 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching P08964 from www.uniprot.org...
The NucPred score for your sequence is 0.96 (see score help below)
1 MTGGQSCSSNMIVWIPDEKEVFVKGELMSTDINKNKFTGQEEQIGIVHPL 50
51 DSTEVSNLVQVRISDVFPVNPSTFDKVENMSELTHLNEPSVLYNLEKRYD 100
101 CDLIYTYSGLFLVAINPYHNLNLYSEDHINLYHNKHNRLSKSRLDENSHE 150
151 KLPPHIFAIAEEAYENLLSEGKDQSILVTGESGAGKTENTKKILQYLASI 200
201 TSGSPSNIAPVSGSSIVESFEMKILQSNPILESFGNAQTVRNNNSSRFGK 250
251 FIKIEFNEHGMINGAHIEWYLLEKSRIVHQNSKERNYHIFYQLLSGLDDS 300
301 ELKNLRLKSRNVKDYKILSNSNQDIIPGINDVENFKELLSALNIIGFSKD 350
351 QIRWIFQVVAIILLIGNIEFVSDRAEQASFKNDVSAICSNLGVDEKDFQT 400
401 AILRPRSKAGKEWVSQSKNSQQAKFILNALSRNLYERLFGYIVDMINKNL 450
451 DHGSATLNYIGLLDIAGFEIFENNSFEQLCINYTNEKLQQFFNNHMFVLE 500
501 QSEYLKENIQWDYIDYGKDLQLTIDLIESKGPPTGVLPLLDEEAVLPKST 550
551 DESFYSKLISTWDQNSSKFKRSRLKNGFILKHYAGDVEYTVEGWLSKNKD 600
601 PLNDNLLSLLSSSQNDIISKLFQPEGEKSSSAGVEANISNQEVKKSARTS 650
651 TFKTTSSRHREQQITLLNQLASTHPHFVRCIIPNNVKKVKTFNRRLILDQ 700
701 LRCNGVLEGIRLAREGYPNRIAFQEFFQRYRILYPENSTTTTFSSKLKAS 750
751 TKQNCEFLLTSLQLDTKVYKIGNTKLFFKAGVLADLEKQKDVKLNNIMIK 800
801 LTATIRGYTVRKEITYHLQKLKKTRVIGNTFRLYNRLVKEDPWFNLFIRI 850
851 KPLLTSSNDMTRTKKFNEQINKLKNDLQEMESKKKFLEEKNQKTVNELEN 900
901 TQDLLNQEKENLRKNESLLNRVKTSSETLQKQFDDLVSEKDEISREKLEV 950
951 AQNLEEAHQKIQGLQETIREREATLEKLHSKNNELIKQISDLNCDISKEQ 1000
1001 SSQSLIKESKLKLENEIKRLKDVINSKEEEIKSFNDKLSSSEEDLDIKLV 1050
1051 TLEKNCNIAMSRLQSLVTENSDLRSKNENFKKEKAALNNQLKNKESELLK 1100
1101 MKEKIDNHKKELATFSKQRDDAVSEHGKITAELKETRIQLTEYKSNYQKI 1150
1151 KEEYSNFQRETKEQEQKKRNSLVESLNDSKIKELEARLSQEISLNQYLNK 1200
1201 RISGNSVETNISSTRRSTSYSDDPLDKEDIIKKYYDLQLAFTEITRNLEN 1250
1251 EIEEKKNLISRLRFTETRLASSSFEDQKIKAQMKKLKKLIQDMDPSIPLD 1300
1301 SILNEPLDNCPDKESDINKLMLEVDYLKRQLDIETRAHYDAENAISALHS 1350
1351 KFRKIQGESSLSSSDIYKLKFEASEERVKSLEDKLKTMPLRDRTNLPVGD 1400
1401 IIKNRDSISKYEEEIRYYKLENYKLQEILNESNGKLSQLTLDLRQSKSKE 1450
1451 ALLSEQLDRLQKDLESTERQKELLSSTIKQQKQQFENCMDDLQGNELRLR 1500
1501 EHIHALKQAEEDVKNMASIIEKLKTQNKQKEKLIWEREMERNDSDMQLQE 1550
1551 TLLELKRVQDVKKILSDDLAHLKERLSAVEDRSQYTDEINRLKEELNCSL 1600
1601 KAETNLKKEFATLKYKLETSTNDSEAKISDLLKQLDHYTKVVEMLNNEKD 1650
1651 AISLAEKELYQKYEALNTECESLKGKIVSLTKIKQELESDLNQKTDALQI 1700
1701 SNAALSSSTQKNKEITEKIKYLEETLQLQMEQNSRNGELVKTLQASCNGY 1750
1751 KDKFDDEKQKNIDLYEENQTLQKLNTDLQLQLKNLHERLSDTTEKNAWLS 1800
1801 KIHELENMVSLETDLKYEEMKKNKSLERAVEELQTKNSQQTDVIELANKN 1850
1851 RSEFEEATLKYEAQISDLEKYISQQELEMKKSIRDNSSYRDKVQEMAQEI 1900
1901 EFWKSRYESTMIGSKNIDSNNAQSKIFS 1928
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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