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
O24145 UniProt NPD GO	4CL1_TOBAC	4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1) (4-coumaroyl-CoA synthase 1)	0.05	-	nuc	0					547
Q6TGZ5 UniProt NPD GO	HPPD_BRARE	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.05	-	cyt	0					397
Q22633 UniProt NPD GO	HPPD_CAEEL	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.05	-	cyt	0					393
Q00415 UniProt NPD GO	HPPD_COCIM	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (T-cell reactive protein ...	0.05	-	cyt	0					399
Q875N2 UniProt NPD GO	RS16_KLULA	40S ribosomal protein S16	0.05	-	cyt	0					143
Q7SFJ9 UniProt NPD GO	RS16_NEUCR	40S ribosomal protein S16	0.05	-	cyt	0					142
Q32PD5 UniProt NPD GO	RS19_BOVIN	40S ribosomal protein S19	0.05	-	cyt	0					144
P39019 UniProt NPD GO	RS19_HUMAN	40S ribosomal protein S19	0.05	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [IDA] nucleolus [IDA]	603474		144
Q5R8M9 UniProt NPD GO	RS19_PONPY	40S ribosomal protein S19	0.05	-	cyt	0					144
Q29308 UniProt NPD GO	RS19_PIG	40S ribosomal protein S19 (Fragment)	0.05	-	nuc	0					135
O18789 UniProt NPD GO	RS2_BOVIN	40S ribosomal protein S2	0.05	+	nuc	0					293
P27952 UniProt NPD GO	RS2_RAT	40S ribosomal protein S2	0.05	+	nuc	0					293
P15880 UniProt NPD GO	RS2_HUMAN	40S ribosomal protein S2 (S4) (LLRep3 protein)	0.05	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603624		293
P25444 UniProt NPD GO	RS2_MOUSE	40S ribosomal protein S2 (S4) (LLRep3 protein)	0.05	+	nuc	0					293
Q6PUF8 UniProt NPD GO	RS21_BOMMO	40S ribosomal protein S21	0.05	-	cyt	0					83
Q962Q8 UniProt NPD GO	RS21_SPOFR	40S ribosomal protein S21	0.05	-	cyt	0					83
Q6CW21 UniProt NPD GO	RS22_KLULA	40S ribosomal protein S22	0.05	-	cyt	0					129
P33953 UniProt NPD GO	RS22_KLUMA	40S ribosomal protein S22 (Ribosomal protein S15a)	0.05	-	cyt	0					129
Q873W8 UniProt NPD GO	RS23_ASPFU	40S ribosomal protein S23	0.05	-	mit	0					145
P49201 UniProt NPD GO	RS23B_ARATH	40S ribosomal protein S23-2 (S12)	0.05	-	mit	0					142
Q90YS0 UniProt NPD GO	RS4_ICTPU	40S ribosomal protein S4	0.05	-	mit	0					262
Q642H9 UniProt NPD GO	RS4X_BRARE	40S ribosomal protein S4, X isoform	0.05	-	mit	0					262
P49041 UniProt NPD GO	RS5_CAEEL	40S ribosomal protein S5	0.05	-	cyt	0					210
P38981 UniProt NPD GO	RSSA_URECA	40S ribosomal protein SA (p40) (34/67 kDa laminin-binding protein)	0.05	-	nuc	0					317
P38979 UniProt NPD GO	RSSA_DROME	40S ribosomal protein SA (p40) (Stubarista protein) (Laminin receptor homolog) (K14)	0.05	-	nuc	0	Cytoplasm				270
P80787 UniProt NPD GO	CWP10_TOBAC	48 kDa cell wall protein (Fragment)	0.05	-	cyt	0	Cell wall				23
P92979 UniProt NPD GO	APR1_ARATH	5'-adenylylsulfate reductase 1, chloroplast precursor (EC 1.8.4.9) (Adenosine 5'-phosphosulfate 5'-a ...	0.05	-	cyt	0	Plastid; chloroplast (Potential)				465
P05694 UniProt NPD GO	METE_YEAST	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) (Methionine synt ...	0.05	-	cyt	0		cytoplasm [IDA]			766
