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
O73698 UniProt NPD GO	PUT2_FUGRU	Putative protein 2 (PUT2) (Fragment)	0.21	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	late endosome [ISS] lysosome [ISS]			187
Q9M158 UniProt NPD GO	Y4105_ARATH	Putative protein At4g01050	0.21	-	nuc	0				1VEE	466
P78860 UniProt NPD GO	YBOF_SCHPO	Putative ribosomal RNA methyltransferase C2G2.15c (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransfera ...	0.21	-	cyt	0					218
Q12385 UniProt NPD GO	ICT1_YEAST	Putative serine protease ICT1 (EC 3.4.21.-) (Increased copper tolerance protein 1)	0.21	-	mit	0					394
Q12026 UniProt NPD GO	YL053_YEAST	Putative uncharacterized protein YLR053C	0.21	-	nuc	0					108
P53979 UniProt NPD GO	YNB3_YEAST	Putative uncharacterized protein YNL013C	0.21	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				125
O00764 UniProt NPD GO	PDXK_HUMAN	Pyridoxal kinase (EC 2.7.1.35) (Pyridoxine kinase)	0.21	-	cyt	0	Cytoplasm		179020	2F7K	312
Q42736 UniProt NPD GO	PPDK_FLAPR	Pyruvate, phosphate dikinase, chloroplast precursor (EC 2.7.9.1) (Pyruvate, orthophosphate dikinase) ...	0.21	-	cyt	0	Plastid; chloroplast				956
P11155 UniProt NPD GO	PPDK_MAIZE	Pyruvate, phosphate dikinase, chloroplast precursor (EC 2.7.9.1) (Pyruvate, orthophosphate dikinase) ...	0.21	-	cyt	0	Plastid; chloroplast			1VBH	947
Q9UUJ0 UniProt NPD GO	PVG5_SCHPO	Pyruvylated Gal-beta-1,3-epitope synthesis protein 5 (PvGal synthesis protein 5)	0.21	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				372
P34149 UniProt NPD GO	RACC_DICDI	RAS-related protein racC	0.21	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				192
Q9ZWI7 UniProt NPD GO	RER1C_ARATH	RER1C protein (AtRER1C)	0.21	-	end	4	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			212
Q5F3B2 UniProt NPD GO	RN166_CHICK	RING finger protein 166	0.21	-	nuc	0					244
Q5XIL0 UniProt NPD GO	RN167_RAT	RING finger protein 167 precursor	0.21	-	end	1	Membrane; single-pass membrane protein (Potential)				349
Q94BY6 UniProt NPD GO	ATL1I_ARATH	RING-H2 finger protein ATL1I	0.21	-	nuc	1					226
P20756 UniProt NPD GO	HB2P_RABIT	RLA class II histocompatibility antigen, DP beta chain precursor (D10 haplotype)	0.21	-	end	1	Membrane; single-pass type I membrane protein (Potential)				257
Q09696 UniProt NPD GO	MED1_SCHPO	RNA polymerase II mediator complex subunit 1 (RNA polymerase II mediator complex protein pmc2)	0.21	-	mit	0	Nucleus (Probable)	mediator complex [IDA]			454
O14198 UniProt NPD GO	MED18_SCHPO	RNA polymerase II mediator complex subunit 18 (Cell separation protein sep11) (RNA polymerase II med ...	0.21	-	cyt	0		mediator complex [IDA]			207
Q9UKM9 UniProt NPD GO	RALY_HUMAN	RNA-binding protein Raly (hnRNP associated with lethal yellow homolog) (Autoantigen p542)	0.21	-	nuc	0	Nucleus (Probable)	heterogeneous nuclear ribonucleoprotein com... [TAS] nucleus [TAS]		1WF1	306
Q9SU67 UniProt NPD GO	RAC8_ARATH	Rac-like GTP-binding protein ARAC8 (GTPase protein ROP10)	0.21	-	cyt	0	Membrane; lipid-anchor				208
O04369 UniProt NPD GO	RAC1_LOTJA	Rac-like GTP-binding protein RAC1	0.21	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				197
P22278 UniProt NPD GO	RAS1_RHIRA	Ras-like protein 1	0.21	-	cyt	0	Cell membrane; lipid-anchor				203
Q58DS5 UniProt NPD GO	RAB13_BOVIN	Ras-related protein Rab-13	0.21	-	nuc	0	Cell membrane; cell-cell junction; tight junction; lipid-anchor; cytoplasmic side (By similarity). C ...				203
P59190 UniProt NPD GO	RAB15_HUMAN	Ras-related protein Rab-15	0.21	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				212
