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
Q5JZY3 UniProt NPD GO	EPHAA_HUMAN	Ephrin type-A receptor 10 precursor (EC 2.7.10.1)	0.34	-	nuc	0	Isoform 1, isoform 3: Cell membrane; single-pass type I membrane protein (Probable). Isoform 2: Secr ...				1008
O54782 UniProt NPD GO	MA2B2_MOUSE	Epididymis-specific alpha-mannosidase precursor (EC 3.2.1.24) (Mannosidase alpha class 2B member 2)	0.34	-	mit	0	Secreted protein				1018
Q6R8F2 UniProt NPD GO	CADH1_BOVIN	Epithelial-cadherin precursor (E-cadherin) (Cadherin-1) (CD324 antigen) [Contains: E-Cad/CTF1; E-Cad ...	0.34	-	end	1	Cell membrane; cell-cell junction; single-pass type I membrane protein. Colocalizes with DLG7 at sit ...				882
Q9R0T4 UniProt NPD GO	CADH1_RAT	Epithelial-cadherin precursor (E-cadherin) (Uvomorulin) (Cadherin-1) (CD324 antigen) [Contains: E-Ca ...	0.34	-	end	1	Cell membrane; cell-cell junction; single-pass type I membrane protein. Colocalizes with DLG7 at sit ...				886
O88339 UniProt NPD GO	EPN1_RAT	Epsin-1 (EPS-15-interacting protein 1)	0.34	-	mit	0	Cytoplasm. Cell membrane; peripheral membrane protein. Nucleus. Associated with the cytoplasmic memb ...			1KY6	575
P16452 UniProt NPD GO	EPB42_HUMAN	Erythrocyte membrane protein band 4.2 (Erythrocyte protein 4.2) (P4.2)	0.34	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side. Cytoplasmic surface of erythrocyte membranes. Cytopla ...	cytoskeleton [TAS] plasma membrane [TAS]	177070		690
P49222 UniProt NPD GO	EPB42_MOUSE	Erythrocyte membrane protein band 4.2 (Erythrocyte protein 4.2) (P4.2)	0.34	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side. Cytoplasmic surface of erythrocyte membranes. Cytopla ...				690
O80337 UniProt NPD GO	ERF1A_ARATH	Ethylene-responsive transcription factor 1A (Ethylene-responsive element-binding factor 1A) (EREBP-1 ...	0.34	+	nuc	0	Nucleus (Probable)			3GCC	268
P41378 UniProt NPD GO	IF4A_WHEAT	Eukaryotic initiation factor 4A (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A) (eIF-4A)	0.34	-	cyt	0					414
P32481 UniProt NPD GO	IF2G_YEAST	Eukaryotic translation initiation factor 2 subunit gamma (eIF-2-gamma)	0.34	+	mit	0		eukaryotic translation initiation factor 2 ... [IMP] multi-eIF complex [IDA] ribosome [TAS]			527
O75821 UniProt NPD GO	IF34_HUMAN	Eukaryotic translation initiation factor 3 subunit 4 (eIF-3 delta) (eIF3 p44) (eIF-3 RNA-binding sub ...	0.34	-	nuc	0			603913	2CQ0	320
Q9LUB6 UniProt NPD GO	SNE_ARATH	F-box protein SNE (Protein SNEEZY) (Sleepy protein 2)	0.34	-	nuc	0	Nucleus (By similarity)				157
Q5VMP0 UniProt NPD GO	MAX2_ORYSA	F-box/LRR-repeat MAX2 homolog (F-box and leucine-rich repeat MAX2 homolog)	0.34	-	mit	0					720
Q07981 UniProt NPD GO	FAR1_HELAS	FMRFamide-related peptides type HF-4 precursor (HeptaFaRP) [Contains: FMRFamide-like; ENNNGYIRF-amid ...	0.34	-	exc	0	Secreted protein				305
Q96I24 UniProt NPD GO	FUBP3_HUMAN	Far upstream element-binding protein 3 (FUSE-binding protein 3)	0.34	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	603536		572
P49327 UniProt NPD GO	FAS_HUMAN	Fatty acid synthase (EC 2.3.1.85) [Includes: [Acyl-carrier-protein] S-acetyltransferase (EC 2.3.1.38 ...	0.34	-	nuc	0	Cytoplasm		600212	2CG5	2511
P19097 UniProt NPD GO	FAS2_YEAST	Fatty acid synthase subunit alpha (EC 2.3.1.86) [Includes: Acyl carrier; 3-oxoacyl-[acyl-carrier-pro ...	0.34	-	cyt	0		mitochondrion [IDA]			1887
O19906 UniProt NPD GO	GLTB_CYACA	Ferredoxin-dependent glutamate synthase (EC 1.4.7.1) (Fd-GOGAT)	0.34	-	mit	0	Plastid; chloroplast; chloroplast stroma				1549
O46414 UniProt NPD GO	FRIH_BOVIN	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit)	0.34	-	nuc	0		plasma membrane [ISS]			180
Q95MP7 UniProt NPD GO	FRIH_CANFA	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit)	0.34	-	nuc	0		plasma membrane [ISS]			182
Q9XT73 UniProt NPD GO	FRIH_TRIVU	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit)	0.34	-	nuc	0		plasma membrane [ISS]			182
O77469 UniProt NPD GO	FBLN1_CAEEL	Fibulin-1 precursor	0.34	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				728
P37889 UniProt NPD GO	FBLN2_MOUSE	Fibulin-2 precursor	0.34	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				1221
