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
Q5DRD9 UniProt NPD GO	PCDBA_PANTR	Protocadherin beta 10 precursor (PCDH-beta10)	0.19	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				798
Q9Y5E6 UniProt NPD GO	PCDB3_HUMAN	Protocadherin beta 3 precursor (PCDH-beta3)	0.19	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606329		796
Q6FUG4 UniProt NPD GO	COX10_CANGA	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.19	-	nuc	4	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				451
Q61038 UniProt NPD GO	PSYR_MOUSE	Psychosine receptor (G-protein coupled receptor 65) (T cell death-associated protein 8)	0.19	-	end	7 *	Membrane; multi-pass membrane protein				337
P35248 UniProt NPD GO	SFTPD_RAT	Pulmonary surfactant-associated protein D precursor (SP-D) (PSP-D) (CP4)	0.19	-	exc	0	Secreted protein; extracellular space	endocytic vesicle [ISS] extracellular region [ISS] lysosome [ISS]			374
Q8GYA3 UniProt NPD GO	OPRL1_ARATH	Putative 12-oxophytodienoate reductase-like protein 1 (EC 1.3.1.-)	0.19	-	mit	0					324
Q9SZB4 UniProt NPD GO	RH43_ARATH	Putative DEAD-box ATP-dependent RNA helicase 43 (EC 3.6.1.-)	0.19	-	cyt	0					542
O89086 UniProt NPD GO	RBM3_MOUSE	Putative RNA-binding protein 3 (RNA-binding motif protein 3)	0.19	-	nuc	0					153
Q95JP6 UniProt NPD GO	KAD7_MACFA	Putative adenylate kinase 7 (EC 2.7.4.3) (Fragment)	0.19	-	nuc	0					533
Q8LQ36 UniProt NPD GO	ATX3_ORYSA	Putative ataxin-3 homolog (EC 3.4.22.-)	0.19	-	cyt	0	Nucleus (By similarity)				336
Q94715 UniProt NPD GO	CATL2_PARTE	Putative cathepsin L2 precursor (EC 3.4.22.15) (Fragment)	0.19	-	cyt	0	Secreted protein				294
O42890 UniProt NPD GO	AMO_SCHPO	Putative copper amine oxidase (EC 1.4.3.6)	0.19	-	cyt	0					794
Q10176 UniProt NPD GO	OST1_SCHPO	Putative dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ost1 precursor (EC 2 ...	0.19	-	exc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	external side of plasma membrane [TAS]			450
Q10348 UniProt NPD GO	YDA6_SCHPO	Putative endonuclease C1F12.06c (EC 3.1.-.-)	0.19	-	mit	0					252
Q9C7P6 UniProt NPD GO	IF4E4_ARATH	Putative eukaryotic translation initiation factor 4E-4 (eIF4E type 4) (eIF-4E type 4) (mRNA cap-bind ...	0.19	-	nuc	0					240
O42872 UniProt NPD GO	RRP41_SCHPO	Putative exosome complex exonuclease RRP41 (EC 3.1.13.-) (Ribosomal RNA-processing protein 41)	0.19	-	cyt	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				242
O22775 UniProt NPD GO	GT2_ARATH	Putative glycosyltransferase 2 (EC 2.4.-.-) (AtGT2)	0.19	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				461
Q9VZL7 UniProt NPD GO	GR63A_DROME	Putative gustatory receptor 63a	0.19	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			512
P56173 UniProt NPD GO	ILB6_CAEEL	Putative insulin-like peptide beta-type 6 precursor	0.19	-	nuc	0					99
Q75EN3 UniProt NPD GO	ATG15_ASHGO	Putative lipase ATG15 (EC 3.1.1.3) (Autophagy-related protein 15)	0.19	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				544
Q7G794 UniProt NPD GO	LOX3_ORYSA	Putative lipoxygenase 3 (EC 1.13.11.12)	0.19	-	cyt	0					866
P82722 UniProt NPD GO	LCR7_ARATH	Putative low-molecular-weight cysteine-rich protein LCR7	0.19	-	nuc	0					84
Q9LSJ5 UniProt NPD GO	MDR20_ARATH	Putative multidrug resistance protein 20 (P-glycoprotein 18)	0.19	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				1225
Q9V3Q2 UniProt NPD GO	OR35A_DROME	Putative odorant receptor 35a	0.19	-	end	4	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			409
Q9VHS4 UniProt NPD GO	OR85A_DROME	Putative odorant receptor 85a	0.19	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				397
