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
P21749 UniProt NPD GO	SALA_DROSI	Protein spalt-accessory precursor	0.05	-	cyt	0	Secreted protein (By similarity)				139
P41568 UniProt NPD GO	SUI11_ARATH	Protein translation factor SUI1 homolog 1	0.05	-	cyt	0					113
Q752H7 UniProt NPD GO	SC61A_ASHGO	Protein transport protein SEC61 subunit alpha	0.05	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				480
Q3T104 UniProt NPD GO	SC61G_BOVIN	Protein transport protein SEC61 subunit gamma	0.05	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				68
P60058 UniProt NPD GO	SC61G_CANFA	Protein transport protein SEC61 subunit gamma	0.05	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein	endoplasmic reticulum membrane [NAS] integral to endoplasmic reticulum membrane [NAS]			68
Q7T207 UniProt NPD GO	SC61G_HARAN	Protein transport protein SEC61 subunit gamma	0.05	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				68
P60059 UniProt NPD GO	SC61G_HUMAN	Protein transport protein SEC61 subunit gamma	0.05	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS] integral to endoplasmic reticulum membrane [ISS]	609215		68
P60060 UniProt NPD GO	SC61G_MOUSE	Protein transport protein SEC61 subunit gamma	0.05	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS] integral to endoplasmic reticulum membrane [ISS]			68
Q11118 UniProt NPD GO	WOS2_SCHPO	Protein wos2 (p21)	0.05	-	cyt	0					186
P31559 UniProt NPD GO	YCF12_EUGGR	Protein ycf12	0.05	-	mit	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q65Z57 UniProt NPD GO	YPEL3_CERAE	Protein yippee-like 3	0.05	-	cyt	0					119
P61236 UniProt NPD GO	YPEL3_HUMAN	Protein yippee-like 3	0.05	-	cyt	0			609724		119
P61237 UniProt NPD GO	YPEL3_MOUSE	Protein yippee-like 3	0.05	-	cyt	0					119
Q9URW3 UniProt NPD GO	YIPL_SCHPO	Protein yippee-like PJ691.02	0.05	-	nuc	0					131
Q9UU91 UniProt NPD GO	YOP1_SCHPO	Protein yop1	0.05	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				182
P87014 UniProt NPD GO	MAM4_SCHPO	Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) (Isoprenylcysteine carboxylmethyltran ...	0.05	-	end	5 *	Membrane; multi-pass membrane protein (Probable)				236
P20717 UniProt NPD GO	PADI2_RAT	Protein-arginine deiminase type-2 (EC 3.5.3.15) (Protein-arginine deiminase type II) (Peptidylargini ...	0.05	-	mit	0	Cytoplasm (By similarity)				665
Q08188 UniProt NPD GO	TGM3_HUMAN	Protein-glutamine gamma-glutamyltransferase E precursor (EC 2.3.2.13) (TGase E) (TGE) (TG(E)) (Trans ...	0.05	-	cyt	0		cornified envelope [ISS] cytoplasm [IDA] extrinsic to internal side of plasma membrane [IDA]	600238	1VJJ	693
O08675 UniProt NPD GO	PAR3_MOUSE	Proteinase-activated receptor 3 precursor (PAR-3) (Thrombin receptor-like 2) (Coagulation factor II ...	0.05	-	end	8 *	Membrane; multi-pass membrane protein				369
Q9R1Q7 UniProt NPD GO	PLP2_MOUSE	Proteolipid protein 2	0.05	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)	plasma membrane [ISS]			152
Q6NV32 UniProt NPD GO	PTMA_BRARE	Prothymosin alpha	0.05	-	nuc	0	Nucleus (By similarity)				105
Q5U274 UniProt NPD GO	PTMAA_XENLA	Prothymosin alpha-A	0.05	-	cyt	0	Nucleus (By similarity)				111
Q9N0P9 UniProt NPD GO	PIM1_BOVIN	Proto-oncogene serine/threonine-protein kinase pim-1 (EC 2.7.11.1)	0.05	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				313
Q28923 UniProt NPD GO	YES_CANFA	Proto-oncogene tyrosine-protein kinase Yes (EC 2.7.10.2) (p61-Yes) (c-Yes)	0.05	-	nuc	0	Cytoplasm; cytosol (By similarity)				538
