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
Q9BBS7 UniProt NPD GO	RPOC2_LOTJA	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.87	-	nuc	0	Plastid; chloroplast				1332
P12227 UniProt NPD GO	RPOC2_PEA	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.87	+	nuc	0	Plastid; chloroplast				1163
P59764 UniProt NPD GO	DOCK4_MOUSE	Dedicator of cytokinesis protein 4	0.87	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity)				1978
P18170 UniProt NPD GO	DEC12_DROME	Defective chorion-1 protein, FC106 isoform precursor [Contains: Defective chorion-1 protein, FC106 i ...	0.87	-	exc	0	Secreted protein	chorion [IDA] extracellular region [IDA]			950
P24585 UniProt NPD GO	DEG1_CAEEL	Degenerin deg-1 (Degeneration of certain neurons protein 1)	0.87	-	mit	2	Membrane; multi-pass membrane protein				778
Q9Y238 UniProt NPD GO	DLEC1_HUMAN	Deleted in lung and esophageal cancer protein 1 (Deleted in lung cancer protein 1) (DLC-1)	0.87	-	mit	0	Cytoplasm	cytoplasm [IDA]	604050		1755
O43150 UniProt NPD GO	DDEF2_HUMAN	Development and differentiation-enhancing factor 2 (Pyk2 C-terminus-associated protein) (PAP) (Paxil ...	0.87	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein. Cell mem ...		603817		1006
Q6PFD5 UniProt NPD GO	DLGP3_MOUSE	Disks large-associated protein 3 (DAP-3) (SAP90/PSD-95-associated protein 3) (SAPAP3) (PSD-95/SAP90- ...	0.87	-	nuc	0	Cell membrane; peripheral membrane protein. Postsynaptic density of neuronal cells	synapse [IDA]			977
P97838 UniProt NPD GO	DLGP3_RAT	Disks large-associated protein 3 (DAP-3) (SAP90/PSD-95-associated protein 3) (SAPAP3) (PSD-95/SAP90- ...	0.87	-	nuc	0	Cell membrane; peripheral membrane protein. Postsynaptic density of neuronal cells	dendritic spine [IDA] membrane fraction [IDA] postsynaptic membrane [IDA]			977
Q9V3D5 UniProt NPD GO	DYRK2_DROME	Dual specificity tyrosine-phosphorylation-regulated kinase 2 (EC 2.7.12.1) (dDyrk2) (Protein smell i ...	0.87	-	nuc	0	Cytoplasm	cytosol [IDA]			722
O08788 UniProt NPD GO	DYNA_MOUSE	Dynactin-1 (150 kDa dynein-associated polypeptide) (DP-150) (DAP-150) (p150-glued)	0.87	-	end	0	Cytoplasm				1281
Q9C1M7 UniProt NPD GO	DYHC_ASHGO	Dynein heavy chain, cytosolic (DYHC)	0.87	-	nuc	0	Cytoplasm (By similarity). Probably binds indirectly to the inner plasma membrane (By similarity)				4083
Q9VDW3 UniProt NPD GO	DMDB_DROME	Dystrophin, isoform B	0.87	-	nuc	0		cytoskeleton [ISS] dystrophin-associated glycoprotein complex [ISS]			1669
Q13191 UniProt NPD GO	CBLB_HUMAN	E3 ubiquitin-protein ligase CBL-B (EC 6.3.2.-) (Signal transduction protein CBL-B) (SH3-binding prot ...	0.87	-	nuc	0	Cytoplasm. Upon EGF stimulation, associates with endocytic vesicles		604491	2BZ8	982
Q8BL66 UniProt NPD GO	EEA1_MOUSE	Early endosome antigen 1	0.87	-	nuc	0	Cytoplasm (By similarity). Endosome; early endosome; early endosomal membrane; peripheral membrane p ...	early endosome [IDA]			1411
Q75E67 UniProt NPD GO	ELOA1_ASHGO	Elongin-A	0.87	-	nuc	0					332
Q9P6L5 UniProt NPD GO	SLA2_SCHPO	Endocytosis protein end4 (SLA2 protein homolog)	0.87	-	nuc	0	Cytoplasm. Localizes at cell ends during interphase and to the medial ring at cell division	actin cortical patch [IDA] cell cortex of cell tip [IDA]			1092
Q99814 UniProt NPD GO	EPAS1_HUMAN	Endothelial PAS domain-containing protein 1 (EPAS-1) (Member of PAS protein 2) (MOP2) (Hypoxia-induc ...	0.87	-	nuc	0			603349	1P97	870
Q5R9R1 UniProt NPD GO	EDRF1_PONPY	Erythroid differentiation-related factor 1	0.87	-	nuc	0	Nucleus (Probable)				1204
Q9YHZ7 UniProt NPD GO	ESR1_ICTPU	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.87	-	nuc	0	Nucleus				617
P57753 UniProt NPD GO	ESR1_MICUN	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha) (Fragment)	0.87	-	nuc	0	Nucleus				525
O60841 UniProt NPD GO	IF2P_HUMAN	Eukaryotic translation initiation factor 5B (eIF-5B) (Translation initiation factor IF-2)	0.87	+	nuc	0			606086		1220
