 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching P34358 from www.uniprot.org...
The NucPred score for your sequence is 0.54 (see score help below)
1 MNRLRQFSLLLWKDWVLLRRNKVWTLFELIIPCLLLGPLVYLVVKNADHT 50
51 SSPENIYDNFQVKGTVEDVFLESNFIKPIYKRWCLRSDVVVGYTSKDAAA 100
101 KRTVDDLMKKFAERFQSAKLKLSVKNESSEEQLLTVLRNDLPMLNETFCA 150
151 INSYAAGVVFDEVDVTNKKLNYRILLGKTPEETWHLTETSYNPYGPSSGR 200
201 YSRIPSSPPYWTSAFLTFQHAIESSFLSSVQSGAPDLPITLRGLPEPRYK 250
251 TSSVSAFIDFFPFIWAFVTFINVIHITREIAAENHAVKPYLTAMGLSTFM 300
301 FYAAHVVMAFLKFFVIFLCSIIPLTFVMEFVSPAALIVTVLMYGLGAVIF 350
351 GAFVASFFNNTNSAIKAILVAWGAMIGISYKLRPELDQISSCFLYGLNIN 400
401 GAFALAVEAISDYMRRERELNLTNMFNDSSLHFSLGWALVMMIVDILWMS 450
451 IGALVVDHIRTSADFSLRTLFDFEAPEDDENQTDGVTAQNTRINEQVRNR 500
501 VRRSDMEIQMNPMASTSLNPPNADSDSLLEGSTEADGARDTARADIIVRN 550
551 LVKIWSTTGERAVDGLSLRAVRGQCSILLGHNGAGKSTTFSSIAGIIRPT 600
601 NGRITICGYDVGNEPGETRRHIGMCPQYNPLYDQLTVSEHLKLVYGLKGA 650
651 REKDFKQDMKRLLSDVKLDFKENEKAVNLSGGMKRKLCVCMALIGDSEVV 700
701 LLDEPTAGMDPGARQDVQKLVEREKANRTILLTTHYMDEAERLGDWVFIM 750
751 SHGKLVASGTNQYLKQKFGTGYLLTVVLDHNGDKRKMAVILTDVCTHYVK 800
801 EAERGEMHGQQIEIILPEARKKEFVPLFQALEAIQDRNYRSNVFDNMPNT 850
851 LKSQLATLEMRSFGLSLNTLEQVFITIGDKVDKAIASRQNSRISHNSRNA 900
901 SEPSLKPAGYDTQSSTKSADSYQKLMDSQARGPEKSGVAKMVAQFISIMR 950
951 KKFLYSRRNWAQLFTQVLIPIILLGLVGSLTTLKSNNTDQFSVRSLTPSG 1000
1001 IEPSKVVWRFENGTIPEEAANFEKILRKSGGFEVLNYNTKNPLPNITKSL 1050
1051 IGEMPPATIGMTMNSDNLEALFNMRYYHVLPTLISMINRARLTGTVDAEI 1100
1101 SSGVFLYSKSTSNSNLLPSQLIDVLLAPMLILIFAMVTSTFVMFLIEERT 1150
1151 CQFAHQQFLTGISPITFYSASLIYDGILYSLICLIFLFMFLAFHWMYDHL 1200
1201 AIVILFWFLYFFSSVPFIYAVSFLFQSPSKANVLLIIWQVVISGAALLAV 1250
1251 FLIFMIFNIDEWLKSILVNIFMFLLPSYAFGSAIITINTYGMILPSEELM 1300
1301 NWDHCGKNAWLMGTFGVCSFALFVLLQFKFVRRFLSQVWTVRRSSHNNVQ 1350
1351 PMMGDLPVCESVSEERERVHRVNSQNSALVIKDLTKTFGRFTAVNELCLA 1400
1401 VDQKECFGLLGVNGAGKTTTFNILTGQSFASSGEAMIGGRDVTELISIGY 1450
1451 CPQFDALMLDLTGRESLEILAQMHGFENYKAKAELILECVGMIAHADKLV 1500
1501 RFYSGGQKRKISVGVALLAPTQMIILDEPTAGIDPKARREVWELLLWCRE 1550
1551 HSNSALMLTSHSMDECEALCSRIAVLNRGSLIAIGSSQELKSLYGNNYTM 1600
1601 TLSLYEPNQRDMVVQLVQTRLPNSVLKTTSTNKTLNLKWQIPKEKEDCWS 1650
1651 AKFEMVQALAKDLGVKDFILAQSSLEETFLRLAGLDEDQLDTHSTVEISH 1700
1701 STHV 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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