NucPred on Proteomes

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

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q6C3P1 UniProt NPD GO	ALG13_YARLI	UDP-N-acetylglucosamine transferase subunit ALG13 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.09	-	mit	1 *	Endoplasmic reticulum (By similarity)				196
P40004 UniProt NPD GO	YEA4_YEAST	UDP-N-acetylglucosamine transporter YEA4	0.09	-	end	6 *	Membrane; multi-pass membrane protein (By similarity). Endoplasmic reticulum	endoplasmic reticulum [IDA]			342
Q9SA77 UniProt NPD GO	ARAE1_ARATH	UDP-arabinose 4-epimerase 1 (EC 5.1.3.5) (UDP-D-xylose 4-epimerase 1)	0.09	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein				419
Q6BMV3 UniProt NPD GO	HUT1_DEBHA	UDP-galactose transporter homolog 1	0.09	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				354
P09875 UniProt NPD GO	UDB1_RAT	UDP-glucuronosyltransferase 2B1 precursor (EC 2.4.1.17) (UDPGT) (UDPGTr-2)	0.09	-	nuc	1	Microsome				529
Q7ZZY8 UniProt NPD GO	UTS2B_BRARE	UII beta precursor [Contains: Urophysin beta; Urotensin II-beta (UII-beta) (U-II-beta)]	0.09	-	exc	0	Secreted protein				125
P30085 UniProt NPD GO	KCY_HUMAN	UMP-CMP kinase (EC 2.7.4.14) (Cytidylate kinase) (Deoxycytidylate kinase) (Cytidine monophosphate ki ...	0.09	-	cyt	0	Nucleus. Mainly. Cytoplasm	cytoplasm [TAS] nucleus [TAS]	191710	1TEV	196
P38857 UniProt NPD GO	YHW2_YEAST	UPF0041 protein YHR162W	0.09	-	mit	0		mitochondrion [IDA]			129
Q9BSU1 UniProt NPD GO	CP070_HUMAN	UPF0183 protein C16orf70	0.09	-	cyt	0					422
Q9V8F3 UniProt NPD GO	U279_DROME	UPF0279 protein CG14505	0.09	-	mit	0					119
Q876Z1 UniProt NPD GO	YCB2_ASHGO	UPF0357 protein AAL017W precursor	0.09	-	nuc	1 *					134
P32861 UniProt NPD GO	UGPA1_YEAST	UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (UDP-glucose pyrophosphorylase) (UDPGP) (U ...	0.09	-	mit	0		cytoplasm [IDA]			499
O35156 UniProt NPD GO	UGPA1_CRIGR	UTP--glucose-1-phosphate uridylyltransferase 1 (EC 2.7.7.9) (UDP-glucose pyrophosphorylase 1) (UDPGP ...	0.09	-	cyt	0	Cytoplasm				507
Q07131 UniProt NPD GO	UGPA1_HUMAN	UTP--glucose-1-phosphate uridylyltransferase 1 (EC 2.7.7.9) (UDP-glucose pyrophosphorylase 1) (UDPGP ...	0.09	-	cyt	0	Cytoplasm	cytoplasm [NAS]	191750		507
Q12238 UniProt NPD GO	UVI31_SCHPO	UV-induced protein uvi31	0.09	-	nuc	0					102
Q6BNQ5 UniProt NPD GO	UCR7_DEBHA	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit VII)	0.09	-	nuc	0	Mitochondrion; mitochondrial inner membrane (Potential)				126
P48503 UniProt NPD GO	UCRQ_NEUCR	Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C precursor (EC 1.10.2.2) (Ub ...	0.09	-	cyt	0	Mitochondrion; mitochondrial inner membrane				107
Q4V7R3 UniProt NPD GO	COQ5_XENLA	Ubiquinone biosynthesis methyltransferase COQ5, mitochondrial precursor (EC 2.1.1.-)	0.09	-	mit	0	Mitochondrion (By similarity)				310
O94453 UniProt NPD GO	COQ4_SCHPO	Ubiquinone biosynthesis protein COQ4 homolog	0.09	-	cyt	0					272
P97478 UniProt NPD GO	COQ7_MOUSE	Ubiquinone biosynthesis protein COQ7 homolog (Coenzyme Q biosynthesis protein 7 homolog) (Timing pro ...	0.09	-	mit	0					217
Q60HC8 UniProt NPD GO	UCHL1_MACFA	Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12) (EC 6.-.-.-) (UCH-L1) (Ubiquitin thi ...	0.09	-	nuc	0	Cytoplasm (By similarity). Found both cytoplasmic and nuclear in cytotrophoblasts and decidual cells ...				223
P42747 UniProt NPD GO	UBC14_ARATH	Ubiquitin-conjugating enzyme E2 14 (EC 6.3.2.19) (Ubiquitin-protein ligase 14) (Ubiquitin carrier pr ...	0.09	-	cyt	0					167
