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
Q00583 UniProt NPD GO	HMDH3_HEVBR	3-hydroxy-3-methylglutaryl-coenzyme A reductase 3 (EC 1.1.1.34) (HMG-CoA reductase 3)	0.20	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Mitochondrion; m ...				586
P27796 UniProt NPD GO	THIK_YEAST	3-ketoacyl-CoA thiolase, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase) (Acetyl-CoA acyltra ...	0.20	-	nuc	0	Peroxisome			1PXT	417
Q99N90 UniProt NPD GO	RM36_MOUSE	39S ribosomal protein L36, mitochondrial precursor (L36mt) (MRP-L36)	0.20	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IDA]			102
P33442 UniProt NPD GO	RS3A_YEAST	40S ribosomal protein S1-A (RP10A)	0.20	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			254
Q08745 UniProt NPD GO	RS10A_YEAST	40S ribosomal protein S10-A	0.20	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			105
P14130 UniProt NPD GO	RS14_DROME	40S ribosomal protein S14	0.20	-	cyt	0					151
P13471 UniProt NPD GO	RS14_RAT	40S ribosomal protein S14	0.20	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [ISS]			150
Q9FIX6 UniProt NPD GO	RS15E_ARATH	40S ribosomal protein S15-5	0.20	-	cyt	0	Cytoplasm				149
Q86CT3 UniProt NPD GO	RS21_BRABE	40S ribosomal protein S21	0.20	-	nuc	0					85
P26782 UniProt NPD GO	RS24_YEAST	40S ribosomal protein S24 (RP50)	0.20	-	mit	0		cytosolic small ribosomal subunit (sensu Eu... [TAS] mitochondrion [IDA]			134
Q95Y04 UniProt NPD GO	RS28_CAEEL	40S ribosomal protein S28	0.20	-	mit	0					65
P49204 UniProt NPD GO	RS4_ARATH	40S ribosomal protein S4	0.20	-	mit	0	Cytoplasm (By similarity)				262
Q9VA91 UniProt NPD GO	RS7_DROME	40S ribosomal protein S7	0.20	-	nuc	0					194
O22518 UniProt NPD GO	RSSA_SOYBN	40S ribosomal protein SA (p40)	0.20	-	cyt	0	Cytoplasm				310
P80386 UniProt NPD GO	AAKB1_RAT	5'-AMP-activated protein kinase subunit beta-1 (AMPK beta-1 chain) (AMPKb) (5'-AMP-activated protein ...	0.20	-	nuc	0				1Z0N	269
Q9MYP4 UniProt NPD GO	AAKG3_PIG	5'-AMP-activated protein kinase subunit gamma-3 (AMPK gamma-3 chain) (AMPK gamma3)	0.20	-	end	0					514
Q8C5P5 UniProt NPD GO	NT5D1_MOUSE	5'-nucleotidase domain-containing protein 1 (5'-nucleotidase cytosolic II-like protein 1)	0.20	-	cyt	0					467
P19327 UniProt NPD GO	5HT1A_RAT	5-hydroxytryptamine 1A receptor (5-HT-1A) (Serotonin receptor 1A) (5-HT1A)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				422
Q6XXY0 UniProt NPD GO	5HT1A_VULVU	5-hydroxytryptamine 1A receptor (5-HT-1A) (Serotonin receptor 1A) (5-HT1A)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				423
P49144 UniProt NPD GO	5HT1B_RABIT	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B) (5-HT-1D-beta)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				390
P30966 UniProt NPD GO	5HT5A_MOUSE	5-hydroxytryptamine 5A receptor (5-HT-5A) (Serotonin receptor 5A) (5-HT-5)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				357
P35364 UniProt NPD GO	5HT5A_RAT	5-hydroxytryptamine 5A receptor (5-HT-5A) (Serotonin receptor 5A) (REC17)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				357
Q9LRN8 UniProt NPD GO	RK3B_ARATH	50S ribosomal protein L3-2, chloroplast precursor	0.20	-	mit	0	Plastid; chloroplast (Potential)	mitochondrion [IDA]			324
Q93VT9 UniProt NPD GO	RL101_ARATH	60S ribosomal protein L10-1	0.20	-	mit	0		cytosolic ribosome (sensu Eukaryota) [IDA]			220
Q08770 UniProt NPD GO	RL102_ARATH	60S ribosomal protein L10-2 (Wilms tumor suppressor protein homolog)	0.20	-	mit	0					221
Q93W22 UniProt NPD GO	RL103_ARATH	60S ribosomal protein L10-3	0.20	-	mit	0					221
Q63507 UniProt NPD GO	RL14_RAT	60S ribosomal protein L14	0.20	-	nuc	0					213
P46288 UniProt NPD GO	RM27_CRYNE	60S ribosomal protein L27, mitochondrial precursor	0.20	-	mit	0	Mitochondrion (By similarity)				183
Q9VZS5 UniProt NPD GO	RL28_DROME	60S ribosomal protein L28	0.20	-	nuc	0					144
P46780 UniProt NPD GO	RL28_XENLA	60S ribosomal protein L28 (Fragment)	0.20	-	nuc	0					33
Q6P0V6 UniProt NPD GO	RL8_BRARE	60S ribosomal protein L8	0.20	-	mit	0	Cytoplasm				256
