 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q90508 from www.uniprot.org...
The NucPred score for your sequence is 0.51 (see score help below)
1 MKAVVLALTLAFVAGQNFAPEFAAGKTYVYKYEALILGGLPEEGLARAGL 50
51 KISTKLLLSAADQNTYMLKLVEPELSEYSGIWPKDPAVPATKLTAALAPQ 100
101 LAIPIKFEYTNGVVGKVFAPEEVSTLVLNIYRGILNILQLNIKKTHKVYD 150
151 LQEVGTQGVCKTLYSISEDARIENILLTKTRDLSNCQERLNKDIGLAYTE 200
201 KCDKCQEETKNLRGTTTLSYVLKPVADAVMILKAYVNELIQFSPFSEANG 250
251 AAQMRTKQSLEFLEIEKEPIPSVKAEYRHRGSLKYEFSDELLQTPLQLIK 300
301 ISDAPAQVAEVLKHLATYNIEDVHENAPLKFLELVQLLRIARYEDLEMYW 350
351 NQYKKMSPHRHWFLDTIPATGTFAGLRFIKEKFMAEEITIAEAAQAFITA 400
401 VHMVTADPEVIKLFESLVDSDKVVENPLLREVVFLGYGTMVNKYCNKTVD 450
451 CPVELIKPIQQRLSDAIAKNEEENIILYIKVLGNAGHPSSFKSLTKIMPI 500
501 HGTAAVSLPMTIHVEAIMALRNIAKKESRMVQELALQLYMDKALHPELRM 550
551 LSCIVLFETSPSMGLVTTVANSVKTEENLQVASFTYSHMKSLSRSPATIH 600
601 PDVAAACSAAMKILGTKLDRLSLRYSKAVHVDLYNSSLAVGAAATAFYIN 650
651 DAATFMPKSFVAKTKGFIAGSTAEVLEIGANIEGLQELILKNPALSESTD 700
701 RITKMKRVIKALSEWRSLPTSKPLASVYVKFFGQEIGFANIDKPMIDKAV 750
751 KFGKELPIQEYGREALKALLLSGINFHYAKPVLAAEMRRILPTVAGIPME 800
801 LSLYSAAVAAASVEIKPNTSPRLSADFDVKTLLETDVELKAEIRPMVAMD 850
851 TYAVMGLNTDIFQAALVARAKLHSVVPAKIAARLNIKEGDFKLEALPVDV 900
901 PENITSMNVTTFAVARNIEEPLVERITPLLPTKVLVPIPIRRHTSKLDPT 950
951 RNSMLDSSELLPMEEEDVEPIPEYKFRRFAKKYCAKHIGVGLKACFKFAS 1000
1001 QNGASIQDIVLYKLAGSHNFSFSVTPIEGEVVERLEMEVKVGAKAAEKLV 1050
1051 KRINLSEDEETEEGGPVLVKLNKILSSRRNSSSSSSSSSSSSSESRSSRS 1100
1101 SSSSSSSSRSSRKIDLAARTNSSSSSSSRRSRSSSSSSSSSSSSSSSSSS 1150
1151 SSRRSSSSSSSSSSSSSRSSRRVNSTRSSSSSSRTSSASSLASFFSDSSS 1200
1201 SSSSSDRRSKEVMEKFQRLHKKMVASGSSASSVEAIYKEKKYLGEEEAVV 1250
1251 AVILRAVKADKRMVGYQLGFYLDKPNARVQIIVANISSDSNWRICADAVV 1300
1301 LSKHKVTTKISWGEQCRKYSTNVTGETGIVSSSPAARLRVSWERLPSTLK 1350
1351 RYGKMVNKYVPVKILSDLIHTKRENSTRNISVIAVATSEKTIDIITKTPM 1400
1401 SSVYNVTMHLPMCIPIDEIKGLSPFDEVIDKIHFMVSKAAAAECSFVEDT 1450
1451 LYTFNNRSYKNKMPSSCYQVAAQDCTDELKFMVLLRKDSSEQHHINVKIS 1500
1501 EIDIDMFPKDDNVTVKVNEMEIPPPACLTATQQLPLKIKTKRRGLAVYAP 1550
1551 SHGLQEVYFDRKTWRIKVADWMKGKTCGLCGKADGEIRQEYHTPNGRVAK 1600
1601 NSISFAHSWILPAESCRDASECRLKLESVQLEKQLTIHGEDSTCFSVEPV 1650
1651 PRCLPGCLPVKTTPVTVGFSCLASDPQTSVYDRSVDLRQTTQAHLACSCN 1700
1701 TKCS 1704
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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