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
O01824 UniProt NPD GO	PDXK_CAEEL	Putative pyridoxal kinase (EC 2.7.1.35) (Pyridoxine kinase)	0.06	-	cyt	0					321
Q09201 UniProt NPD GO	YP22_CAEEL	Putative sideroflexin-like protein AH6.2	0.06	-	cyt	4	Membrane; multi-pass membrane protein (Potential)				329
Q00713 UniProt NPD GO	STCQ_EMENI	Putative sterigmatocystin biosynthesis protein stcQ	0.06	-	cyt	0					274
Q8MPZ7 UniProt NPD GO	ISL1_CAEEL	Putative trypsin inhibitor isl-1 precursor (Inhibitor of serine protease-like protein 1)	0.06	-	nuc	0	Secreted protein (Potential)				100
P39559 UniProt NPD GO	YAM3_YEAST	Putative uncharacterized protein YA5053W	0.06	-	cyt	0	Membrane; multi-pass membrane protein (Potential)				98
P39989 UniProt NPD GO	YEC8_YEAST	Putative uncharacterized protein YEL028W precursor	0.06	-	vac	1 *					153
Q8K183 UniProt NPD GO	PDXK_MOUSE	Pyridoxal kinase (EC 2.7.1.35) (Pyridoxine kinase)	0.06	-	cyt	0	Cytoplasm (By similarity)				312
O35331 UniProt NPD GO	PDXK_RAT	Pyridoxal kinase (EC 2.7.1.35) (Pyridoxine kinase)	0.06	-	cyt	0	Cytoplasm (By similarity)				312
Q6FJA3 UniProt NPD GO	PDC1_CANGA	Pyruvate decarboxylase (EC 4.1.1.1)	0.06	-	cyt	0					564
Q12629 UniProt NPD GO	PDC1_KLULA	Pyruvate decarboxylase (EC 4.1.1.1)	0.06	-	cyt	0					563
P33149 UniProt NPD GO	PDC1_KLUMA	Pyruvate decarboxylase (EC 4.1.1.1)	0.06	-	cyt	0					564
P51846 UniProt NPD GO	PDC2_TOBAC	Pyruvate decarboxylase isozyme 2 (EC 4.1.1.1) (PDC)	0.06	-	mit	0					614
P26268 UniProt NPD GO	ODPT_ASCSU	Pyruvate dehydrogenase E1 component alpha subunit type II, mitochondrial precursor (EC 1.2.4.1) (PDH ...	0.06	-	cyt	0	Mitochondrion; mitochondrial matrix				391
O13366 UniProt NPD GO	ODPA_KLULA	Pyruvate dehydrogenase E1 component alpha subunit, mitochondrial precursor (EC 1.2.4.1) (PDHE1-A)	0.06	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				412
P31865 UniProt NPD GO	KPYK_TRIRE	Pyruvate kinase (EC 2.7.1.40) (PK)	0.06	-	cyt	0					538
P55964 UniProt NPD GO	KPYG_RICCO	Pyruvate kinase isozyme G, chloroplast (EC 2.7.1.40) (Fragment)	0.06	-	cyt	0	Plastid; chloroplast				418
P12928 UniProt NPD GO	KPYR_RAT	Pyruvate kinase isozymes R/L (EC 2.7.1.40) (L-PK)	0.06	-	cyt	0					574
Q9UT27 UniProt NPD GO	PVG1_SCHPO	Pyruvyltransferase 1 precursor (EC 2.-.-.-) (Pyruvylated Gal-beta-1,3-epitope synthesis protein 1) ( ...	0.06	-	exc	1 *	Secreted protein (Potential)				401
P37207 UniProt NPD GO	PHCA_PORCR	R-phycocyanin-1 subunit alpha (R-phycocyanin I alpha chain)	0.06	-	cyt	0	Plastid; chloroplast				162
P84861 UniProt NPD GO	PHEA_POLUR	R-phycoerythrin alpha chain	0.06	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen. Periphery of the rods of the phycobilisome			1LIA	164
Q6NXM2 UniProt NPD GO	RCBT1_MOUSE	RCC1 and BTB domain-containing protein 1 (Regulator of chromosome condensation and BTB domain-contai ...	0.06	-	cyt	0	Nucleus (Potential)				531
Q8GT74 UniProt NPD GO	ATL2B_ARATH	RING-H2 finger protein ATL2B (NEP1-interacting protein 2)	0.06	-	end	1 *					241
Q8GT75 UniProt NPD GO	ATL4M_ARATH	RING-H2 finger protein ATL4M (NEP1-interacting protein 1)	0.06	-	end	3 *					236
Q9LZV8 UniProt NPD GO	ATL5A_ARATH	RING-H2 finger protein ATL5A	0.06	-	nuc	1 *					159
Q9FKX5 UniProt NPD GO	ATL5P_ARATH	RING-H2 finger protein ATL5P	0.06	-	end	3 *					221
Q9SUS5 UniProt NPD GO	RHA1B_ARATH	RING-H2 zinc finger protein RHA1b	0.06	-	cyt	0					157
Q9WTZ1 UniProt NPD GO	RBX2_MOUSE	RING-box protein 2 (Rbx2) (RING finger protein 7) (Sensitive to apoptosis gene protein)	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			113
