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
Q8BKE5 UniProt NPD GO	FSBP_MOUSE	Fibrinogen silencer-binding protein	0.61	-	nuc	0	Nucleus (Potential)				299
P70379 UniProt NPD GO	FGF14_MOUSE	Fibroblast growth factor 14 (FGF-14) (Fibroblast growth factor homologous factor 4) (FHF-4)	0.61	-	nuc	0	Nucleus (Probable)				247
Q03898 UniProt NPD GO	FIN1_YEAST	Filament protein FIN1 (Filaments in between nuclei protein 1)	0.61	-	nuc	0	Nucleus. Cytoplasm. Cytoskeleton, spindle pole. Nuclear during early bud formation, located at the s ...	intermediate filament [IDA] nucleus [IDA]			291
Q9UM11 UniProt NPD GO	FZR_HUMAN	Fizzy-related protein homolog (Fzr) (Cdh1/Hct1 homolog) (hCDH1) (CDC20-like protein 1)	0.61	-	nuc	0	Isoform 2: Nucleus. Isoform 3: Cytoplasm	anaphase-promoting complex [TAS]	603619		496
O35346 UniProt NPD GO	FAK1_RAT	Focal adhesion kinase 1 (EC 2.7.10.2) (FADK 1) (pp125FAK)	0.61	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side. Constituent of focal adhesion ...	focal adhesion [TAS]			1055
Q05397 UniProt NPD GO	FAK1_HUMAN	Focal adhesion kinase 1 (EC 2.7.10.2) (FADK 1) (pp125FAK) (Protein-tyrosine kinase 2)	0.61	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side. Constituent of focal adhesion ...	cytoskeleton [TAS]	600758	1OW8	1052
Q07342 UniProt NPD GO	FOXA2_BRARE	Forkhead box protein A2 (Axial protein)	0.61	+	nuc	0	Nucleus				409
Q9I9E1 UniProt NPD GO	FOXH1_BRARE	Forkhead box protein H1 (Forkhead activin signal transducer 1) (Fast-1) (Schmalspur protein)	0.61	-	nuc	0	Nucleus				472
Q8K3Q3 UniProt NPD GO	FOXN4_MOUSE	Forkhead box protein N4	0.61	-	nuc	0	Nucleus (Potential)				521
Q9Y653 UniProt NPD GO	GPR56_HUMAN	G-protein coupled receptor 56 precursor (TM7XN1 protein)	0.61	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	606854		693
Q8IZP9 UniProt NPD GO	GPR64_HUMAN	G-protein coupled receptor 64 precursor (Epididymis-specific protein 6) (He6 receptor)	0.61	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	300572		1017
P38875 UniProt NPD GO	GPI16_YEAST	GPI transamidase component GPI16 precursor	0.61	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	GPI-anchor transamidase complex [IPI]			602
Q12344 UniProt NPD GO	GYP5_YEAST	GTPase-activating protein GYP5	0.61	-	nuc	0	Cytoplasm. Bud. Bud neck	bud neck [IDA] bud tip [IDA] cytosol [IDA] Golgi-associated vesicle [IDA] incipient bud site [IDA] plasma membrane [IDA] soluble fraction [IDA]			894
P09379 UniProt NPD GO	GYP7_YARLI	GTPase-activating protein GYP7 (GAP for YPT7)	0.61	-	cyt	0					730
P28473 UniProt NPD GO	GBRG3_RAT	Gamma-aminobutyric-acid receptor gamma-3 subunit precursor (GABA(A) receptor)	0.61	-	end	4	Membrane; multi-pass membrane protein				467
Q8TB36 UniProt NPD GO	GDAP1_HUMAN	Ganglioside-induced differentiation-associated protein 1 (GDAP1)	0.61	-	nuc	2	Cytoplasm (By similarity)		608340		358
P02892 UniProt NPD GO	BAB3_BABBO	Gene BABR protein 3 (Fragment)	0.61	-	nuc	0					212
P22890 UniProt NPD GO	GLUC_OCTDE	Glucagon precursor [Contains: Glicentin; Glicentin-related polypeptide (GRPP); Oxyntomodulin (OXY) ( ...	0.61	-	vac	0	Secreted protein				180
P16649 UniProt NPD GO	TUP1_YEAST	Glucose repression regulatory protein TUP1 (Flocculation suppressor protein) (Repressor AER2)	0.61	-	nuc	0		nucleus [IDA]		1ERJ	713
O08795 UniProt NPD GO	GLU2B_MOUSE	Glucosidase 2 subunit beta precursor (Glucosidase II subunit beta) (Protein kinase C substrate, 60.1 ...	0.61	-	end	0	Endoplasmic reticulum	alpha-glucosidase II complex [IPI] endoplasmic reticulum [TAS]			521
Q5IS45 UniProt NPD GO	NMDE1_PANTR	Glutamate [NMDA] receptor subunit epsilon 1 precursor (N-methyl D-aspartate receptor subtype 2A) (NR ...	0.61	-	end	4	Membrane; multi-pass membrane protein (By similarity)				1464
Q12879 UniProt NPD GO	NMDE1_HUMAN	Glutamate [NMDA] receptor subunit epsilon 1 precursor (N-methyl D-aspartate receptor subtype 2A) (NR ...	0.61	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	138253		1464
