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
Q8SRW8 UniProt NPD GO	RL21_ENCCU	60S ribosomal protein L21	0.33	-	mit	0					160
P46778 UniProt NPD GO	RL21_HUMAN	60S ribosomal protein L21	0.33	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	603636		159
O09167 UniProt NPD GO	RL21_MOUSE	60S ribosomal protein L21	0.33	-	mit	0					159
P91914 UniProt NPD GO	RL27_CAEEL	60S ribosomal protein L27	0.33	+	cyt	0					136
Q9XGL4 UniProt NPD GO	RL31_CYAPA	60S ribosomal protein L31	0.33	-	cyt	0					119
Q9IA76 UniProt NPD GO	RL31_PAROL	60S ribosomal protein L31	0.33	-	nuc	0					124
O22608 UniProt NPD GO	RL5_DUNSA	60S ribosomal protein L5	0.33	-	mit	0					271
P05737 UniProt NPD GO	RL7A_YEAST	60S ribosomal protein L7-A (L6A) (YL8A) (RP11)	0.33	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	243
Q12213 UniProt NPD GO	RL7B_YEAST	60S ribosomal protein L7-B (L6B) (YL8B)	0.33	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			243
P36639 UniProt NPD GO	8ODP_HUMAN	7,8-dihydro-8-oxoguanine triphosphatase (EC 3.1.6.-) (8-oxo-dGTPase) (Nucleoside diphosphate-linked ...	0.33	-	cyt	0			600312	1IRY	197
Q8BQU3 UniProt NPD GO	ACN9_MOUSE	ACN9 protein homolog, mitochondrial precursor	0.33	-	mit	0	Mitochondrion (Potential)	mitochondrial intermembrane space [ISS]			125
Q8K410 UniProt NPD GO	ADA32_MOUSE	ADAM 32 precursor (A disintegrin and metalloproteinase domain 32)	0.33	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				750
P61208 UniProt NPD GO	ARL4C_MOUSE	ADP-ribosylation factor-like protein 4C (ADP-ribosylation factor-like 7)	0.33	+	mit	0	Nucleus (By similarity)				192
P56559 UniProt NPD GO	ARL4C_HUMAN	ADP-ribosylation factor-like protein 4C (ADP-ribosylation factor-like protein 7) (ADP-ribosylation f ...	0.33	+	mit	0	Nucleus (By similarity)	nucleus [TAS]	604787		192
Q2PWT8 UniProt NPD GO	AP4M1_RAT	AP-4 complex subunit mu-1 (Adapter-related protein complex 4 mu-1 subunit) (Mu subunit of AP-4) (AP- ...	0.33	-	nuc	0	Golgi apparatus; trans-Golgi network. Associated with the trans-Golgi network. Found in soma and den ...				453
O74754 UniProt NPD GO	ATPG_SCHPO	ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)	0.33	-	mit	0	Mitochondrion (By similarity)				301
P24783 UniProt NPD GO	DBP2_YEAST	ATP-dependent RNA helicase DBP2 (EC 3.6.1.-) (DEAD box protein 2) (p68-like protein)	0.33	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			546
Q5KJJ2 UniProt NPD GO	FAL1_CRYNE	ATP-dependent RNA helicase FAL1 (EC 3.6.1.-)	0.33	-	cyt	0	Nucleus; nucleolus (By similarity)				396
Q2UPY3 UniProt NPD GO	IF4A_ASPOR	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.33	-	cyt	0	Cytoplasm (By similarity)				421
P16641 UniProt NPD GO	SMC7_SCHMA	ATP:guanidino kinase SMC74 (EC 2.7.3.-) (ATP:guanidino phosphotransferase)	0.33	-	cyt	0					675
Q8NBU5 UniProt NPD GO	ATAD1_HUMAN	ATPase family AAA domain-containing protein 1	0.33	-	mit	0					361
Q9D5T0 UniProt NPD GO	ATAD1_MOUSE	ATPase family AAA domain-containing protein 1	0.33	-	mit	0					361
Q505J9 UniProt NPD GO	ATAD1_RAT	ATPase family AAA domain-containing protein 1	0.33	-	mit	0					361
Q38710 UniProt NPD GO	TPSDV_ABIGR	Abietadiene synthase, chloroplast precursor ((-)-abieta-7(8),13(14)-diene synthase) (Abietadiene cyc ...	0.33	-	nuc	0	Plastid; chloroplast (By similarity)				868
Q6CUY0 UniProt NPD GO	ACN9_KLULA	Acetate non-utilizing protein 9, mitochondrial precursor	0.33	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				129
Q9P7Y2 UniProt NPD GO	ACN9_SCHPO	Acetate non-utilizing protein 9, mitochondrial precursor	0.33	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				115
Q04401 UniProt NPD GO	ACN9_YEAST	Acetate non-utilizing protein 9, mitochondrial precursor	0.33	-	mit	0	Mitochondrion; mitochondrial intermembrane space	mitochondrial intermembrane space [IDA]			133
