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
Q27665 UniProt NPD GO	K6PF_HAECO	6-phosphofructokinase (EC 2.7.1.11) (Phosphofructokinase) (Phosphohexokinase)	0.15	-	mit	0					789
P17858 UniProt NPD GO	K6PL_HUMAN	6-phosphofructokinase, liver type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phospho ...	0.15	-	cyt	0		6-phosphofructokinase complex [IDA]	171860		779
P51349 UniProt NPD GO	CH60_PORPU	60 kDa chaperonin (Protein Cpn60) (groEL protein)	0.15	-	cyt	0	Plastid; chloroplast				528
Q90YX1 UniProt NPD GO	RLA0_ICTPU	60S acidic ribosomal protein P0 (L10E)	0.15	-	cyt	0					317
Q9SPB3 UniProt NPD GO	RL10_VITRI	60S ribosomal protein L10 (QM protein homolog)	0.15	-	nuc	0					220
Q6FRF5 UniProt NPD GO	RL10A_CANGA	60S ribosomal protein L10a	0.15	+	nuc	0					217
P59230 UniProt NPD GO	R10A2_ARATH	60S ribosomal protein L10a-2	0.15	+	nuc	0					216
Q3T0U2 UniProt NPD GO	RL14_BOVIN	60S ribosomal protein L14	0.15	-	nuc	0					213
P36528 UniProt NPD GO	RM17_YEAST	60S ribosomal protein L17, mitochondrial precursor (YmL17/YmL30)	0.15	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			281
O22644 UniProt NPD GO	RL23A_FRIAG	60S ribosomal protein L23A	0.15	-	nuc	0					154
P46776 UniProt NPD GO	RL27A_HUMAN	60S ribosomal protein L27a	0.15	+	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	603637		147
Q5R1X0 UniProt NPD GO	RL27A_PANTR	60S ribosomal protein L27a	0.15	+	mit	0					147
Q5REY2 UniProt NPD GO	RL27A_PONPY	60S ribosomal protein L27a	0.15	+	mit	0					147
P36534 UniProt NPD GO	RM40_YEAST	60S ribosomal protein L40, mitochondrial precursor (YmL40)	0.15	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			297
Q42064 UniProt NPD GO	RL83_ARATH	60S ribosomal protein L8-3	0.15	-	mit	0					258
Q05866 UniProt NPD GO	GRP78_PLAFO	78 kDa glucose-regulated protein homolog precursor (GRP 78)	0.15	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				655
P59769 UniProt NPD GO	GRP78_ASPAW	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.15	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum lumen [NAS]			672
P83617 UniProt NPD GO	GRP78_ASPKA	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.15	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum lumen [ISS]			672
P83616 UniProt NPD GO	GRP78_ASPNG	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.15	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum lumen [NAS]			672
P16474 UniProt NPD GO	GRP78_YEAST	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.15	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [IDA] endoplasmic reticulum lumen [TAS]			682
P49382 UniProt NPD GO	ADT_KLULA	ADP,ATP carrier protein (ADP/ATP translocase) (Adenine nucleotide translocator) (ANT)	0.15	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				305
Q09188 UniProt NPD GO	ADT_SCHPO	ADP,ATP carrier protein (ADP/ATP translocase) (Adenine nucleotide translocator) (ANT)	0.15	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IGI]			322
P31167 UniProt NPD GO	ADT1_ARATH	ADP,ATP carrier protein 1, mitochondrial precursor (ADP/ATP translocase 1) (Adenine nucleotide trans ...	0.15	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				381
O08697 UniProt NPD GO	ARL2_RAT	ADP-ribosylation factor-like protein 2	0.15	-	nuc	0		cytosol [IDA] Golgi apparatus [IDA]			184
Q00275 UniProt NPD GO	ATP6_APILI	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.15	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P14092 UniProt NPD GO	ATP6_CHICK	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.15	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50681 UniProt NPD GO	ATP6_COTJA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.15	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q8SPH6 UniProt NPD GO	ATP5J_MACFA	ATP synthase coupling factor 6, mitochondrial precursor (EC 3.6.3.14) (ATPase subunit F6)	0.15	-	mit	0					108
