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
P05744 UniProt NPD GO	RL33A_YEAST	60S ribosomal protein L33-A (L37A) (YL37) (RP47)	0.04	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			106
P41056 UniProt NPD GO	RL33B_YEAST	60S ribosomal protein L33-B (L37B) (YL37) (RP47)	0.04	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			106
P49180 UniProt NPD GO	RL35A_CAEEL	60S ribosomal protein L35a	0.04	-	mit	0					123
P49167 UniProt NPD GO	RL38_YEAST	60S ribosomal protein L38	0.04	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			78
Q10232 UniProt NPD GO	RL9A_SCHPO	60S ribosomal protein L9-A	0.04	-	cyt	0					190
P80826 UniProt NPD GO	CWP02_ARATH	65 kDa cell wall protein (Fragment)	0.04	-		0	Cell wall				5
P90587 UniProt NPD GO	WD66_PHYPO	66 kDa stress protein (p66)	0.04	-	cyt	0					601
Q5E9J5 UniProt NPD GO	DHCR7_BOVIN	7-dehydrocholesterol reductase (EC 1.3.1.21) (7-DHC reductase) (Sterol delta-7-reductase)	0.04	-	mit	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				475
Q9Y1C1 UniProt NPD GO	EMAP_LYTVA	77 kDa echinoderm microtubule-associated protein (Fragment)	0.04	-	mit	1					664
Q86UN6 UniProt NPD GO	AKA28_HUMAN	A-kinase anchor protein 14 (Protein kinase A-anchoring protein 14) (A-kinase anchor protein 28 kDa)	0.04	-	nuc	0	Cytoplasm (Probable)		300462		197
Q753H5 UniProt NPD GO	IZH1_ASHGO	ADIPOR-like receptor IZH1	0.04	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				317
Q27312 UniProt NPD GO	NADA_APLKU	ADP-ribosyl cyclase precursor (EC 3.2.2.5) (NAD(+) nucleosidase) (NADase) (NAD glycohydrolase) (ADRC ...	0.04	-	cyt	0	Localized to vesicles or granules within ova of all stages				282
P84081 UniProt NPD GO	ARF2_BOVIN	ADP-ribosylation factor 2	0.04	-	cyt	0		Golgi apparatus [ISS]			181
Q8BSL7 UniProt NPD GO	ARF2_MOUSE	ADP-ribosylation factor 2	0.04	-	cyt	0		Golgi apparatus [IDA]		1J2J	181
P51823 UniProt NPD GO	ARF2_ORYSA	ADP-ribosylation factor 2	0.04	-	cyt	0					180
P84082 UniProt NPD GO	ARF2_RAT	ADP-ribosylation factor 2	0.04	-	cyt	0		Golgi apparatus [ISS]			181
Q9QXJ4 UniProt NPD GO	ARL10_MOUSE	ADP-ribosylation factor-like protein 10 (ADP-ribosylation factor-like membrane-associated protein)	0.04	-	end	1 *					243
Q58DI9 UniProt NPD GO	ARL11_BOVIN	ADP-ribosylation factor-like protein 11	0.04	-	cyt	0					182
Q969Q4 UniProt NPD GO	ARL11_HUMAN	ADP-ribosylation factor-like protein 11 (ADP-ribosylation factor-like tumor suppressor protein 1)	0.04	-	cyt	0			609351		196
Q6QRN9 UniProt NPD GO	ADT3_PIG	ADP/ATP translocase 3 (Adenine nucleotide translocator 2) (ANT 3) (ADP,ATP carrier protein 3) (Solut ...	0.04	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				297
P81072 UniProt NPD GO	AMPD1_RABIT	AMP deaminase 1 (EC 3.5.4.6) (Myoadenylate deaminase) (AMP deaminase isoform M) (Fragment)	0.04	-	nuc	0					26
Q8BFR6 UniProt NPD GO	ZFAN1_MOUSE	AN1-type zinc finger protein 1	0.04	-	nuc	0				1WYS	268
Q00381 UniProt NPD GO	AP2S_YEAST	AP-2 complex subunit sigma (Clathrin assembly protein 2 small chain) (Adaptin small chain) (Clathrin ...	0.04	-	nuc	0	Component of the coat surrounding the cytoplasmic face of the plasma membrane coated vesicles				147
Q2YDH6 UniProt NPD GO	AP3S1_BOVIN	AP-3 complex subunit sigma-1 (Adapter-related protein complex 3 sigma-1 subunit) (Sigma-adaptin 3a) ...	0.04	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				193
Q9DCR2 UniProt NPD GO	AP3S1_MOUSE	AP-3 complex subunit sigma-1 (Adapter-related protein complex 3 sigma-1 subunit) (Sigma-adaptin 3a) ...	0.04	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	Golgi trans face [TAS]			193
Q92572 UniProt NPD GO	AP3S1_HUMAN	AP-3 complex subunit sigma-1 (Adapter-related protein complex 3 sigma-1 subunit) (Sigma-adaptin 3a) ...	0.04	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	membrane coat adaptor complex [TAS] transport vesicle [TAS]	601507		193
Q9VES1 UniProt NPD GO	AR6P1_DROME	ARL-6-interacting protein 1 homolog	0.04	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				197
P40373 UniProt NPD GO	HIS1_SCHPO	ATP phosphoribosyltransferase (EC 2.4.2.17) (ATP-PRTase) (ATP-PRT)	0.04	-	cyt	0	Cytoplasm (By similarity)				310
P41291 UniProt NPD GO	ATP6_BALMU	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P24945 UniProt NPD GO	ATP6_BALPH	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P00847 UniProt NPD GO	ATP6_BOVIN	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P24888 UniProt NPD GO	ATP6_CAEEL	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				199
Q9ZZ62 UniProt NPD GO	ATP6_CANFA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P14413 UniProt NPD GO	ATP6_CRIGR	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q9TA24 UniProt NPD GO	ATP6_LOXAF	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				222
P48178 UniProt NPD GO	ATP6_ONCMY	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				223
Q36454 UniProt NPD GO	ATP6_ORNAN	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q9T9W0 UniProt NPD GO	ATP6_PANTR	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P92719 UniProt NPD GO	ATP6_PONPP	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	vac	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q35920 UniProt NPD GO	ATP6_SALSA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O78752 UniProt NPD GO	ATP6_SHEEP	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.04	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
O03570 UniProt NPD GO	ATP6_TROHI	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6) (Fragment)	0.04	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				212
O03359 UniProt NPD GO	ATP6_TROMO	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6) (Fragment)	0.04	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				212
Q757N0 UniProt NPD GO	ATPD_ASHGO	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)	0.04	-	mit	0	Mitochondrion				158
O47036 UniProt NPD GO	ATPE_PICAB	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.04	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
P56384 UniProt NPD GO	AT5G3_MOUSE	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.04	-	cyt	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				141
P34836 UniProt NPD GO	ATP8_ANOGA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.04	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
P33506 UniProt NPD GO	ATP8_ANOQU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.04	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
Q00276 UniProt NPD GO	ATP8_APILI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.04	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				52
Q9MJC0 UniProt NPD GO	ATP8_ARBLI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.04	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54

You are viewing entries 76101 to 76150 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.