Q08213 UniProt NPD GO	NGL1_YEAST	RNA exonuclease NGL1 (EC 3.1.-.-)	0.06	-	mit	0		mitochondrion [IDA]			363
Q3E7C1 UniProt NPD GO	TFB5_YEAST	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.06	-	nuc	0	Nucleus	nucleus [IDA] transcription factor TFIIH complex [IDA]			72
P18211 UniProt NPD GO	HB2D_RAT	RT1 class II histocompatibility antigen, D-1 beta chain precursor	0.06	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				264
Q8RWG8 UniProt NPD GO	RBP1B_ARATH	Ran-binding protein 1 homolog b	0.06	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity)				217
P41920 UniProt NPD GO	YRB1_YEAST	Ran-specific GTPase-activating protein 1 (Ran-binding protein 1) (RANBP1) (Perinuclear array-localiz ...	0.06	-	nuc	0	Cytoplasm. Nucleus. Shuttles between the nucleus and cytoplasm	cytoplasm [IDA] nucleus [IDA]			201
Q09717 UniProt NPD GO	RANG_SCHPO	Ran-specific GTPase-activating protein 1 (Ran-binding protein 1) (RANBP1) (Spi1-binding protein)	0.06	-	nuc	0	Cytoplasm. Mainly				215
P28187 UniProt NPD GO	ARA4_ARATH	Ras-related protein ARA-4	0.06	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				214
Q6DHC1 UniProt NPD GO	RAB18_BRARE	Ras-related protein Rab-18	0.06	-	cyt	0					205
Q5M7U5 UniProt NPD GO	RAB19_RAT	Ras-related protein Rab-19	0.06	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
Q9ULC3 UniProt NPD GO	RAB23_HUMAN	Ras-related protein Rab-23	0.06	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		606144		237
P24408 UniProt NPD GO	RAB9A_CANFA	Ras-related protein Rab-9A (Rab-9)	0.06	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)			1S8F	201
Q99P75 UniProt NPD GO	RAB9A_RAT	Ras-related protein Rab-9A (Rab-9)	0.06	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
Q9R0M6 UniProt NPD GO	RAB9A_MOUSE	Ras-related protein Rab-9A (Rab-9) (Sid 99)	0.06	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)			1YZL	201
Q40520 UniProt NPD GO	RB11C_TOBAC	Ras-related protein Rab11C	0.06	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				222
P34143 UniProt NPD GO	RABC_DICDI	Ras-related protein RabC	0.06	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				196
Q99396 UniProt NPD GO	CY42_TRYBB	Receptor-type adenylate cyclase GRESAG 4.2 (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase) ...	0.06	-	mit	0	Cell membrane; multi-pass membrane protein (By similarity)				572
P32313 UniProt NPD GO	OPSR_CARAU	Red-sensitive opsin (Red cone photoreceptor pigment)	0.06	-	end	7	Membrane; multi-pass membrane protein				357
P35231 UniProt NPD GO	REG3A_RAT	Regenerating islet-derived protein 3 alpha precursor (Reg III-alpha) (Pancreatitis-associated protei ...	0.06	-	mit	0	Secreted protein				174
P25031 UniProt NPD GO	REG3B_RAT	Regenerating islet-derived protein 3 beta precursor (Reg III-beta) (Pancreatitis-associated protein ...	0.06	-	end	0	Secreted protein. Found in the apical region of pancreatic acinar cells				175
P21827 UniProt NPD GO	RCC1_YEAST	Regulator of chromosome condensation (Protein PRP20) (Pheromone response pathway component SRM1)	0.06	-	cyt	0	Nucleus	nuclear chromatin [IDA] nucleus [TAS]			482
Q9FFE0 UniProt NPD GO	RRAA2_ARATH	Regulator of ribonuclease-like protein 2	0.06	-	cyt	0					166
P11184 UniProt NPD GO	RELX_BALAC	Relaxin [Contains: Relaxin B chain; Relaxin A chain]	0.06	-	cyt	0	Secreted protein				54
Q8HY17 UniProt NPD GO	REL3_PIG	Relaxin-3 precursor (Insulin-like peptide INSL7) (Insulin-like peptide 7) [Contains: Relaxin-3 B cha ...	0.06	-	exc	0	Secreted protein				140

You are viewing entries 73051 to 73100 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.