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
P13506 UniProt NPD GO	EPD1_CARAU	Ependymin-1 precursor (Ependymin I) (EPD-I)	0.01	-	exc	0	Secreted protein				215
O75715 UniProt NPD GO	GPX5_HUMAN	Epididymal secretory glutathione peroxidase precursor (EC 1.11.1.9) (Epididymis-specific glutathione ...	0.01	-	exc	0	Secreted protein		603435		221
P28714 UniProt NPD GO	GPX5_MACFA	Epididymal secretory glutathione peroxidase precursor (EC 1.11.1.9) (Epididymis-specific glutathione ...	0.01	-	exc	0	Secreted protein				221
Q6JVE9 UniProt NPD GO	LCN8_HUMAN	Epididymal-specific lipocalin-8 precursor	0.01	-	mit	0	Secreted protein (By similarity)				175
P54850 UniProt NPD GO	EMP1_RABIT	Epithelial membrane protein 1 (EMP-1) (Tumor-associated membrane protein) (Squamous cell-specific pr ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein				160
O54698 UniProt NPD GO	S29A1_RAT	Equilibrative nucleoside transporter 1 (Equilibrative nitrobenzylmercaptopurine riboside-sensitive n ...	0.01	-	end	11 *	Membrane; multi-pass membrane protein				456
Q9BZD2 UniProt NPD GO	S29A3_HUMAN	Equilibrative nucleoside transporter 3 (Solute carrier family 29 member 3)	0.01	-	end	11	Membrane; multi-pass membrane protein				475
Q99P65 UniProt NPD GO	S29A3_MOUSE	Equilibrative nucleoside transporter 3 (Solute carrier family 29 member 3)	0.01	-	end	11	Membrane; multi-pass membrane protein				475
P05088 UniProt NPD GO	PHAE_PHAVU	Erythroagglutinating phytohemagglutinin precursor (PHA-E)	0.01	-	exc	0					275
P10095 UniProt NPD GO	EST5_DROMO	Esterase-5 (EC 3.1.1.1) (Fragment)	0.01	-	cyt	0					38
P37058 UniProt NPD GO	DHB3_HUMAN	Estradiol 17-beta-dehydrogenase 3 (EC 1.1.1.62) (17-beta-HSD 3) (Testicular 17-beta-hydroxysteroid d ...	0.01	-	nuc	3 *		microsome [TAS]	605573		310
Q9GME3 UniProt NPD GO	DHB8_CALJA	Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62) (17-beta-HSD 8) (17-beta-hydroxysteroid dehydrogenas ...	0.01	-	cyt	0					134
Q9XT00 UniProt NPD GO	DHB8_PIG	Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62) (17-beta-HSD 8) (17-beta-hydroxysteroid dehydrogenas ...	0.01	-	exc	0					259
Q9D4V0 UniProt NPD GO	EKI1_MOUSE	Ethanolamine kinase 1 (EC 2.7.1.82) (EKI 1) (Fragment)	0.01	-	mit	1 *	Cytoplasm (By similarity)				412
P20461 UniProt NPD GO	IF2G_PIG	Eukaryotic translation initiation factor 2 subunit 3 (Eukaryotic translation initiation factor 2 sub ...	0.01	-	cyt	0					22
P33887 UniProt NPD GO	IF2G_RABIT	Eukaryotic translation initiation factor 2 subunit 3 (Eukaryotic translation initiation factor 2 sub ...	0.01	-	cyt	0					152
P07260 UniProt NPD GO	IF4E_YEAST	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein) (eIF-4F 25 k ...	0.01	-	cyt	0		cytoplasm [IDA] eukaryotic translation initiation factor 4F... [TAS] nucleus [IDA] ribosome [TAS]		1RF8	213
Q9AXQ7 UniProt NPD GO	IF5A_DIACA	Eukaryotic translation initiation factor 5A (eIF-5A)	0.01	-	cyt	0					160
Q9AXJ4 UniProt NPD GO	IF5A_MANES	Eukaryotic translation initiation factor 5A (eIF-5A)	0.01	-	nuc	0					160
P62924 UniProt NPD GO	IF5A_SPOEX	Eukaryotic translation initiation factor 5A (eIF-5A)	0.01	-	cyt	0					160
P62925 UniProt NPD GO	IF5A_SPOFR	Eukaryotic translation initiation factor 5A (eIF-5A)	0.01	-	cyt	0					160
P13651 UniProt NPD GO	IF5A_DICDI	Eukaryotic translation initiation factor 5A (eIF-5A) (eIF-4D)	0.01	-	cyt	0					169
P26564 UniProt NPD GO	IF5A1_MEDSA	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (eIF-4D)	0.01	-	cyt	0					161
Q6EWQ7 UniProt NPD GO	IF5A1_BOVIN	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (eIF-5A1) (Eukaryotic initiation factor 5A ...	0.01	-	mit	0					153
P63242 UniProt NPD GO	IF5A1_MOUSE	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (eIF-5A1) (Eukaryotic initiation factor 5A ...	0.01	-	mit	0		cytoplasm [IDA] nucleus [IDA]			153
