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
Q7Z5A9 UniProt NPD GO	F19A1_HUMAN	Protein FAM19A1 precursor (Chemokine-like protein TAFA-1)	0.07	-	nuc	1 *	Secreted protein				133
Q7Z5A8 UniProt NPD GO	F19A3_HUMAN	Protein FAM19A3 precursor (Chemokine-like protein TAFA-3)	0.07	-	end	1 *	Secreted protein				133
Q7TPG6 UniProt NPD GO	F19A3_MOUSE	Protein FAM19A3 precursor (Chemokine-like protein TAFA-3)	0.07	-	mit	0	Secreted protein (By similarity)				132
Q96LR4 UniProt NPD GO	F19A4_HUMAN	Protein FAM19A4 precursor (Chemokine-like protein TAFA-4)	0.07	-	mit	1 *	Secreted protein				140
Q9N0D3 UniProt NPD GO	F19A4_MACFA	Protein FAM19A4 precursor (Chemokine-like protein TAFA-4)	0.07	-	mit	1 *	Secreted protein (By similarity)				140
O75063 UniProt NPD GO	FA20B_HUMAN	Protein FAM20B precursor	0.07	-	end	1 *	Secreted protein (Potential)				409
Q2HJ63 UniProt NPD GO	FA26B_BOVIN	Protein FAM26B	0.07	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				323
Q9HA72 UniProt NPD GO	FA26B_HUMAN	Protein FAM26B	0.07	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				323
Q9D8N2 UniProt NPD GO	FAM45_MOUSE	Protein FAM45	0.07	-	cyt	0					357
Q43312 UniProt NPD GO	H2A7_WHEAT	Protein H2A.7 (wcH2A-4) (wcH2A-10)	0.07	-	nuc	0	Nucleus (By similarity)				133
Q12382 UniProt NPD GO	HSD1_YEAST	Protein HSD1 (High-copy suppressor of SLY1 defect protein 1)	0.07	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	integral to endoplasmic reticulum membrane [IDA]			290
O88824 UniProt NPD GO	JTB_MOUSE	Protein JTB precursor	0.07	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				146
Q9C801 UniProt NPD GO	MOS2_ARATH	Protein MOS2	0.07	-	mit	0	Nucleus	nucleus [IDA]			462
P42882 UniProt NPD GO	NMT1_ASPPA	Protein NMT1 homolog	0.07	-	cyt	0					342
P06781 UniProt NPD GO	RHO2_YEAST	Protein RHO2	0.07	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	intracellular [TAS]			192
P53047 UniProt NPD GO	RTA1_YEAST	Protein RTA1	0.07	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				317
P50117 UniProt NPD GO	S10A9_RABIT	Protein S100-A9 (S100 calcium-binding protein A9) (Calgranulin-B) (Migration inhibitory factor-relat ...	0.07	-	nuc	0					118
P97816 UniProt NPD GO	S100G_MOUSE	Protein S100-G (S100 calcium-binding protein G) (Vitamin D-dependent calcium-binding protein, intest ...	0.07	-	nuc	0		apical plasma membrane [IDA] basolateral plasma membrane [IDA]			78
P38992 UniProt NPD GO	SUR2_YEAST	Protein SUR2 (Syringomycin response protein 2)	0.07	+	nuc	4 *	Membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum [TAS]			349
Q6UWE3 UniProt NPD GO	U3045_HUMAN	Protein UNQ3045/PRO9861 precursor	0.07	-	mit	1 *	Secreted protein (Probable)				153
P31287 UniProt NPD GO	WNT6_XENLA	Protein Wnt-6 (XWnt-6) (Fragment)	0.07	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				129
P31289 UniProt NPD GO	WNT7B_XENLA	Protein Wnt-7b (XWnt-7b) (Fragment)	0.07	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				135
Q4P0H0 UniProt NPD GO	YOP1_USTMA	Protein YOP1	0.07	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				172
P53584 UniProt NPD GO	YTP1_YEAST	Protein YTP1	0.07	-	end	10 *	Membrane; multi-pass membrane protein				459
Q9US09 UniProt NPD GO	BTN1_SCHPO	Protein btn1	0.07	-	end	8 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)	vacuolar membrane (sensu Fungi) [IDA]			396
Q27367 UniProt NPD GO	CRQ_DROME	Protein croquemort (d-CD36)	0.07	-	cyt	1 *	Membrane; multi-pass membrane protein				457
