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
Q01231 UniProt NPD GO	CXA5_MOUSE	Gap junction alpha-5 protein (Connexin-40) (Cx40)	0.15	-	end	3 *	Membrane; multi-pass membrane protein				357
P81498 UniProt NPD GO	PEPC_SUNMU	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C-1)	0.15	-	vac	0	Secreted protein				389
P46627 UniProt NPD GO	GASR_RABIT	Gastrin/cholecystokinin type B receptor (CCK-B receptor) (CCK-BR) (Cholecystokinin-2 receptor) (CCK2 ...	0.15	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS] plasma membrane [ISS]			452
O93510 UniProt NPD GO	GELS_CHICK	Gelsolin precursor (Actin-depolymerizing factor) (ADF) (Brevin) (Homogenin)	0.15	-	mit	1 *	Secreted protein				778
P38090 UniProt NPD GO	AGP2_YEAST	General amino acid permease AGP2	0.15	-	end	12	Membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum membrane [IDA] integral to plasma membrane [IDA] vacuolar membrane [IDA]			596
Q6F596 UniProt NPD GO	GGPPS_RAT	Geranylgeranyl pyrophosphate synthetase (GGPP synthetase) (GGPPSase) (Geranylgeranyl diphosphate syn ...	0.15	-	cyt	0	Cytoplasm (Potential)	soluble fraction [ISS]			300
Q8AUU1 UniProt NPD GO	GHRL_CARAU	Ghrelin precursor [Contains: Ghrelin-12; Ghrelin-19]	0.15	-	exc	0	Secreted protein (By similarity)	extracellular space [ISS]			103
Q9CWG1 UniProt NPD GO	GLIP1_MOUSE	Glioma pathogenesis-related protein 1 precursor (GliPR 1)	0.15	-	nuc	1					255
P09687 UniProt NPD GO	GLUC_SCYCA	Glucagon precursor [Contains: Glucagon-29; Glucagon-33; Glucagon-like peptide] (Fragments)	0.15	-	nuc	0	Secreted protein				62
P53626 UniProt NPD GO	E13B_TRIHA	Glucan endo-1,3-beta-glucosidase BGN13.1 precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase B ...	0.15	-	exc	0	Secreted protein				762
P08017 UniProt NPD GO	AMYG_SACFI	Glucoamylase GLU1 precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohyd ...	0.15	-	exc	0				2FBA	519
P55231 UniProt NPD GO	GLGL3_ARATH	Glucose-1-phosphate adenylyltransferase large subunit 3, chloroplast precursor (EC 2.7.7.27) (ADP-gl ...	0.15	-	cyt	0	Plastid; chloroplast				521
P54385 UniProt NPD GO	DHE3_DROME	Glutamate dehydrogenase, mitochondrial precursor (EC 1.4.1.3) (GDH)	0.15	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)				562
P39086 UniProt NPD GO	GRIK1_HUMAN	Glutamate receptor, ionotropic kainate 1 precursor (Glutamate receptor 5) (GluR-5) (GluR5) (Excitato ...	0.15	-	end	3	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	138245		918
Q92947 UniProt NPD GO	GCDH_HUMAN	Glutaryl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.7) (GCD)	0.15	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	231670	1SIR	438
P80031 UniProt NPD GO	GSTP1_PIG	Glutathione S-transferase P (EC 2.5.1.18) (GST P1-1) (GST class-pi)	0.15	-	cyt	0				2GSR	207
P30711 UniProt NPD GO	GSTT1_HUMAN	Glutathione S-transferase theta-1 (EC 2.5.1.18) (GST class-theta-1) (Glutathione transferase T1-1)	0.15	-	mit	0	Cytoplasm		600436	2C3T	239
P51855 UniProt NPD GO	GSHB_MOUSE	Glutathione synthetase (EC 6.3.2.3) (Glutathione synthase) (GSH synthetase) (GSH-S)	0.15	-	cyt	0					474
P21696 UniProt NPD GO	GPD1_SCHPO	Glycerol-3-phosphate dehydrogenase [NAD+] 1 (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.15	-	cyt	0	Cytoplasm				385
Q4R806 UniProt NPD GO	GATM_MACFA	Glycine amidinotransferase, mitochondrial precursor (EC 2.1.4.1) (L-arginine:glycine amidinotransfer ...	0.15	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				423
Q99069 UniProt NPD GO	GRP1_SORBI	Glycine-rich RNA-binding protein 1 (Fragment)	0.15	+	cyt	0					142
Q03251 UniProt NPD GO	GRP8_ARATH	Glycine-rich RNA-binding protein 8 (Protein CCR1)	0.15	+	cyt	0					169
P49311 UniProt NPD GO	GRP2_SINAL	Glycine-rich RNA-binding protein GRP2A	0.15	+	cyt	0	Nucleus				169
P27484 UniProt NPD GO	GRP2_NICSY	Glycine-rich protein 2	0.15	+	cyt	0					214
P09466 UniProt NPD GO	PAEP_HUMAN	Glycodelin precursor (GD) (Pregnancy-associated endometrial alpha-2 globulin) (PEG) (PAEG) (Placenta ...	0.15	-	mit	0			173310		180
Q06135 UniProt NPD GO	GAS2_YEAST	Glycolipid-anchored surface protein 2 precursor	0.15	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cytoplasm [IDA]			555
