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
Q09136 UniProt NPD GO	AAPK1_PIG	5'-AMP-activated protein kinase catalytic subunit alpha-1 (EC 2.7.11.1) (AMPK alpha-1 chain) (63 kDa ...	0.07	-	cyt	0					132
P58108 UniProt NPD GO	AAKG1_BOVIN	5'-AMP-activated protein kinase subunit gamma-1 (AMPK gamma-1 chain) (AMPKg)	0.07	-	cyt	0					330
P80385 UniProt NPD GO	AAKG1_RAT	5'-AMP-activated protein kinase subunit gamma-1 (AMPK gamma-1 chain) (AMPKg)	0.07	-	cyt	0					330
Q7RVY5 UniProt NPD GO	HEM1_NEUCR	5-aminolevulinate synthase, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic acid synthase) ( ...	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				544
P36688 UniProt NPD GO	RK12_NICSY	50S ribosomal protein L12, chloroplast precursor (CL12)	0.07	-	mit	0	Plastid; chloroplast				186
P11893 UniProt NPD GO	RK24_PEA	50S ribosomal protein L24, chloroplast precursor (CL24)	0.07	-	nuc	0	Plastid; chloroplast				194
P80785 UniProt NPD GO	CWP08_TOBAC	52 kDa cell wall protein (Fragment)	0.07	-		0	Cell wall				10
P52209 UniProt NPD GO	6PGD_HUMAN	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	0.07	-	cyt	0			172200		482
Q9DCD0 UniProt NPD GO	6PGD_MOUSE	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	0.07	-	cyt	0					482
Q9CQ60 UniProt NPD GO	6PGL_MOUSE	6-phosphogluconolactonase (EC 3.1.1.31) (6PGL)	0.07	-	cyt	0					257
O08848 UniProt NPD GO	RO60_MOUSE	60 kDa SS-A/Ro ribonucleoprotein (60 kDa Ro protein) (60 kDa ribonucleoprotein Ro) (RoRNP) (TROVE do ...	0.07	-	cyt	0	Cytoplasm (By similarity)				538
Q00531 UniProt NPD GO	JI60_HORVU	60 kDa jasmonate-induced protein (EC 3.2.2.22) (rRNA N-glycosidase)	0.07	-	cyt	0					560
P91913 UniProt NPD GO	RLA1_CAEEL	60S acidic ribosomal protein P1	0.07	-	cyt	0					111
Q9LVC9 UniProt NPD GO	RLA32_ARATH	60S acidic ribosomal protein P3-2	0.07	-	mit	0					120
O74836 UniProt NPD GO	RL1B_SCHPO	60S ribosomal protein L1-B (L10a)	0.07	+	cyt	0					216
O94238 UniProt NPD GO	RL14_SCHPO	60S ribosomal protein L14	0.07	-	cyt	0					134
P36105 UniProt NPD GO	RL14A_YEAST	60S ribosomal protein L14-A	0.07	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			138
P38754 UniProt NPD GO	RL14B_YEAST	60S ribosomal protein L14-B	0.07	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			138
Q9P843 UniProt NPD GO	RL27_CANAL	60S ribosomal protein L27	0.07	-	cyt	0					136
Q9M5M6 UniProt NPD GO	RL30_EUPES	60S ribosomal protein L30	0.07	-	nuc	0					112
Q9LSA3 UniProt NPD GO	RL303_ARATH	60S ribosomal protein L30-3	0.07	-	nuc	0					112
Q29187 UniProt NPD GO	RL4_PIG	60S ribosomal protein L4 (L1) (Fragment)	0.07	-	nuc	0					101
P32904 UniProt NPD GO	RM06_YEAST	60S ribosomal protein L6, mitochondrial precursor (YmL16) (MRP-L6)	0.07	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			214
P49210 UniProt NPD GO	RL9_ORYSA	60S ribosomal protein L9	0.07	-	nuc	0					190
Q07929 UniProt NPD GO	SP63_STRPU	63 kDa sperm flagellar membrane protein precursor	0.07	-	exc	0	Flagellum; flagellar membrane; lipid-anchor; GPI-anchor. Attached to the flagellar membrane by a GPI ...				470
Q26613 UniProt NPD GO	EMAP_STRPU	77 kDa echinoderm microtubule-associated protein	0.07	-	mit	1					686
P31692 UniProt NPD GO	ADT_CHLKE	ADP,ATP carrier protein (ADP/ATP translocase) (Adenine nucleotide translocator) (ANT)	0.07	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				339
