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
P38720 UniProt NPD GO	6PGD1_YEAST	6-phosphogluconate dehydrogenase, decarboxylating 1 (EC 1.1.1.44)	0.02	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA]			489
Q03393 UniProt NPD GO	PTPS_HUMAN	6-pyruvoyl tetrahydrobiopterin synthase (EC 4.2.3.12) (PTPS) (PTP synthase)	0.02	-	mit	0			261640		145
Q90W95 UniProt NPD GO	PTPS_POERE	6-pyruvoyl tetrahydrobiopterin synthase (EC 4.2.3.12) (PTPS) (PTP synthase)	0.02	-	cyt	0					147
P50345 UniProt NPD GO	RLA0_LUPLU	60S acidic ribosomal protein P0	0.02	-	end	0					322
Q96TJ5 UniProt NPD GO	RLA0_NEUCR	60S acidic ribosomal protein P0	0.02	-	mit	0					313
P41095 UniProt NPD GO	RLA0_ORYSA	60S acidic ribosomal protein P0	0.02	-	cyt	0					318
O74864 UniProt NPD GO	RLA0_SCHPO	60S acidic ribosomal protein P0	0.02	-	nuc	0					312
Q9U3U0 UniProt NPD GO	RLA0_CERCA	60S acidic ribosomal protein P0 (CcP0)	0.02	-	cyt	0					317
P47826 UniProt NPD GO	RLA0_CHICK	60S acidic ribosomal protein P0 (L10E)	0.02	-	cyt	0					316
P19945 UniProt NPD GO	RLA0_RAT	60S acidic ribosomal protein P0 (L10E)	0.02	-	cyt	0					317
O04204 UniProt NPD GO	RLA01_ARATH	60S acidic ribosomal protein P0-1	0.02	-	cyt	0					317
P22684 UniProt NPD GO	RLA1_DICDI	60S acidic ribosomal protein P1	0.02	-	cyt	0					113
P26643 UniProt NPD GO	RLA1_TRYCR	60S acidic ribosomal protein P1	0.02	-	cyt	0					109
P08570 UniProt NPD GO	RLA1_DROME	60S acidic ribosomal protein P1 (RP21C) (Acidic ribosomal protein RPA2)	0.02	-	cyt	0					112
Q8LCW9 UniProt NPD GO	RLA11_ARATH	60S acidic ribosomal protein P1-1	0.02	-	cyt	0					112
O23095 UniProt NPD GO	RLA12_ARATH	60S acidic ribosomal protein P1-2	0.02	-	cyt	0					113
Q8LEQ0 UniProt NPD GO	RLA13_ARATH	60S acidic ribosomal protein P1-3	0.02	-	cyt	0					113
P27055 UniProt NPD GO	RLA2_BABBO	60S acidic ribosomal protein P2 (L12EI)	0.02	-	cyt	0					112
P23632 UniProt NPD GO	RLA2_TRYCR	60S acidic ribosomal protein P2-A (P) (P-JL5) (L12E)	0.02	-	cyt	0					107
Q9C285 UniProt NPD GO	RL12_NEUCR	60S ribosomal protein L12	0.02	-	cyt	0					165
Q9FF52 UniProt NPD GO	RL123_ARATH	60S ribosomal protein L12-3	0.02	-	cyt	0					166
P08792 UniProt NPD GO	RL25_PICJA	60S ribosomal protein L25	0.02	-	mit	0					142
Q05462 UniProt NPD GO	RL27_PEA	60S ribosomal protein L27	0.02	-	cyt	0					135
Q8LCL3 UniProt NPD GO	RL272_ARATH	60S ribosomal protein L27-2	0.02	-	cyt	0					135
Q21930 UniProt NPD GO	RL28_CAEEL	60S ribosomal protein L28	0.02	-	nuc	0					125
P24002 UniProt NPD GO	RL37_TETTH	60S ribosomal protein L37 (P1 type)	0.02	-	nuc	0					109
P51401 UniProt NPD GO	RL9B_YEAST	60S ribosomal protein L9-B (L8) (YL11) (RP25)	0.02	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			191
P80844 UniProt NPD GO	CWP23_ARATH	64 kDa cell wall protein (Fragment)	0.02	-		0	Cell wall				10
Q9Z2Z8 UniProt NPD GO	DHCR7_RAT	7-dehydrocholesterol reductase (EC 1.3.1.21) (7-DHC reductase) (Sterol delta-7-reductase)	0.02	-	mit	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				471
P80815 UniProt NPD GO	CWP19_LYCES	76 kDa cell wall protein (Fragment)	0.02	-		0	Cell wall				18
P80514 UniProt NPD GO	HR83_TRITO	83 kDa hypersensitivity protein (Protein IV) (Fragment)	0.02	-	cyt	0					26
