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
O65268 UniProt NPD GO	ASPG4_ARATH	Putative L-asparaginase 4 precursor (EC 3.5.1.1) (L-asparagine amidohydrolase 4) [Contains: L-aspara ...	0.08	-	cyt	0					407
Q9VCG2 UniProt NPD GO	OPA31_DROME	Putative OPA3-like protein CG13602	0.08	-	cyt	0					111
Q09442 UniProt NPD GO	YP85_CAEEL	Putative RNA-binding protein C08B11.5	0.08	-	nuc	0					388
Q9FI17 UniProt NPD GO	ARAE4_ARATH	Putative UDP-arabinose 4-epimerase 4 (EC 5.1.3.5) (UDP-D-xylose 4-epimerase 4)	0.08	-	mit	1	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Potential) ...				436
P38694 UniProt NPD GO	YHJ9_YEAST	Putative aldehyde dehydrogenase-like protein YHR039C (EC 1.2.1.-)	0.08	-	end	1 *		endoplasmic reticulum [IDA]			644
Q9ZSI1 UniProt NPD GO	EXP17_ARATH	Putative alpha-expansin 17 precursor (AtEXPA17) (At-EXP17) (AtEx17) (Ath-ExpAlpha-1.13)	0.08	-	mit	1 *	Cell wall; peripheral membrane protein				255
Q19425 UniProt NPD GO	YSPK_CAEEL	Putative amino-acid permease F13H10.3	0.08	-	end	11	Membrane; multi-pass membrane protein (Potential)				615
Q09735 UniProt NPD GO	YA55_SCHPO	Putative aminopeptidase C13A11.05 in chromosome I (EC 3.4.11.-)	0.08	-	mit	0	Cytoplasm (By similarity)				513
P43546 UniProt NPD GO	AAD16_YEAST	Putative aryl-alcohol dehydrogenase AAD16 (EC 1.1.1.-)	0.08	-	cyt	0					152
Q2QRX6 UniProt NPD GO	DRTS_ORYSA	Putative bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolat ...	0.08	-	cyt	0					494
P60300 UniProt NPD GO	CLCG_ARATH	Putative chloride channel-like protein CLC-g	0.08	-	end	13	Membrane; multi-pass membrane protein				763
Q08651 UniProt NPD GO	YO246_YEAST	Putative dehydrogenase YOR246C (EC 1.1.1.-)	0.08	-	mit	1 *	Lipid particle; lipid particle membrane; multi-pass membrane protein (Potential)	lipid particle [IDA]			330
O74918 UniProt NPD GO	RRP45_SCHPO	Putative exosome complex exonuclease RRP45 (EC 3.1.13.-) (Ribosomal RNA-processing protein 45)	0.08	-	mit	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				291
O65399 UniProt NPD GO	E131_ARATH	Putative glucan endo-1,3-beta-glucosidase 1 precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolas ...	0.08	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				402
Q9VQE7 UniProt NPD GO	G23AA_DROME	Putative gustatory receptor 23a, isoform A	0.08	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			383
P58958 UniProt NPD GO	G39AC_DROME	Putative gustatory receptor 39a, isoform D	0.08	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			381
O61369 UniProt NPD GO	PICO_DROAN	Putative inorganic phosphate cotransporter	0.08	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			483
Q9V7S5 UniProt NPD GO	PICO_DROME	Putative inorganic phosphate cotransporter	0.08	-	end	10 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			529
P82778 UniProt NPD GO	LCR64_ARATH	Putative low-molecular-weight cysteine-rich protein LCR64 precursor	0.08	-	nuc	1 *					90
Q61585 UniProt NPD GO	G0S2_MOUSE	Putative lymphocyte G0/G1 switch protein 2 (G0S2-like protein)	0.08	-	mit	1 *					103
Q10442 UniProt NPD GO	YDE9_SCHPO	Putative mitochondrial carrier C12B10.09	0.08	-	mit	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				345
Q09982 UniProt NPD GO	NLP32_CAEEL	Putative neuropeptide-like protein 32 precursor [Contains: YGGWG-amide; GGW-amide; GG-amide; GYG-ami ...	0.08	+	exc	1 *	Secreted protein (Potential)				105
O45830 UniProt NPD GO	NDX1_CAEEL	Putative nudix hydrolase 1 (EC 3.6.1.-)	0.08	-	cyt	0					365
Q9W1P8 UniProt NPD GO	OR59B_DROME	Putative odorant receptor 59b	0.08	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			398
