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
Q4PHA8 UniProt NPD GO	BRO1_USTMA	Vacuolar protein-sorting protein BRO1 (BRO domain-containing protein 1)	0.58	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				1076
Q6CJL0 UniProt NPD GO	SNF7_KLULA	Vacuolar sorting protein SNF7 (Vacuolar protein sorting-associated protein VPS32)	0.58	-	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				232
Q02725 UniProt NPD GO	VTC3_YEAST	Vacuolar transporter chaperone 3 (Phosphate metabolism protein 2)	0.58	-	end	3	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuolar membrane [IDA]			835
P37370 UniProt NPD GO	VRP1_YEAST	Verprolin	0.58	-	nuc	0		actin cortical patch [IDA]			817
P48616 UniProt NPD GO	VIME_BOVIN	Vimentin	0.58	-	mit	0		cytoplasm [ISS] intermediate filament [ISS]			465
P08670 UniProt NPD GO	VIME_HUMAN	Vimentin	0.58	-	mit	0		cytoplasm [IDA] cytoskeleton [TAS] intermediate filament [IDA]	193060	1GK7	465
P02544 UniProt NPD GO	VIME_MESAU	Vimentin	0.58	-	mit	0		cytoplasm [ISS] intermediate filament [ISS]			464
P20152 UniProt NPD GO	VIME_MOUSE	Vimentin	0.58	-	mit	0		cytoplasm [ISS] type III intermediate filament [TAS]			465
Q5R1W8 UniProt NPD GO	VIME_PANTR	Vimentin	0.58	-	mit	0					465
P31000 UniProt NPD GO	VIME_RAT	Vimentin	0.58	-	mit	0	Nucleus; nucleoplasm; nuclear matrix	cytoplasm [ISS] type III intermediate filament [TAS]			465
P24790 UniProt NPD GO	VIM4_XENLA	Vimentin 4	0.58	-	mit	0					463
P21614 UniProt NPD GO	VTDB_MOUSE	Vitamin D-binding protein precursor (DBP) (Group-specific component) (Gc-globulin) (VDB)	0.58	-	exc	0	Secreted protein				476
Q9JJV4 UniProt NPD GO	CCG4_MOUSE	Voltage-dependent calcium channel gamma-4 subunit (Neuronal voltage-gated calcium channel gamma-4 su ...	0.58	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				327
P87141 UniProt NPD GO	MIP1_SCHPO	WD repeat protein mip1	0.58	-	end	0	Cytoplasm	cytoplasm [IDA]			1313
Q15007 UniProt NPD GO	WTAP_HUMAN	Wilms' tumor 1-associating protein (WT1-associated protein) (Putative pre-mRNA-splicing regulator fe ...	0.58	-	nuc	0	Nucleus; nucleolus	nuclear membrane [IDA] nucleus [IDA]	605442		396
Q9ER69 UniProt NPD GO	WTAP_MOUSE	Wilms' tumor 1-associating protein (WT1-associated protein) (Putative pre-mRNA-splicing regulator fe ...	0.58	-	nuc	0	Nucleus; nucleolus (By similarity)	nucleoplasm [IDA]			396
Q86Y38 UniProt NPD GO	XYLT1_HUMAN	Xylosyltransferase 1 (EC 2.4.2.26) (Xylosyltransferase I) (XylT-I) (XT-I) (Peptide O-xylosyltransfer ...	0.58	+	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...		608124		959
Q52V16 UniProt NPD GO	ZFY_GORGO	Zinc finger Y-chromosomal protein	0.58	+	nuc	0	Nucleus				801
P10754 UniProt NPD GO	ZFP13_MOUSE	Zinc finger protein 13 (Zfp-13) (Krox-8 protein)	0.58	-	nuc	0	Nucleus (Potential)				512
P49910 UniProt NPD GO	ZN165_HUMAN	Zinc finger protein 165 (LD65) (Zinc finger and SCAN domain-containing protein 7)	0.58	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	600834		485
Q9HBT7 UniProt NPD GO	ZN287_HUMAN	Zinc finger protein 287	0.58	-	nuc	0	Nucleus (Probable)				754
P17040 UniProt NPD GO	ZNF31_HUMAN	Zinc finger protein 31 (Zinc finger protein KOX29) (Zinc finger and SCAN domain-containing protein 2 ...	0.58	-	nuc	0	Nucleus (Potential)				977
Q53GI3 UniProt NPD GO	ZN394_HUMAN	Zinc finger protein 394	0.58	-	nuc	0	Nucleus (Potential)				561
Q9Z2K3 UniProt NPD GO	ZN394_RAT	Zinc finger protein 394 (Zinc finger protein 94) (Zfp-94) (Zinc finger protein Y1) (RLZF-Y)	0.58	-	nuc	0	Nucleus (Potential)				536
