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
Q00941 UniProt NPD GO	CSF2R_MOUSE	Granulocyte-macrophage colony-stimulating factor receptor alpha chain precursor (GM-CSF-R-alpha) (GM ...	0.06	-	end	1	Membrane; single-pass type I membrane protein (Potential)				388
Q03238 UniProt NPD GO	GRAM_RAT	Granzyme M precursor (EC 3.4.21.-) (Met-ase) (Natural killer cell granular protease) (RNK-Met-1) (Fr ...	0.06	-	nuc	0	Granules of large granular lymphocytes				258
Q6GPJ9 UniProt NPD GO	GRB2B_XENLA	Growth factor receptor-bound protein 2-B (Adapter protein GRB2-B) (SH2/SH3 adapter GRB2-B)	0.06	-	cyt	0		cytosol [ISS]			229
O08725 UniProt NPD GO	GHSR_RAT	Growth hormone secretagogue receptor type 1 (GHS-R) (GH-releasing peptide receptor) (GHRP) (Ghrelin ...	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]			364
P32082 UniProt NPD GO	GHRHR_MOUSE	Growth hormone-releasing hormone receptor precursor (GHRH receptor) (GRF receptor) (GRFR)	0.06	-	end	5 *	Membrane; multi-pass membrane protein				423
O46678 UniProt NPD GO	GROA_SHEEP	Growth-regulated alpha protein precursor (CXCL1)	0.06	-	exc	0	Secreted protein				103
O46676 UniProt NPD GO	GROA_BOVIN	Growth-regulated protein homolog alpha precursor (GRO-alpha)	0.06	-	mit	0	Secreted protein				104
Q08326 UniProt NPD GO	MSS4_RAT	Guanine nucleotide exchange factor MSS4 (Rab-interacting factor)	0.06	-	cyt	0				1HXR	123
P63214 UniProt NPD GO	GBG3_BOVIN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-3 subunit precursor	0.06	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				75
P63215 UniProt NPD GO	GBG3_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-3 subunit precursor	0.06	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		608941		75
P63216 UniProt NPD GO	GBG3_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-3 subunit precursor	0.06	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				75
Q9UK08 UniProt NPD GO	GBG8_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-8 subunit precursor (Gamma-9)	0.06	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	extracellular region [NAS]			70
Q93134 UniProt NPD GO	GBLP_BIOGL	Guanine nucleotide-binding protein subunit beta 2-like 1 (Receptor of activated protein kinase C) (R ...	0.06	-	cyt	0					316
O42248 UniProt NPD GO	GBLP_BRARE	Guanine nucleotide-binding protein subunit beta 2-like 1 (Receptor of activated protein kinase C) (R ...	0.06	-	cyt	0					317
O42249 UniProt NPD GO	GBLP_ORENI	Guanine nucleotide-binding protein subunit beta 2-like 1 (Receptor of activated protein kinase C) (R ...	0.06	-	cyt	0					317
P32621 UniProt NPD GO	GDA1_YEAST	Guanosine-diphosphatase (EC 3.6.1.42) (GDPase)	0.06	-	vac	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi apparatus [TAS]			518
P14434 UniProt NPD GO	HA2B_MOUSE	H-2 class II histocompatibility antigen, A-B alpha chain precursor (IAalpha)	0.06	-	end	1	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [IDA] lysosome [IDA] MHC class II protein complex [IDA] plasma membrane [IDA]		1MUJ	256
P01910 UniProt NPD GO	HA2K_MOUSE	H-2 class II histocompatibility antigen, A-K alpha chain precursor	0.06	-	end	1	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [IDA] lysosome [IDA] MHC class II protein complex [IDA] plasma membrane [IDA]		1JL4	256
P04227 UniProt NPD GO	HA2Q_MOUSE	H-2 class II histocompatibility antigen, A-Q alpha chain (Fragment)	0.06	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [IDA] lysosome [IDA] MHC class II protein complex [IDA] plasma membrane [IDA]			221
P14437 UniProt NPD GO	HA2S_MOUSE	H-2 class II histocompatibility antigen, A-S alpha chain	0.06	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				233
P14438 UniProt NPD GO	HA2U_MOUSE	H-2 class II histocompatibility antigen, A-U alpha chain (Fragment)	0.06	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [IDA] lysosome [IDA] MHC class II protein complex [IDA] plasma membrane [IDA]		1U3H	227
P04231 UniProt NPD GO	HB23_MOUSE	H-2 class II histocompatibility antigen, E-S beta chain (Fragment)	0.06	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				232
Q9P7H0 UniProt NPD GO	NHP2_SCHPO	H/ACA ribonucleoprotein complex subunit 2 (H/ACA snoRNP protein NHP2) (High mobility group-like nucl ...	0.06	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA] small nucleolar ribonucleoprotein complex [ISS]			154
