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
P62275 UniProt NPD GO	RS29_RAT	40S ribosomal protein S29	0.30	-	mit	0					55
P79891 UniProt NPD GO	RS3_AMBME	40S ribosomal protein S3	0.30	-	mit	0					253
P40910 UniProt NPD GO	RS3A_CANAL	40S ribosomal protein S3aE (S1)	0.30	+	nuc	0					255
P10852 UniProt NPD GO	4F2_MOUSE	4F2 cell-surface antigen heavy chain (4F2hc)	0.30	-	nuc	1	Membrane; single-pass type II membrane protein				526
P08909 UniProt NPD GO	5HT2C_RAT	5-hydroxytryptamine 2C receptor (5-HT-2C) (Serotonin receptor 2C) (5-HT2C) (5-HTR2C) (5HT-1C)	0.30	+	end	8 *	Membrane; multi-pass membrane protein	external side of plasma membrane [IDA] plasma membrane [IMP]			460
P35365 UniProt NPD GO	5HT5B_RAT	5-hydroxytryptamine 5B receptor (5-HT-5B) (Serotonin receptor 5B) (MR22)	0.30	-	end	7	Membrane; multi-pass membrane protein				370
Q5IS65 UniProt NPD GO	5HT6R_PANTR	5-hydroxytryptamine 6 receptor (5-HT-6) (Serotonin receptor 6)	0.30	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				440
Q17239 UniProt NPD GO	5HTR_BOMMO	5-hydroxytryptamine receptor (5-HT receptor) (Serotonin receptor)	0.30	-	end	7	Membrane; multi-pass membrane protein				446
Q06030 UniProt NPD GO	RK121_SECCE	50S ribosomal protein L12-1, chloroplast precursor (CL12-1)	0.30	-	mit	0	Plastid; chloroplast				174
P30956 UniProt NPD GO	RK28_TOBAC	50S ribosomal protein L28, chloroplast precursor (CL28)	0.30	-	mit	0	Plastid; chloroplast				151
Q7RZS0 UniProt NPD GO	RL10A_NEUCR	60S ribosomal protein L10a	0.30	+	nuc	0					217
Q3T087 UniProt NPD GO	RL11_BOVIN	60S ribosomal protein L11	0.30	-	cyt	0					177
Q6QMZ8 UniProt NPD GO	RL11_CHILA	60S ribosomal protein L11	0.30	-	cyt	0					177
Q8SSG9 UniProt NPD GO	RL11_ENCCU	60S ribosomal protein L11	0.30	-	mit	0					165
Q9CXW4 UniProt NPD GO	RL11_MOUSE	60S ribosomal protein L11	0.30	-	cyt	0					177
Q29205 UniProt NPD GO	RL11_PIG	60S ribosomal protein L11	0.30	-	cyt	0					177
P62914 UniProt NPD GO	RL11_RAT	60S ribosomal protein L11	0.30	-	cyt	0					177
P62913 UniProt NPD GO	RL11_HUMAN	60S ribosomal protein L11 (CLL-associated antigen KW-12)	0.30	-	cyt	0			604175		177
Q07761 UniProt NPD GO	RL23A_TOBAC	60S ribosomal protein L23a (L25)	0.30	-	nuc	0					154
Q84WM0 UniProt NPD GO	RL292_ARATH	60S ribosomal protein L29-2	0.30	-	nuc	0					61
P49669 UniProt NPD GO	RL4_TRYBB	60S ribosomal protein L4 (L1)	0.30	+	mit	0					374
Q06090 UniProt NPD GO	RM51_YEAST	60S ribosomal protein L51, mitochondrial precursor	0.30	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			140
Q9FZ76 UniProt NPD GO	RL61_ARATH	60S ribosomal protein L6-1	0.30	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [IDA]			233
Q9TT92 UniProt NPD GO	ATS5_BOVIN	ADAMTS-5 (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 5) (ADAM-TS 5 ...	0.30	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				207
P37996 UniProt NPD GO	ARL3_RAT	ADP-ribosylation factor-like protein 3 (ARD3)	0.30	-	cyt	0					182
Q06185 UniProt NPD GO	ATP5I_MOUSE	ATP synthase e chain, mitochondrial (EC 3.6.3.14)	0.30	-	nuc	0					70
P05631 UniProt NPD GO	ATPG_BOVIN	ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)	0.30	-	nuc	0	Mitochondrion			2CK3	298
P18260 UniProt NPD GO	ATPAM_HELAN	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.30	-	cyt	0	Mitochondrion				510
P45844 UniProt NPD GO	ABCG1_HUMAN	ATP-binding cassette sub-family G member 1 (White protein homolog) (ATP-binding cassette transporter ...	0.30	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	integral to plasma membrane [IC] membrane fraction [TAS]	603076		678
