 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q460N5 from www.uniprot.org...
The NucPred score for your sequence is 0.49 (see score help below)
1 MAVPGSFPLLVEGSWGPDPPKNLNTKLQMYFQSPKRSGGGECEVRQDPRS 50
51 PSRFLVFFYPEDVRQKVLERKNHELVWQGKGTFKLTVQLPATPDEIDHVF 100
101 EEELLTKESKTKEDVKEPDVSEELDTKLPLDGGLDKMEDIPEECENISSL 150
151 VAFENLKANVTDIMLILLVENISGLSNDDFQVEIIRDFDVAVVTFQKHID 200
201 TIRFVDDCTKHHSIKQLQLSPRLLEVTNTIRVENLPPGADDYSLKLFFEN 250
251 PYNGGGRVANVEYFPEESSALIEFFDRKVLDTIMATKLDFNKMPLSVFPY 300
301 YASLGTALYGKEKPLIKLPAPFEESLDLPLWKFLQKKNHLIEEINDEMRR 350
351 CHCELTWSQLSGKVTIRPAATLVNEGRPRIKTWQADTSTTLSSIRSKYKV 400
401 NPIKVDPTMWDTIKNDVKDDRILIEFDTLKEMVILAGKSEDVQSIEVQVR 450
451 ELIESTTQKIKREEQSLKEKMIISPGRYFLLCHSSLLDHLLTECPEIEIC 500
501 YDRVTQHLCLKGPSADVYKAKCEIQEKVYTMAQKNIQVSPEIFQFLQQVN 550
551 WKEFSKCLFIAQKILALYELEGTTVLLTSCSSEALLEAEKQMLSALNYKR 600
601 IEVENKEVLHGKKWKGLTHNLLKKQNSSPNTVIINELTSETTAEVIITGC 650
651 VKEVNETYKLLFNFVEQNMKIERLVEVKPSLVIDYLKTEKKLFWPKIKKV 700
701 NVQVSFNPENKQKGILLTGSKTEVLKAVDIVKQVWDSVCVKSVHTDKPGA 750
751 KQFFQDKARFYQSEIKRLFGCYIELQENEVMKEGGSPAGQKCFSRTVLAP 800
801 GVVLIVQQGDLARLPVDVVVNASNEDLKHYGGLAAALSKAAGPELQADCD 850
851 QIVKREGRLLPGNATISKAGKLPYHHVIHAVGPRWSGYEAPRCVYLLRRA 900
901 VQLSLCLAEKYKYRSIAIPAISSGVFGFPLGRCVETIVSAIKENFQFKKD 950
951 GHCLKEIYLVDVSEKTVEAFAEAVKTVFKATLPDTAAPPGLPPAAAGPGK 1000
1001 TSWEKGSLVSPGGLQMLLVKEGVQNAKTDVVVNSVPLDLVLSRGPLSKSL 1050
1051 LEKAGPELQEELDTVGQGVAVSMGTVLKTSSWNLDCRYVLHVVAPEWRNG 1100
1101 STSSLKIMEDIIRECMEITESLSLKSIAFPAIGTGNLGFPKNIFAELIIS 1150
1151 EVFKFSSKNQLKTLQEVHFLLHPSDHENIQAFSDEFARRANGNLVSDKIP 1200
1201 KAKDTQGFYGTVSSPDSGVYEMKIGSIIFQVASGDITKEEADVIVNSTSN 1250
1251 SFNLKAGVSKAILECAGQNVERECSQQAQQRKNDYIITGGGFLRCKNIIH 1300
1301 VIGGNDVKSSVSSVLQECEKKNYSSICLPAIGTGNAKQHPDKVAEAIIDA 1350
1351 IEDFVQKGSAQSVKKVKVVIFLPQVLDVFYANMKKREGTQLSSQQSVMSK 1400
1401 LASFLGFSKQSPQKKNHLVLEKKTESATFRVCGENVTCVEYAISWLQDLI 1450
1451 EKEQCPYTSEDECIKDFDEKEYQELNELQKKLNINISLDHKRPLIKVLGI 1500
1501 SRDVMQARDEIEAMIKRVRLAKEQESRADCISEFIEWQYNDNNTSHCFNK 1550
1551 MTNLKLEDARREKKKTVDVKINHRHYTVNLNTYTATDTKGHSLSVQRLTK 1600
1601 SKVDIPAHWSDMKQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIER 1650
1651 IQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRS 1700
1701 YAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTH 1750
1751 GNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFR 1800
1801 K 1801
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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