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
Q08586 UniProt NPD GO	FCPC_PHATR	Fucoxanthin-chlorophyll a-c binding protein C, chloroplast precursor	0.04	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				197
Q08587 UniProt NPD GO	FCPD_PHATR	Fucoxanthin-chlorophyll a-c binding protein D, chloroplast precursor	0.04	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				197
P10173 UniProt NPD GO	FUMH_PIG	Fumarate hydratase, mitochondrial (EC 4.2.1.2) (Fumarase)	0.04	-	cyt	0					466
Q7SX99 UniProt NPD GO	FUMH_BRARE	Fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fumarase)	0.04	-	mit	0	Mitochondrion (By similarity)				509
P07954 UniProt NPD GO	FUMH_HUMAN	Fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fumarase)	0.04	-	mit	0	Mitochondrion. Cytoplasm	cytoplasm [TAS] mitochondrion [TAS]	606812		510
Q60HF9 UniProt NPD GO	FUMH_MACFA	Fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fumarase)	0.04	-	mit	0	Mitochondrion (By similarity). Cytoplasm (By similarity)				510
P14408 UniProt NPD GO	FUMH_RAT	Fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fumarase)	0.04	-	mit	0	Mitochondrion. Cytoplasm				507
O94552 UniProt NPD GO	FUMH_SCHPO	Fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fumarase)	0.04	-	cyt	0	Mitochondrion (Potential)				482
Q5RDW0 UniProt NPD GO	FAHD1_PONPY	Fumarylacetoacetate hydrolase domain-containing protein 1 (EC 3.-.-.-)	0.04	-	cyt	0					224
P70259 UniProt NPD GO	GP143_MOUSE	G-protein coupled receptor 143 (Ocular albinism type 1 protein homolog) (MOA1)	0.04	-	end	5 *	Melanosome; melanosomal membrane; multi-pass membrane protein (By similarity). Targeted to intracell ...				405
Q6BD04 UniProt NPD GO	GPR54_ORENI	G-protein coupled receptor 54	0.04	-	end	7 *	Membrane; multi-pass membrane protein				377
Q96A29 UniProt NPD GO	FUCT1_HUMAN	GDP-fucose transporter 1 (Solute carrier family 35 member C1)	0.04	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein		605881		364
Q8K3X3 UniProt NPD GO	GMDS_CRIGR	GDP-mannose 4,6 dehydratase (EC 4.2.1.47) (GDP-D-mannose dehydratase) (GMD)	0.04	-	cyt	0					372
Q941R4 UniProt NPD GO	GONS1_ARATH	GDP-mannose transporter	0.04	-	end	9 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein				333
Q6FXQ5 UniProt NPD GO	GPI14_CANGA	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.04	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				431
Q5F380 UniProt NPD GO	PIGM_CHICK	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Phosphatidylinositol- ...	0.04	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				418
Q8C2R7 UniProt NPD GO	PIGM_MOUSE	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Phosphatidylinositol- ...	0.04	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				423
Q4WQ21 UniProt NPD GO	GPI18_ASPFU	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.04	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				441
Q2UJS7 UniProt NPD GO	GPI18_ASPOR	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Glycosylphosphatidy ...	0.04	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				434
Q9NUD9 UniProt NPD GO	PIGV_HUMAN	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Phosphatidylinosito ...	0.04	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				493
Q75BG9 UniProt NPD GO	GPI10_ASHGO	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.04	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				595
Q753C1 UniProt NPD GO	SMP3_ASHGO	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.04	+	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				498
O13883 UniProt NPD GO	PIGU_SCHPO	GPI transamidase component GAB1 homolog	0.04	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				408
Q6PBT6 UniProt NPD GO	GFRP_BRARE	GTP cyclohydrolase 1 feedback regulatory protein (GTP cyclohydrolase I feedback regulatory protein) ...	0.04	-	cyt	0					89
P25160 UniProt NPD GO	ARL1_DROME	GTP-binding ADP-ribosylation factor homolog 1 protein	0.04	-	cyt	0					180