P84769 UniProt NPD GO	PHCY_LIOMA	Pseudohemocyanin (Fragment)	0.05	-		0					12
P49874 UniProt NPD GO	SFTPA_PIG	Pulmonary surfactant-associated protein A precursor (SP-A) (PSP-A) (PSAP)	0.05	-	exc	0	Secreted protein; extracellular space				249
P35245 UniProt NPD GO	PSPC_MUSVI	Pulmonary surfactant-associated protein C precursor (SP-C)	0.05	-	gol	1 *	Secreted protein; extracellular space				190
P27781 UniProt NPD GO	CUP9_DROME	Pupal cuticle protein Edg-91 precursor (Ecdysone-dependent protein 91)	0.05	-	exc	0					159
Q09131 UniProt NPD GO	PPAF_SOYBN	Purple acid phosphatase precursor (EC 3.1.3.2) (Manganese(II) purple acid phosphatase)	0.05	-	mit	0	Secreted protein	extracellular space [IDA]			464
Q2R1D5 UniProt NPD GO	14338_ORYSA	Putative 14-3-3-like protein GF14-H (G-box factor 14-3-3 homolog H)	0.05	-	cyt	0					230
Q02961 UniProt NPD GO	YP113_YEAST	Putative 2-hydroxyacid dehydrogenase YPL113C (EC 1.-.-.-)	0.05	-	cyt	0					396
O14140 UniProt NPD GO	SEM1_SCHPO	Putative 26 proteasome complex subunit sem1	0.05	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			71
P87316 UniProt NPD GO	ATP5E_SCHPO	Putative ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14)	0.05	-	nuc	0	Mitochondrion				67
Q22021 UniProt NPD GO	ATPK_CAEEL	Putative ATP synthase f chain, mitochondrial (EC 3.6.3.14)	0.05	-	cyt	0					153
Q9T0E0 UniProt NPD GO	PMAX_ARATH	Putative ATPase, plasma membrane-like	0.05	-	end	9	Membrane; multi-pass membrane protein (Potential)				813
Q67WR5 UniProt NPD GO	FCL2_ORYSA	Putative GDP-L-fucose synthase 2 (EC 1.1.1.271) (GDP-4-keto-6-deoxy-D-mannose-3, 5-epimerase-4-reduc ...	0.05	-	cyt	0					347
Q9FRA7 UniProt NPD GO	Y5940_ORYSA	Putative REF/SRPP-like protein Os05g05940	0.05	-	mit	0					253
Q9M0R7 UniProt NPD GO	ATL4A_ARATH	Putative RING-H2 finger protein ATL4A	0.05	-	mit	1 *					132
Q9VU68 UniProt NPD GO	WDR1_DROME	Putative actin-interacting protein 1 (AIP1)	0.05	-	cyt	0					608
P46562 UniProt NPD GO	AL7A1_CAEEL	Putative aldehyde dehydrogenase family 7 member A1 homolog (EC 1.2.1.3) (ALH-9)	0.05	-	mit	0					531
O59831 UniProt NPD GO	YCUB_SCHPO	Putative amino-acid permease C965.11c	0.05	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				537
Q40784 UniProt NPD GO	AAPC_PENCL	Putative apospory-associated protein C	0.05	-	cyt	0					329
Q19087 UniProt NPD GO	DNPEP_CAEEL	Putative aspartyl aminopeptidase (EC 3.4.11.21)	0.05	-	cyt	0	Cytoplasm (By similarity)				470
P0C130 UniProt NPD GO	IAA28_ORYSA	Putative auxin-responsive protein IAA28 (Indoleacetic acid-induced protein 28)	0.05	-	cyt	0	Nucleus (By similarity)				162
P0C131 UniProt NPD GO	IAA29_ORYSA	Putative auxin-responsive protein IAA29 (Indoleacetic acid-induced protein 29)	0.05	-	cyt	0	Nucleus (By similarity)				171
P83344 UniProt NPD GO	XYNB_PRUPE	Putative beta-D-xylosidase (EC 3.2.1.-) (PpAz152) (Fragment)	0.05	-	cyt	0					461
Q10462 UniProt NPD GO	CAH5_CAEEL	Putative carbonic anhydrase 5 precursor (EC 4.2.1.1) (Carbonate dehydratase 5)	0.05	-	exc	1 *	Secreted protein (Potential)				310
Q9U700 UniProt NPD GO	CX51_CONTE	Putative conotoxin Tx5.1 precursor	0.05	-	exc	0	Secreted protein				62
Q8X0J4 UniProt NPD GO	CYB5L_NEUCR	Putative cytochrome b5 B11H24.095	0.05	-	cyt	0					83
Q9LMI4 UniProt NPD GO	ADSL4_ARATH	Putative delta-9 desaturase-like 4 protein (EC 1.14.19.-)	0.05	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				319

You are viewing entries 75451 to 75500 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.