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

NucPred

Fetching P54939 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MVALSLKISIGNVVKTMQFEPSTMVYDACRMIRERVPEAQMGQPNDFGLF    50
  51  LSDEDPKKGIWLEAGKALDYYMLRNGDTMEYKKKQRPLKIRMLDGTVKTV   100
 101  MVDDSKTVTDMLTTICARIGITNYDEYSLVREIMEEKKEEVTGTLKKDKT   150
 151  LLRDEKKMEKLKQKLHTDDELNWLDHGRTLREQGIDDNETLLLRRKFFYS   200
 201  DQNVDSRDPVQLNLLYVQARDDILNGSHPVSFDKACEFAGYQCQIQFGPH   250
 251  NEQKHKPGFLELKDFLPKEYIKQKGERKIFMAHKNCGNMSEIEAKVRYVK   300
 301  LARSLKTYGVSFFLVKEKMKGKNKLVPRLLGITKECVMRVDEKTKEVIQE   350
 351  WSLTNIKRWAASPKSFTLDFGDYQDGYYSVQTTEGEQIAQLIAGYIDIIL   400
 401  KKKKSKDHFGLEGDEESTMLEDSVSPKKSTVLQQQFNRVGKAELGSVALP   450
 451  AIMRTGAGGPENFQVGTMPQAQMQITSGQMHRGHMPPLTSAQQALTGTIN   500
 501  SSMQAVNAAQATLDDFETLPPLGQDAASKAWRKNKMDESKHEIHSQADAI   550
 551  TAGTASVVNLTAGDPADTDYTAVGCAVTTISSNLTEMSKGVKLLAALMED   600
 601  EGGNGRQLLQAAKNLASAVSDLLKTAQPASAEPRQNLLQAAGLVGQTSGE   650
 651  LLQQIGESDTDPRFQDMLMQLAKAVASAAAALVLKAKNVAQKTEDSALQT   700
 701  QVIAAATQCALSTSQLVACTKVVAPTISSPVCQEQLIEAGKLVAKSAEGC   750
 751  VEASKAATNDDQLLKQVGVAATAVTQALNDLLQHIKQHATGGQPIGRYDQ   800
 801  ATDTILNVTENIFSSMGDAGEMVRQARILAQATSDLVNAIKADAEGETDL   850
 851  ENSRKLLSAAKILADATAKMVEAAKGAAAHPDSEEQQQRLREAAEGLRMA   900
 901  TNAAAQNAIKKKLVHKLEHAAKQAAASATQTIAAAQHAAASNKNPAAQQQ   950
 951  LVQSCKVVADQIPMLVQGVRGSQSQPDSPSAQLALIAASQNFLQPGGKMV  1000
1001  AAAKATVPTITDQASAMQLSQCAKNLAAALAELRTAAQKAQEACGPLEID  1050
1051  SALGLVQSLERDLKEAKAAARDGKLKPLPGETMEKCAQDLGNSTKAVTSA  1100
1101  IAHLLGEVAQGNENYTGIAAREVAQALRSLSQAARGVAANSSDPQAQNAM  1150
1151  LECASDVMDKANNLIEEARKAVAKPGDPDSQQRLVQVAKAVSQALNRCVN  1200
1201  CLPGQRDVDAAIRMVGEASKRLLSDSFPPSNKTFQEAQSQLNRAAAGLNQ  1250
1251  SANELVQASRGTPQDLAKSSGKFGQDFNEFLQAGVEMASLSPTKEDQAQV  1300
1301  VSNLKSISMSSSKLLLAAKALSADPTSPNLKSQLAAAARAVTDSINQLIT  1350
1351  MCTQQAPGQKECDNALRELETVKELLENPTQTVNDMSYFSCLDSVMENSK  1400
1401  VLGESMAGISQNAKNSKLPEFGESISAASKALCGLTEAAAQAAYLVGVSD  1450
1451  PNSQAGQQGLVDPTQFARANQAIQMACQNLVDPACTQSQVLSAATIVAKH  1500
1501  TSALCNTCRLASSRTANPVAKRQFVQPAKEVANSTANLVKTIKALDGAFN  1550
1551  EENRERCRAATAPLIEAVDNLTAFASNPEFATVPAQISPEGRRAMEPIVT  1600
1601  SAKTMLESSAGLIQTARSLAVNPKDPPQWSVLAGHSRTVSDSIKKLITNM  1650
1651  RDKAPGQRECDEAIDVLNRCMREVDQASLAAISQQLAPREGISQEALHNQ  1700
1701  MITAVQEINNLIEPVASAARAEASQLGHKVSQMAQYFEPLILAAIGAASK  1750
1751  TPNHQQQMNLLDQTKTLAESALQMLYTAKEAGGNPKQAAHTQEALEEAVQ  1800
1801  MMKEAVEDLTTTLNEAASAAGVVGGMVDSITQAINQLDEGPMGEPEGTFV  1850
1851  DYQTTMVKTAKAIAVTVQEMVTKSTTNPDELGILANQLTNDYGQLAQQAK  1900
1901  PAALTAENEEIGSHIKRRVQELGHGCAALVTKAGALQCSPSDAYTKKELI  1950
1951  ESARKVSEKVSHVLAALQAGNRGTQACITAASAVSGIIADLDTTIMFATA  2000
2001  GTLNRENSETFADHREGILKTAKALVEDTKVLVQNATASQEKLAQAAQSS  2050
2051  VSTITRLAEVVKLGAASLGSEDPETQVVLINAVKDVAKALGDLIGATKAA  2100
2101  AGKAGDDPAVYQLKNSAKVMVTNVTSLLKTVKAVEDEATKGTRALEATIE  2150
2151  HIRQELAVFSSPVPPAQVSTPEDFIRMTKGITMATAKAVAAGNSCRQEDV  2200
2201  IATANLSRRAIADMLRACKEAAYHPEVSADVRQRALRFGKECADGYLELL  2250
2251  EHVLVILQKPTHELKQQLAGYSKRVASSVTELIQAAEAMKGTEWVDPEDP  2300
2301  TVIAENELLGAAAAIEAAAKKLEQLKPRAKPKQADESLDFEEQILEAAKS  2350
2351  IAAATSALVKAASAAQRELVAQGKVGVIPANAVDDGQWSQGLISAARMVA  2400
2401  AATNNLCEAANAAVQGHASEEKLISSAKQVAASTAQLLVACKVKADHDSE  2450
2451  AMKRLQAAGNAVKRASDNLVKAAQKAAAFQDHDETVVVKEKMVGGIAQII  2500
2501  AAQEEMLRKERELEEARKKLAMIRQQQYKFLPTELRDEEQN           2541

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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