P21333 UniProt NPD GO	FLNA_HUMAN	Filamin-A (Alpha-filamin) (Filamin-1) (Endothelial actin-binding protein) (Actin-binding protein 280 ...	0.34	-	cyt	0	Cytoplasm; cell cortex	actin cytoskeleton [TAS]	300017	2BRQ	2646
Q8BTM8 UniProt NPD GO	FLNA_MOUSE	Filamin-A (Alpha-filamin) (Filamin-1) (Endothelial actin-binding protein) (Actin-binding protein 280 ...	0.34	-	cyt	0	Cytoplasm; cell cortex (By similarity)	Golgi trans face [IDA]			2646
Q12841 UniProt NPD GO	FSTL1_HUMAN	Follistatin-related protein 1 precursor (Follistatin-like 1)	0.34	-	exc	0	Secreted protein (Potential)	extracellular space [TAS]	605547		308
Q14488 UniProt NPD GO	FOXGC_HUMAN	Forkhead box protein G1C (Forkhead-related protein FKHL3) (HFK3) (Fragment)	0.34	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	605524		224
Q6AXT1 UniProt NPD GO	FHL5_RAT	Four and a half LIM domains protein 5 (FHL-5)	0.34	-	nuc	0	Nucleus (By similarity). Nuclei of round and elongated spermatids (By similarity)				284
Q5RCN4 UniProt NPD GO	FZD6_PONPY	Frizzled-6 precursor (Fz-6)	0.34	+	end	7	Membrane; multi-pass membrane protein				707
Q9BDS7 UniProt NPD GO	GPR15_MACFA	G-protein coupled receptor 15	0.34	-	end	7 *	Membrane; multi-pass membrane protein				359
P49685 UniProt NPD GO	GPR15_HUMAN	G-protein coupled receptor 15 (BOB)	0.34	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601166		360
Q9BG77 UniProt NPD GO	GPR15_PANTR	G-protein coupled receptor 15 (BOB)	0.34	-	end	7 *	Membrane; multi-pass membrane protein				360
P53782 UniProt NPD GO	CCND2_XENLA	G1/S-specific cyclin-D2	0.34	-	cyt	0					291
P30281 UniProt NPD GO	CCND3_HUMAN	G1/S-specific cyclin-D3	0.34	-	nuc	0	Cytoplasm. Nucleus		123834		292
O22929 UniProt NPD GO	GC5L_ARATH	GCN5-like protein 1 (RT14 protein homolog)	0.34	-	nuc	0					152
Q9USP5 UniProt NPD GO	GPI8_SCHPO	GPI-anchor transamidase precursor (EC 3.-.-.-) (GPI transamidase)	0.34	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	endoplasmic reticulum lumen [ISS]			380
P79800 UniProt NPD GO	RASK_MELGA	GTPase KRas (K-Ras 2) (Ki-Ras) (K-ras)	0.34	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity)				188
O42277 UniProt NPD GO	RASK_ORYLA	GTPase KRas (Ki-Ras) (K-ras)	0.34	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity)				188
Q5EFX7 UniProt NPD GO	RASK_RIVMA	GTPase KRas (Ki-Ras) (K-ras)	0.34	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity)				188
P11844 UniProt NPD GO	CRGA_HUMAN	Gamma crystallin A (Gamma crystallin 5)	0.34	-	cyt	0			123660	1LER	173
Q9WV18 UniProt NPD GO	GABR1_MOUSE	Gamma-aminobutyric acid type B receptor, subunit 1 precursor (GABA-B receptor 1) (GABA-B-R1) (Gb1)	0.34	-	end	7	Cell membrane; multi-pass membrane protein (By similarity). Moreover coexpression of GABA-B-R1 and G ...	cytoplasm [IDA]			960
P63137 UniProt NPD GO	GBRB2_MOUSE	Gamma-aminobutyric-acid receptor beta-2 subunit precursor (GABA(A) receptor)	0.34	-	cyt	4 *	Membrane; multi-pass membrane protein				474
P22723 UniProt NPD GO	GBRG2_MOUSE	Gamma-aminobutyric-acid receptor gamma-2 subunit precursor (GABA(A) receptor)	0.34	-	end	4	Membrane; multi-pass membrane protein				474
P34904 UniProt NPD GO	GBRG4_CHICK	Gamma-aminobutyric-acid receptor gamma-4 subunit precursor (GABA(A) receptor)	0.34	-	end	4	Membrane; multi-pass membrane protein				457
P47870 UniProt NPD GO	GBRB2_HUMAN	Gamma-aminobutyric-acid receptor subunit beta-2 precursor (GABA(A) receptor)	0.34	-	cyt	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600232		474
P63138 UniProt NPD GO	GBRB2_RAT	Gamma-aminobutyric-acid receptor subunit beta-2 precursor (GABA(A) receptor)	0.34	-	cyt	4 *	Membrane; multi-pass membrane protein				474
P17990 UniProt NPD GO	HOG1_HORVU	Gamma-hordein-1 precursor	0.34	-	exc	0	Cytoplasm. Vacuole. Cytoplasmic (as globules) and vacuolar (as protein bodies)				305
O93533 UniProt NPD GO	CXB6_CHICK	Gap junction beta-6 protein (Connexin-31) (Cx31)	0.34	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				263
P18722 UniProt NPD GO	ZG46_XENLA	Gastrula zinc finger protein XLCGF46.1 (Fragment)	0.34	-	nuc	0	Nucleus (Potential)				280
P18727 UniProt NPD GO	ZG52_XENLA	Gastrula zinc finger protein XLCGF52.1 (Fragment)	0.34	-	nuc	0	Nucleus (Potential)				223

You are viewing entries 36651 to 36700 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.