Q06849 UniProt NPD GO	ARL2_DROME	GTP-binding ADP-ribosylation factor homolog 2 protein	0.04	-	nuc	0					184
P84557 UniProt NPD GO	RAN_POPEU	GTP-binding nuclear protein Ran (Fragments)	0.04	-	nuc	0	Nucleus (By similarity)				28
Q63942 UniProt NPD GO	RAB3D_RAT	GTP-binding protein Rab-3D	0.04	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				219
P11620 UniProt NPD GO	YPT1_SCHPO	GTP-binding protein ypt1	0.04	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				203
P80399 UniProt NPD GO	GGN5_RANRU	Gaegurin-5 precursor	0.04	-	end	0	Secreted protein				65
Q801X7 UniProt NPD GO	AJL1_ANGJA	Galactose-binding lectin l-1 (Galectin) (Ajl-1)	0.04	-	cyt	0	Secreted protein	extracellular region [IDA]			142
P02872 UniProt NPD GO	LECG_ARAHY	Galactose-binding lectin precursor (Agglutinin) (PNA)	0.04	-	vac	0				2TEP	273
Q866E4 UniProt NPD GO	FUT1_ALOCA	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.04	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
Q866C7 UniProt NPD GO	FUT1_ATEBE	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.04	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
Q866C9 UniProt NPD GO	FUT1_LAGLA	Galactoside 2-alpha-L-fucosyltransferase 1 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.04	-	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				366
P97353 UniProt NPD GO	SEC1_MOUSE	Galactoside 2-alpha-L-fucosyltransferase 3 (EC 2.4.1.69) (GDP-L-fucose:beta-D-galactoside 2-alpha-L- ...	0.04	-	nuc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				368
Q9UHV8 UniProt NPD GO	PP13_HUMAN	Galactoside-binding soluble lectin 13 (EC 3.1.1.5) (Placental tissue protein 13) (Placenta protein 1 ...	0.04	-	cyt	0			608717	1F87	139
P10683 UniProt NPD GO	GALA_RAT	Galanin precursor [Contains: Galanin; Galanin message-associated peptide (GMAP)]	0.04	-	exc	1 *	Secreted protein				124
Q91VD1 UniProt NPD GO	LEG12_MOUSE	Galectin-12	0.04	-	cyt	0	Nucleus	mitochondrion [IDA] nucleus [IDA]			314
Q9P4R8 UniProt NPD GO	CGL2_COPCI	Galectin-2 (Galectin II) (Cgl-II)	0.04	-	cyt	0	Secreted protein. Detected in extracellular matrix, cell wall and cytoplasmic membrane-bound bodies			1ULG	150
Q9QZU7 UniProt NPD GO	BODG_RAT	Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine,2-oxoglutarate dioxygenase) (Gam ...	0.04	-	cyt	0	Cytoplasm				387
P56711 UniProt NPD GO	CXG7A_CONPE	Gamma-conotoxin PnVIIA	0.04	-	nuc	0	Secreted protein				32
Q5G235 UniProt NPD GO	PEN2_BOVIN	Gamma-secretase subunit PEN-2 (Presenilin enhancer protein 2)	0.04	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				101
Q9NZ42 UniProt NPD GO	PEN2_HUMAN	Gamma-secretase subunit PEN-2 (Presenilin enhancer protein 2)	0.04	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [IDA] Golgi apparatus [IDA] integral to plasma membrane [IDA]	607632		101
Q9CQR7 UniProt NPD GO	PEN2_MOUSE	Gamma-secretase subunit PEN-2 (Presenilin enhancer protein 2)	0.04	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to plasma membrane [ISS]			101
Q9FY84 UniProt NPD GO	PEN2_ARATH	Gamma-secretase subunit PEN2-like protein	0.04	-	cyt	2	Membrane; multi-pass membrane protein (Potential)				146
Q8JHF0 UniProt NPD GO	PEN2_BRARE	Gamma-secretase subunit Psenen (Presenilin enhancer protein 2 homolog)	0.04	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				101
P28233 UniProt NPD GO	CXA6_RAT	Gap junction alpha-6 protein (Connexin-33) (Cx33)	0.04	-	end	3 *	Membrane; multi-pass membrane protein	connexon complex [TAS]			286
O75712 UniProt NPD GO	CXB3_HUMAN	Gap junction beta-3 protein (Connexin-31) (Cx31)	0.04	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [NAS]	603324		270
P01281 UniProt NPD GO	GIP_PIG	Gastric inhibitory polypeptide (GIP) (Glucose-dependent insulinotropic polypeptide)	0.04	-	cyt	0	Secreted protein				42

You are viewing entries 77051 to 77100 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.