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
Q9CRD4 UniProt NPD GO	DBND2_MOUSE	Dysbindin domain-containing protein 2	0.41	-	nuc	0					158
Q9EQP2 UniProt NPD GO	EHD4_MOUSE	EH-domain-containing protein 4 (mPAST2)	0.41	-	nuc	0					541
P41969 UniProt NPD GO	ELK1_MOUSE	ETS domain-containing protein Elk-1	0.41	+	nuc	0	Nucleus				429
Q96KS0 UniProt NPD GO	EGLN2_HUMAN	Egl nine homolog 2 (EC 1.14.11.-) (Hypoxia-inducible factor prolyl hydroxylase 1) (HIF-prolyl hydrox ...	0.41	-	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]	606424		407
Q68FR6 UniProt NPD GO	EF1G_RAT	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.41	-	cyt	0					436
O93796 UniProt NPD GO	EF3_CANGA	Elongation factor 3 (EF-3)	0.41	+	nuc	0					1045
O43281 UniProt NPD GO	EFS_HUMAN	Embryonal Fyn-associated substrate (HEFS)	0.41	-	nuc	0		cytoplasm [TAS]	609906		561
P54197 UniProt NPD GO	CHI2_COCIM	Endochitinase 2 precursor (EC 3.2.1.14)	0.41	-	nuc	0					860
P97740 UniProt NPD GO	EDN1_CAVPO	Endothelin-1 precursor (ET-1) (Preproendothelin-1) (PPET1) (Fragment)	0.41	-	nuc	0	Secreted protein				149
Q9JHL3 UniProt NPD GO	ECEL1_RAT	Endothelin-converting enzyme-like 1 (EC 3.4.24.-) (Xce protein) (Damage-induced neuronal endopeptida ...	0.41	-	cyt	1	Membrane; single-pass type II membrane protein				775
Q3SZC0 UniProt NPD GO	ERH_BOVIN	Enhancer of rudimentary homolog	0.41	-	nuc	0					104
P84090 UniProt NPD GO	ERH_HUMAN	Enhancer of rudimentary homolog	0.41	-	nuc	0			601191	1W9G	104
P84089 UniProt NPD GO	ERH_MOUSE	Enhancer of rudimentary homolog	0.41	-	nuc	0				1WZ7	104
P0C0K7 UniProt NPD GO	EPHB6_RAT	Ephrin type-B receptor 6 precursor (Tyrosine-protein kinase-defective receptor EPH-6)	0.41	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				1013
O15197 UniProt NPD GO	EPHB6_HUMAN	Ephrin type-B receptor 6 precursor (Tyrosine-protein kinase-defective receptor EPH-6) (HEP)	0.41	-	end	1	Membrane; single-pass type I membrane protein		602757		1006
Q5RDJ3 UniProt NPD GO	MA2B2_PONPY	Epididymis-specific alpha-mannosidase precursor (EC 3.2.1.24) (Mannosidase alpha class 2B member 2)	0.41	-	mit	0	Secreted protein (Potential)				1009
P49157 UniProt NPD GO	EPO_PIG	Erythropoietin precursor	0.41	-	exc	1 *	Secreted protein				194
Q00387 UniProt NPD GO	EP45_XENLA	Estrogen-regulated protein EP45 precursor	0.41	-	end	0	Secreted protein; extracellular space				436
Q41741 UniProt NPD GO	IF4A_MAIZE	Eukaryotic initiation factor 4A (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A) (eIF-4A)	0.41	-	cyt	0					410
P41377 UniProt NPD GO	IF4A2_ARATH	Eukaryotic initiation factor 4A-2 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-2) (eIF-4A-2) (DEAD ...	0.41	-	cyt	0	Cytoplasm (By similarity)				412
P41380 UniProt NPD GO	IF4A3_NICPL	Eukaryotic initiation factor 4A-3 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-3) (eIF-4A-3)	0.41	-	cyt	0					391
Q4R8K5 UniProt NPD GO	IF4A1_MACFA	Eukaryotic initiation factor 4A-I (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-1) (eIF4A-I) (eIF-4 ...	0.41	-	nuc	0					406
Q5R5F5 UniProt NPD GO	IF4A1_PONPY	Eukaryotic initiation factor 4A-I (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-1) (eIF4A-I) (eIF-4 ...	0.41	-	nuc	0					406
P56820 UniProt NPD GO	IF37_ARATH	Eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta) (eIF3d) (p66)	0.41	-	nuc	0					591
Q8JZQ9 UniProt NPD GO	IF39_MOUSE	Eukaryotic translation initiation factor 3 subunit 9 (eIF-3 eta) (eIF3 p116)	0.41	-	cyt	0					803
O74846 UniProt NPD GO	SEC6_SCHPO	Exocyst complex component sec6	0.41	-	cyt	0	Cytoplasm (By similarity)	cell cortex of cell tip [IDA] exocyst [IDA]			730
