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
P52799 UniProt NPD GO	EFNB2_HUMAN	Ephrin-B2 precursor (EPH-related receptor tyrosine kinase ligand 5) (LERK-5) (HTK ligand) (HTK-L)	0.33	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	600527		333
O43556 UniProt NPD GO	SGCE_HUMAN	Epsilon-sarcoglycan precursor (Epsilon-SG)	0.33	-	mit	1	Sarcolemma; sarcolemmal membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS] sarcoglycan complex [TAS]	604149		438
Q9S814 UniProt NPD GO	EIN2_ARATH	Ethylene-insensitive protein 2 (EIN-2) (AtEIN2) (Cytokinin-resistant protein AtCKR1)	0.33	+	end	11 *	Membrane; multi-pass membrane protein (Potential)				1294
Q9MAI5 UniProt NPD GO	ERF8_ARATH	Ethylene-responsive transcription factor 8 (Ethylene-responsive element-binding factor 8) (EREBP-8) ...	0.33	-	nuc	0	Nucleus (Probable)				185
P20459 UniProt NPD GO	IF2A_YEAST	Eukaryotic translation initiation factor 2 subunit alpha (eIF-2-alpha)	0.33	-	nuc	0		cytoplasm [IDA] eukaryotic translation initiation factor 2 ... [IMP] multi-eIF complex [IDA] ribosome [TAS]		2A1A	304
Q98TT6 UniProt NPD GO	4EBP_BRARE	Eukaryotic translation initiation factor 4E-1A-binding protein (eIF4E-1A-binding protein) (4E-BP)	0.33	-	nuc	0					112
P48724 UniProt NPD GO	IF5_PHAVU	Eukaryotic translation initiation factor 5 (eIF-5)	0.33	-	nuc	0					443
Q7TSL3 UniProt NPD GO	FBX11_RAT	F-box only protein 11	0.33	-	cyt	0					843
Q86XK2 UniProt NPD GO	FBX11_HUMAN	F-box only protein 11 (Vitiligo-associated protein VIT-1)	0.33	-	cyt	0		ubiquitin ligase complex [NAS]	607871		843
Q8N1E6 UniProt NPD GO	FXL14_HUMAN	F-box/LRR-repeat protein 14 (F-box and leucine-rich repeat protein 14)	0.33	-	nuc	0			609081		418
Q8BFZ4 UniProt NPD GO	FXL21_MOUSE	F-box/LRR-repeat protein 21 (F-box and leucine-rich repeat protein 21) (F-box/LRR-repeat protein 3B) ...	0.33	-	mit	0					434
Q5ALL8 UniProt NPD GO	POB3_CANAL	FACT complex subunit POB3 (Facilitates chromatin transcription complex subunit POB3)	0.33	-	mit	0	Nucleus (By similarity)				538
Q66JX5 UniProt NPD GO	FR1OP_MOUSE	FGFR1 oncogene partner	0.33	-	nuc	0	Centrosome. Associated with gamma-tubulin (By similarity)				399
Q6CWE8 UniProt NPD GO	FKBP3_KLULA	FK506-binding protein 3 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.33	+	nuc	0	Nucleus; nucleolus (By similarity)				418
O75344 UniProt NPD GO	FKBP6_HUMAN	FK506-binding protein 6 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (36 k ...	0.33	-	cyt	0			604839		327
Q06434 UniProt NPD GO	GLTB_ANTSP	Ferredoxin-dependent glutamate synthase (EC 1.4.7.1) (Fd-GOGAT)	0.33	-	nuc	0	Plastid; chloroplast; chloroplast stroma				1536
P41348 UniProt NPD GO	FTRC1_SPIOL	Ferredoxin-thioredoxin reductase catalytic chain, chloroplast precursor (EC 1.18.-.-) (FTR-C) (Ferre ...	0.33	-	mit	0	Plastid; chloroplast				144
Q99MX2 UniProt NPD GO	FHL17_MOUSE	Ferritin heavy polypeptide-like 17	0.33	-	nuc	0					176
O43320 UniProt NPD GO	FGF16_HUMAN	Fibroblast growth factor 16 (FGF-16)	0.33	-	cyt	0	Secreted protein (By similarity)	extracellular space [TAS]	603724		207
Q9Y2H6 UniProt NPD GO	FNDC3_HUMAN	Fibronectin type-III domain-containing protein 3a	0.33	-	cyt	1				2CRZ	1134
P62706 UniProt NPD GO	FBS1_HUMAN	Fibrosin-1	0.33	-	nuc	0	Secreted protein (By similarity)		608601		177
P38894 UniProt NPD GO	FLO5_YEAST	Flocculation protein FLO5 precursor (Flocculin-5)	0.33	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			1075
P79763 UniProt NPD GO	FSHR_CHICK	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.33	-	end	7	Membrane; multi-pass membrane protein				693
Q9WTX7 UniProt NPD GO	FHL5_MOUSE	Four and a half LIM domains protein 5 (FHL-5) (Activator of cAMP-responsive element modulator in tes ...	0.33	-	nuc	0	Nucleus. Nuclei of round and elongated spermatids				284
Q9XI80 UniProt NPD GO	FUT6_ARATH	Fucosyltransferase 6 (EC 2.4.1.-) (AtFUT6)	0.33	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				537
Q13069 UniProt NPD GO	GAGE5_HUMAN	G antigen 5 (GAGE-5)	0.33	-	nuc	0			604247		117
Q13070 UniProt NPD GO	GAGE6_HUMAN	G antigen 6 (GAGE-6)	0.33	-	nuc	0			604248		117