P82443 UniProt NPD GO	CWP35_TOBAC	50 kDa cell wall protein (Fragment)	0.05	-		0	Cell wall				10
P02398 UniProt NPD GO	RK12_SPIOL	50S ribosomal protein L12, chloroplast precursor (CL12)	0.05	-	mit	0	Plastid; chloroplast. And other plastids				189
Q9SKX4 UniProt NPD GO	RK3A_ARATH	50S ribosomal protein L3-1, chloroplast precursor	0.05	-	mit	0	Plastid; chloroplast (Potential)				271
Q93572 UniProt NPD GO	RLA0_CAEEL	60S acidic ribosomal protein P0	0.05	-	cyt	0					311
Q8TFM9 UniProt NPD GO	RLA2_FUSCU	60S acidic ribosomal protein P2 (Allergen Fus c 1)	0.05	-	exc	0					109
Q9LUK2 UniProt NPD GO	RLA25_ARATH	60S acidic ribosomal protein P2-5	0.05	-	cyt	0					114
Q94793 UniProt NPD GO	RL11_TOXCA	60S ribosomal protein L11 (Fragment)	0.05	-	cyt	0					125
Q8SR84 UniProt NPD GO	RL12_ENCCU	60S ribosomal protein L12	0.05	-	nuc	0					166
P17079 UniProt NPD GO	RL12_YEAST	60S ribosomal protein L12 (L15) (YL23)	0.05	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	165
P05749 UniProt NPD GO	RL22A_YEAST	60S ribosomal protein L22-A (YL31) (RP4)	0.05	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			120
P04451 UniProt NPD GO	RL23_YEAST	60S ribosomal protein L23 (L17)	0.05	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	136
O74538 UniProt NPD GO	RL27B_SCHPO	60S ribosomal protein L27-B	0.05	-	mit	0					136
Q5I7K9 UniProt NPD GO	RL30_WHEAT	60S ribosomal protein L30	0.05	-	nuc	0				1YSH	112
Q9LDU6 UniProt NPD GO	ST7R_ARATH	7-dehydrocholesterol reductase (EC 1.3.1.21) (7-DHC reductase) (Sterol delta-7-reductase) (Dwarf5 pr ...	0.05	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				432
Q60813 UniProt NPD GO	ADM1A_MOUSE	ADAM 1a precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 1a) (Fertilin alpha 1a s ...	0.05	-	mit	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS] lipid raft [IDA]			791
Q26365 UniProt NPD GO	ADT_DROME	ADP,ATP carrier protein (ADP/ATP translocase) (Adenine nucleotide translocator) (ANT) (Stress sensit ...	0.05	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IEP]			312
Q7PQV7 UniProt NPD GO	ADT2_ANOGA	ADP,ATP carrier protein 2 (ADP/ATP translocase 2) (Adenine nucleotide translocator 2) (ANT 2)	0.05	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				300
Q01976 UniProt NPD GO	ADPP_YEAST	ADP-ribose pyrophosphatase (EC 3.6.1.13) (ADP-ribose diphosphatase) (Adenosine diphosphoribose pyrop ...	0.05	-	mit	0		cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			231
Q9MZ03 UniProt NPD GO	CD38_RABIT	ADP-ribosyl cyclase 1 (EC 3.2.2.5) (Cyclic ADP-ribose hydrolase 1) (cADPr hydrolase 1) (CD38 homolog ...	0.05	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Microsome; microsomal membrane; single-pass typ ...	microsome [IDA] plasma membrane [IDA]			298
P91924 UniProt NPD GO	ARF_DUGJA	ADP-ribosylation factor	0.05	-	cyt	0					182
O23778 UniProt NPD GO	ARF1_CATRO	ADP-ribosylation factor 1	0.05	-	cyt	0					180
P51822 UniProt NPD GO	ARF1_DAUCA	ADP-ribosylation factor 1	0.05	-	cyt	0					180

You are viewing entries 73601 to 73650 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.