O43037 UniProt NPD GO	MGN_SCHPO	Protein mago nashi homolog	0.07	-	cyt	0					147
P49599 UniProt NPD GO	PP2C3_ARATH	Protein phosphatase 2C PPH1 (EC 3.1.3.16) (PP2C)	0.07	-	nuc	0					388
P49443 UniProt NPD GO	PP2CA_MOUSE	Protein phosphatase 2C isoform alpha (EC 3.1.3.16) (PP2C-alpha) (IA) (Protein phosphatase 1A)	0.07	-	nuc	0					382
P35814 UniProt NPD GO	PP2CA_RABIT	Protein phosphatase 2C isoform alpha (EC 3.1.3.16) (PP2C-alpha) (IA) (Protein phosphatase 1A)	0.07	-	nuc	0					382
P53693 UniProt NPD GO	RDS1_SCHPO	Protein rds1	0.07	-	vac	0					402
Q6FRY3 UniProt NPD GO	SC61A_CANGA	Protein transport protein SEC61 subunit alpha	0.07	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				479
Q6CPY9 UniProt NPD GO	SC61A_KLULA	Protein transport protein SEC61 subunit alpha	0.07	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				480
Q19967 UniProt NPD GO	SC61G_CAEEL	Protein transport protein SEC61 subunit gamma	0.07	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)	cell [IDA]			68
Q5R7J8 UniProt NPD GO	TP4A1_PONPY	Protein tyrosine phosphatase type IVA protein 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 4a1) (Pr ...	0.07	-	mit	0	Cell membrane (By similarity). Endosome; early endosome (By similarity). Endoplasmic reticulum (By s ...				173
Q3ZBE7 UniProt NPD GO	YPEL5_BOVIN	Protein yippee-like 5	0.07	-	cyt	0					121
Q65Z55 UniProt NPD GO	YPEL5_CERAE	Protein yippee-like 5	0.07	-	cyt	0					121
P62699 UniProt NPD GO	YPEL5_HUMAN	Protein yippee-like 5	0.07	-	cyt	0			609726		121
P62700 UniProt NPD GO	YPEL5_MOUSE	Protein yippee-like 5	0.07	-	cyt	0					121
Q5RDU7 UniProt NPD GO	YPEL5_PONPY	Protein yippee-like 5	0.07	-	cyt	0					121
Q9U3G6 UniProt NPD GO	YPL1_CAEEL	Protein yippee-like F37A8.5	0.07	-	cyt	0					137
Q27873 UniProt NPD GO	PIMT_CAEEL	Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) (Protein-beta-aspartate methyltransferase) ...	0.07	-	cyt	0	Cytoplasm				225
Q08642 UniProt NPD GO	PADI2_MOUSE	Protein-arginine deiminase type-2 (EC 3.5.3.15) (Protein-arginine deiminase type II) (Peptidylargini ...	0.07	-	nuc	0	Cytoplasm (By similarity)				673
O60507 UniProt NPD GO	TPS1_HUMAN	Protein-tyrosine sulfotransferase 1 (EC 2.8.2.20) (Tyrosylprotein sulfotransferase-1) (TPST-1)	0.07	-	cyt	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	membrane fraction [TAS]	603125		370
Q96RI0 UniProt NPD GO	PAR4_HUMAN	Proteinase-activated receptor 4 precursor (PAR-4) (Thrombin receptor-like 3) (Coagulation factor II ...	0.07	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	602779		385
Q95LJ0 UniProt NPD GO	PIM1_FELCA	Proto-oncogene serine/threonine-protein kinase pim-1 (EC 2.7.11.1)	0.07	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				313
Q6KF82 UniProt NPD GO	PHCY1_HOMAM	Pseudohemocyanin-1 precursor (Fragment)	0.07	-	cyt	0					684
Q6FS81 UniProt NPD GO	PUS5_CANGA	Pseudouridylate synthase PUS5 (EC 5.4.99.-) (Pseudouridine synthase 5) (Uracil hydrolyase PUS5)	0.07	-	cyt	0	Mitochondrion (By similarity)				223
Q6RXL1 UniProt NPD GO	SFTPA_BOVIN	Pulmonary surfactant-associated protein A (SP-A) (PSP-A) (PSAP) (Fragment)	0.07	-	nuc	0	Secreted protein; extracellular space (By similarity)				92
Q9TUC5 UniProt NPD GO	SFTPA_MACMU	Pulmonary surfactant-associated protein A (SP-A) (PSP-A) (PSAP) (Fragment)	0.07	-	cyt	0	Secreted protein; extracellular space (By similarity)				165

You are viewing entries 70851 to 70900 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.