P63121 UniProt NPD GO	VPK5_HUMAN	HERV-K_19p13.11 provirus ancestral Pro protein (EC 3.4.23.-) (HERV-K113 envelope protein) (Protease) ...	0.06	-	cyt	0					156
P63131 UniProt NPD GO	VPK12_HUMAN	HERV-K_1q22 provirus ancestral Pro protein (EC 3.4.23.-) (HERV-K102 Pro protein) (HERV-K(III) Pro pr ...	0.06	-	cyt	0					156
P10265 UniProt NPD GO	VPK10_HUMAN	HERV-K_5q33.3 provirus ancestral Pro protein (EC 3.4.23.-) (HERV-K10 Pro protein) (HERV-K107 Pro pro ...	0.06	-	cyt	0					156
Q9Y6I0 UniProt NPD GO	VPK2_HUMAN	HERV-K_7p22.1 provirus ancestral Pro protein (EC 3.4.23.-) (HERV-K(HML-2.HOM) Pro protein) (HERV-K10 ...	0.06	-	cyt	0					156
Q9BW72 UniProt NPD GO	HIG2A_HUMAN	HIG1 domain family member 2A	0.06	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				106
Q9QZ23 UniProt NPD GO	HIRP5_MOUSE	HIRA-interacting protein 5 (mHIRIP5)	0.06	-	cyt	0		cytosol [IDA]		1VEH	199
P79483 UniProt NPD GO	2B31_HUMAN	HLA class II histocompatibility antigen, DRB3-1 beta chain precursor (MHC class I antigen DRB3*1)	0.06	-	end	1 *	Membrane; single-pass type I membrane protein				266
O74261 UniProt NPD GO	HSP60_CANAL	Heat shock protein 60, mitochondrial precursor (60 kDa chaperonin) (Protein Cpn60)	0.06	-	mit	0	Mitochondrion				566
Q7ZWG6 UniProt NPD GO	HCP1_BRARE	Heme carrier protein 1	0.06	-	end	9	Membrane; multi-pass membrane protein (By similarity)				481
P22765 UniProt NPD GO	HEMTB_LINUN	Hemerythrin beta chain	0.06	-	cyt	0					117
P83180 UniProt NPD GO	HCYB_PONLE	Hemocyanin B chain	0.06	-	cyt	1	Secreted protein; extracellular space				566
P82300 UniProt NPD GO	HCY5_HOMAM	Hemocyanin subunit 5 (Fragment)	0.06	-	cyt	0	Secreted protein; extracellular space				27
P07413 UniProt NPD GO	HBAD_PASMO	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.06	-	cyt	0					141
Q9YGW1 UniProt NPD GO	HBB_MUSGR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.06	-	cyt	0				1GCW	137
P09105 UniProt NPD GO	HBAT_HUMAN	Hemoglobin subunit theta-1 (Hemoglobin theta-1 chain) (Theta-1-globin)	0.06	-	mit	0		hemoglobin complex [TAS]	142240		141
Q7M413 UniProt NPD GO	GLB5_OLIMA	Hemoglobin, extracellular, major globin chain a5	0.06	-	nuc	0	Secreted protein			2D2N	142
Q7M418 UniProt NPD GO	GLBC_OLIMA	Hemoglobin, extracellular, major globin chain c	0.06	-	mit	0	Secreted protein			2D2N	147
P26227 UniProt NPD GO	HTIB_MANSE	Hemolymph trypsin inhibitor B (BPI-type) (Fragment)	0.06	-	cyt	0					53
P20058 UniProt NPD GO	HEMO_RABIT	Hemopexin precursor	0.06	-	exc	0	Secreted protein			1QJS	460
O93995 UniProt NPD GO	COQ3_CANAL	Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (EC 2.1.1.114) (Dihydroxyhexa ...	0.06	-	cyt	0	Mitochondrion; mitochondrial matrix (Probable)				327
P04806 UniProt NPD GO	HXKA_YEAST	Hexokinase-1 (EC 2.7.1.1) (Hexokinase-A) (Hexokinase PI)	0.06	-	cyt	0				1HKG	485
Q2KNB4 UniProt NPD GO	HXK3_ORYSA	Hexokinase-3 (EC 2.7.1.1) (Hexokinase-8)	0.06	-	nuc	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein (By similarity)				500
Q07249 UniProt NPD GO	FCERG_CAVPO	High affinity immunoglobulin epsilon receptor gamma-subunit precursor (FceRI gamma) (IgE Fc receptor ...	0.06	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				86
P20491 UniProt NPD GO	FCERG_MOUSE	High affinity immunoglobulin epsilon receptor gamma-subunit precursor (FceRI gamma) (IgE Fc receptor ...	0.06	-	end	2 *	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] integral to plasma membrane [IDA] lipid raft [TAS]			86
Q01362 UniProt NPD GO	FCERB_HUMAN	High affinity immunoglobulin epsilon receptor subunit beta (FcERI) (IgE Fc receptor, subunit beta) ( ...	0.06	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	147138		244
P25025 UniProt NPD GO	CXCR2_HUMAN	High affinity interleukin-8 receptor B (IL-8R B) (CXCR-2) (GRO/MGSA receptor) (IL-8 receptor type 2) ...	0.06	-	end	6	Membrane; multi-pass membrane protein	cytoplasm [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	146928		360
O02228 UniProt NPD GO	SC5A7_CAEEL	High-affinity choline transporter 1	0.06	-	end	13 *	Membrane; multi-pass membrane protein (Probable)	integral to membrane [ISS] membrane [IC]			576

You are viewing entries 72201 to 72250 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.