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
O65731 UniProt NPD GO	RS5_CICAR	40S ribosomal protein S5 (Fragment)	0.24	-	cyt	0					197
Q9VFE4 UniProt NPD GO	RS5B_DROME	40S ribosomal protein S5b	0.24	-	nuc	0					230
P50890 UniProt NPD GO	RSSA_CHICK	40S ribosomal protein SA (p40) (34/67 kDa laminin receptor) (37LRP)	0.24	-	nuc	0	Cytoplasm				296
Q26264 UniProt NPD GO	SM41_HEMPU	41 kDa spicule matrix protein precursor (HSM41) (HPSMC)	0.24	-	exc	0	Secreted protein				407
P07147 UniProt NPD GO	TYRP1_MOUSE	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (EC 1.14.18.-) (DHICA oxidase) (Tyrosinase-r ...	0.24	-	end	2 *	Melanosome; melanosomal membrane; single-pass type I membrane protein (Potential)	melanosome [IDA]			537
Q29003 UniProt NPD GO	5HT1E_PIG	5-hydroxytryptamine 1E receptor (5-HT-1E) (Serotonin receptor 1E) (5-HT1E) (Fragment)	0.24	-	end	4 *	Membrane; multi-pass membrane protein				149
P31388 UniProt NPD GO	5HT6R_RAT	5-hydroxytryptamine 6 receptor (5-HT-6) (Serotonin receptor 6) (ST-B17)	0.24	-	end	7 *	Membrane; multi-pass membrane protein				436
P16862 UniProt NPD GO	K6PF2_YEAST	6-phosphofructokinase subunit beta (EC 2.7.1.11) (Phosphofructokinase 2) (Phosphohexokinase) (6PF-1- ...	0.24	-	cyt	0	Cytoplasm	6-phosphofructokinase complex [IMP] cytoplasm [IDA]			958
P47859 UniProt NPD GO	K6PP_RABIT	6-phosphofructokinase type C (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosphofruct ...	0.24	-	nuc	0					791
P41805 UniProt NPD GO	RL10_YEAST	60S ribosomal protein L10 (L9) (Ubiquinol-cytochrome C reductase complex subunit VI-requiring protei ...	0.24	-	mit	0	Cytoplasm	cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	221
Q9VTP4 UniProt NPD GO	R10AB_DROME	60S ribosomal protein L10a-2	0.24	+	nuc	0					217
O46160 UniProt NPD GO	RL14_LUMRU	60S ribosomal protein L14	0.24	-	nuc	0					152
Q9SIM4 UniProt NPD GO	RL141_ARATH	60S ribosomal protein L14-1	0.24	-	cyt	0					134
Q9UUC1 UniProt NPD GO	RL21A_SCHPO	60S ribosomal protein L21-A	0.24	-	mit	0					160
O42706 UniProt NPD GO	RL21B_SCHPO	60S ribosomal protein L21-B	0.24	-	mit	0					160
Q19869 UniProt NPD GO	RL26_CAEEL	60S ribosomal protein L26	0.24	-	nuc	0					142
Q7S7F1 UniProt NPD GO	RL30_NEUCR	60S ribosomal protein L30	0.24	-	nuc	0					109
Q757D7 UniProt NPD GO	RL31_ASHGO	60S ribosomal protein L31	0.24	-	nuc	0					114
P04649 UniProt NPD GO	RL31_YEAST	60S ribosomal protein L31 (L34) (YL28)	0.24	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	112
Q9XHE4 UniProt NPD GO	RL37A_GOSHI	60S ribosomal protein L37a	0.24	-	nuc	0					92
Q9ZRS8 UniProt NPD GO	RL37A_PSEMZ	60S ribosomal protein L37a	0.24	-	cyt	0					92
Q8SSM6 UniProt NPD GO	RL8_ENCCU	60S ribosomal protein L8	0.24	-	nuc	0	Cytoplasm				239
O60733 UniProt NPD GO	PA2G6_HUMAN	85 kDa calcium-independent phospholipase A2 (EC 3.1.1.4) (iPLA2) (CaI-PLA2) (Group VI phospholipase ...	0.24	-	mit	0	Isoform LH-iPLA2: Membrane; peripheral membrane protein. Isoform SH-iPLA2: Cytoplasm		603604		806
P97570 UniProt NPD GO	PA2G6_RAT	85 kDa calcium-independent phospholipase A2 (EC 3.1.1.4) (iPLA2) (CaI-PLA2) (Group VI phospholipase ...	0.24	-	mit	0	Cytoplasm				751
Q9Y4W6 UniProt NPD GO	AFG32_HUMAN	AFG3-like protein 2 (EC 3.4.24.-) (Paraplegin-like protein)	0.24	+	end	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrion [TAS]	604581		797
Q07456 UniProt NPD GO	AMBP_MOUSE	AMBP protein precursor [Contains: Alpha-1-microglobulin; Inter-alpha-trypsin inhibitor light chain ( ...	0.24	-	exc	0	Secreted protein	extracellular region [ISS] plasma membrane [ISS]			349
Q9HFE5 UniProt NPD GO	AP1M1_SCHPO	AP-1 complex subunit mu-1 (Mu(1)-adaptin) (Clathrin assembly protein complex 1 medium chain)	0.24	-	cyt	0					426