Q755N4 UniProt NPD GO	DBP2_ASHGO	ATP-dependent RNA helicase DBP2 (EC 3.6.1.-)	0.30	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				557
Q4I7K4 UniProt NPD GO	DED1_GIBZE	ATP-dependent RNA helicase DED1 (EC 3.6.1.-)	0.30	+	cyt	0	Cytoplasm (By similarity)				675
Q6FJG1 UniProt NPD GO	FAL1_CANGA	ATP-dependent RNA helicase FAL1 (EC 3.6.1.-)	0.30	-	cyt	0	Nucleus; nucleolus (By similarity)				399
Q2U070 UniProt NPD GO	DBP2_ASPOR	ATP-dependent RNA helicase dbp2 (EC 3.6.1.-)	0.30	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				554
Q4TZY1 UniProt NPD GO	IRK12_BOVIN	ATP-sensitive inward rectifier potassium channel 12 (Potassium channel, inwardly rectifying subfamil ...	0.30	-	end	3	Membrane; multi-pass membrane protein				427
P52187 UniProt NPD GO	IRK12_MOUSE	ATP-sensitive inward rectifier potassium channel 12 (Potassium channel, inwardly rectifying subfamil ...	0.30	-	end	3	Membrane; multi-pass membrane protein				427
P52188 UniProt NPD GO	IRK12_RAT	ATP-sensitive inward rectifier potassium channel 12 (Potassium channel, inwardly rectifying subfamil ...	0.30	-	end	3	Membrane; multi-pass membrane protein				427
O70339 UniProt NPD GO	IRK15_CAVPO	ATP-sensitive inward rectifier potassium channel 15 (Potassium channel, inwardly rectifying subfamil ...	0.30	-	end	2	Membrane; multi-pass membrane protein				375
Q99712 UniProt NPD GO	IRK15_HUMAN	ATP-sensitive inward rectifier potassium channel 15 (Potassium channel, inwardly rectifying subfamil ...	0.30	-	mit	2	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602106		375
Q12154 UniProt NPD GO	GET3_YEAST	ATPase GET3 (EC 3.6.3.16) (Arsenical pump-driving ATPase) (Arsenite-translocating ATPase) (Arsenical ...	0.30	-	cyt	0	Cytoplasm. Endoplasmic reticulum. Golgi apparatus	endoplasmic reticulum [IDA] GET complex [IMP]			354
Q5EA59 UniProt NPD GO	ABHD4_BOVIN	Abhydrolase domain-containing protein 4 (EC 3.1.1.-) (Lyso-N-acylphosphatidylethanolamine lipase) (A ...	0.30	-	cyt	0					342
Q751X1 UniProt NPD GO	ACN9_ASHGO	Acetate non-utilizing protein 9, mitochondrial precursor	0.30	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				125
Q5KLU1 UniProt NPD GO	ACN9_CRYNE	Acetate non-utilizing protein 9, mitochondrial precursor	0.30	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				164
P56293 UniProt NPD GO	ACCD_CHLVU	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.30	-	cyt	0	Plastid; chloroplast				411
P52769 UniProt NPD GO	ACCD_PINTH	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.30	-	cyt	0	Plastid; chloroplast				321
Q9ZSK2 UniProt NPD GO	ADF6_ARATH	Actin-depolymerizing factor 6 (ADF-6) (AtADF6)	0.30	-	cyt	0					146
Q5AXH1 UniProt NPD GO	ARP6_EMENI	Actin-like protein arp6	0.30	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				479
P32061 UniProt NPD GO	STAD_CUCSA	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.30	-	mit	0	Plastid; chloroplast. In green tissue, found in chloroplasts. Plastid. In non-photosynthetic tissue, ...				396
P22337 UniProt NPD GO	STAD_RICCO	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.30	-	mit	0	Plastid; chloroplast. In green tissue, found in chloroplasts. Plastid. In non-photosynthetic tissue, ...			1OQB	396
Q9Y305 UniProt NPD GO	ACOT9_HUMAN	Acyl-coenzyme A thioesterase 9 (EC 3.1.2.-) (Acyl-CoA thioesterase 9) (Acyl-CoA thioester hydrolase ...	0.30	-	mit	0		mitochondrion [ISS]			406
Q9C9W9 UniProt NPD GO	ADO3_ARATH	Adagio protein 3 (Flavin-binding kelch repeat F-box protein 1) (F-box only protein 2a) (FBX2a)	0.30	-	cyt	0	Nucleus (By similarity)				619

You are viewing entries 40051 to 40100 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.