Q96JC4 UniProt NPD GO	ZN479_HUMAN	Zinc finger protein 479 (Zinc finger protein Kr19) (HKr19)	0.58	-	nuc	0	Nucleus (Potential)				524
Q6ZNG1 UniProt NPD GO	ZN600_HUMAN	Zinc finger protein 600	0.58	-	nuc	0	Nucleus (Probable)				722
Q9H0M5 UniProt NPD GO	ZN700_HUMAN	Zinc finger protein 700	0.58	-	nuc	0	Nucleus (Potential)				742
Q13433 UniProt NPD GO	S39A6_HUMAN	Zinc transporter SLC39A6 precursor (Solute carrier family 39 member 6) (Estrogen-regulated protein L ...	0.58	+	end	6	Cell membrane; multi-pass membrane protein		608731		749
Q9FFX4 UniProt NPD GO	KNU_ARATH	Zinc-finger protein KNUCKLES	0.58	-	nuc	0	Nucleus (Probable)				161
Q3UEI1 UniProt NPD GO	PDE4C_MOUSE	cAMP-specific 3',5'-cyclic phosphodiesterase 4C (EC 3.1.4.17)	0.58	-	nuc	0					686
Q61410 UniProt NPD GO	KGP2_MOUSE	cGMP-dependent protein kinase 2 (EC 2.7.11.12) (CGK 2) (cGKII) (Type II cGMP-dependent protein kinas ...	0.58	-	cyt	0					762
Q9P6M8 UniProt NPD GO	PABPX_SCHPO	mRNA export factor crp79 (Polyadenylate-binding protein crp79) (Poly(A)-binding protein) (PABP) (Mei ...	0.58	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA]			710
Q09807 UniProt NPD GO	PALA_SCHPO	pH-response regulator protein palA/rim20	0.58	-	nuc	0					701
Q52FM1 UniProt NPD GO	PALF_MAGGR	pH-response regulator protein palF/RIM8	0.58	-	nuc	0					770
Q9TLW9 UniProt NPD GO	TILS_CYACA	tRNA(Ile)-lysidine synthase (EC 6.3.4.-) (tRNA(Ile)-lysidine synthetase) (tRNA(Ile)-2-lysyl-cytidine ...	0.58	-	cyt	0	Plastid; chloroplast				314
Q99002 UniProt NPD GO	1433_TRIHA	14-3-3 protein homolog (Th1433)	0.57	+	nuc	0					262
Q60432 UniProt NPD GO	OXRP_CRIGR	150 kDa oxygen-regulated protein precursor (Orp150) (Hypoxia up-regulated 1) (170 kDa glucose-regula ...	0.57	-	gol	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				999
O61199 UniProt NPD GO	ODO1_CAEEL	2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2) (Alpha-ketoglutarate ...	0.57	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				1029
Q8HXY4 UniProt NPD GO	ODBA_MACFA	2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial precursor (EC 1.2.4.4) (Branched-chain a ...	0.57	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				445
Q5AYZ1 UniProt NPD GO	RT10_EMENI	30S ribosomal protein S10, mitochondrial precursor (Mitochondrial ribosomal small subunit protein 10 ...	0.57	-	mit	0	Mitochondrion (By similarity)				272
P49697 UniProt NPD GO	EM55_FUGRU	55 kDa erythrocyte membrane protein (p55) (Membrane protein, palmitoylated 1)	0.57	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				467
Q95ZE8 UniProt NPD GO	RL14_DROVI	60S ribosomal protein L14	0.57	-	nuc	0		ribosome [ISS]			160
P61369 UniProt NPD GO	RL15_SILAS	60S ribosomal protein L15	0.57	-	nuc	0					203
P17932 UniProt NPD GO	RL32P_MOUSE	60S ribosomal protein L32'	0.57	-	nuc	0					134
O97231 UniProt NPD GO	RL44_PLAF7	60S ribosomal protein L44	0.57	+	nuc	0					103
Q9HF88 UniProt NPD GO	RL44_CRYNE	60S ribosomal protein L44 (60S ribosomal protein L41)	0.57	-	nuc	0					105
Q9SAI5 UniProt NPD GO	RL71_ARATH	60S ribosomal protein L7-1	0.57	+	nuc	0					247
P60040 UniProt NPD GO	RL72_ARATH	60S ribosomal protein L7-2	0.57	-	cyt	0					242
Q966C6 UniProt NPD GO	RL7A_CAEEL	60S ribosomal protein L7a	0.57	-	nuc	0					264
Q01241 UniProt NPD GO	NF70_LOLPE	70 kDa neurofilament protein (NF70)	0.57	-	nuc	0					615

You are viewing entries 20551 to 20600 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.