Q9UVR2 UniProt NPD GO	UBC1_MAGGR	Ubiquitin-conjugating enzyme E2-16 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.09	-	nuc	0					147
O74196 UniProt NPD GO	UBC1_COLGL	Ubiquitin-conjugating enzyme E2-16 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.09	-	nuc	0					147
O74983 UniProt NPD GO	MMS2_SCHPO	Ubiquitin-conjugating enzyme spm2 (Ubiquitin-conjugating enzyme variant MMS2 homolog) (UEV MMS2)	0.09	-	nuc	0					139
P38219 UniProt NPD GO	YBN5_YEAST	Uncharacterized GTP-binding protein YBR025C	0.09	-	cyt	0	Cytoplasm	cytoplasm [IDA]			394
P53295 UniProt NPD GO	YG3Y_YEAST	Uncharacterized GTP-binding protein YGR173W	0.09	-	nuc	0		cytoplasm [IDA]			368
Q12185 UniProt NPD GO	YD018_YEAST	Uncharacterized acyltransferase YDR018C (EC 2.3.-.-)	0.09	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				396
Q3E7A6 UniProt NPD GO	YM007_YEAST	Uncharacterized mitochondrial protein YML007C-A	0.09	-	mit	0	Mitochondrion	mitochondrion [IDA]			36
Q8N5C1 UniProt NPD GO	CF188_HUMAN	Uncharacterized protein C6orf188	0.09	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				309
Q9URS8 UniProt NPD GO	Y464_KLULA	Uncharacterized protein KLLA0D02464g	0.09	-	cyt	0					227
P38260 UniProt NPD GO	YBV1_YEAST	Uncharacterized protein YBR101C	0.09	-	cyt	0		cytosol [IDA] cytosolic ribosome (sensu Eukaryota) [IPI]			290
P38281 UniProt NPD GO	YB01_YEAST	Uncharacterized protein YBR151W	0.09	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			316
P38348 UniProt NPD GO	YB9Q_YEAST	Uncharacterized protein YBR272C	0.09	-	cyt	0		cytoplasm [IDA]			480
Q3E774 UniProt NPD GO	YD159_YEAST	Uncharacterized protein YDL159W-A	0.09	-	cyt	0					43
Q07716 UniProt NPD GO	YD237_YEAST	Uncharacterized protein YDL237W precursor	0.09	-	gol	1 *					390
Q12156 UniProt NPD GO	YD063_YEAST	Uncharacterized protein YDR063W	0.09	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			149
P40100 UniProt NPD GO	YE15_YEAST	Uncharacterized protein YER185W	0.09	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				303
Q8TGU1 UniProt NPD GO	YG188_YEAST	Uncharacterized protein YGL188C-A	0.09	-	nuc	0					46
P53262 UniProt NPD GO	YG2T_YEAST	Uncharacterized protein YGR106C precursor	0.09	-	end	1	Vacuole; vacuolar membrane; single-pass type I membrane protein (Potential)	vacuolar membrane (sensu Fungi) [IDA]			265
P40544 UniProt NPD GO	YIC3_YEAST	Uncharacterized protein YIL023C	0.09	-	end	5	Membrane; multi-pass membrane protein (Probable)				346
P46999 UniProt NPD GO	YJQ0_YEAST	Uncharacterized protein YJL160C precursor	0.09	-	exc	0	Secreted protein (Potential)				287
Q3E766 UniProt NPD GO	YM175_YEAST	Uncharacterized protein YMR175W-A	0.09	-	exc	0					64
Q8TGS2 UniProt NPD GO	YO19A_YEAST	Uncharacterized protein YOL019W-A	0.09	-	mit	0					50
Q3E807 UniProt NPD GO	YO011_YEAST	Uncharacterized protein YOR011W-A	0.09	-	cyt	0					68
Q3E832 UniProt NPD GO	YO072_YEAST	Uncharacterized protein YOR072W-B	0.09	-	cyt	0					53
O42851 UniProt NPD GO	YFHE_SCHPO	Uncharacterized trans-sulfuration enzyme C23A1.14c	0.09	-	cyt	0					398
P83602 UniProt NPD GO	NF05_NAEFO	Unknown protein NF005 from 2D-PAGE (Fragment)	0.09	-	nuc	0					23
P80633 UniProt NPD GO	UC27_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 688) (Fragment)	0.09	-		0					15
P38642 UniProt NPD GO	UF04_MOUSE	Unknown protein from 2D-PAGE of fibroblasts (P46) (Fragment)	0.09	-		0					7

You are viewing entries 67251 to 67300 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

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.)

Go back to the NucPred Home Page.