P49658 UniProt NPD GO	IRK6_MESAU	G protein-activated inward rectifier potassium channel 2 (GIRK2) (Potassium channel, inwardly rectif ...	0.33	-	end	2	Membrane; multi-pass membrane protein				425
P25008 UniProt NPD GO	CCNC_DROME	G1/S-specific cyclin-C	0.33	-	mit	0	Nucleus				267
P49706 UniProt NPD GO	CCND2_CHICK	G1/S-specific cyclin-D2	0.33	-	cyt	0					291
P48961 UniProt NPD GO	CCND3_RAT	G1/S-specific cyclin-D3	0.33	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				293
Q8CFX1 UniProt NPD GO	G6PE_MOUSE	GDH/6PGL endoplasmic bifunctional protein precursor [Includes: Glucose 1-dehydrogenase (EC 1.1.1.47) ...	0.33	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity). Microsomes, endoplasmic reticulu ...	microsome [IDA]			789
Q8WZK2 UniProt NPD GO	MCD4_SCHPO	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-) (Immunosuppresant and temperature-sensitive pr ...	0.33	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				935
P49018 UniProt NPD GO	GPI8_YEAST	GPI-anchor transamidase precursor (EC 3.-.-.-) (GPI transamidase)	0.33	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	endoplasmic reticulum lumen [TAS] GPI-anchor transamidase complex [IPI]			411
Q6XQG9 UniProt NPD GO	G3ST2_PIG	Galactose 3-O-sulfotransferase 2 (EC 2.8.2.-) (Gal3ST-2) (Galbeta1-3GalNAc 3'-sulfotransferase 2) (B ...	0.33	-	nuc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)				398
Q9P2W7 UniProt NPD GO	B3GA1_HUMAN	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.33	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	integral to membrane [TAS]	151290	1V84	334
P10067 UniProt NPD GO	CRGD_RAT	Gamma crystallin D (Gamma crystallin 2-2)	0.33	-	cyt	0					173
Q06255 UniProt NPD GO	CRG5_XENLA	Gamma crystallin-5 (Gamma crystallin V) (Gamma-5-CRY) (Fragment)	0.33	-	cyt	0					132
Q9UBS5 UniProt NPD GO	GABR1_HUMAN	Gamma-aminobutyric acid type B receptor, subunit 1 precursor (GABA-B receptor 1) (GABA-B-R1) (Gb1)	0.33	-	end	7	Cell membrane; multi-pass membrane protein. Moreover coexpression of GABA-B-R1 and GABA-B-R2 appears ...	integral to plasma membrane [TAS]	603540		961
Q9ERD8 UniProt NPD GO	PARVG_MOUSE	Gamma-parvin	0.33	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side (By similarity). Constituent o ...				331
Q9SPE5 UniProt NPD GO	SNAG_ARATH	Gamma-soluble NSF attachment protein (Gamma-SNAP) (N-ethylmaleimide-sensitive factor attachment prot ...	0.33	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				291
P57764 UniProt NPD GO	GSDC1_HUMAN	Gasdermin domain-containing protein 1	0.33	-	nuc	0					484
Q6ZMI3 UniProt NPD GO	GLDN_HUMAN	Gliomedin	0.33	-	nuc	1 *	Cell membrane; single-pass type II membrane protein. Localizes to the nodes of Ranvier (By similarit ...		608603		551
Q93ZW0 UniProt NPD GO	G6PD4_ARATH	Glucose-6-phosphate 1-dehydrogenase 4, chloroplast precursor (EC 1.1.1.49) (G6PD4) (G6PDH4)	0.33	-	exc	0	Plastid; chloroplast (By similarity)				625
P37830 UniProt NPD GO	G6PD_SOLTU	Glucose-6-phosphate 1-dehydrogenase, cytoplasmic isoform (EC 1.1.1.49) (G6PD)	0.33	-	nuc	0	Cytoplasm				511
P19490 UniProt NPD GO	GRIA1_RAT	Glutamate receptor 1 precursor (GluR-1) (GluR-A) (GluR-K1) (Glutamate receptor ionotropic, AMPA 1) ( ...	0.33	-	end	3	Membrane; multi-pass membrane protein	cell soma [IDA] dendritic shaft [IDA] early endosome [IDA] ionotropic glutamate receptor complex [TAS] synapse [IMP]			907
P22756 UniProt NPD GO	GRIK1_RAT	Glutamate receptor, ionotropic kainate 1 precursor (Glutamate receptor 5) (GluR-5) (GluR5)	0.33	-	end	3	Membrane; multi-pass membrane protein	plasma membrane [IMP]		2F36	949
Q43794 UniProt NPD GO	SYE_TOBAC	Glutamyl-tRNA synthetase (EC 6.1.1.17) (Glutamate--tRNA ligase) (GluRS)	0.33	+	cyt	0					569
O23732 UniProt NPD GO	GSHB_BRAJU	Glutathione synthetase, chloroplast precursor (EC 6.3.2.3) (Glutathione synthase) (GSH synthetase) ( ...	0.33	-	mit	0	Plastid; chloroplast (Potential)				530
P02861 UniProt NPD GO	GLT1_WHEAT	Glutenin, high molecular weight subunit PC256 (Fragment)	0.33	-	nuc	0					101

You are viewing entries 37551 to 37600 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.