMAGLDETIAKLT 1000
1001 KEKKALQEAHQQTLDDLQAEEDKVNTLTKAKIKLEQQVDDLEGSLEQEKK 1050
1051 IRMDLERAKRKLEGDLKLAQESTMDVENDKQQLDEKLKKKEFEMSNLQSK 1100
1101 IEDEQALGMQLQKKIKELQARIEELEEEIEAERASRAKAEKQRSDLSREL 1150
1151 EEISERLEEAGGATSAQIEMNKKREAEFQKMRRDLEEATLQHEATAATLR 1200
1201 KKHADSVAELGEQIDNLQRVKQKLEKEKSEMKMEIDDLASNMEVISKSKG 1250
1251 NLEKMCRTLEDQVSELKTKEEEQQRLINELTAQRGRLQTESGEYSRQLDE 1300
1301 KDSLVSQLSRGKQAFTQQIEELKRQLEEEIKAKSALAHALQSSRHDCDLL 1350
1351 REQYEEEQEAKAELQRAMSKANSEVAQWRTKYETDAIQRTEELEEAKKKL 1400
1401 AQRLQDAEEHVEAVNAKCASLEKTKQRLQNEVEDLMIDVERTNAACAALD 1450
1451 KKQRNFDKILAEWKQKYEETHAELEASQKESRSLSTELFKIKNAYEESLD 1500
1501 HLETLKRENKNLQQEISDLTEQIAEGGKRIHELEKIKKQIEQEKSELQAA 1550
1551 LEEAEASLEHEEGKILRIQLELNQVKSEIDRKIAEKDEEIDQLKRNHIRV 1600
1601 VESMQSTLDAEIRSRNDAIRLKKKMEGDLNEMEIQLNHSNRMAAEALRNY 1650
1651 RNTQGILKDTQLHLDDALRGQEDLKEQLAMVERRANLLQAEIEELRATLE 1700
1701 QTERSRKIAEQELLDASERVQLLHTQNTSLINTKKKLETDISQIQGEMED 1750
1751 IVQEARNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNLEQTVKDL 1800
1801 QHRLDEAEQLALKGGKKQIQKLEARVRELEGEVENEQKRNVEAIKGLRKH 1850
1851 ERRVKELTYQTEEDRKNVLRLQDLVDKLQSKVKAYKRQAEEAEEQSNVNL 1900
1901 AKFRKIQHELEEAEERADIAESQVNKLRVKSREVHTKIISEE 1942
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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