SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q60952 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  METGSPGLNMKPQSLQLVLEGQVLALQQQMAENQAASWRKLKNSQEAQKR    50
  51  QATLVRKLQAKVLQYRSWCQDLEKRLEATGGLIPQRWESVEEPNLEQLLI   100
 101  RLEEEQQRCESLVEVNTELRLHMEKADVVNKALQEDVEKLTVDWSRARDE   150
 151  LVRKESQWRMEQEFFKGYLRGEHGRLLNLWREVVTFRRHFLKMKSATDRD   200
 201  LTELKAEHARLSGSLLTCCLRLTLRAQSRESSGSGRTEESEPARLLLLVA   250
 251  KTQALEKEAHEKSQELMQLKSHGDLEKAELQDRVTELSALLTQSQKQNED   300
 301  YEKMVKALRETMEILETNHAELMEHEASLSRNAQEEKLSLQQVIKAITQA   350
 351  LASVEEEDTVTQSSGHEDSLQSDCNGLSQFDPQDPDRALTLVQSVLTRRQ   400
 401  QAVQDLRQQLSGCQEAMSFLQQQHDQWEEEGRALREKLQKLTGERDALAG   450
 451  QTVGLQGEVDSLSRERELLQKARGELQQQLEVLEQEAWRLRRMNMELQLQ   500
 501  GDSAQGEKLEQQEELHLAVRERERLQETLVGLEAKQSESLSELLTLREAL   550
 551  ESSRLEGELLKQERVEVAAALARAEQSIVELSGSENSLKAEVADLRAAAV   600
 601  KLGALNEALALDKVELNQQLLQLEQENQSLCSRVEAAEQLRSALQVDLAE   650
 651  AERRREALWEKKTQLETQLQKAEEAGAELQAELRGTREEKEELKDKLSEA   700
 701  HHQQETATAHLEQLHQDAERQEETLARAVQEKEALVRERAALEVRLQAVE   750
 751  RDRQDLTEHVLGLRSAKEQLESNLFEAQQQNSVIQVTKGQLEVQIQTIIQ   800
 801  AKEVIQGEVKCLKLELDAERTRAEQEWDAVARQLAQAEQEGQASLERQKV   850
 851  AHEEEVNRLQEKWEKERSWLQQELDKTLETLERERAELETKLREQQTEME   900
 901  AIRAQREEERSQADSALYQMQLETEKERVSLLETLLRTQKELADASQQLE   950
 951  RLRQDMKIQKLKEQETTGMLQAQLQETQQELKEAAQQHRDDLAAFQKDKL  1000
1001  DLQKQVEDLMSQLVAHDDSQRLVKEEIEEKVKVAQECSRIQKELEKENAS  1050
1051  LALSLVEKEKRLLILQEADSVRQQELSSLRQDIQEAQEGQRELGVQVELL  1100
1101  RQEVKEKEADFVAREAQLLEELEASRVAEQQLRASLWAQEAKATQLQLQL  1150
1151  RSTESQLEALVAEQQPENQAQAQLASLCSVLQQALGSACESRPELRGGGD  1200
1201  SAPTLWGPDPDQNGASRLFKRWSLPTALSPEAVALALQKLHQDVWKARQA  1250
1251  RDDLRDQVQKLVQRLTDTEAQKSQVHSELQDLQRQLSQSQEEKSKWEGRQ  1300
1301  NSLESELRDLHETAASLQSRLRQAELQKMEAQNDRELLQASKEKLSAQVE  1350
1351  HLQACVAEAQAQADAAAVLEEDLRTARSALKLKNEELESERERAQALQEQ  1400
1401  GELKVAQGKALQENLALLAQTLSNREREVETLQAEVQELEKQREMQKAAL  1450
1451  ELLSLDLKKRSREVDLQQEQIQELEQCRSVLEHLPMAVQEREQKLSVQRD  1500
1501  QIRELENDREAQRSVLEHQLLDLEQKAQVIESQRGQIQDLKKQLGTLECL  1550
1551  ALELEESHHKVESQQKMITELEGQREMQRVALTHLTLDLEERSQELQAQS  1600
1601  SQLHELENHSTHLAKELQERDQEVTSQRQQIDELQKQQEQLAQALERKGQ  1650
1651  ELVLQKERIQVLEDQRTLQTKILEEDLEQIKHSLRERSQELASQWQLVHE  1700
1701  RADDGKSPSKGQRGSLEHLKLILRDKEKEVECQQERIQELQGHMGQLEQQ  1750
1751  LQGLHRKVGETSLLLTHREQETATLQQHLQEAKEQGELREQVLQGQLEEA  1800
1801  QRDLAQRDHELETLRQEKQQTQDQEESMKLKTSALQAALEQAHATLKERQ  1850
1851  GELEEHREQVRRLQEELEVEGRQVRALEEVLGDLRAESREHEKAVLALQQ  1900
1901  RCAEQAQEHEAEARTLQDSWLQAQATLTEQEQELAALRAENQYSRRQEEA  1950
1951  AVSQAEALQEALSKAQAALQEKEQSLLEQAELSHTLEASTAALQATLDTC  2000
2001  QASARQLEEALRIREGEIQAQALQHHEVTQHLQQELCQKKEELRQLLEKA  2050
2051  GARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVAQREEEILMLRE  2100
2101  ASSPRHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDLA  2150
2151  LSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSRQALEEQQS  2200
2201  GGPHSTSRADQGPKVGQGSQSGEVETEPSPGVEEKERLTQRLERLQQAVA  2250
2251  ELEVDRSKLQCHNAQLRTALEQVERERRKLKRDSVRASRAGSLEARETMT  2300
2301  SSPTQQDGRGSQRGSSDSVLVVELQREVALLRAQLALERKQRQDYIARSV  2350
2351  QTSRELAGLHHSLSHSLLTVAQAPEATVLEAETRKLDESLNQSLTSPGPC  2400
2401  LLHPSLDTTQNTHR                                      2414

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

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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