P31963 UniProt NPD GO	MFA2_USTMA	A2-specific pheromone (Mating factor A2)	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				38
Q09749 UniProt NPD GO	ADRL_SCHPO	ADIPOR-like receptor spbc12c2.09c	0.02	-	end	7	Membrane; multi-pass membrane protein (Potential)				324
P11076 UniProt NPD GO	ARF1_YEAST	ADP-ribosylation factor 1	0.02	-	cyt	0		cytosol [TAS] Golgi-associated vesicle [TAS]			180
Q94231 UniProt NPD GO	ARF11_CAEEL	ADP-ribosylation factor 1-like 1 (ADP-ribosylation factor-related protein 1.1) (ADP-ribosylation fac ...	0.02	-	cyt	0					178
Q2YDM1 UniProt NPD GO	ARL1_BOVIN	ADP-ribosylation factor-like protein 1	0.02	-	cyt	0					181
P40616 UniProt NPD GO	ARL1_HUMAN	ADP-ribosylation factor-like protein 1	0.02	-	cyt	0			603425	1UPT	181
P61211 UniProt NPD GO	ARL1_MOUSE	ADP-ribosylation factor-like protein 1	0.02	-	cyt	0					181
P61212 UniProt NPD GO	ARL1_RAT	ADP-ribosylation factor-like protein 1	0.02	-	cyt	0				1R4A	181
Q8N8L6 UniProt NPD GO	ARL10_HUMAN	ADP-ribosylation factor-like protein 10	0.02	-	end	1 *					244
Q96KC2 UniProt NPD GO	ARL5B_HUMAN	ADP-ribosylation factor-like protein 5B (ADP-ribosylation factor-like protein 8)	0.02	-	cyt	0			608909	1YZG	179
Q9D4P0 UniProt NPD GO	ARL5B_MOUSE	ADP-ribosylation factor-like protein 5B (ADP-ribosylation factor-like protein 8)	0.02	-	cyt	0					179
O88848 UniProt NPD GO	ARL6_MOUSE	ADP-ribosylation factor-like protein 6	0.02	-	cyt	0	Cytoplasm	cytoplasm [IDA] membrane [IDA]			186
P81073 UniProt NPD GO	AMPD1_CHICK	AMP deaminase 1 (EC 3.5.4.6) (Myoadenylate deaminase) (AMP deaminase isoform M) (Fragment)	0.02	-	mit	0					26
P47795 UniProt NPD GO	AP1M_DISOM	AP-1 complex subunit mu (Clathrin coat assembly protein AP47 homolog) (Clathrin coat-associated prot ...	0.02	-	mit	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				418
P53680 UniProt NPD GO	AP2S1_HUMAN	AP-2 complex subunit sigma-1 (Adapter-related protein complex 2 sigma-1 subunit) (Clathrin coat asse ...	0.02	-	mit	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane	AP-2 adaptor complex [TAS]	602242		142
P62743 UniProt NPD GO	AP2S1_MOUSE	AP-2 complex subunit sigma-1 (Adapter-related protein complex 2 sigma-1 subunit) (Sigma-adaptin 3b) ...	0.02	-	mit	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane			1GW5	142
Q5R940 UniProt NPD GO	AP2S1_PONPY	AP-2 complex subunit sigma-1 (Adapter-related protein complex 2 sigma-1 subunit) (Sigma-adaptin 3b) ...	0.02	-	mit	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane (By ...				142
P62744 UniProt NPD GO	AP2S1_RAT	AP-2 complex subunit sigma-1 (Adapter-related protein complex 2 sigma-1 subunit) (Sigma-adaptin 3b) ...	0.02	-	mit	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane	AP-2 adaptor complex [IDA]			142
Q9WVL1 UniProt NPD GO	AP4S1_MOUSE	AP-4 complex subunit sigma-1 (Adapter-related protein complex 4 sigma-1 subunit) (Sigma subunit of A ...	0.02	-	cyt	0	Golgi apparatus; trans-Golgi network (By similarity). Associated with the trans-Golgi network. Found ...	Golgi trans face [TAS]			144

You are viewing entries 82201 to 82250 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.