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
O88343 UniProt NPD GO	S4A4_MOUSE	Electrogenic sodium bicarbonate cotransporter 1 (Sodium bicarbonate cotransporter) (Na(+)/HCO3(-) co ...	0.52	+	end	9	Cell membrane; basolateral cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			1079
Q9C7S7 UniProt NPD GO	ERO1_ARATH	Endoplasmic oxidoreductin-1 precursor (EC 1.8.4.-)	0.52	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side				469
Q14162 UniProt NPD GO	SREC_HUMAN	Endothelial cells scavenger receptor precursor (Acetyl LDL receptor) (Scavenger receptor class F mem ...	0.52	-	exc	0	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [IDA]	607873		830
O65020 UniProt NPD GO	ETO1_ARATH	Ethylene-overproduction protein 1	0.52	-	cyt	0					951
Q40479 UniProt NPD GO	ERF2_TOBAC	Ethylene-responsive transcription factor 2 (Ethylene-responsive element-binding factor 2) (EREBP-2) ...	0.52	-	nuc	0	Nucleus				233
Q9HGI4 UniProt NPD GO	ERF2_ZYGRO	Eukaryotic peptide chain release factor GTP-binding subunit (ERF2) (Translation release factor 3) (P ...	0.52	-	cyt	0	Cytoplasm (Probable)				662
Q8CJG1 UniProt NPD GO	I2C1_MOUSE	Eukaryotic translation initiation factor 2C 1 (eIF2C 1) (eIF-2C 1) (Argonaute-1) (Piwi/argonaute fam ...	0.52	-	cyt	0					857
Q9H9G7 UniProt NPD GO	I2C3_HUMAN	Eukaryotic translation initiation factor 2C 3 (eIF2C 3) (eIF-2C 3) (Argonaute-3)	0.52	-	cyt	0			607355		860
O94513 UniProt NPD GO	IF36_SCHPO	Eukaryotic translation initiation factor 3 subunit 6 (eIF-3 p48)	0.52	-	cyt	0	Cytoplasm	cytoplasm [IDA]			501
O74562 UniProt NPD GO	SEC8_SCHPO	Exocyst complex component sec8	0.52	-	nuc	0	Cytoplasm. Associated with the actinomyosin ring at the division site and at the cell tips	cell cortex of cell tip [IDA] exocyst [IDA]			1088
Q7SZC2 UniProt NPD GO	XPO2_BRARE	Exportin-2 (Exp2) (Importin-alpha re-exporter) (Chromosome segregation 1-like protein)	0.52	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				971
Q9PTU3 UniProt NPD GO	XPO2_PAGMA	Exportin-2 (Exp2) (Importin-alpha re-exporter) (Chromosome segregation 1-like protein) (Cellular apo ...	0.52	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				971
P13983 UniProt NPD GO	EXTN_TOBAC	Extensin precursor (Cell wall hydroxyproline-rich glycoprotein)	0.52	-	exc	0	Secreted protein; extracellular space; extracellular matrix				620
P35384 UniProt NPD GO	CASR_BOVIN	Extracellular calcium-sensing receptor precursor (CaSR) (Parathyroid Cell calcium-sensing receptor)	0.52	-	end	7	Membrane; multi-pass membrane protein				1085
P47144 UniProt NPD GO	ECM27_YEAST	Extracellular matrix protein 27	0.52	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				725
Q99502 UniProt NPD GO	EYA1_HUMAN	Eyes absent homolog 1 (EC 3.1.3.48)	0.52	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		601653		592
Q9JJ19 UniProt NPD GO	NHERF_RAT	Ezrin-radixin-moesin-binding phosphoprotein 50 (EBP50) (Na(+)/H(+) exchange regulatory cofactor NHE- ...	0.52	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity). Colocalizes with actin in mi ...				355
O75426 UniProt NPD GO	FBX24_HUMAN	F-box only protein 24	0.52	-	nuc	0		ubiquitin ligase complex [NAS]	609097		580
P87053 UniProt NPD GO	POF1_SCHPO	F-box/WD repeat protein pof1 (Skp1-binding protein 1)	0.52	-	nuc	0		SCF ubiquitin ligase complex [IDA]			605
Q5B2X8 UniProt NPD GO	SPT16_EMENI	FACT complex subunit spt16 (Facilitates chromatin transcription complex subunit spt16)	0.52	+	cyt	0	Nucleus (By similarity)				1049
Q5R776 UniProt NPD GO	FAKD2_PONPY	FAST kinase domains-containing protein 2	0.52	-	mit	0					693
O88182 UniProt NPD GO	FGF18_RAT	Fibroblast growth factor 18 precursor (FGF-18)	0.52	-	exc	0	Secreted protein				207
P11088 UniProt NPD GO	FILA_MOUSE	Filaggrin (Fragment)	0.52	-	nuc	0		cornified envelope [IDA]			336
Q61080 UniProt NPD GO	FOXF1_MOUSE	Forkhead box protein F1 (Forkhead-related protein FKHL5) (Forkhead-related transcription factor 1) ( ...	0.52	-	nuc	0	Nucleus				353
P32298 UniProt NPD GO	GRK4_HUMAN	G protein-coupled receptor kinase 4 (EC 2.7.11.16) (G protein-coupled receptor kinase GRK4) (ITI1)	0.52	+	cyt	0			137026		578