Q9LTR9 UniProt NPD GO	NMT1_ARATH	Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) (Peptide N-myristoyltransferase 1) (Myristo ...	0.15	-	cyt	0	Cytoplasm. Mostly associated to ribosomes. Present to a lower extent in mitochondria				434
Q86XS8 UniProt NPD GO	GOLI_HUMAN	Goliath homolog precursor (RING finger protein 130)	0.15	-	end	2	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [ISS]			419
O13050 UniProt NPD GO	GTHB1_CYPCA	Gonadotropin beta-1 subunit precursor (Gonadotropin beta-I chain) (GTH-I-beta) (Follicle-stimulating ...	0.15	-	mit	0	Secreted protein				130
P28676 UniProt NPD GO	GRAN_HUMAN	Grancalcin	0.15	-	cyt	0	Cytoplasm. 50%. Membrane. 50%. The remainder being attached to the membranes and granules	cytoplasm [TAS] plasma membrane [TAS]	607030	1K95	217
Q43093 UniProt NPD GO	SSG2_PEA	Granule-bound starch synthase 2, chloroplast precursor (EC 2.4.1.21) (Granule-bound starch synthase ...	0.15	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Soluble and granule-bound (By similarity)				752
P11052 UniProt NPD GO	CSF2_BOVIN	Granulocyte-macrophage colony-stimulating factor precursor (GM-CSF) (Colony-stimulating factor) (CSF ...	0.15	-	nuc	0	Secreted protein				143
P13366 UniProt NPD GO	GRAG_MOUSE	Granzyme G precursor (EC 3.4.21.-) (CTL serine protease 1) (MCSP-1)	0.15	-	exc	0	Cytoplasmic granule. Cytoplasmic granules of cytolytic T-lymphocytes				248
P09341 UniProt NPD GO	GROA_HUMAN	Growth-regulated protein alpha precursor (CXCL1) (Melanoma growth stimulatory activity) (MGSA) (Neut ...	0.15	-	mit	0	Secreted protein	extracellular space [TAS]	155730	1ROD	107
Q63741 UniProt NPD GO	BB1_RAT	Growth-regulating protein BB1	0.15	-	nuc	0					57
Q3SZC1 UniProt NPD GO	GRPE1_BOVIN	GrpE protein homolog 1, mitochondrial precursor (Mt-GrpE#1) (mt-GrpE)	0.15	-	mit	0	Mitochondrion; mitochondrial matrix				217
Q75C01 UniProt NPD GO	GRPE_ASHGO	GrpE protein homolog, mitochondrial precursor	0.15	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				212
P14428 UniProt NPD GO	HA1Q_MOUSE	H-2 class I histocompatibility antigen, K-Q alpha chain (H-2K(Q)) (Fragment)	0.15	-	cyt	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			328
P20040 UniProt NPD GO	HB24_MOUSE	H-2 class II histocompatibility antigen, E-Q beta chain precursor (E-W17)	0.15	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				264
Q5RC65 UniProt NPD GO	NOLA2_PONPY	H/ACA ribonucleoprotein complex subunit 2 (Nucleolar protein family A member 2)	0.15	-	nuc	0	Nucleus; nucleolus (By similarity). Also localized to Cajal bodies (coiled bodies) (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			153
Q9NX24 UniProt NPD GO	NOLA2_HUMAN	H/ACA ribonucleoprotein complex subunit 2 (Nucleolar protein family A member 2) (snoRNP protein NHP2 ...	0.15	-	nuc	0	Nucleus; nucleolus. Nucleus; nucleoplasm; Cajal body. Also localized to Cajal bodies (coiled bodies) ...	small nucleolar ribonucleoprotein complex [ISS]	606470		153
P63127 UniProt NPD GO	VPK4_HUMAN	HERV-K_6q14.1 provirus ancestral Pro protein (EC 3.4.23.-) (HERV-K109 Pro protein) (HERV-K(C6) Pro p ...	0.15	-	cyt	0					156
P63122 UniProt NPD GO	VPK6_HUMAN	HERV-K_8p23.1 provirus ancestral Pro protein (EC 3.4.23.-) (HERV-K115 Pro protein) (Protease) (Prote ...	0.15	-	cyt	0					156
P48720 UniProt NPD GO	HSP70_BLAEM	Heat shock 70 kDa protein	0.15	-	cyt	0					649
P25840 UniProt NPD GO	HSP70_CHLRE	Heat shock 70 kDa protein	0.15	-	cyt	0					650
P26413 UniProt NPD GO	HSP70_SOYBN	Heat shock 70 kDa protein	0.15	-	cyt	0					645
P19378 UniProt NPD GO	HSP7C_CRIGR	Heat shock cognate 71 kDa protein (Heat shock 70 kDa protein 8)	0.15	-	cyt	0	Cytoplasm (By similarity). Translocates rapidly from the cytoplasm to the nuclei, and especially to ...				646
O16076 UniProt NPD GO	HSP83_DROPE	Heat shock protein 83 (HSP 82) (Fragment)	0.15	-	cyt	0	Cytoplasm	centrosome [ISS]			269
P87222 UniProt NPD GO	HSP75_CANAL	Heat shock protein SSB1	0.15	-	cyt	0	Cytoplasm. Associated with translating ribosomes; may bind directly to the nascent polypeptide (By s ...				613
P39987 UniProt NPD GO	HSP7E_YEAST	Heat shock protein SSC3, mitochondrial precursor (Extracellular matrix protein 10)	0.15	-	mit	0	Mitochondrion; mitochondrial matrix. Found in mitochondrial nucleoids	mitochondrial nucleoid [IDA] mitochondrion [IDA]			644

You are viewing entries 56951 to 57000 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.