Q27238 UniProt NPD GO	ADT1_ANOGA	ADP,ATP carrier protein 1 (ADP/ATP translocase 1) (Adenine nucleotide translocator 1) (ANT 1)	0.07	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				301
Q63072 UniProt NPD GO	BST1_RAT	ADP-ribosyl cyclase 2 precursor (EC 3.2.2.5) (Cyclic ADP-ribose hydrolase 2) (cADPr hydrolase 2) (Bo ...	0.07	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				319
Q7RVM2 UniProt NPD GO	ARF_NEUCR	ADP-ribosylation factor	0.07	-	cyt	0					184
P34212 UniProt NPD GO	ARL5_CAEEL	ADP-ribosylation factor-like protein 5	0.07	-	nuc	0					177
Q2KJ96 UniProt NPD GO	ARL5A_BOVIN	ADP-ribosylation factor-like protein 5A	0.07	-	mit	0					179
Q9Y689 UniProt NPD GO	ARL5A_HUMAN	ADP-ribosylation factor-like protein 5A	0.07	-	mit	0			608960	1ZJ6	179
P51646 UniProt NPD GO	ARL5A_RAT	ADP-ribosylation factor-like protein 5A	0.07	-	mit	0					179
Q5R4G5 UniProt NPD GO	ARL6_PONPY	ADP-ribosylation factor-like protein 6	0.07	-	cyt	0	Cytoplasm (By similarity)				186
Q8VEH3 UniProt NPD GO	ARL8A_MOUSE	ADP-ribosylation factor-like protein 8A (ADP-ribosylation factor-like protein 10B) (Novel small G pr ...	0.07	-	cyt	0	Endosome; late endosome (By similarity). Lysosome (By similarity)				186
Q6BRU4 UniProt NPD GO	HIS1_DEBHA	ATP phosphoribosyltransferase (EC 2.4.2.17) (ATP-PRTase) (ATP-PRT)	0.07	-	cyt	0	Cytoplasm (By similarity)				304
Q32644 UniProt NPD GO	ATP6_CAPHI	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.07	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P92480 UniProt NPD GO	ATP6_EQUAS	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.07	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P00846 UniProt NPD GO	ATP6_HUMAN	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.07	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	proton-transporting ATP synthase complex, c... [NAS]	551500		226
P92664 UniProt NPD GO	ATP6_MACRO	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.07	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q35538 UniProt NPD GO	ATP6_PETMA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.07	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				237
Q00521 UniProt NPD GO	ATP6_PHOVI	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.07	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P21571 UniProt NPD GO	ATP5J_RAT	ATP synthase coupling factor 6, mitochondrial precursor (EC 3.6.3.14) (ATPase subunit F6)	0.07	-	mit	0					108
Q02849 UniProt NPD GO	ATPD_ANTSP	ATP synthase delta chain, chloroplast (EC 3.6.3.14)	0.07	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane				183
Q96251 UniProt NPD GO	ATPO_ARATH	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral pr ...	0.07	-	mit	0	Mitochondrion				238
P69445 UniProt NPD GO	ATPE_AEGCO	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
P69446 UniProt NPD GO	ATPE_AEGCR	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
Q7YJW6 UniProt NPD GO	ATPE_CALFE	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.07	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				132
Q85FT3 UniProt NPD GO	ATPE_CYAME	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.07	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				131

You are viewing entries 69351 to 69400 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.