Q9VAW0 UniProt NPD GO	OR98B_DROME	Putative odorant receptor 98b	0.08	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				384
Q10245 UniProt NPD GO	YD1F_SCHPO	Putative oxidoreductase C4G9.15 (EC 1.-.-.-)	0.08	-	nuc	1 *					341
Q20735 UniProt NPD GO	SMS2_CAEEL	Putative phosphatidylcholine:ceramide cholinephosphotransferase 2 (EC 2.7.-.-) (Sphingomyelin syntha ...	0.08	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			335
Q7XD66 UniProt NPD GO	RIP6_ORYSA	Putative ripening-related protein 6 precursor	0.08	-	exc	0	Secreted protein (Potential)				167
P56346 UniProt NPD GO	MIND_CHLVU	Putative septum site-determining protein minD	0.08	-	cyt	0	Plastid; chloroplast				282
Q9MUM5 UniProt NPD GO	MIND_MESVI	Putative septum site-determining protein minD	0.08	-	cyt	0	Plastid; chloroplast				286
P25565 UniProt NPD GO	YCA2_YEAST	Putative uncharacterized protein YCL002C	0.08	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				251
P40558 UniProt NPD GO	YIA3_YEAST	Putative uncharacterized protein YIL003W	0.08	-	cyt	0		cytoplasm [IDA]			293
P40570 UniProt NPD GO	YIT4_YEAST	Putative uncharacterized protein YIR014W	0.08	-	end	0	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			242
Q9MAS5 UniProt NPD GO	VA726_ARATH	Putative vesicle-associated membrane protein 726 (AtVAMP726)	0.08	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				220
P35487 UniProt NPD GO	ODPAT_MOUSE	Pyruvate dehydrogenase E1 component alpha subunit, testis-specific form, mitochondrial precursor (EC ...	0.08	-	mit	0					391
P22122 UniProt NPD GO	RHO_DISOM	RAS-like GTP-binding protein O-RHO	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				192
Q94124 UniProt NPD GO	RAC2_CAEEL	RAS-related protein rac-2	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				195
P34148 UniProt NPD GO	RACB_DICDI	RAS-related protein racB	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				195
Q24817 UniProt NPD GO	RACD_ENTHI	RAS-related protein racD (Fragment)	0.08	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				198
O82246 UniProt NPD GO	Y2778_ARATH	REF/SRPP-like protein At2g47780	0.08	-	cyt	0					235
O15258 UniProt NPD GO	RER1_HUMAN	RER1 protein	0.08	-	end	3 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	integral to Golgi membrane [IDA]			196
Q9CQU3 UniProt NPD GO	RER1_MOUSE	RER1 protein	0.08	-	end	3 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				196
Q7TMV1 UniProt NPD GO	RN139_MOUSE	RING finger protein 139	0.08	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [ISS] integral to membrane [ISS]			668
Q8N4F7 UniProt NPD GO	RN175_HUMAN	RING finger protein 175	0.08	-	end	5	Membrane; multi-pass membrane protein (Potential)				328
Q8L9W3 UniProt NPD GO	ATL5J_ARATH	RING-H2 finger protein ATL5J	0.08	-	mit	1 *					163
P62878 UniProt NPD GO	RBX1_MOUSE	RING-box protein 1 (Rbx1)	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	anaphase-promoting complex [TAS] ubiquitin ligase complex [TAS]			108
P62877 UniProt NPD GO	RBX1_HUMAN	RING-box protein 1 (Rbx1) (Regulator of cullins 1) (RING finger protein 75) (Protein ZYP)	0.08	-	cyt	0	Cytoplasm. Nucleus		603814	1U6G	108
Q9W5E1 UniProt NPD GO	RBX1A_DROME	RING-box protein 1A (Regulator of cullins 1a) (dRbx1)	0.08	-	cyt	0	Cytoplasm. Nucleus	nucleus [IDA] SCF ubiquitin ligase complex [IDA]			108
Q6CE69 UniProt NPD GO	REXO4_YARLI	RNA exonuclease 4 (EC 3.1.-.-)	0.08	-	mit	0	Nucleus (By similarity)				291
Q6FM86 UniProt NPD GO	TFB5_CANGA	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.08	-	cyt	0	Nucleus (By similarity)				73

You are viewing entries 68901 to 68950 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.