Q21389 UniProt NPD GO	LGE1_CAEEL	Glycosyltransferase-like protein LARGE (EC 2.4.-.-)	0.61	-	vac	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				631
Q10039 UniProt NPD GO	SYG_CAEEL	Glycyl-tRNA synthetase (EC 6.1.1.14) (Glycine--tRNA ligase) (GlyRS)	0.61	-	nuc	0					742
Q9Y5P4 UniProt NPD GO	C43BP_HUMAN	Goodpasture antigen-binding protein (EC 2.7.11.9) (GPBP) (Collagen type IV alpha-3-binding protein) ...	0.61	+	cyt	0			604677		624
O60383 UniProt NPD GO	GDF9_HUMAN	Growth/differentiation factor 9 precursor (GDF-9)	0.61	-	exc	1 *	Secreted protein (By similarity)		601918		454
Q9ESX5 UniProt NPD GO	DKC1_MOUSE	H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-) (Dyskerin) (Nucleolar protein family A membe ...	0.61	+	nuc	0	Nucleus; nucleolus. Nucleus; nucleoplasm; Cajal body. Also localized to Cajal bodies (coiled bodies) ...				508
O60832 UniProt NPD GO	DKC1_HUMAN	H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-) (Dyskerin) (Nucleolar protein family A membe ...	0.61	+	nuc	0	Nucleus; nucleolus. Nucleus; nucleoplasm; Cajal body. Also localized to Cajal bodies (coiled bodies) ...	nucleolus [TAS] nucleoplasm [TAS] telomerase holoenzyme complex [IDA]	305000		513
O95714 UniProt NPD GO	HERC2_HUMAN	HECT domain and RCC1-like domain-containing protein 2	0.61	-	nuc	0			605837		4834
Q4U2R1 UniProt NPD GO	HERC2_MOUSE	HECT domain and RCC1-like domain-containing protein 2	0.61	-	end	0		mitochondrial inner membrane [IDA]			4836
P61583 UniProt NPD GO	NP8_HUMAN	HERV-K_3q12.3 provirus Np9 protein (HERV-K(II) Np9 protein)	0.61	-	nuc	0	Nucleus (By similarity). When overexpressed (By similarity)				75
Q9HDB9 UniProt NPD GO	GAK8_HUMAN	HERV-K_3q12.3 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K(II) Gag protein) [Contain ...	0.61	-	nuc	0	Cell membrane. Cytoplasmic membrane (in a transfection system) (By similarity)				666
Q9UQG0 UniProt NPD GO	POK20_HUMAN	HERV-K_3q27.3 provirus ancestral Pol protein [Includes: Reverse transcriptase (RT) (EC 2.7.7.49); Ri ...	0.61	-	mit	0					969
P10266 UniProt NPD GO	POK10_HUMAN	HERV-K_5q33.3 provirus ancestral Pol protein (HERV-K10 Pol protein) (HERV-K107 Pol protein) [Include ...	0.61	-	cyt	0					1014
Q9GKX7 UniProt NPD GO	HS90A_HORSE	Heat shock protein HSP 90-alpha (HSP 86) (Fragment)	0.61	-	cyt	0	Cytoplasm				719
P70106 UniProt NPD GO	GUC2C_CAVPO	Heat-stable enterotoxin receptor precursor (GC-C) (Intestinal guanylate cyclase) (EC 4.6.1.2) (STA r ...	0.61	-	end	1	Membrane; single-pass type I membrane protein				1076
P81172 UniProt NPD GO	HEPC_HUMAN	Hepcidin precursor (Liver-expressed antimicrobial peptide) (LEAP-1) (Putative liver tumor regressor) ...	0.61	-	exc	1 *	Secreted protein	extracellular region [NAS]	602390	1M4F	84
Q27442 UniProt NPD GO	H2B_ANOGA	Histone H2B	0.61	+	nuc	0	Nucleus				123
P83837 UniProt NPD GO	H2B_CYPCA	Histone H2B (Fragment)	0.61	+	nuc	0	Nucleus				28
P0C1H4 UniProt NPD GO	H2B5_CHICK	Histone H2B 5 (H2B V)	0.61	+	nuc	0	Nucleus				125
Q9D2U9 UniProt NPD GO	H2B3A_MOUSE	Histone H2B type 3-A	0.61	+	nuc	0	Nucleus			2F8N	125
Q8SQP4 UniProt NPD GO	H4_ENCCU	Histone H4	0.61	-	nuc	0	Nucleus (By similarity)				103
P49749 UniProt NPD GO	EVX2_MOUSE	Homeobox even-skipped homolog protein 2 (EVX-2)	0.61	+	nuc	0	Nucleus				475
P22544 UniProt NPD GO	BARH1_DROAN	Homeobox protein B-H1 (Homeobox BarH1 protein)	0.61	-	nuc	0	Nucleus (Potential)				606
P15142 UniProt NPD GO	HM7X_CHICK	Homeobox protein CHOX-7 (Fragment)	0.61	+	nuc	0	Nucleus (Probable)				124
P53773 UniProt NPD GO	DLL1_XENLA	Homeobox protein DLL-1 (DLL) (XDLL)	0.61	+	nuc	0	Nucleus (Potential)				250
P70396 UniProt NPD GO	DLX5_MOUSE	Homeobox protein DLX-5	0.61	+	nuc	0	Nucleus (Potential)				289
P50901 UniProt NPD GO	HOX3_BRAFL	Homeobox protein HOX3	0.61	+	nuc	0	Nucleus				411
P31245 UniProt NPD GO	HXA2_MOUSE	Homeobox protein Hox-A2 (Hox-1.11) (Hox1.11)	0.61	+	nuc	0	Nucleus				372
O43365 UniProt NPD GO	HXA3_HUMAN	Homeobox protein Hox-A3 (Hox-1E)	0.61	+	nuc	0	Nucleus		142954		443

You are viewing entries 18451 to 18500 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.