P12218 UniProt NPD GO	ACCD_ORYSA	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.33	-	mit	0	Plastid; chloroplast				106
Q00761 UniProt NPD GO	ACCD_PHYPA	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.33	-	cyt	0	Plastid; chloroplast				315
P04760 UniProt NPD GO	ACHG_MOUSE	Acetylcholine receptor protein subunit gamma precursor	0.33	-	end	4	Membrane; multi-pass membrane protein	Golgi apparatus [IDA] plasma membrane [IDA] postsynaptic membrane [IDA]			519
P48182 UniProt NPD GO	ACR2_CAEEL	Acetylcholine receptor subunit beta-type acr-2 precursor	0.33	-	end	4	Membrane; multi-pass membrane protein				575
Q03637 UniProt NPD GO	COLQ_TORMA	Acetylcholinesterase collagenic tail peptide precursor (AChE Q subunit)	0.33	-	exc	0					471
Q06990 UniProt NPD GO	ASPX_PAPHA	Acrosomal protein SP-10 precursor (Acrosomal vesicle protein 1)	0.33	-	exc	0	Acrosome. Nascent acrosomal vesicle of Golgi phase spermatids				285
P30174 UniProt NPD GO	ADF_BRANA	Actin-depolymerizing factor (ADF) (Fragment)	0.33	-	cyt	0					126
Q9PW36 UniProt NPD GO	ACLC_AGKAC	Acutolysin-C precursor (EC 3.4.24.-)	0.33	-	nuc	0	Secreted protein				417
P07872 UniProt NPD GO	ACOX1_RAT	Acyl-coenzyme A oxidase 1, peroxisomal (EC 1.3.3.6) (Palmitoyl-CoA oxidase) (AOX) [Contains: Acyl-Co ...	0.33	-	pox	0	Peroxisome			2DDH	661
Q8WYK0 UniProt NPD GO	ACO12_HUMAN	Acyl-coenzyme A thioesterase 12 (EC 3.1.2.1) (Acyl-CoA thioesterase 12) (Acyl-CoA thioester hydrolas ...	0.33	-	cyt	0	Cytoplasm (By similarity)	cytosol [ISS]			555
P06750 UniProt NPD GO	AGGL_RICCO	Agglutinin precursor (RCA) [Contains: Agglutinin A chain (EC 3.2.2.22) (rRNA N-glycosidase); Aggluti ...	0.33	-	cyt	0				1RZO	564
P25304 UniProt NPD GO	AGRN_RAT	Agrin precursor	0.33	-	nuc	1 *	Synaptic basal lamina at the neuromuscular junction	basal lamina [ISS]			1959
Q06834 UniProt NPD GO	ASR1_YEAST	Alcohol-sensitive RING finger protein 1	0.33	-	nuc	0	Cytoplasm. Predominantly. Nucleus. Accumulates in the nucleus specifically upon alcohol stress. Shut ...	cytoplasm [IDA] nucleus [IDA]			288
P31756 UniProt NPD GO	ALLN_ALLAS	Alliin lyase precursor (EC 4.4.1.4) (Alliinase) (Cysteine sulphoxide lyase) (Fragment)	0.33	-	mit	0	Vacuole				447
P55009 UniProt NPD GO	AIF1_RAT	Allograft inflammatory factor 1 (AIF-1) (Ionized calcium-binding adapter molecule 1) (Microglia resp ...	0.33	-	nuc	0					147
Q91311 UniProt NPD GO	CRYAA_RANCA	Alpha crystallin A chain	0.33	-	nuc	0					173
Q01338 UniProt NPD GO	ADA2A_MOUSE	Alpha-2A adrenergic receptor (Alpha-2A adrenoceptor) (Alpha-2A adrenoreceptor) (Alpha-2AAR)	0.33	-	end	7 *	Membrane; multi-pass membrane protein				450
P18871 UniProt NPD GO	ADA2A_PIG	Alpha-2A adrenergic receptor (Alpha-2A adrenoceptor) (Alpha-2A adrenoreceptor) (Alpha-2AAR)	0.33	-	end	7 *	Membrane; multi-pass membrane protein				450
P45561 UniProt NPD GO	AMEL_PIG	Amelogenin precursor (Amelogenin 173A/173B) (Leucine-rich amelogenin peptide) (LRAP)	0.33	-	exc	0	Secreted protein; extracellular space; extracellular matrix				189
Q708S8 UniProt NPD GO	ACC2A_BRARE	Amiloride-sensitive cation channel 2-A, neuronal (Acid-sensing ion channel 1.1) (ZASIC1.1)	0.33	-	mit	1	Cell membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [IDA]			557
Q9TSZ7 UniProt NPD GO	GCST_CANFA	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.33	-	mit	0	Mitochondrion (By similarity)				403
Q8R1C9 UniProt NPD GO	APBB3_MOUSE	Amyloid beta A4 precursor protein-binding family B member 3	0.33	-	cyt	0					486
Q95241 UniProt NPD GO	A4_SAISC	Amyloid beta A4 protein precursor (APP) (ABPP) (Alzheimer disease amyloid protein homolog) [Contains ...	0.33	-	end	1	Membrane; single-pass type I membrane protein (By similarity). Cell surface protein that rapidly bec ...			1RW6	751

You are viewing entries 37301 to 37350 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.