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
P43075 UniProt NPD GO	TRNL_CANAL	tRNA ligase (EC 6.5.1.3)	0.42	-	mit	0					832
Q9T390 UniProt NPD GO	TILS_NEPOL	tRNA(Ile)-lysidine synthase (EC 6.3.4.-) (tRNA(Ile)-lysidine synthetase) (tRNA(Ile)-2-lysyl-cytidine ...	0.42	-	cyt	0	Plastid; chloroplast				367
Q8K582 UniProt NPD GO	DUS1L_RAT	tRNA-dihydrouridine synthase 1-like (EC 1.-.-.-) (Liver regeneration-related protein LRRG08/LRRG09)	0.42	-	cyt	0					438
Q9T065 UniProt NPD GO	1A18_ARATH	1-aminocyclopropane-1-carboxylate synthase 8 (EC 4.4.1.14) (ACC synthase 8) (S-adenosyl-L-methionine ...	0.41	-	cyt	0					469
Q5XHK2 UniProt NPD GO	143BA_XENLA	14-3-3 protein beta/alpha-A	0.41	-	nuc	0	Cytoplasm (By similarity)				244
P29309 UniProt NPD GO	1433_XENLA	14-3-3-like protein (Fragment)	0.41	-	nuc	0					235
P78578 UniProt NPD GO	PRS6B_ASPNG	26S protease regulatory subunit 6B homolog	0.41	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				423
Q9V3P6 UniProt NPD GO	PSD1_DROME	26S proteasome non-ATPase regulatory subunit 1 (26S proteasome regulatory subunit RPN2) (26S proteas ...	0.41	-	cyt	0		proteasome regulatory particle (sensu Eukar... [IDA]			1020
Q3SYT7 UniProt NPD GO	PSD8_BOVIN	26S proteasome non-ATPase regulatory subunit 8	0.41	-	mit	0					257
P48556 UniProt NPD GO	PSD8_HUMAN	26S proteasome non-ATPase regulatory subunit 8 (26S proteasome regulatory subunit S14) (p31)	0.41	-	mit	0		proteasome regulatory particle (sensu Eukar... [TAS]			257
P38886 UniProt NPD GO	RPN10_YEAST	26S proteasome regulatory subunit RPN10	0.41	-	nuc	0		proteasome complex (sensu Eukaryota) [IMP] proteasome regulatory particle, base subcom... [IPI]			267
Q9Y3D3 UniProt NPD GO	RT16_HUMAN	28S ribosomal protein S16, mitochondrial precursor (S16mt) (MRP-S16)	0.41	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]	609204		137
O77082 UniProt NPD GO	RS10_DICDI	40S ribosomal protein S10	0.41	-	nuc	0	Cytoplasm (By similarity)				153
Q9T029 UniProt NPD GO	RS25B_ARATH	40S ribosomal protein S25-2	0.41	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [IDA]			108
Q8L953 UniProt NPD GO	RS27D_ARATH	40S ribosomal protein S27-4	0.41	-	nuc	0					84
P31753 UniProt NPD GO	RS27A_ASPOF	40S ribosomal protein S27a	0.41	+	nuc	0					78
P68203 UniProt NPD GO	RS27A_SPOFR	40S ribosomal protein S27a	0.41	+	nuc	0					80
Q42262 UniProt NPD GO	RS3A_ARATH	40S ribosomal protein S3a	0.41	-	nuc	0					261
P49396 UniProt NPD GO	RS3A_BRARA	40S ribosomal protein S3a (S phase-specific protein BIS289)	0.41	-	nuc	0					261
P50894 UniProt NPD GO	RS7_FUGRU	40S ribosomal protein S7	0.41	-	nuc	0					194
P55935 UniProt NPD GO	RS9_DROME	40S ribosomal protein S9	0.41	-	cyt	0					195
Q7S7R6 UniProt NPD GO	RT09_NEUCR	40S ribosomal protein S9, mitochondrial precursor	0.41	-	mit	0	Mitochondrion (Potential)				314
O14006 UniProt NPD GO	RT09_SCHPO	40S ribosomal protein S9, mitochondrial precursor	0.41	-	nuc	0	Mitochondrion (Potential)				132
O08890 UniProt NPD GO	5HT1F_CAVPO	5-hydroxytryptamine 1F receptor (5-HT-1F) (Serotonin receptor 1F) (5-HT1F)	0.41	-	end	7 *	Membrane; multi-pass membrane protein				366
P26785 UniProt NPD GO	RL16B_YEAST	60S ribosomal protein L16-B (YL15) (RP23)	0.41	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			197
P48162 UniProt NPD GO	R23A1_CAEEL	60S ribosomal protein L23a 1	0.41	-	mit	0					147