Q5R7Y8 UniProt NPD GO	RL8_PONPY	60S ribosomal protein L8	0.20	-	mit	0	Cytoplasm				256
Q6PBF0 UniProt NPD GO	RL8_XENTR	60S ribosomal protein L8	0.20	-	mit	0	Cytoplasm				256
P32388 UniProt NPD GO	RM49_YEAST	60S ribosomal protein MRP49, mitochondrial precursor	0.20	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			137
P36604 UniProt NPD GO	GRP78_SCHPO	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.20	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum lumen [IDA] nuclear membrane [IDA]			663
Q16956 UniProt NPD GO	GRP78_APLCA	78 kDa glucose-regulated protein precursor (GRP 78) (BiP) (Protein 1603)	0.20	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				667
Q90593 UniProt NPD GO	GRP78_CHICK	78 kDa glucose-regulated protein precursor (GRP 78) (Immunoglobulin heavy chain-binding protein) (Bi ...	0.20	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	cell surface [ISS] intracellular [ISS]			652
P14928 UniProt NPD GO	LEA1_HORVU	ABA-inducible protein PHV A1	0.20	-	nuc	0					213
Q9PSZ3 UniProt NPD GO	ADA11_XENLA	ADAM 11 (A disintegrin and metalloproteinase domain 11) (Metalloproteinase-like, disintegrin-like, a ...	0.20	-	nuc	1	Membrane; single-pass type I membrane protein				452
Q41629 UniProt NPD GO	ADT1_WHEAT	ADP,ATP carrier protein 1, mitochondrial precursor (ADP/ATP translocase 1) (Adenine nucleotide trans ...	0.20	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				331
P25083 UniProt NPD GO	ADT1_SOLTU	ADP,ATP carrier protein, mitochondrial precursor (ADP/ATP translocase) (Adenine nucleotide transloca ...	0.20	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				386
Q66HA6 UniProt NPD GO	ARL8B_RAT	ADP-ribosylation factor-like protein 8B	0.20	-	cyt	0	Endosome; late endosome (By similarity). Lysosome (By similarity). Alternatively, may localize with ...				186
Q9NVJ2 UniProt NPD GO	ARL8B_HUMAN	ADP-ribosylation factor-like protein 8B (ADP-ribosylation factor-like protein 10C) (Novel small G pr ...	0.20	-	cyt	0	Endosome; late endosome. Lysosome. According to Ref.1 it localizes with microtubules at the spindle ...	cytoplasm [IDA] midbody [IDA] spindle midzone [IDA]		2AL7	186
Q9CQW2 UniProt NPD GO	ARL8B_MOUSE	ADP-ribosylation factor-like protein 8B (ADP-ribosylation factor-like protein 10C) (Novel small G pr ...	0.20	-	cyt	0	Endosome; late endosome (By similarity). Lysosome (By similarity). Alternatively, may localize with ...				186
Q10567 UniProt NPD GO	AP1B1_HUMAN	AP-1 complex subunit beta-1 (Adapter-related protein complex 1 beta-1 subunit) (Beta-adaptin 1) (Ada ...	0.20	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...		600157		949
O35643 UniProt NPD GO	AP1B1_MOUSE	AP-1 complex subunit beta-1 (Adapter-related protein complex 1 beta-1 subunit) (Beta-adaptin 1) (Ada ...	0.20	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	Golgi trans face [TAS]		1W63	943
O43079 UniProt NPD GO	AP1B1_SCHPO	AP-1 complex subunit beta-1 (Beta(1)-adaptin) (Clathrin assembly protein large beta-1 chain) (Clathr ...	0.20	-	mit	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane (By ...				683
P35603 UniProt NPD GO	AP2M_CAEEL	AP-2 complex subunit mu (Clathrin coat assembly protein AP50) (Clathrin coat-associated protein AP50 ...	0.20	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane	AP-2 adaptor complex [NAS] membrane coat adaptor complex [NAS]			441
Q9JKW0 UniProt NPD GO	AR6P1_MOUSE	ARL-6-interacting protein 1 (ADP-ribosylation-like factor 6-interacting protein 1) (Aip-1) (Protein ...	0.20	-	end	4 *	Membrane; multi-pass membrane protein (By similarity). Predominantly localized to intracytoplasmic m ...	cytoplasm [IDA] cytosol [IDA] integral to membrane [IDA] translocon complex [IPI]			203
O78477 UniProt NPD GO	ATPF_GUITH	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.20	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				182

You are viewing entries 50251 to 50300 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.