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
Q8R2L5 UniProt NPD GO	RT18C_MOUSE	28S ribosomal protein S18c, mitochondrial precursor (MRP-S18-c) (Mrps18c) (MRP-S18-1)	0.22	-	nuc	0	Mitochondrion				143
P22434 UniProt NPD GO	PDE1_YEAST	3',5'-cyclic-nucleotide phosphodiesterase 1 (EC 3.1.4.17) (PDEase 1) (Low-affinity cAMP phosphodiest ...	0.22	-	cyt	0					369
Q03163 UniProt NPD GO	HMDH_CATRO	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.22	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				601
O14289 UniProt NPD GO	LEU2_SCHPO	3-isopropylmalate dehydratase (EC 4.2.1.33) (Isopropylmalate isomerase) (Alpha-IPM isomerase) (IPMI) ...	0.22	-	cyt	0					758
P07264 UniProt NPD GO	LEU2_YEAST	3-isopropylmalate dehydratase (EC 4.2.1.33) (Isopropylmalate isomerase) (Alpha-IPM isomerase) (IPMI) ...	0.22	-	cyt	0					779
Q3T0F4 UniProt NPD GO	RS10_BOVIN	40S ribosomal protein S10	0.22	-	nuc	0	Cytoplasm (By similarity)				165
P46783 UniProt NPD GO	RS10_HUMAN	40S ribosomal protein S10	0.22	-	nuc	0	Cytoplasm	cytosolic small ribosomal subunit (sensu Eu... [IDA]	603632		165
O77302 UniProt NPD GO	RS10_LUMRU	40S ribosomal protein S10	0.22	-	cyt	0	Cytoplasm (By similarity)				156
P41094 UniProt NPD GO	RS18_DROME	40S ribosomal protein S18	0.22	-	nuc	0	Cytoplasm				152
Q9C2P2 UniProt NPD GO	RS29_NEUCR	40S ribosomal protein S29	0.22	-	mit	0					56
Q08364 UniProt NPD GO	RS5_PODCA	40S ribosomal protein S5	0.22	-	nuc	0					210
Q9ZUT9 UniProt NPD GO	RS5A_ARATH	40S ribosomal protein S5-1	0.22	-	cyt	0					207
P38984 UniProt NPD GO	RSSA_CHLVR	40S ribosomal protein SA (p40) (33 kDa laminin-binding protein)	0.22	-	cyt	0	Cytoplasm				293
P78698 UniProt NPD GO	HEM1_KLULA	5-aminolevulinate synthase, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic acid synthase) ( ...	0.22	-	nuc	0	Mitochondrion; mitochondrial matrix				570
Q9N2B7 UniProt NPD GO	5HT1B_GORGO	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				390
Q8UUG8 UniProt NPD GO	5HT2B_TETFL	5-hydroxytryptamine 2B receptor (5-HT-2B) (Serotonin receptor 2B)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				471
Q62758 UniProt NPD GO	5HT4R_RAT	5-hydroxytryptamine 4 receptor (5-HT-4) (Serotonin receptor 4) (5-HT4)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				406
Q29006 UniProt NPD GO	5HT4R_PIG	5-hydroxytryptamine 4 receptor (5-HT-4) (Serotonin receptor 4) (5-HT4) (Fragment)	0.22	-	end	2 *	Membrane; multi-pass membrane protein				137
Q91559 UniProt NPD GO	5HT7R_XENLA	5-hydroxytryptamine 7 receptor (5-HT-7) (Serotonin receptor 7)	0.22	-	end	7	Membrane; multi-pass membrane protein				425
Q9ZST0 UniProt NPD GO	RK5_ORYSA	50S ribosomal protein L5, chloroplast precursor	0.22	-	mit	0	Plastid; chloroplast				279
P45633 UniProt NPD GO	RL10_MAIZE	60S ribosomal protein L10 (QM protein homolog)	0.22	-	mit	0					220
P46287 UniProt NPD GO	RL11_MEDSA	60S ribosomal protein L11 (L5)	0.22	-	cyt	0	Cytoplasm				181
Q6FWF4 UniProt NPD GO	RL31_CANGA	60S ribosomal protein L31	0.22	-	nuc	0					113
Q5QM99 UniProt NPD GO	RL37A_ORYSA	60S ribosomal protein L37a	0.22	-	cyt	0				1YSH	92