Q8HXB8 UniProt NPD GO	RL29_MACFA	60S ribosomal protein L29	0.41	-	nuc	0					156
Q6CJR7 UniProt NPD GO	RL3_KLULA	60S ribosomal protein L3	0.41	+	mit	0	Cytoplasm (By similarity)				387
P59671 UniProt NPD GO	RL3_NEUCR	60S ribosomal protein L3	0.41	+	mit	0	Cytoplasm (By similarity)				392
P14126 UniProt NPD GO	RL3_YEAST	60S ribosomal protein L3 (YL1) (RP1) (Maintenance of killer protein 8) (Trichodermin resistance prot ...	0.41	+	mit	0	Cytoplasm	cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	386
Q9UTI8 UniProt NPD GO	RL44_SCHPO	60S ribosomal protein L44	0.41	-	nuc	0					105
Q9UWE4 UniProt NPD GO	RL44_COPCI	60S ribosomal protein L44 (60S ribosomal protein L41)	0.41	-	nuc	0					105
Q8LBI1 UniProt NPD GO	RL51_ARATH	60S ribosomal protein L5-1	0.41	-	mit	0	Cytoplasm. Nucleus; nucleolus				301
P47991 UniProt NPD GO	RL6_CAEEL	60S ribosomal protein L6	0.41	-	mit	0					217
Q9ESP7 UniProt NPD GO	ATS4_RAT	ADAMTS-4 precursor (EC 3.4.24.82) (A disintegrin and metalloproteinase with thrombospondin motifs 4) ...	0.41	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [TAS]			630
Q9JHT5 UniProt NPD GO	AMER1_MOUSE	AMME syndrome candidate gene 1 protein homolog	0.41	-	nuc	0					344
Q9UNQ0 UniProt NPD GO	ABCG2_HUMAN	ATP-binding cassette sub-family G member 2 (Placenta-specific ATP-binding cassette transporter) (Bre ...	0.41	-	end	6	Cell membrane; multi-pass membrane protein	integral to membrane [TAS]	603756		655
Q75C39 UniProt NPD GO	DBP5_ASHGO	ATP-dependent RNA helicase DBP5 (EC 3.6.1.-)	0.41	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				467
Q4P733 UniProt NPD GO	DED1_USTMA	ATP-dependent RNA helicase DED1 (EC 3.6.1.-)	0.41	+	cyt	0	Cytoplasm (By similarity)				672
P33310 UniProt NPD GO	MDL1_YEAST	ATP-dependent permease MDL1, mitochondrial precursor (ABC transporter MDL1) (Multidrug resistance-li ...	0.41	-	end	5	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			695
Q4WHK3 UniProt NPD GO	ACN9_ASPFU	Acetate non-utilizing protein 9, mitochondrial precursor	0.41	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				129
P0C146 UniProt NPD GO	ACN9_MAGGR	Acetate non-utilizing protein 9, mitochondrial precursor	0.41	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				123
P06680 UniProt NPD GO	PRPH_MESAU	Acidic proline-rich protein HP43A precursor	0.41	-	nuc	0					183
Q9QXD1 UniProt NPD GO	ACOX2_MOUSE	Acyl-coenzyme A oxidase 2, peroxisomal (EC 1.17.99.3) (3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-ch ...	0.41	-	cyt	0	Peroxisome (By similarity)				681
P28039 UniProt NPD GO	AOAH_HUMAN	Acyloxyacyl hydrolase precursor (EC 3.1.1.77) [Contains: Acyloxyacyl hydrolase small subunit; Acylox ...	0.41	-	exc	0			102593		575
Q9TU18 UniProt NPD GO	AGRP_PIG	Agouti-related protein precursor	0.41	-	exc	0	Secreted protein (By similarity)				134
Q90404 UniProt NPD GO	AGRN_DISOM	Agrin (Fragment)	0.41	-	nuc	0	Synaptic basal lamina at the neuromuscular junction (By similarity)				1328
P02505 UniProt NPD GO	CRYAA_RHEAM	Alpha crystallin A chain	0.41	-	nuc	0					173
P02509 UniProt NPD GO	CRYAA_SQUAC	Alpha crystallin A chain	0.41	-	nuc	0					177
P15823 UniProt NPD GO	ADA1B_RAT	Alpha-1B adrenergic receptor (Alpha 1B-adrenoceptor) (Alpha 1B-adrenoreceptor)	0.41	+	end	7 *	Membrane; multi-pass membrane protein				515

You are viewing entries 30851 to 30900 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.