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

NucPred

Fetching P12270 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MAAVLQQVLERTELNKLPKSVQNKLEKFLADQQSEIDGLKGRHEKFKVES    50
  51  EQQYFEIEKRLSHSQERLVNETRECQSLRLELEKLNNQLKALTEKNKELE   100
 101  IAQDRNIAIQSQFTRTKEELEAEKRDLIRTNERLSQELEYLTEDVKRLNE   150
 151  KLKESNTTKGELQLKLDELQASDVSVKYREKRLEQEKELLHSQNTWLNTE   200
 201  LKTKTDELLALGREKGNEILELKCNLENKKEEVSRLEEQMNGLKTSNEHL   250
 251  QKHVEDLLTKLKEAKEQQASMEEKFHNELNAHIKLSNLYKSAADDSEAKS   300
 301  NELTRAVEELHKLLKEAGEANKAIQDHLLEVEQSKDQMEKEMLEKIGRLE   350
 351  KELENANDLLSATKRKGAILSEEELAAMSPTAAAVAKIVKPGMKLTELYN   400
 401  AYVETQDQLLLEKLENKRINKYLDEIVKEVEAKAPILKRQREEYERAQKA   450
 451  VASLSVKLEQAMKEIQRLQEDTDKANKQSSVLERDNRRMEIQVKDLSQQI   500
 501  RVLLMELEEARGNHVIRDEEVSSADISSSSEVISQHLVSYRNIEELQQQN   550
 551  QRLLVALRELGETREREEQETTSSKITELQLKLESALTELEQLRKSRQHQ   600
 601  MQLVDSIVRQRDMYRILLSQTTGVAIPLHASSLDDVSLASTPKRPSTSQT   650
 651  VSTPAPVPVIESTEAIEAKAALKQLQEIFENYKKEKAENEKIQNEQLEKL   700
 701  QEQVTDLRSQNTKISTQLDFASKRYEMLQDNVEGYRREITSLHERNQKLT   750
 751  ATTQKQEQIINTMTQDLRGANEKLAVAEVRAENLKKEKEMLKLSEVRLSQ   800
 801  QRESLLAEQRGQNLLLTNLQTIQGILERSETETKQRLSSQIEKLEHEISH   850
 851  LKKKLENEVEQRHTLTRNLDVQLLDTKRQLDTETNLHLNTKELLKNAQKE   900
 901  IATLKQHLSNMEVQVASQSSQRTGKGQPSNKEDVDDLVSQLRQTEEQVND   950
 951  LKERLKTSTSNVEQYQAMVTSLEESLNKEKQVTEEVRKNIEVRLKESAEF  1000
1001  QTQLEKKLMEVEKEKQELQDDKRRAIESMEQQLSELKKTLSSVQNEVQEA  1050
1051  LQRASTALSNEQQARRDCQEQAKIAVEAQNKYERELMLHAADVEALQAAK  1100
1101  EQVSKMASVRQHLEETTQKAESQLLECKASWEERERMLKDEVSKCVCRCE  1150
1151  DLEKQNRLLHDQIEKLSDKVVASVKEGVQGPLNVSLSEEGKSQEQILEIL  1200
1201  RFIRREKEIAETRFEVAQVESLRYRQRVELLERELQELQDSLNAEREKVQ  1250
1251  VTAKTMAQHEELMKKTETMNVVMETNKMLREEKERLEQDLQQMQAKVRKL  1300
1301  ELDILPLQEANAELSEKSGMLQAEKKLLEEDVKRWKARNQHLVSQQKDPD  1350
1351  TEEYRKLLSEKEVHTKRIQQLTEEIGRLKAEIARSNASLTNNQNLIQSLK  1400
1401  EDLNKVRTEKETIQKDLDAKIIDIQEKVKTITQVKKIGRRYKTQYEELKA  1450
1451  QQDKVMETSAQSSGDHQEQHVSVQEMQELKETLNQAETKSKSLESQVENL  1500
1501  QKTLSEKETEARNLQEQTVQLQSELSRLRQDLQDRTTQEEQLRQQITEKE  1550
1551  EKTRKAIVAAKSKIAHLAGVKDQLTKENEELKQRNGALDQQKDELDVRIT  1600
1601  ALKSQYEGRISRLERELREHQERHLEQRDEPQEPSNKVPEQQRQITLKTT  1650
1651  PASGERGIASTSDPPTANIKPTPVVSTPSKVTAAAMAGNKSTPRASIRPM  1700
1701  VTPATVTNPTTTPTATVMPTTQVESQEAMQSEGPVEHVPVFGSTSGSVRS  1750
1751  TSPNVQPSISQPILTVQQQTQATAFVQPTQQSHPQIEPANQELSSNIVEV  1800
1801  VQSSPVERPSTSTAVFGTVSATPSSSLPKRTREEEEDSTIEASDQVSDDT  1850
1851  VEMPLPKKLKSVTPVGTEEEVMAEESTDGEVETQVYNQDSQDSIGEGVTQ  1900
1901  GDYTPMEDSEETSQSLQIDLGPLQSDQQTTTSSQDGQGKGDDVIVIDSDD  1950
1951  EEEDDDENDGEHEDYEEDEEDDDDDEDDTGMGDEGEDSNEGTGSADGNDG  2000
2001  YEADDAEGGDGTDPGTETEESMGGGEGNHRAADSQNSGEGNTGAAESSFS  2050
2051  QEVSREQQPSSASERQAPRAPQSPRRPPHPLPPRLTIHAPPQELGPPVQR  2100
2101  IQMTRRQSVGRGLQLTPGIGGMQQHFFDDEDRTVPSTPTLVVPHRTDGFA  2150
2151  EAIHSPQVAGVPRFRFGPPEDMPQTSSSHSDLGQLASQGGLGMYETPLFL  2200
2201  AHEEESGGRSVPTTPLQVAAPVTVFTESTTSDASEHASQSVPMVTTSTGT  2250
2251  LSTTNETATGDDGDEVFVEAESEGISSEAGLEIDSQQEEEPVQASDESDL  2300
2301  PSTSQDPPSSSSVDTSSSQPKPFRRVRLQTTLRQGVRGRQFNRQRGVSHA  2350
2351  MGGRGGINRGNIN                                       2363

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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