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
Q61694 UniProt NPD GO	3BHS5_MOUSE	3 beta-hydroxysteroid dehydrogenase type 5 (3 beta-hydroxysteroid dehydrogenase type V) (3Beta-HSD V ...	0.32	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...	mitochondrial inner membrane [IDA]			372
P56937 UniProt NPD GO	DHB7_HUMAN	3-keto-steroid reductase (EC 1.1.1.270) (Estradiol 17-beta-dehydrogenase 7) (EC 1.1.1.62) (17-beta-H ...	0.32	-	mit	0	Membrane; single-pass membrane protein		606756		341
Q6FM05 UniProt NPD GO	RT10_CANGA	30S ribosomal protein S10, mitochondrial precursor (Mitochondrial ribosomal small subunit protein 10 ...	0.32	-	mit	0	Mitochondrion (By similarity)				235
O35465 UniProt NPD GO	FKBP8_MOUSE	38 kDa FK506-binding protein homolog (FKBPR38) (FK506-binding protein 8) (muFKBP38)	0.32	-	nuc	1		integral to endoplasmic reticulum membrane [IDA] mitochondrial envelope [IDA]			355
Q95KE5 UniProt NPD GO	RM43_BOVIN	39S ribosomal protein L43, mitochondrial precursor (L43mt) (MRP-L43)	0.32	-	mit	0	Mitochondrion				159
P93841 UniProt NPD GO	ISPE_LYCES	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, chloroplast precursor (EC 2.7.1.148) (CMK) (4-(cy ...	0.32	+	mit	0	Plastid; chloroplast (By similarity)				401
P48151 UniProt NPD GO	RS18_ENTHI	40S ribosomal protein S18	0.32	-	nuc	0	Cytoplasm				155
Q962R1 UniProt NPD GO	RS18_SPOFR	40S ribosomal protein S18	0.32	-	nuc	0	Cytoplasm				152
O74893 UniProt NPD GO	RS20_SCHPO	40S ribosomal protein S20	0.32	-	nuc	0					118
P02377 UniProt NPD GO	RS24_XENLA	40S ribosomal protein S24 (S19)	0.32	-	nuc	0					132
Q06559 UniProt NPD GO	RS3_DROME	40S ribosomal protein S3	0.32	-	cyt	0	Cytoplasm. Nucleus				246
Q56JV9 UniProt NPD GO	RS3A_BOVIN	40S ribosomal protein S3a	0.32	+	nuc	0					263
P61247 UniProt NPD GO	RS3A_HUMAN	40S ribosomal protein S3a	0.32	+	nuc	0		cytosol [ISS] cytosolic small ribosomal subunit (sensu Eu... [IDA] nucleus [ISS] ribosome [ISS]	180478		263
Q801S3 UniProt NPD GO	RS3A_XENLA	40S ribosomal protein S3a	0.32	+	nuc	0					263
O73813 UniProt NPD GO	RS3A_ORYLA	40S ribosomal protein S3a (V-fos transformation effector protein)	0.32	+	nuc	0					265
P49242 UniProt NPD GO	RS3A_RAT	40S ribosomal protein S3a (V-fos transformation effector protein) [Contains: 40S ribosomal protein S ...	0.32	+	nuc	0		cytosol [ISS] nucleus [ISS] ribosome [ISS]			263
Q90YR7 UniProt NPD GO	RS7_ICTPU	40S ribosomal protein S7	0.32	-	nuc	0					194
Q9JM14 UniProt NPD GO	NT5C_MOUSE	5'(3')-deoxyribonucleotidase, cytosolic type (EC 3.1.3.-) (Cytosolic 5',3'-pyrimidine nucleotidase) ...	0.32	-	mit	0	Cytoplasm				200
Q28948 UniProt NPD GO	AAPK2_PIG	5'-AMP-activated protein kinase catalytic subunit alpha-2 (EC 2.7.11.1) (AMPK alpha-2 chain)	0.32	-	cyt	0					552
Q5RD00 UniProt NPD GO	AAPK2_PONPY	5'-AMP-activated protein kinase catalytic subunit alpha-2 (EC 2.7.11.1) (AMPK alpha-2 chain)	0.32	-	cyt	0					552
Q9XS79 UniProt NPD GO	HEM1_DELLE	5-aminolevulinate synthase, nonspecific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic aci ...	0.32	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				640
Q60F97 UniProt NPD GO	5HT2C_CANFA	5-hydroxytryptamine 2C receptor (5-HT-2C) (Serotonin receptor 2C) (5-HT2C) (5-HTR2C)	0.32	+	end	8 *	Membrane; multi-pass membrane protein (By similarity)				458
P34968 UniProt NPD GO	5HT2C_MOUSE	5-hydroxytryptamine 2C receptor (5-HT-2C) (Serotonin receptor 2C) (5-HT2C) (5-HTR2C) (5HT-1C)	0.32	+	end	8 *	Membrane; multi-pass membrane protein				459
P46098 UniProt NPD GO	5HT3R_HUMAN	5-hydroxytryptamine 3 receptor precursor (5-HT-3) (Serotonin-gated ion channel receptor) (5-HT3R)	0.32	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182139		478