Q8K386 UniProt NPD GO	RAB15_MOUSE	Ras-related protein Rab-15	0.21	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				212
Q9ULW5 UniProt NPD GO	RAB26_HUMAN	Ras-related protein Rab-26	0.21	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		605455	2G6B	256
O95755 UniProt NPD GO	RAB36_HUMAN	Ras-related protein Rab-36	0.21	-	mit	0	Golgi apparatus; Golgi membrane; lipid-anchor	Golgi apparatus [TAS]	605662		333
Q40523 UniProt NPD GO	RB11A_TOBAC	Ras-related protein Rab11A	0.21	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				216
P29687 UniProt NPD GO	RAB5_TOBAC	Ras-related protein Rab5	0.21	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200
P49800 UniProt NPD GO	RGS5_RAT	Regulator of G-protein signaling 5 (RGS5)	0.21	-	nuc	0					181
Q14257 UniProt NPD GO	RCN2_HUMAN	Reticulocalbin-2 precursor (Calcium-binding protein ERC-55) (E6-binding protein) (E6BP)	0.21	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS]	602584		317
Q13956 UniProt NPD GO	CNCG_HUMAN	Retinal cone rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase gamma-subunit (EC 3.1.4.17) (GM ...	0.21	-	nuc	0			610024		83
O55175 UniProt NPD GO	CNCG_SPETR	Retinal cone rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase gamma-subunit (EC 3.1.4.17) (GM ...	0.21	-	nuc	0					83
Q9SFC6 UniProt NPD GO	GDIR_ARATH	Rho GDP-dissociation inhibitor 1 (Rho GDI-1) (AtRhoGDI1)	0.21	-	nuc	0	Cytoplasm (By similarity)				240
O46530 UniProt NPD GO	RNAS6_SAGOE	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.21	-	exc	0	Secreted protein				150
O46529 UniProt NPD GO	RNAS6_SAISC	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.21	-	exc	0	Secreted protein				150
P23540 UniProt NPD GO	RNMC_MOMCH	Ribonuclease MC (EC 3.1.27.1) (RNase MC)	0.21	-	nuc	0				1V9H	191
P87351 UniProt NPD GO	RNAS1_AXIPR	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.21	-	nuc	0	Secreted protein				124
Q5GAN6 UniProt NPD GO	RNS10_HUMAN	Ribonuclease-like protein 10 precursor	0.21	-	exc	1 *	Secreted protein (By similarity)				216
Q9XG99 UniProt NPD GO	KPRS2_SPIOL	Ribose-phosphate pyrophosphokinase 2, chloroplast precursor (EC 2.7.6.1) (Phosphoribosyl pyrophospha ...	0.21	-	mit	0	Plastid; chloroplast (Potential)				395
Q08961 UniProt NPD GO	RKM1_YEAST	Ribosomal N-lysine methyltransferase 1 (EC 2.1.1.-)	0.21	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			583
P22851 UniProt NPD GO	RIPB_LUFCY	Ribosome-inactivating protein luffin-B (EC 3.2.2.22) (rRNA N-glycosidase)	0.21	-	nuc	0				1NIO	250
P27664 UniProt NPD GO	PDE6A_MOUSE	Rod cGMP-specific 3',5'-cyclic phosphodiesterase alpha-subunit (EC 3.1.4.35) (GMP-PDE alpha)	0.21	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				858
Q3E784 UniProt NPD GO	SLO1_YEAST	SCOCO-like protein 1	0.21	-	nuc	0		cytoplasm [NAS]			85
Q9WUZ7 UniProt NPD GO	SH3BG_MOUSE	SH3 domain-binding glutamic acid-rich protein (SH3BGR protein)	0.21	-	mit	0					214
Q5RCJ9 UniProt NPD GO	SPFH1_PONPY	SPFH domain-containing protein 1 precursor	0.21	-	mit	1 *	Membrane; peripheral membrane protein (Probable)				346
O09181 UniProt NPD GO	UBC9_MESAU	SUMO-1-conjugating enzyme UBC9 (EC 6.3.2.19) (SUMO-1-protein ligase) (Ubiquitin-conjugating enzyme E ...	0.21	-	nuc	0					158
Q5QA93 UniProt NPD GO	HSV2_PICAN	SVP1-like protein 2	0.21	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Cytoplasmic vesicle; cytopl ...				360
Q8IWL8 UniProt NPD GO	STH_HUMAN	Saitohin	0.21	-	nuc	0			607067		128
P24471 UniProt NPD GO	SCHS_LYMST	Schistosomin	0.21	-	nuc	0	Secreted protein				79

You are viewing entries 50001 to 50050 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.