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
Q3E754 UniProt NPD GO	RS21B_YEAST	40S ribosomal protein S21-B (S26)	0.08	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			87
Q9M5Z9 UniProt NPD GO	RS23_EUPES	40S ribosomal protein S23	0.08	-	nuc	0					142
P47961 UniProt NPD GO	RS4_CRIGR	40S ribosomal protein S4	0.08	-	mit	0					262
Q76N24 UniProt NPD GO	RS4X_CERAE	40S ribosomal protein S4, X isoform	0.08	-	mit	0		ribosome [ISS]			262
P62705 UniProt NPD GO	RS4X_FELCA	40S ribosomal protein S4, X isoform	0.08	-	mit	0		ribosome [ISS]			262
Q76MY1 UniProt NPD GO	RS4X_MACFU	40S ribosomal protein S4, X isoform	0.08	-	mit	0		ribosome [ISS]			262
P62704 UniProt NPD GO	RS4X_MESAU	40S ribosomal protein S4, X isoform	0.08	-	mit	0		ribosome [ISS]			262
P62702 UniProt NPD GO	RS4X_MOUSE	40S ribosomal protein S4, X isoform	0.08	-	mit	0		ribosome [ISS]			262
P62703 UniProt NPD GO	RS4X_RAT	40S ribosomal protein S4, X isoform	0.08	-	mit	0		ribosome [ISS]			262
P62701 UniProt NPD GO	RS4X_HUMAN	40S ribosomal protein S4, X isoform (Single copy abundant mRNA protein) (SCR10)	0.08	-	mit	0		ribosome [IDA]	312760		262
P51427 UniProt NPD GO	RS5B_ARATH	40S ribosomal protein S5-2	0.08	-	cyt	0					207
P46771 UniProt NPD GO	RSSA_STRPU	40S ribosomal protein SA (p40) (34/67 kDa laminin-binding protein) (Fragment)	0.08	-	mit	0	Cytoplasm				264
P54619 UniProt NPD GO	AAKG1_HUMAN	5'-AMP-activated protein kinase subunit gamma-1 (AMPK gamma-1 chain) (AMPKg)	0.08	-	cyt	0			602742		331
Q09138 UniProt NPD GO	AAKG1_PIG	5'-AMP-activated protein kinase subunit gamma-1 (AMPK gamma-1 chain) (AMPKg) (38 kDa subunit)	0.08	-	cyt	0					330
Q6FXE3 UniProt NPD GO	HEM1_CANGA	5-aminolevulinate synthase, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic acid synthase) ( ...	0.08	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				530
P47898 UniProt NPD GO	5HT5A_HUMAN	5-hydroxytryptamine 5A receptor (5-HT-5A) (Serotonin receptor 5A) (5-HT-5)	0.08	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601305		357
Q42699 UniProt NPD GO	METE_CATRO	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) (Vitamin-B12-ind ...	0.08	-	nuc	0	Cytoplasm (Potential)				765
P93263 UniProt NPD GO	METE_MESCR	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) (Vitamin-B12-ind ...	0.08	-	nuc	0	Cytoplasm (Potential)				765
P27683 UniProt NPD GO	RK24_SPIOL	50S ribosomal protein L24, chloroplast precursor (CL24)	0.08	-	mit	0	Plastid; chloroplast				191
O60037 UniProt NPD GO	6PGD_CUNEL	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	0.08	-	cyt	0					485
P42700 UniProt NPD GO	RO60_XENLA	60 kDa SS-A/Ro ribonucleoprotein (60 kDa Ro protein) (60 kDa ribonucleoprotein Ro) (RoRNP) (TROVE do ...	0.08	-	mit	0	Cytoplasm			1YVR	538
P53027 UniProt NPD GO	RL10A_PIG	60S ribosomal protein L10a (Fragment)	0.08	+	nuc	0					164
P59231 UniProt NPD GO	R10A3_ARATH	60S ribosomal protein L10a-3	0.08	+	nuc	0					217
P08093 UniProt NPD GO	RL2_SCHPO	60S ribosomal protein L2 (K5) (K37) (KD4)	0.08	-	mit	0					253
P05732 UniProt NPD GO	RL20_SCHPO	60S ribosomal protein L20 (YL17)	0.08	-	cyt	0					175
P56628 UniProt NPD GO	RL22B_YEAST	60S ribosomal protein L22-B	0.08	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			121
Q07760 UniProt NPD GO	RL23_TOBAC	60S ribosomal protein L23	0.08	-	mit	0					140
