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

NucPred

Fetching Q12397 from www.uniprot.org...

The NucPred score for your sequence is 0.33 (see score help below)

   1  MASHAEPTRLFLFGDQTYDFVADLRDLLNIRNNPILVAFLEQSHHVIRAQ    50
  51  MIRELPPKEHKQARTASLAELLQKYVDRKLPSAFQTALSCVTQIGLFMRQ   100
 101  FDDPRVLYPHANDSYVLGVCTGSLAAAAISCSTSLSELLPIAVQTVLVAF   150
 151  RLGLWAEKVRDNLEISETNQTQPWSAVCHVPPEEVAIAIDRFSHKKVRSP   200
 201  VYRAQRPWITATSAKTTTVSASPDILSQLASQAPFTNSKLWREIPIYVPA   250
 251  HNNHLFSSRDVDDILATTNENPWSTFGAQIPFLSSVTGKLAWVRNYRDLL   300
 301  HLALSQCLIEPIRWDVVEAEVPRLLKDRDGLDTLTIVAFTTVLSKSLSNA   350
 351  LVTEGIKPAEPPTSINKTPERYSHRPGSDRGKLAIVSMSGRFPEAPSTDS   400
 401  FWDLLYKGLDVCKEVPLRRWDVKTHVDPSGKARNKGATRWGCWLDFAGEF   450
 451  DPRFFSISPKEAPQMDPAQRMALMSTYEAMERGGIVPDTTPSTQRNRIGV   500
 501  FHGVTSNDWMETNTAQNIDTYFITGGNRGFIPGRINFCFEFSGPSYSNDT   550
 551  ACSSSLAAIHLACNSLWRGDCDTAVAGGTNMIFTPDGHTGLDKGFFLSRT   600
 601  GNCKAFDDAADGYCRAEGVGTVFIKRLEDALAENDPILATILDIKTNHSA   650
 651  MSDSMTRPFKPAQIDNMSALLSTAGISPLDLSYIEMHGTGTQVGDAVEME   700
 701  SVLSLFAPDETFRPRDKPLYVGSAKANIGHGEGVSGVTSLIKVLLMMKND   750
 751  TIPPHCGIKPGSRINRNYPDLPARNVHIAFEPKPWPRTDTPRRVLINNFS   800
 801  AAGGNTAVLVEDAPVRDPVTASDPRTSHIVTVSGHVGKSLKLNLEKLRDH   850
 851  LVKRPEINPSELSYTTTARRWHHPHRVSITGANTMEILRNVESAIARGHG   900
 901  VNRPATKPKIVIACSGQGSQYTGMGWQLYNSYPTFRSDLERFDQLARSYG   950
 951  FPSFLEVYTSKPVGDSMEDLLPVIVQLALVSLEMALGNLLGSFGLKPSAV  1000
1001  IGHSLGEYAALYISGVLSAADTLYLVGMRAKLLQERCQRGTHAMLAVRAS  1050
1051  PVTLCEVLAESNCEVACHNGPNDTVLSGPLKEVMNLQNSLSATGIKGTLL  1100
1101  KLPFAFHSAQVQPILEEFKNVARGVTFHKPQIPVLSPLLVKVIDEKGTVD  1150
1151  PVYLARHCREPVKMVSVLEHARDQHIITDRTIVIDVGPKALMAGMIKTTL  1200
1201  DKDTSSALPTLGPSLDVWKSLTNILGTLYSRGLDINWVAYHEPFGSAKKV  1250
1251  IELPSYGWDLKDYFIPYKGEWCLHRHEIRCSCATPGKETATSDYQLPSDE  1300
1301  QVAAKRPSKQDESKEAYPEIVATTTVHRVVEEKTEPLGATLVVETDISRP  1350
1351  DVNQIAQGHLVDGIPLCTPSVYADIALHVGRYSMNRLRASHPGAMDGVVD  1400
1401  VADMVIDKALIPHGKSPQLLRTTLTMTWPPKAAATTRSAKIKFATYFADG  1450
1451  KLDTEHATCTVRFTSEAQLKSLQKKVPEYQERIKKLGEGLRQGQFIRYTT  1500
1501  KSGYKLMSSMASFHRDYKLLNHLILNEADNEAVSTMDFSAAKSEGTFAAH  1550
1551  PAYVDAITQVGGFAMNANDNTDIQQEVFVNHGWDSFQVYQPLVKGKTYEV  1600
1601  YVRMTEDEKGDLVHGDTIVLYGDAVVAFFKGLSLRRVPRRGLRMVLQQAS  1650
1651  DKAARLHGNQQAVKTQAPQRAALKQKPQSSPTQPHASKVAYSRSATSPTA  1700
1701  GKPVVAARDLSREGDDKFKAVLSVISEESGVALGELTADTNFADIGIDSL  1750
1751  SSMVIGSRLREDLGLELGAEFSLFIDCPTVRSLKTLLSGSAVSVNNDKDE  1800
1801  LEPGQEAETAAPEQLDLRIGDAAPSKVRDANIEPLDLGDELFRNVLRIVS  1850
1851  EESGVALDELSAETVFADIGIDSLSSMVITSRFREDLGMSLDSSFNLFEE  1900
1901  VPTVARLQEFFGTTSGSTTGSSGSGSSEDETDSIPSTPEEYTTADTRVPE  1950
1951  CRPTTSVVLQGLPQMAKQILFMLPDGGGSASSYLTIPRLHADVAIVGLNC  2000
2001  PYARDPENMNCTHQSMIQSFCNEIKRRQPEGPYHLGGWSSGGAFAYVTAE  2050
2051  ALINAGNEVHSLIIIDAPVPQVMEKLPTSFYEYCNNLGLFSNQPGGTTDG  2100
2101  TAQPPPYLIPHFQATVDVMLDYRVAPLKTNRMPKVGIIWASETVMDEDNA  2150
2151  PKMKGMHFMVQKRKDFGPDGWDVVCPGAVFDIVRAEGANHFTLMTKEHVY  2200
2201  LVRELIDRVMG                                         2211

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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