Q32PB9 UniProt NPD GO	RL38_BOVIN	60S ribosomal protein L38	0.22	-	nuc	0					69
Q8HXB9 UniProt NPD GO	RL38_MACFA	60S ribosomal protein L38	0.22	-	nuc	0					69
Q3T0S6 UniProt NPD GO	RL8_BOVIN	60S ribosomal protein L8	0.22	-	mit	0	Cytoplasm (By similarity)				256
P62917 UniProt NPD GO	RL8_HUMAN	60S ribosomal protein L8	0.22	-	mit	0	Cytoplasm		604177		256
P62918 UniProt NPD GO	RL8_MOUSE	60S ribosomal protein L8	0.22	-	mit	0	Cytoplasm (By similarity)				256
P62919 UniProt NPD GO	RL8_RAT	60S ribosomal protein L8	0.22	-	mit	0	Cytoplasm (By similarity)				256
P41116 UniProt NPD GO	RL8_XENLA	60S ribosomal protein L8	0.22	-	mit	0	Cytoplasm				256
P61312 UniProt NPD GO	ADM2_RAT	ADM2 precursor (Intermedin) [Contains: Adrenomedullin-2 (Intermedin-long) (IMDL); Intermedin-short ( ...	0.22	-	exc	1 *	Secreted protein				146
Q5XIG0 UniProt NPD GO	NUDT9_RAT	ADP-ribose pyrophosphatase, mitochondrial precursor (EC 3.6.1.13) (ADP-ribose diphosphatase) (Adenos ...	0.22	-	mit	0	Mitochondrion (By similarity)				350
Q2TA37 UniProt NPD GO	ARL2_BOVIN	ADP-ribosylation factor-like protein 2	0.22	-	nuc	0					184
P36404 UniProt NPD GO	ARL2_HUMAN	ADP-ribosylation factor-like protein 2	0.22	-	nuc	0			601175		184
P13619 UniProt NPD GO	AT5F1_BOVIN	ATP synthase B chain, mitochondrial precursor (EC 3.6.3.14)	0.22	-	mit	0	Mitochondrion				256
P24539 UniProt NPD GO	AT5F1_HUMAN	ATP synthase B chain, mitochondrial precursor (EC 3.6.3.14)	0.22	-	mit	0	Mitochondrion	mitochondrial matrix [TAS] mitochondrion [TAS]	603270		256
Q9CQQ7 UniProt NPD GO	AT5F1_MOUSE	ATP synthase B chain, mitochondrial precursor (EC 3.6.3.14)	0.22	-	mit	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrion [IDA]			256
P13618 UniProt NPD GO	ATP5J_PIG	ATP synthase coupling factor 6, mitochondrial (EC 3.6.3.14) (ATPase subunit F6)	0.22	-	nuc	0					76
Q24407 UniProt NPD GO	ATP5J_DROME	ATP synthase coupling factor 6, mitochondrial precursor (EC 3.6.3.14) (ATPase subunit F6)	0.22	-	nuc	0					106
P12113 UniProt NPD GO	ATPG_CHLRE	ATP synthase gamma chain, chloroplast precursor (EC 3.6.3.14)	0.22	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				358
P41314 UniProt NPD GO	ATP8_DIDMA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.22	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				69
P56757 UniProt NPD GO	ATPA_ARATH	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q7YJY4 UniProt NPD GO	ATPA_CALFE	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q49L13 UniProt NPD GO	ATPA_EUCGG	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q332Y4 UniProt NPD GO	ATPA_LACSA	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				508
Q9BBS3 UniProt NPD GO	ATPA_LOTJA	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				510
Q2MIB5 UniProt NPD GO	ATPA_LYCES	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q3C1H4 UniProt NPD GO	ATPA_NICSY	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q33C53 UniProt NPD GO	ATPA_NICTO	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507

You are viewing entries 48051 to 48100 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.