 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q29011 from www.uniprot.org...
The NucPred score for your sequence is 0.47 (see score help below)
1 MTTLLLVFVTLRVIAAAISVEVSEPDNSLSVSIPQPSPLRVLLGGSLTIP 50
51 CYFIDPMHPVTTAPSTAPLAPRIKWSRVSKEKEVVLLVATEGQVRVNSAY 100
101 QDRVTLPNYPAIPSDATLEIQNLRSNDSGIYRCEVMHGIEDSEATLEVVV 150
151 KGIVFHYRAISTRYTLDFDRAQRACLQNSAIIATPEQLQAAYEDGFHQCD 200
201 AGWLADQTVRYPIHTPREGCYGDKDEFPGVRTYGIRDTNETYDVYCFAEE 250
251 MEGEVFYATSPEKFTFQEAANECRRLGARLATTGQLYLAWQGGMDMCSAG 300
301 WLADRSVRYPISKARPNCGGNLLGVRTVYLHANQTGYPDPSSRYDAICYT 350
351 GEDFVDIPENFFGVGGEEDITIQTVTWPDVELPLPRNITEGEARGTVILT 400
401 VKPVFEFSPTAPEPEEPFTFAPGTGATAFPEAENRTGEATRPWAFPEEST 450
451 PGLGAPTAFTSEDLVVQVTMAPGATEFPGQPRLPGGVVFHYRPGSSRYSL 500
501 TFEEAQQACLRTGAVIASPEQLQAAYEAGYEQCDAGWLQDQTVRYPIVSP 550
551 RTPCVGDKDSTPGVRTYGVRPPSETYDVYCYVDRLEGEVFFATRLEQFTF 600
601 REAQEFCESQNATLASTGQLYAAWSRGLDKCYAGWLADGSLRYPIVTPRP 650
651 ACGGDKPGVRTVYLYPNQTGLLDPLSRHHAFCFRGVSAVAPSPGEEEGGT 700
701 PTSLPDLEERIATQVGPGVAAVPVGEETTEVAAFTTEPENRTEWEFVYTP 750
751 VGTSPLPGIPPTWPPTSAATEEGTEGPSATEAPSTSEEPFPSEKPFPSEE 800
801 PFPSEEPFPSEKPSASEEPFPSEQPSTLSAPVPSRTELPGSGEVSGAPEV 850
851 SGDFTGSGEVSGHLDYSGQPSGEIASGLPSEDLDSSGLTSAVGSGLPVES 900
901 GLASGDEDKITWSSTSKVDRLPSGGEGPEGSVSGVEDLSGLPSGEGPEIS 950
951 ASGVEDLSRLPSGEGPEISASGVEDLSRLPSGEGPEISASGIEDISQLPS 1000
1001 GEGPEISASGIEDLSRLPSGEGPEISASGVEDLSRLPSGEGPEISASGVE 1050
1051 DISQLPSGEGPEISASGVEDLSRLPSGEGPEISASGVEDISQLPSGEGPE 1100
1101 ISASGVEDLSRLPSGEGPEISASGVEDLSRLPSGEGPEISASGVEDISQL 1150
1151 PSGEGPEISASGVEDLSRLPSGEGPEISASGVEDISQLPSGEGPEISVSG 1200
1201 VEDLSRLPSGEGPEISASGVEDLSRLPSGEGPEISASGVEDISQLPSGEG 1250
1251 PEISASGVEDLSRLPSGEGPEISASGVEDLSRLPSGEGPDISASGVEDLS 1300
1301 RLPSGEGPEISASGIEDLSRLPSGEGPEISASGVEDLSRLPSGEGPEISA 1350
1351 SGVEDISQLPSGEGPEISASGVEDLSRLPSGEGPEISASGVEDISQLPSG 1400
1401 EGPEISASGVEDLSRLPSGEGPEISASGVEDISQLPSGEGPEISASGVED 1450
1451 LSRLPSGGEGHLETSASGVEDLSGIPSGGEDHLESSASGVGDLSGLPSGR 1500
1501 EGLEIYASGAEDLSGLTSGKEDLAGSASGDLDVGRMPSGTLESGQAPEVS 1550
1551 GLPSGFSGEYSGVDLGSGPSSGLPDFSELPSGFPTVSLVDTTLVEMVTAT 1600
1601 TASELEGRGTIGVSGAGETFGLPFSELDISGGASGHPSGAELSGQASGSP 1650
1651 DISGETSGLFDVSGQPSGFPDISGGTSGLFEVSGQPSGFSGATSGVTELS 1700
1701 GLSSGQPDISGDASGVLSGVGQPFGLTDVSGETSGVPDLSGQPSGWPGFS 1750
1751 GMPSGTPDLVSSATSGSGESSGITFVDTSLVEVTPTTRKEEEGLGSVELS 1800
1801 GLPSGEADLSGASGVVDVSGLASGATDSSGFTSQPPEFSGLPSGVTEVSG 1850
1851 ESSGVEIGSSLPSGAYDGSGLPLSAPTVYLVDRTLVESVTQAPTAQEAGE 1900
1901 GPPGTLELSGAHSGVPDMSGDHSGSVDLSGLQSGLAEPSGEPASTPYFSG 1950
1951 DFSVTTDISGDSSAATSTSGEASGLPEVTLIASEFVEGVTEPTVSQELGQ 2000
2001 RPPVTHTPQLFESSGEASASGDVPRFPGSGVEAPPIPESSRESSAYPEAE 2050
2051 TGASAAPEASGGASGSPDLTEATSAFHEADLEGTSGLGVSVSTSAFQEGT 2100
2101 REVSAAPEVSRESTTTYDVGPEASGLPLATPVSSGDRTEVSGDLSGHTSG 2150
2151 LEVAISTAIPEYAWTQQTQRPAEAPLEIESSSPVHSGEEMPTAKPATSQT 2200
2201 EASIPTPPGQTDESEATTADQKLCENGWTKFQGHCYRHFPDRATWVDAES 2250
2251 QCRKQQSHLSSIVTPEEQEFVNNNAQDYQWIGLNDKTIEGDFRWSDGHSL 2300
2301 QFENWRPNQPDNFFATGEDCVVMIWHEKGEWNDVPCNYQLPFTCKKGTVA 2350
2351 CGEPPVVEHARIFGQKKDRYEINSLVRYQCTEGFVQRHVPTIRCQPSGHW 2400
2401 EEPRITCTDPATYKRRLQKRSSRSLRRSRPSTGP 2434
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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