| Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q3UHF7 from www.uniprot.org...
The NucPred score for your sequence is 0.99 (see score help below)
1 MDTGDTALGQKATSRSGETDSVSGRWRQEQSAVLKMSTFSSQEGPRQPQI 50
51 DPEQIGNAASAQLFGSGKLASPGEGLHQVTEKQYPPHRPSPYPCQHSLSF 100
101 PQHSLSQGMTHSHKPHQSLEGPPWLFPGPLPSVASEDLFPFPMHGHSGGY 150
151 PRKKISNLNPAYSQYSQKSIEQAEDAHKKEHKPKKPGKYICPYCSRACAK 200
201 PSVLKKHIRSHTGERPYPCIPCGFSFKTKSNLYKHRKSHAHAIKAGLVPF 250
251 TESSVSKLDLEAGFIDVEAEIHSDGEQSTDTDEESSLFAEASDKVSPGPP 300
301 VPLDIASRGGYHGSLEESLGGPMKVPILIIPKSGIPLASEGSQYLSSEML 350
351 PNPSLNAKADDSHTVKQKLALRLSEKKGQDSEPSLNLLSPHSKGSTDSGY 400
401 FSRSESAEQQISPPNTNAKSYEEIIFGKYCRLSPRNTLSVTPTGQERTAM 450
451 GRRGIMEPLPHLNTRLEVKMFEDPISQLNPSKGEMDPGQINMLKTTKFNS 500
501 ECRQPQAIPSSVRNEGKPYPGNFLGSNPMLLEAPVDSSPLIRSNSMPTSS 550
551 ATNLSVPPSLRGSHSFDERMTGSDDVFYPGTVGIPPQRMLRRQAAFELPS 600
601 VQEGHMESEHPARVSKGLASPSLKEKKLLPGDRPGYDYDVCRKPYKKWED 650
651 SETLKQSYLGSFKQGGEYFMDPSVPVQGVPTMFGTTCENRKRRKEKSVGD 700
701 EEDVPMICGGMGNAPVGMMSSEYDPKLQDGGRSGFAMTAHESLAHGHSDR 750
751 LDPARPQLPSRSPSLGSEDLPLAADPDKMTDLGKKPPGNVISVIQHTNSL 800
801 SRPNSFERSESTEMVACPQDKTPSPAETCDSEVLEAPVSPEWAPPGDGGE 850
851 SGSKPTPSQQVPQHSYHAQPRLVRQHNIQVPEIRVTEEPDKPEKEKEAPT 900
901 KEPEKPVEEFQWPQRSETLSQLPAEKLPPKKKRLRLADLEHSSGESSFES 950
951 TGTGLSRSPSQESNLSHSSSFSMSFDREETVKLTAPPKQDESGKHSEFLT 1000
1001 VPAGSYSLSVPGHHHQKEMRRCSSEQMPCPHPTEVPEIRSKSFDYGNLSH 1050
1051 APVAGTSPSTLSPSRERKKCFLVRQASFSGSPEIAQGEAGVDPSVKQEHM 1100
1101 EHLHAGLRAAWSSVLPPLPGDDPGKQVGTCGPLSSGPPLHLTQQQIMHMD 1150
1151 SQESLRNPLIQPTSYMTSKHLPEQPHLFPHQDAVPFSPIQNALFQFQYPT 1200
1201 VCMVHLPAQQPPWWQTHFPHPFAPHPQNSYSKPPFQADLHSSYPLEHVAE 1250
1251 HTGKKSADYPHAKEQTYPCYSGTSGLHSKNLPLKFPSDPGSKSTETPTEQ 1300
1301 LLREDFASENAGPLQSLPGTVVPVRIQTHVPSYGSVMYTSISQILGQNSP 1350
1351 AIVICKVDENMTQRTLVTNAAMQGIGLNIAQVLGQHTGLEKYPLWKVPQT 1400
1401 LPLGLESSIPLCLPSTSDNAASLGGSKRMLSPASSLELFMETKQQKRVKE 1450
1451 EKMYGQIVEELSAVELTNSDIKKGLSRPQKPQLVRQGCASEPKDGCFQSR 1500
1501 SSSFSSLSPSSSQDHPSASGPFPPNREILPGSRAPPRRKFSGPSESRESS 1550
1551 DELDMDETSSDMSMSPQSSALPTGGGQQEEEGKARKLPVSMLVHMASGPG 1600
1601 GNVANSTLLFTDVADFQQILQFPSLRTTTTVSWCFLNYTKPSFVQQATFK 1650
1651 SSVYASWCISSCNPNPSGLNTKTTLALLRSKQKITAEIYTLAAMHRPGAG 1700
1701 KLTSSSVWKQFAQMKPDAPFLFGNKLERKLAGNVLKERGKGEIHGDKDLG 1750
1751 SKQTEPIRIKIFEGGYKSNEDYVYVRGRGRGKYICEECGIRCKKPSMLKK 1800
1801 HIRTHTDVRPYVCKLCNFAFKTKGNLTKHMKSKAHMKKCLELGVSMTSVD 1850
1851 DTETEEAENMEELHKTSEKHSMSGISTDHQFSDAEESDGEDGDDNDDDDE 1900
1901 DDDDFDDQGDLTPKTRSRSTSPQPPRFSSLPVNVGAVAHGVPSDSSLGHS 1950
1951 SLISYLVTLPSIQVTQLMTPSDSCDDTQMTEYQRLFQSKSTDSEPDKDRL 2000
2001 DIPSSMDEEAMLSSEPSSSPRDFSPSSYRSSPGYDSSPCRDNSPKRYLIP 2050
2051 KGDLSPRRHLSPRRDLSPMRHLSPRKEAALRREMSQGDASPRRHLSPRRP 2100
2101 LSPGKDITARRDLSPRRERRYMTTIRAPSPRRALYPNPPLSMGQYLQTEP 2150
2151 IVLGPPNLRRGIPQVPYFSLYGDQEGAYEHHGSSLFPEGPTDYVFSHLPL 2200
2201 HSQQQVRAPIPMVPVGGIQMVHSLPPALSGLHPPPTLPLPTEGSEEKKGA 2250
2251 PGEAFAKDPYILSRRHEKQAPQVLQSSGLPSSPSSPRLLMKQSTSEDSLN 2300
2301 STEREQEENIQTCTKAIASLRIATEEAALLGADPPTWVQESPQKPLESAH 2350
2351 VSIRHFGGPEPGQPCTSAAHPDLHDGEKDTFGTSQTAVAHPTFYSKSSVD 2400
2401 EKRVDFQSSKELSLSTEEGNEPSPEKNQLH 2430
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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