Q9TL15 UniProt NPD GO	ATPF_NEPOL	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.24	-	end	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				176
Q40609 UniProt NPD GO	ATPF_OCHNE	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.24	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				178
Q24251 UniProt NPD GO	ATP5H_DROME	ATP synthase D chain, mitochondrial (EC 3.6.3.14)	0.24	-	nuc	0					178
P56385 UniProt NPD GO	ATP5I_HUMAN	ATP synthase e chain, mitochondrial (EC 3.6.3.14)	0.24	-	nuc	1 *			601519		68
P29419 UniProt NPD GO	ATP5I_RAT	ATP synthase e chain, mitochondrial (EC 3.6.3.14)	0.24	-	cyt	0		mitochondrion [IDA]			70
Q8WI12 UniProt NPD GO	ATPE_PSINU	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.24	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				133
P48896 UniProt NPD GO	ATP8_FELCA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.24	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q2QDA3 UniProt NPD GO	ATPA_CUCSA	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.24	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P05022 UniProt NPD GO	ATPA_MAIZE	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.24	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P08215 UniProt NPD GO	ATPA_PEA	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.24	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				501
Q06735 UniProt NPD GO	ATPAM_BETVU	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.24	-	cyt	0	Mitochondrion	mitochondrion [NAS] proton-transporting ATP synthase complex, c... [NAS]			506
P05494 UniProt NPD GO	ATPAM_MAIZE	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.24	-	cyt	0	Mitochondrion				508
P48410 UniProt NPD GO	ABCD1_MOUSE	ATP-binding cassette sub-family D member 1 (Adrenoleukodystrophy protein) (ALDP)	0.24	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				736
Q64343 UniProt NPD GO	ABCG1_MOUSE	ATP-binding cassette sub-family G member 1 (White protein homolog) (ATP-binding cassette transporter ...	0.24	-	end	7	Membrane; multi-pass membrane protein (Probable)				666
Q9TM05 UniProt NPD GO	CLPC_CYACA	ATP-dependent Clp protease ATP-binding subunit clpA homolog	0.24	-	cyt	0	Plastid; chloroplast				854
Q6FKN8 UniProt NPD GO	DBP5_CANGA	ATP-dependent RNA helicase DBP5 (EC 3.6.1.-)	0.24	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				504
Q6CLR3 UniProt NPD GO	DED1_KLULA	ATP-dependent RNA helicase DED1 (EC 3.6.1.-)	0.24	-	nuc	0	Cytoplasm (By similarity)				627
Q5AWA6 UniProt NPD GO	DBP3_EMENI	ATP-dependent RNA helicase dbp3 (EC 3.6.1.-)	0.24	-	nuc	0	Nucleus; nucleolus (By similarity)				498
Q8JZN3 UniProt NPD GO	IRK14_MOUSE	ATP-sensitive inward rectifier potassium channel 14 (Potassium channel, inwardly rectifying subfamil ...	0.24	-	end	3	Membrane; multi-pass membrane protein				434
Q7G9P4 UniProt NPD GO	ALDO3_ARATH	Abscisic-aldehyde oxidase (EC 1.2.3.14) (Aldehyde oxidase 3) (AO-3) (AtAO-3) (AtAO4)	0.24	-	cyt	0					1332
Q9U968 UniProt NPD GO	A29AB_DROSI	Accessory gland protein Acp29AB precursor	0.24	-	mit	0	Secreted protein (Probable)				234
P14874 UniProt NPD GO	ILV2_BRANA	Acetolactate synthase 2, chloroplast precursor (EC 2.2.1.6) (Acetolactate synthase II) (Acetohydroxy ...	0.24	-	mit	0	Plastid; chloroplast				637
Q27218 UniProt NPD GO	ACH7_CAEEL	Acetylcholine receptor subunit beta-type lev-1 precursor (Levamisole-resistant protein 1)	0.24	-	end	4 *	Membrane; multi-pass membrane protein				507

You are viewing entries 45951 to 46000 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.