Q9Z2G7 UniProt NPD GO	GRK7_SPETR	G protein-coupled receptor kinase 7 precursor (EC 2.7.11.16) (G protein-coupled receptor kinase GRK7 ...	0.52	+	cyt	0	Membrane; lipid-anchor				548
P24861 UniProt NPD GO	CCNA_PATVU	G2/mitotic-specific cyclin-A	0.52	-	nuc	0					426
P30284 UniProt NPD GO	CG21_EMENI	G2/mitotic-specific cyclin-B	0.52	-	nuc	0					478
Q99501 UniProt NPD GO	GA2L1_HUMAN	GAS2-like protein 1 (Growth arrest-specific 2-like 1) (GAS2-related protein on chromosome 22) (GAR22 ...	0.52	-	nuc	0			602128		681
Q8GXL7 UniProt NPD GO	GAT27_ARATH	GATA transcription factor 27 (ZIM-like 1 protein)	0.52	-	nuc	0	Nucleus (Probable)				297
O75791 UniProt NPD GO	GRAP2_HUMAN	GRB2-related adapter protein 2 (GADS protein) (Growth factor receptor-binding protein) (GRBLG) (Grf4 ...	0.52	-	nuc	0		cytoplasm [TAS]	604518		330
Q7RYE7 UniProt NPD GO	GAL7_NEUCR	Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP-glucose-- ...	0.52	-	nuc	0					392
P18861 UniProt NPD GO	CXA7_CHICK	Gap junction alpha-7 protein (Connexin-45) (Cx45)	0.52	-	end	4 *	Membrane; multi-pass membrane protein				394
P14136 UniProt NPD GO	GFAP_HUMAN	Glial fibrillary acidic protein, astrocyte (GFAP)	0.52	-	nuc	0	Cytoplasm. Associated with intermediate filaments	intermediate filament [TAS]	203450		432
O42143 UniProt NPD GO	GLUC1_XENLA	Glucagon-1 precursor (Glucagon I) [Contains: Glucagon; Glucagon-like peptide 1A (GLP-1A); Glucagon-l ...	0.52	-	exc	0	Secreted protein				266
Q6FQ15 UniProt NPD GO	GNT1_CANGA	Glucose N-acetyltransferase 1 (EC 2.4.1.-) (N-acetylglucosaminyltransferase)	0.52	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential). Vacuole; vacuolar ...				501
P14314 UniProt NPD GO	GLU2B_HUMAN	Glucosidase 2 subunit beta precursor (Glucosidase II subunit beta) (Protein kinase C substrate, 60.1 ...	0.52	-	end	0		intracellular [NAS]	177060		527
Q9EQG9 UniProt NPD GO	C43BP_MOUSE	Goodpasture antigen-binding protein (EC 2.7.11.9) (GPBP) (Collagen type IV alpha-3-binding protein) ...	0.52	+	cyt	0					624
Q9XZV3 UniProt NPD GO	GNAO_GEOCY	Guanine nucleotide-binding protein G(o) subunit alpha	0.52	-	cyt	0					358
P30684 UniProt NPD GO	GNAS_LYMST	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.52	-	cyt	0					376
P19627 UniProt NPD GO	GNAZ_RAT	Guanine nucleotide-binding protein G(z) subunit alpha (G(x) alpha chain) (Gz-alpha)	0.52	-	mit	0	Membrane; lipid-anchor	heterotrimeric G-protein complex [TAS]			354
P21278 UniProt NPD GO	GNA11_MOUSE	Guanine nucleotide-binding protein alpha-11 subunit	0.52	-	cyt	0		heterotrimeric G-protein complex [TAS]			359
Q00580 UniProt NPD GO	GPA1_CRYPA	Guanine nucleotide-binding protein subunit alpha	0.52	-	cyt	0					352
O13315 UniProt NPD GO	GPA1_MAGGR	Guanine nucleotide-binding protein subunit alpha	0.52	-	cyt	0					352
Q9LD90 UniProt NPD GO	DKC1_ARATH	H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-) (Nucleolar protein NAP57 homolog) (Nopp-140- ...	0.52	+	nuc	0	Nucleus; nucleolus (By similarity)				565
Q9GM44 UniProt NPD GO	HEAT1_MACFA	HEAT repeat-containing protein 1 (Protein BAP28) (Fragment)	0.52	-	nuc	0	Nucleus; nucleolus (By similarity)				958
P04233 UniProt NPD GO	HG2A_HUMAN	HLA class II histocompatibility antigen gamma chain (HLA-DR antigens-associated invariant chain) (Ia ...	0.52	-	nuc	1 *	Membrane; single-pass type II membrane protein (Potential)	integral to membrane [TAS] intracellular [TAS]	142790	1L3H	296
P27323 UniProt NPD GO	HSP81_ARATH	Heat shock protein 81-1 (HSP81-1) (Heat shock protein 83)	0.52	+	cyt	0	Cytoplasm (Potential)				700
Q07078 UniProt NPD GO	HSP83_ORYSA	Heat shock protein 81-3 (HSP81-3) (Gravity-specific protein GSC 381)	0.52	-	cyt	0	Cytoplasm (Potential)				699
P55204 UniProt NPD GO	GUC2C_PIG	Heat-stable enterotoxin receptor precursor (GC-C) (Intestinal guanylate cyclase) (EC 4.6.1.2) (STA r ...	0.52	-	end	2	Membrane; single-pass type I membrane protein				1073

You are viewing entries 23701 to 23750 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.