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

NucPred

Fetching Q28295 from www.uniprot.org...

The NucPred score for your sequence is 0.54 (see score help below)

   1  MSPTRLVRVLLALALILPGKLCTKGTVGRSSMARCSLFGGDFINTFDESM    50
  51  YSFAGDCSYLLAGDCQEHSVSLIGGFQNGKRVSLSVYLGEFFDIHLFVNG   100
 101  TMLQGTQSISMPYASNGLYLEAEAGYYKLSSEAYGFVARIDGNGNFQVLL   150
 151  SDRYFNKTCGLCGNFNIFAEDDFRTQEGTLTSDPYDFANSWALSSGEQRC   200
 201  KRVSPPSSPCNVSSDEVQQVLWEQCQLLKSASVFARCHPLVDPEPFVALC   250
 251  ERTLCTCVQGMECPCAVLLEYARACAQQGIVLYGWTDHSVCRPACPAGME   300
 301  YKECVSPCTRTCQSLHVKEVCQEQCVDGCSCPEGQLLDEGHCVGSAECSC   350
 351  VHAGQRYPPGASLLQDCHTCICRNSLWICSNEECPGECLVTGQSHFKSFD   400
 401  NRYFTFSGVCHYLLAQDCQDHTFSVVIETVQCADDLDAVCTRSVTVRLPG   450
 451  HHNSLVKLKHGGGVSMDGQDIQIPLLQGDLRIQHTVMASVRLSYGEDLQM   500
 501  DWDGRGRLLVTLSPAYAGKTCGLCGNYNGNRGDDFVTPAGLAEPLVEDFG   550
 551  NAWKLLGACENLQKQHRDPCSLNPRQARFAEEACALLTSSKFEPCHRAVG   600
 601  PQPYVQNCRYDVCSCSDGRDCLCSAVANYAAACARRGVHIAWREPGFCAL   650
 651  SCPQGQVYLQCGTPCNMTCRSLSYPEEDCNEVCLEGCFCPPGLYLDERGD   700
 701  CVPKAQCPCYYDGEIFQPEDIFSDHHTMCYCEDGFMHCTTSGGLGSLLPN   750
 751  PVLSSPRSHRSKRSLSCRPPMVKLVCPADNPRAEGLECAKTCQNYDLQCM   800
 801  STGCVSGCLCPQGMVRHENRCVALERCPCFHQGQEYAPGETVKIDCNTCV   850
 851  CRDRKWNCTDHVCDATCSAIGMAHYLTFDGLKYLFPGECQYVLVQDYCGS   900
 901  NPGTFRILVGNEGCSYPSVKCKKRVTILVEGGEIELFDGEVNVKKPMKDE   950
 951  THFEVVESGQYVILLLGKALSVVWDHRLSISVTLKRTYQEQVCGLCGNFD  1000
1001  GIQNNDFTSSSLQIEEDPVDFGNSWKVNPQCADTKKVPLDSSPAVCHNNI  1050
1051  MKQTMVDSSCRILTSDIFQDCNRLVDPEPFLDICIYDTCSCESIGDCTCF  1100
1101  CDTIAAYAHVCAQHGKVVAWRTATFCPQNCEERNLHENGYECEWRYNSCA  1150
1151  PACPITCQHPEPLACPVQCVEGCHAHCPPGKILDELLQTCIDPEDCPVCE  1200
1201  VAGRRLAPGKKIILNPSDPEHCQICHCDGVNFTCQACREPGSLVVPPTEG  1250
1251  PIGSTTSYVEDTPEPPLHDFHCSRLLDLVFLLDGSSKLSEDEFEVLKVFV  1300
1301  VGMMEHLHISQKRIRVAVVEYHDGSHAYIELKDRKRPSELRRITSQVKYA  1350
1351  GSEVASTSEVLKYTLFQIFGKIDRPEASRIALLLMASQEPSRLARNLVRY  1400