P49208 UniProt NPD GO	RK1_PEA	50S ribosomal protein L1, chloroplast precursor (Fragment)	0.32	-	exc	0	Plastid; chloroplast				208
Q28901 UniProt NPD GO	F263_BOVIN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (6PF-2-K/Fru-2,6-P2ASE brain/placenta-type iso ...	0.32	-	nuc	0					463
P16861 UniProt NPD GO	K6PF1_YEAST	6-phosphofructokinase subunit alpha (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (6PF-1 ...	0.32	-	cyt	0	Cytoplasm	6-phosphofructokinase complex [IMP] cytoplasm [IDA]			987
P52784 UniProt NPD GO	K6PF_CANFA	6-phosphofructokinase, muscle type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosph ...	0.32	-	cyt	0		6-phosphofructokinase complex [ISS]			781
Q9BH80 UniProt NPD GO	R27A2_ENTHI	60S ribosomal protein L27a-2/4	0.32	-	mit	0					149
P58374 UniProt NPD GO	RL30_BRABE	60S ribosomal protein L30	0.32	-	mit	0					114
Q9GP16 UniProt NPD GO	RL31_HELVI	60S ribosomal protein L31	0.32	-	cyt	0					124
Q9M573 UniProt NPD GO	RL31_PERFR	60S ribosomal protein L31	0.32	-	nuc	0					121
Q7KF90 UniProt NPD GO	RL31_SPOFR	60S ribosomal protein L31	0.32	-	cyt	0					124
P51420 UniProt NPD GO	RL313_ARATH	60S ribosomal protein L31-3	0.32	-	nuc	0					119
Q9USR7 UniProt NPD GO	RL38A_SCHPO	60S ribosomal protein L38-1	0.32	-	nuc	0					74
Q9SF40 UniProt NPD GO	RL4A_ARATH	60S ribosomal protein L4-1 (L1)	0.32	-	gol	0					406
P21899 UniProt NPD GO	RL40_TRYBB	60S ribosomal protein L40 (CEP52)	0.32	+	nuc	0					52
P32387 UniProt NPD GO	RM41_YEAST	60S ribosomal protein L41, mitochondrial precursor (YmL41)	0.32	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			263
P53724 UniProt NPD GO	RM50_YEAST	60S ribosomal protein L50, mitochondrial precursor	0.32	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			139
Q6BTA4 UniProt NPD GO	RL7_DEBHA	60S ribosomal protein L7	0.32	-	cyt	0					241
P51998 UniProt NPD GO	RL4P_YEAST	60S ribosomal protein YmL6, mitochondrial precursor	0.32	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			286
Q9P2A4 UniProt NPD GO	ABI3_HUMAN	ABI gene family member 3 (New molecule including SH3) (Nesh)	0.32	-	nuc	0	Cytoplasm. Colocalizes with PAK2 at leading edge of cells	cytoplasm [NAS]	606363		366
Q60411 UniProt NPD GO	ADAM2_CAVPO	ADAM 2 precursor (A disintegrin and metalloproteinase domain 2) (Fertilin subunit beta) (PH-30) (PH3 ...	0.32	-	end	1	Membrane; single-pass type I membrane protein				735
Q8BLI0 UniProt NPD GO	ATL1_MOUSE	ADAMTS-like protein 1 precursor (Punctin-1)	0.32	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				377
Q9BW91 UniProt NPD GO	NUDT9_HUMAN	ADP-ribose pyrophosphatase, mitochondrial precursor (EC 3.6.1.13) (ADP-ribose diphosphatase) (Adenos ...	0.32	-	mit	0	Isoform 1: Mitochondrion	intracellular [NAS]	606022	1QVJ	350
P36405 UniProt NPD GO	ARL3_HUMAN	ADP-ribosylation factor-like protein 3	0.32	-	cyt	0			604695		182
Q9MYT8 UniProt NPD GO	ATP5I_PIG	ATP synthase e chain, mitochondrial (EC 3.6.3.14)	0.32	-	nuc	0					70
Q06908 UniProt NPD GO	ATPG_ODOSI	ATP synthase gamma chain, chloroplast precursor (EC 3.6.3.14)	0.32	-	exc	0	Plastid; chloroplast; chloroplast thylakoid membrane				370
Q6AYJ1 UniProt NPD GO	RECQ1_RAT	ATP-dependent DNA helicase Q1 (EC 3.6.1.-) (DNA-dependent ATPase Q1)	0.32	-	cyt	0	Nucleus (By similarity)				621
Q61655 UniProt NPD GO	DD19A_MOUSE	ATP-dependent RNA helicase DDX19A (EC 3.6.1.-) (DEAD box protein 19A) (DEAD box RNA helicase DEAD5) ...	0.32	-	cyt	0	Cytoplasm (By similarity). Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side (By sim ...				478

You are viewing entries 38201 to 38250 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.