Q9VCS9 UniProt NPD GO	OR94A_DROME	Putative odorant receptor 94a	0.19	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			387
Q965Q4 UniProt NPD GO	SMS3_CAEEL	Putative phosphatidylcholine:ceramide cholinephosphotransferase 3 (EC 2.7.-.-) (Sphingomyelin syntha ...	0.19	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			340
Q09755 UniProt NPD GO	AROF_SCHPO	Putative phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) (Phospho-2-keto-3-deoxyheptonate ...	0.19	-	nuc	0					368
P34516 UniProt NPD GO	YMX8_CAEEL	Putative serine/threonine-protein kinase K06H7.1 (EC 2.7.11.1)	0.19	-	cyt	0					346
Q41141 UniProt NPD GO	PFPB_RICCO	Pyrophosphate--fructose 6-phosphate 1-phosphotransferase subunit beta (EC 2.7.1.90) (PFP) (6-phospho ...	0.19	-	cyt	0					552
P16451 UniProt NPD GO	ODPX_YEAST	Pyruvate dehydrogenase complex protein X component, mitochondrial precursor (Dihydrolipoamide dehydr ...	0.19	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA] pyruvate dehydrogenase complex (sensu Eukar... [TAS]			410
Q9GPQ9 UniProt NPD GO	RACJ_DICDI	RAS-related protein racJ	0.19	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				205
Q9GPQ8 UniProt NPD GO	RACL_DICDI	RAS-related protein racL	0.19	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				196
Q8RXX9 UniProt NPD GO	ATL3B_ARATH	RING-H2 finger protein ATL3B precursor (RING-H2 finger protein ATL6)	0.19	-	end	2 *					398
Q9ZU51 UniProt NPD GO	RHA2B_ARATH	RING-H2 zinc finger protein RHA2b	0.19	-	nuc	0					147
Q750A5 UniProt NPD GO	REXO3_ASHGO	RNA exonuclease 3 (EC 3.1.-.-)	0.19	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				382
Q12090 UniProt NPD GO	REXO3_YEAST	RNA exonuclease 3 (EC 3.1.-.-)	0.19	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			404
Q6CTL5 UniProt NPD GO	TFB5_KLULA	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.19	-	nuc	0	Nucleus (By similarity)				72
Q6Z7L8 UniProt NPD GO	RAC7_ORYSA	Rac-like GTP-binding protein 7 (OsRac7) (GTPase protein ROP5)	0.19	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				197
Q35638 UniProt NPD GO	RHO1_PEA	Rac-like GTP-binding protein RHO1 (GTPase protein ROP1)	0.19	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				197
Q9VIW3 UniProt NPD GO	RGP1_DROME	Ran GTPase-activating protein (RanGAP) (Protein segregation distorter)	0.19	-	cyt	0	Cytoplasm (By similarity)				596
P40389 UniProt NPD GO	RRG1_SCHPO	Rapid response to glucose protein 1	0.19	-	cyt	0					303
P22124 UniProt NPD GO	RAL_DISOM	Ras-related protein O-RAL	0.19	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				206
P35288 UniProt NPD GO	RAB23_MOUSE	Ras-related protein Rab-23 (Rab-15)	0.19	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)			1Z2A	237
P59279 UniProt NPD GO	RAB2B_MOUSE	Ras-related protein Rab-2B	0.19	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				216
Q96AX2 UniProt NPD GO	RAB37_HUMAN	Ras-related protein Rab-37	0.19	-	cyt	0	Secretory granules (By similarity)	ER-Golgi intermediate compartment [IDA]	609956		222
O97572 UniProt NPD GO	RAB7_RABIT	Ras-related protein Rab-7	0.19	-	cyt	0	Endosome; late endosome. Lysosome (By similarity). Phagosome (By similarity). Found on late lysosome ...				207
P35280 UniProt NPD GO	RAB8A_RAT	Ras-related protein Rab-8A	0.19	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				207
P55258 UniProt NPD GO	RAB8A_MOUSE	Ras-related protein Rab-8A (Oncogene c-mel)	0.19	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)			2FU5	207
Q6NUK4 UniProt NPD GO	REEP3_HUMAN	Receptor expression-enhancing protein 3	0.19	-	nuc	3 *	Membrane; multi-pass membrane protein (By similarity)		609348		255

You are viewing entries 52351 to 52400 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.