1401  VQGLKKKKVIVIPVGIGPHASLKQIHLIEKQAPENKAFVFSGVDELEQRR  1450
1451  DEIINYLCDLAPEAPAPTQHPPMAQVTVGSELLGVSSPGPKRNSMVLDVV  1500
1501  FVLEGSDKIGEANFNKSREFMEEVIQRMDVGQDRIHVTVLQYSYMVTVEY  1550
1551  TFSEAQSKGEVLQQVRDIRYRGGNRTNTGLALQYLSEHSFSVSQGDREQV  1600
1601  PNLVYMVTGNPASDEIKRMPGDIQVVPIGVGPHANVQELEKIGWPNAPIL  1650
1651  IHDFEMLPREAPDLVLQRCCSGEGLQIPTLSPTPDCSQPLDVVLLLDGSS  1700
1701  SIPASYFDEMKSFTKAFISRANIGPRLTQVSVLQYGSITTIDVPWNVAYE  1750
1751  KVHLLSLVDLMQQEGGPSQIGDALSFAVRYVTSEVHGARPGASKAVVILV  1800
1801  TDVSVDSVDAAAEAARSNRVTVFPIGIGDRYSEAQLSSLAGPKAGSNMVR  1850
1851  LQRIEDLPTVATLGNSFFHKLCSGFDRVCVDEDGNEKRPGDVWTLPDQCH  1900
1901  TVTCLPDGQTLLKSHRVNCDRGPRPSCPNGQPPLRVEETCGCRWTCPCVC  1950
1951  MGSSTRHIVTFDGQNFKLTGSCSYVLFQNKEQDLEVILHNGACSPGAKET  2000
2001  CMKSIEVKHDGLSVELHSDMQMTVNGRLVSIPYVGGDMEVNVYGTIMYEV  2050
2051  RFNHLGHIFTFTPQNNEFQLQLSPRTFASKTYGLCGICDENGANDFILRD  2100
2101  GTVTTDWKALIQEWTVQQLGKTCQPVPEEQCPVSSSSHCQVLLSELFAEC  2150
2151  HKVLAPATFYAMCQPDSCHPKKVCEAIALYAHLCRTKGVCVDWRRANFCA  2200
2201  MSCPPSLVYNHCEHGCPRLCEGNTSSCGDQPSEGCFCPPNQVMLEGSCVP  2250
2251  EEACTQCISEDGVRHQFLETWVPAHQPCQICTCLSGRKVNCTLQPCPTAR  2300
2301  APTCGPCEVARLRQNAEQCCPEYECVCDLVSCDLPPVPPCEDGLQMTLTN  2350
2351  PGECRPNFTCACRKDECRRESPPSCPPHRTLALRKTQCCDEYECACNCVN  2400
2401  STVSCPLGYLASAVTNDCGCTTTTCFPDKVCVHRGTIYPVGQFWEEACDV  2450
2451  CTCTDLEDSVMGLRVAQCSQKPCEDNCLSGFTYVLHEGECCGRCLPSACE  2500
2501  VVIGSPRGDAQSHWKNVGSHWASPDNPCLINECVRVKEEVFVQQRNVSCP  2550
2551  QLNVPTCPTGFQLSCKTSECCPTCHCEPLEACLLNGTIIGPGKSLMIDVC  2600
2601  TTCRCTVQVGVISGFKLECRKTTCEACPLGYKEEKNQGECCGRCLPIACT  2650
2651  IQLRGGQIMTLKRDETIQDGCDSHFCKVNERGEYIWEKRVTGCPPFDEHK  2700
2701  CLAEGGKIMKIPGTCCDTCEEPECKDIIAKLQRVKVGDCKSEEEVDIHYC  2750
2751  EGKCASKAVYSIHMEDVQDQCSCCSPTQTEPMQVPLRCTNGSLIYHEILN  2800
2801  AMQCRCSPRKCSK                                       2813

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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