Q3T1J1 UniProt NPD GO	IF5A1_RAT	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (eIF-5A1) (Eukaryotic initiation factor 5A ...	0.01	-	mit	0					153
P63241 UniProt NPD GO	IF5A1_HUMAN	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (eIF-5A1) (Eukaryotic initiation factor 5A ...	0.01	-	mit	0			600187	1FH4	153
Q945F4 UniProt NPD GO	IF5A2_MEDSA	Eukaryotic translation initiation factor 5A-2 (eIF-5A-2)	0.01	-	cyt	0					159
Q07460 UniProt NPD GO	IF5A2_CHICK	Eukaryotic translation initiation factor 5A-2 (eIF-5A-2) (eIF-5A2) (Eukaryotic initiation factor 5A ...	0.01	-	cyt	0					152
Q9C505 UniProt NPD GO	IF5A3_ARATH	Eukaryotic translation initiation factor 5A-3 (eIF-5A-3)	0.01	-	cyt	0					158
P56336 UniProt NPD GO	IF5A4_SOLTU	Eukaryotic translation initiation factor 5A-4 (eIF-5A-4) (eIF-4D)	0.01	-	nuc	0					159
O22290 UniProt NPD GO	IF6_ARATH	Eukaryotic translation initiation factor 6 (eIF-6)	0.01	-	cyt	0					247
O57321 UniProt NPD GO	EAA1_AMBTI	Excitatory amino acid transporter 1 (SEAAT1)	0.01	-	end	9 *	Membrane; multi-pass membrane protein				543
P43004 UniProt NPD GO	EAA2_HUMAN	Excitatory amino acid transporter 2 (Sodium-dependent glutamate/aspartate transporter 2)	0.01	-	end	9 *	Membrane; multi-pass membrane protein	membrane fraction [TAS]	600300		574
P43006 UniProt NPD GO	EAA2_MOUSE	Excitatory amino acid transporter 2 (Sodium-dependent glutamate/aspartate transporter 2) (GLT-1)	0.01	-	end	9 *	Membrane; multi-pass membrane protein				572
P31596 UniProt NPD GO	EAA2_RAT	Excitatory amino acid transporter 2 (Sodium-dependent glutamate/aspartate transporter 2) (GLUT-R) (G ...	0.01	-	end	9 *	Membrane; multi-pass membrane protein	dendritic shaft [IDA] presynaptic membrane [IDA]			573
Q9N1R2 UniProt NPD GO	EAA4_CANFA	Excitatory amino acid transporter 4 (Sodium-dependent glutamate/aspartate transporter)	0.01	-	end	8	Membrane; multi-pass membrane protein				564
P48664 UniProt NPD GO	EAA4_HUMAN	Excitatory amino acid transporter 4 (Sodium-dependent glutamate/aspartate transporter)	0.01	-	end	8	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	600637		564
P56637 UniProt NPD GO	SIXE_BUTJU	Excitatory insect toxin Bjxtr-IT precursor (Bj-xtrIT) (BjxtrIT)	0.01	-	mit	0	Secreted protein			1BCG	94
P20394 UniProt NPD GO	EXE3_HELHO	Exendin-3	0.01	-	nuc	0	Secreted protein				39
Q9M0C2 UniProt NPD GO	EXPR2_ARATH	Expansin-related protein 2 precursor (AtEXPR2) (Ath-ExpGamma-1.1)	0.01	-	exc	1 *					123
P83122 UniProt NPD GO	GLB1_PHEHI	Extracellular globin-1 (Globin I) (Erythrocruorin)	0.01	-	cyt	0	Secreted protein				140
P13578 UniProt NPD GO	GLB3_TYLHE	Extracellular globin-2B (Extracellular globin IIB) (Erythrocruorin)	0.01	-	cyt	0					148
P02220 UniProt NPD GO	GLB4_TYLHE	Extracellular globin-2C (Extracellular globin IIC) (Erythrocruorin)	0.01	-	cyt	0	Secreted protein				149
P51547 UniProt NPD GO	SODE_HAECO	Extracellular superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1) (EC-SOD)	0.01	-	mit	0	Secreted protein; extracellular space				183
Q8LEK2 UniProt NPD GO	FA18_ARATH	FAM18-like protein At1g09330	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				186
Q4WLV6 UniProt NPD GO	FKB1A_ASPFU	FK506-binding protein 1A (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyc ...	0.01	-	cyt	0	Cytoplasm (By similarity)				112
O42123 UniProt NPD GO	FKB1A_XENLA	FK506-binding protein 1A (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (12 ...	0.01	-	cyt	0	Cytoplasm (By similarity)				107
P0C1J4 UniProt NPD GO	FKB2A_RHIOR	FK506-binding protein 2A precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rota ...	0.01	-	end	2 *	Membrane; single-pass membrane protein (Potential)				167
P25089 UniProt NPD GO	FPRL2_HUMAN	FMLP-related receptor II (FMLP-R-II) (Formylpeptide receptor-like 2)	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	136539		353

You are viewing entries 88201 to 88250 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.