Q8R3S6 UniProt NPD GO	EXOC1_MOUSE	Exocyst complex component 1 (Exocyst complex component Sec3)	0.87	-	nuc	0					893
O35250 UniProt NPD GO	EXOC7_MOUSE	Exocyst complex component 7 (Exocyst complex component Exo70)	0.87	+	nuc	0	Cytoplasm; cytosol. Cell membrane; peripheral membrane protein. Translocates, as a preformed complex ...				697
Q04110 UniProt NPD GO	ECM11_YEAST	Extracellular matrix protein 11	0.87	-	nuc	0	Nucleus	nucleus [IDA]			302
P40458 UniProt NPD GO	ECM37_YEAST	Extracellular matrix protein 37	0.87	+	nuc	1					529
Q9NWN3 UniProt NPD GO	FBX34_HUMAN	F-box only protein 34	0.87	-	nuc	0			609104		711
Q8C180 UniProt NPD GO	FRS2_MOUSE	Fibroblast growth factor receptor substrate 2 (FGFR substrate 2) (Suc1-associated neurotrophic facto ...	0.87	-	nuc	0	Membrane; lipid-anchor	cytoplasm [IDA] integral to plasma membrane [ISS] plasma membrane [IDA]			507
P20930 UniProt NPD GO	FILA_HUMAN	Filaggrin	0.87	-	nuc	0		cytoplasmic membrane-bound vesicle [IDA] intermediate filament [NAS]	146700		4061
P32028 UniProt NPD GO	FD4_DROME	Fork head domain-containing protein FD4	0.87	+	nuc	0	Nucleus				372
Q3BJS3 UniProt NPD GO	FOXN3_XENLA	Forkhead box protein N3	0.87	+	nuc	0	Nucleus (Potential)				485
Q28G71 UniProt NPD GO	FOXN3_XENTR	Forkhead box protein N3	0.87	+	nuc	0	Nucleus (Potential)				464
Q28H65 UniProt NPD GO	FOXN5_XENTR	Forkhead box protein N5	0.87	-	nuc	0	Nucleus (Potential)				293
O43058 UniProt NPD GO	SEP1_SCHPO	Forkhead protein sep1	0.87	-	nuc	0	Nucleus	nucleus [IDA]			663
P13365 UniProt NPD GO	CG13_YEAST	G1/S-specific cyclin CLN3	0.87	-	mit	0		nucleus [IDA]			580
Q8WWL7 UniProt NPD GO	CCNB3_HUMAN	G2/mitotic-specific cyclin-B3	0.87	-	nuc	0	Nucleus		300456		1395
P40187 UniProt NPD GO	PIG2_YEAST	GSY2-interacting protein PIG2	0.87	+	nuc	0		cytoplasm [IDA]			538
Q9NUQ3 UniProt NPD GO	TXLNG_HUMAN	Gamma-taxilin (Lipopolysaccharide-specific response protein 5)	0.87	+	nuc	0					528
Q8WUA4 UniProt NPD GO	TF3C2_HUMAN	General transcription factor 3C polypeptide 2 (Transcription factor IIIC-subunit beta) (TF3C-beta) ( ...	0.87	-	nuc	0	Nucleus		604883		911
Q8NEA9 UniProt NPD GO	GMCLL_HUMAN	Germ cell-less protein-like 1-like	0.87	-	mit	0	Nucleus; nucleoplasm; nuclear matrix (By similarity)				526
Q92896 UniProt NPD GO	GSLG1_HUMAN	Golgi apparatus protein 1 precursor (Golgi sialoglycoprotein MG-160) (E-selectin ligand 1) (ESL-1) ( ...	0.87	-	cyt	1	Golgi apparatus; Golgi membrane; single-pass type I membrane protein	Golgi membrane [TAS]	600753		1179
Q9CR59 UniProt NPD GO	G45IP_MOUSE	Growth arrest and DNA-damage-inducible proteins-interacting protein 1	0.87	+	mit	0	Nucleus (By similarity)				222
Q7PD79 UniProt NPD GO	GNAS_ANOGA	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.87	-	nuc	0					383
Q292P9 UniProt NPD GO	GNAS_DROPS	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.87	-	nuc	0		plasma membrane [ISS]			382
Q7ZX41 UniProt NPD GO	GNL3_XENLA	Guanine nucleotide-binding protein-like 3 (Nucleostemin-like protein)	0.87	+	nuc	0	Nucleus (By similarity)	nucleolus [ISS] nucleus [ISS]			542
Q90690 UniProt NPD GO	HAND2_CHICK	Heart- and neural crest derivatives-expressed protein 2 (Deciduum, heart, autonomic nervous system a ...	0.87	+	nuc	0					216
P22121 UniProt NPD GO	HSF_KLULA	Heat shock factor protein (HSF) (Heat shock transcription factor) (HSTF)	0.87	-	nuc	0	Nucleus			3HTS	677
Q76LW2 UniProt NPD GO	H6ST2_CHICK	Heparan-sulfate 6-O-sulfotransferase 2 (EC 2.8.2.-) (HS6ST-2) (cHS6ST-2)	0.87	-	exc	1 *	Membrane; single-pass type II membrane protein (Potential)				403
Q80T19 UniProt NPD GO	HEPC2_MOUSE	Hepcidin-2 precursor	0.87	-	exc	0	Secreted protein				83
Q7S9B6 UniProt NPD GO	ESA1_NEUCR	Histone acetyltransferase esa-1 (EC 2.3.1.48)	0.87	-	nuc	0	Nucleus (By similarity)				506

You are viewing entries 5551 to 5600 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.