P14068 UniProt NPD GO	XPO1_SCHPO	Exportin-1 (Chromosome region maintenance protein 1) (Caffeine resistance protein 2)	0.41	-	cyt	0	Nucleus. Localized in the nucleus and at its periphery	nucleus [IDA]			1078
P48603 UniProt NPD GO	CAPZB_DROME	F-actin capping protein subunit beta	0.41	-	nuc	0					276
Q6AY27 UniProt NPD GO	FBX17_RAT	F-box only protein 17	0.41	-	mit	0					250
Q9UJT9 UniProt NPD GO	FBXL7_HUMAN	F-box/LRR-repeat protein 7 (F-box and leucine-rich repeat protein 7) (F-box protein FBL6/FBL7)	0.41	-	nuc	0		ubiquitin ligase complex [NAS]	605656		491
Q9Y297 UniProt NPD GO	FBW1A_HUMAN	F-box/WD repeat protein 1A (F-box and WD repeats protein beta-TrCP) (E3RSIkappaB) (pIkappaBalpha-E3 ...	0.41	-	nuc	0	Cytoplasm		603482	1P22	605
Q13158 UniProt NPD GO	FADD_HUMAN	FADD protein (FAS-associating death domain-containing protein) (Mediator of receptor induced toxicit ...	0.41	-	nuc	0			602457	1E41	208
Q684R7 UniProt NPD GO	FREM1_MOUSE	FRAS1-related extracellular matrix protein 1 precursor (Protein QBRICK)	0.41	-	cyt	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Localizes at the bas ...				2191
Q99PF5 UniProt NPD GO	FUBP2_RAT	Far upstream element-binding protein 2 (FUSE-binding protein 2) (KH type-splicing regulatory protein ...	0.41	-	nuc	0	Nucleus. Cytoplasm. A small proportion is also found in the cytoplasm of neuronal cell bodies and de ...				721
Q71SP7 UniProt NPD GO	FAS_BOVIN	Fatty acid synthase (EC 2.3.1.85) [Includes: [Acyl-carrier-protein] S-acetyltransferase (EC 2.3.1.38 ...	0.41	-	vac	0					2513
Q28275 UniProt NPD GO	FINC_CANFA	Fibronectin (FN) (Fragment)	0.41	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				522
P11276 UniProt NPD GO	FINC_MOUSE	Fibronectin precursor (FN)	0.41	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [IDA]		2MFN	2477
O42182 UniProt NPD GO	FBLN1_BRARE	Fibulin-1 precursor	0.41	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				681
Q5REN1 UniProt NPD GO	FBLI1_PONPY	Filamin-binding LIM protein 1	0.41	-	nuc	0	Cytoplasm; cell cortex (By similarity). Associated with actin stress fiber at cell-ECM focal adhesio ...				375
Q63246 UniProt NPD GO	FOXC2_RAT	Forkhead box protein C2 (Brain factor 3) (BF-3) (HFH-BF-3) (Fragment)	0.41	+	nuc	0	Nucleus (Probable)				101
P51113 UniProt NPD GO	FMR1A_XENLA	Fragile X mental retardation protein 1 homolog-A (Protein FMR-1-A) (FMRP-A) (XFMR1-A)	0.41	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				564
Q96GT9 UniProt NPD GO	GAGD3_HUMAN	G antigen family D member 3 (Protein XAGE-2)	0.41	-	nuc	0			300416		111
Q8WTP9 UniProt NPD GO	GAGD4_HUMAN	G antigen family D member 4 (Placenta-specific gene 6 protein) (Protein XAGE-3)	0.41	-	nuc	0					111
Q8WTQ7 UniProt NPD GO	GRK7_HUMAN	G protein-coupled receptor kinase 7 precursor (EC 2.7.11.16) (G protein-coupled receptor kinase GRK7 ...	0.41	+	cyt	0	Membrane; lipid-anchor		606987		553
P13837 UniProt NPD GO	G156_PARPR	G surface protein, allelic form 156 precursor	0.41	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				2715
Q7TMA4 UniProt NPD GO	GP120_MOUSE	G-protein coupled receptor 120 (G-protein coupled receptor GT01)	0.41	-	end	7 *	Membrane; multi-pass membrane protein				361
P04962 UniProt NPD GO	CCNA_SPISO	G2/mitotic-specific cyclin-A	0.41	-	cyt	0					422
P56201 UniProt NPD GO	G6PE_RABIT	GDH/6PGL endoplasmic bifunctional protein [Includes: Glucose 1-dehydrogenase (EC 1.1.1.47) (Hexose-6 ...	0.41	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Microsomes, endoplasmic reticulum lumen				763
Q5R8Q7 UniProt NPD GO	GTPB1_PONPY	GTP-binding protein 1 (G-protein 1) (GP-1) (GP1)	0.41	-	mit	0					584
P46943 UniProt NPD GO	GUF1_YEAST	GTP-binding protein GUF1 (GTPase GUF1)	0.41	+	mit	0		mitochondrion [IDA]			645

You are viewing entries 31051 to 31100 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.