P30400 UniProt NPD GO	ATPE_CUSRE	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.15	-	cyt	0	Plastid; plastid thylakoid membrane; peripheral membrane protein (By similarity)				136
P06285 UniProt NPD GO	ATPE_MARPO	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.15	-	pox	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				135
P41623 UniProt NPD GO	ATPE_PINTH	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.15	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
P00834 UniProt NPD GO	ATPE_TOBAC	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.15	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				133
P56135 UniProt NPD GO	ATPK_MOUSE	ATP synthase f chain, mitochondrial (EC 3.6.3.14)	0.15	+	nuc	1		mitochondrion [IDA] proton-transporting ATP synthase complex (s... [ISS]			87
O99598 UniProt NPD GO	ATP8_ARTJA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.15	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q9XPI2 UniProt NPD GO	ATP8_CHEMY	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.15	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				61
P24949 UniProt NPD GO	ATP8_MICPE	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.15	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
P05626 UniProt NPD GO	ATPF_YEAST	ATP synthase subunit 4, mitochondrial precursor (EC 3.6.3.14)	0.15	-	nuc	0	Mitochondrion	proton-transporting ATP synthase, stator st... [TAS]			244
P30392 UniProt NPD GO	ATPA_EUGGR	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.15	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				506
P37211 UniProt NPD GO	ATPA_NEUCR	ATP synthase subunit alpha, mitochondrial precursor (EC 3.6.3.14)	0.15	-	mit	0	Mitochondrion				551
P37399 UniProt NPD GO	ATPBM_DAUCA	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.15	-	mit	0	Mitochondrion				547
P22027 UniProt NPD GO	ATP5S_BOVIN	ATP synthase subunit s, mitochondrial precursor (ATP synthase coupling factor B) (Mitochondrial ATP ...	0.15	-	cyt	0	Mitochondrion				200
Q6BRN4 UniProt NPD GO	IF4A_DEBHA	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.15	-	cyt	0	Cytoplasm (By similarity)				397
Q5RBI4 UniProt NPD GO	ABHD5_PONPY	Abhydrolase domain-containing protein 5	0.15	-	cyt	0	Cytoplasm (By similarity). Colocalizated with PLIN and ADRP on the surface of lipid droplets. The lo ...				349
P33738 UniProt NPD GO	MS2B_DROMA	Accessory gland-specific peptide 26Ab precursor (Male accessory gland secretory protein 355B)	0.15	-	exc	0	Secreted protein; extracellular space				90
Q6K2E8 UniProt NPD GO	ILV1_ORYSA	Acetolactate synthase 1, chloroplast precursor (EC 2.2.1.6) (Acetohydroxy-acid synthase 1)	0.15	-	mit	0	Plastid; chloroplast (By similarity)				644
P27818 UniProt NPD GO	ILV1_BRANA	Acetolactate synthase 1, chloroplast precursor (EC 2.2.1.6) (Acetolactate synthase I) (Acetohydroxy- ...	0.15	-	mit	0	Plastid; chloroplast				655
O47039 UniProt NPD GO	ACCD_PICAB	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.15	-	cyt	0	Plastid; chloroplast				319
O60011 UniProt NPD GO	ACS1_KLULA	Acetyl-coenzyme A synthetase 1 (EC 6.2.1.1) (Acetate--CoA ligase 1) (Acyl-activating enzyme 1)	0.15	-	nuc	0	Microsome (Potential)				707
Q6FXI2 UniProt NPD GO	ACS2_CANGA	Acetyl-coenzyme A synthetase 2 (EC 6.2.1.1) (Acetate--CoA ligase 2) (Acyl-activating enzyme 2)	0.15	-	nuc	0					683
P49579 UniProt NPD GO	ACHB_XENLA	Acetylcholine receptor protein subunit beta precursor (Fragment)	0.15	-	end	4	Membrane; multi-pass membrane protein				489

You are viewing entries 56551 to 56600 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.