Q10330 UniProt NPD GO	RL25A_SCHPO	60S ribosomal protein L25-A	0.08	-	mit	0					141
P78987 UniProt NPD GO	RL27A_ERYGR	60S ribosomal protein L27a (L29)	0.08	+	mit	0					149
P08978 UniProt NPD GO	RL28_NEUCR	60S ribosomal protein L28 (L27A) (L29) (CRP1)	0.08	+	mit	0					149
O49884 UniProt NPD GO	RL30_LUPLU	60S ribosomal protein L30	0.08	-	nuc	0					112
Q9SDG6 UniProt NPD GO	RL30_ORYSA	60S ribosomal protein L30	0.08	-	nuc	0					111
Q8SSC8 UniProt NPD GO	RL31_ENCCU	60S ribosomal protein L31	0.08	-	cyt	0					111
Q95Y90 UniProt NPD GO	RL9_CAEEL	60S ribosomal protein L9	0.08	-	nuc	0					189
P30707 UniProt NPD GO	RL9_PEA	60S ribosomal protein L9 (Gibberellin-regulated protein GA)	0.08	-	nuc	0					193
P49209 UniProt NPD GO	RL91_ARATH	60S ribosomal protein L9-1	0.08	-	nuc	0					194
Q9SZX9 UniProt NPD GO	RL92_ARATH	60S ribosomal protein L9-2	0.08	-	nuc	0					194
Q7SXF1 UniProt NPD GO	DHCR7_BRARE	7-dehydrocholesterol reductase (EC 1.3.1.21) (7-DHC reductase) (Sterol delta-7-reductase)	0.08	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				478
Q7ZXH1 UniProt NPD GO	DHCR7_XENLA	7-dehydrocholesterol reductase (EC 1.3.1.21) (7-DHC reductase) (Sterol delta-7-reductase)	0.08	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				473
Q6P4M0 UniProt NPD GO	DHCR7_XENTR	7-dehydrocholesterol reductase (EC 1.3.1.21) (7-DHC reductase) (Sterol delta-7-reductase)	0.08	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				473
P34935 UniProt NPD GO	GRP78_PIG	78 kDa glucose-regulated protein (GRP 78) (Immunoglobulin heavy chain-binding protein) (BiP) (Fragme ...	0.08	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen				262
Q03877 UniProt NPD GO	GP85_TRYCR	85 kDa surface antigen precursor	0.08	-	end	1	Cell membrane; lipid-anchor; GPI-anchor				714
P83408 UniProt NPD GO	ACA_HUMAN	ACA protein (Fragments)	0.08	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...	anchored to membrane [NAS]			139
P56528 UniProt NPD GO	CD38_MOUSE	ADP-ribosyl cyclase 1 (EC 3.2.2.5) (Cyclic ADP-ribose hydrolase 1) (cADPr hydrolase 1) (NIM-R5 antig ...	0.08	-	mit	1 *	Membrane; single-pass type II membrane protein	membrane fraction [IDA]			304
Q64277 UniProt NPD GO	BST1_MOUSE	ADP-ribosyl cyclase 2 precursor (EC 3.2.2.5) (Cyclic ADP-ribose hydrolase 2) (cADPr hydrolase 2) (Bo ...	0.08	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				311
P34727 UniProt NPD GO	ARF_AJECA	ADP-ribosylation factor	0.08	-	cyt	0					182
Q80ZU0 UniProt NPD GO	ARL5A_MOUSE	ADP-ribosylation factor-like protein 5A	0.08	-	mit	0					179
Q5ZKQ8 UniProt NPD GO	ARL8A_CHICK	ADP-ribosylation factor-like protein 8A	0.08	-	cyt	0	Endosome; late endosome (By similarity). Lysosome (By similarity)				186
Q6P8C8 UniProt NPD GO	ARL8A_XENTR	ADP-ribosylation factor-like protein 8A (ADP-ribosylation factor-like protein 10B)	0.08	-	cyt	0	Endosome; late endosome (By similarity). Lysosome (By similarity)				186
Q96BM9 UniProt NPD GO	ARL8A_HUMAN	ADP-ribosylation factor-like protein 8A (ADP-ribosylation factor-like protein 10B) (Novel small G pr ...	0.08	-	cyt	0	Endosome; late endosome. Lysosome	cytoplasm [IDA] midbody [IDA] spindle midzone [IDA]		1ZD9	186

You are viewing entries 67401 to 67450 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.