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
Q9UTP0 UniProt NPD GO	RL30B_SCHPO	60S ribosomal protein L30-2	0.06	-	nuc	0					117
Q09900 UniProt NPD GO	RL38B_SCHPO	60S ribosomal protein L38-2	0.06	-	nuc	0					74
Q02326 UniProt NPD GO	RL6A_YEAST	60S ribosomal protein L6-A (L17) (YL16) (RP18)	0.06	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			175
P50882 UniProt NPD GO	RL9_DROME	60S ribosomal protein L9	0.06	-	mit	0					190
P49076 UniProt NPD GO	ARF_MAIZE	ADP-ribosylation factor	0.06	-	nuc	0					180
P51821 UniProt NPD GO	ARF1_CHLRE	ADP-ribosylation factor 1	0.06	-	nuc	0					180
O48649 UniProt NPD GO	ARF1_SALBA	ADP-ribosylation factor 1	0.06	-	cyt	0					180
Q10943 UniProt NPD GO	ARF12_CAEEL	ADP-ribosylation factor 1-like 2 (ADP-ribosylation factor-related protein 1.2)	0.06	-	cyt	0					180
P49702 UniProt NPD GO	ARF5_CHICK	ADP-ribosylation factor 5	0.06	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			179
Q8IVW1 UniProt NPD GO	ARL14_HUMAN	ADP-ribosylation factor-like protein 14 (ADP-ribosylation factor 7)	0.06	-	cyt	0					177
Q05962 UniProt NPD GO	ADT1_RAT	ADP/ATP translocase 1 (Adenine nucleotide translocator 1) (ANT 1) (ADP,ATP carrier protein 1) (Solut ...	0.06	-	cyt	4	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				297
P02722 UniProt NPD GO	ADT1_BOVIN	ADP/ATP translocase 1 (Adenine nucleotide translocator 1) (ANT 1) (ADP,ATP carrier protein 1) (Solut ...	0.06	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein			2C3E	297
O50016 UniProt NPD GO	AP2S1_MAIZE	AP-2 complex subunit sigma-1 (Clathrin coat assembly protein AP17) (Clathrin coat-associated protein ...	0.06	-	mit	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane				132
Q9Y587 UniProt NPD GO	AP4S1_HUMAN	AP-4 complex subunit sigma-1 (Adapter-related protein complex 4 sigma-1 subunit) (Sigma subunit of A ...	0.06	-	cyt	0	Golgi apparatus; trans-Golgi network. Associated with the trans-Golgi network. Found in soma and den ...		607243		144
Q66I75 UniProt NPD GO	APIP_BRARE	APAF1-interacting protein homolog	0.06	-	cyt	0	Cytoplasm (By similarity)				241
Q9M6A3 UniProt NPD GO	ASC1_LYCES	ASC1 protein (Alternaria stem canker resistance protein 1)	0.06	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				308
Q24439 UniProt NPD GO	ATPO_DROME	ATP synthase O subunit, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.06	-	mit	0					209
P38591 UniProt NPD GO	ATP6_HALGR	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.06	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q8LX27 UniProt NPD GO	ATP6_LEMCA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.06	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P14569 UniProt NPD GO	ATP6_LOCMI	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.06	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				225
O79432 UniProt NPD GO	ATP6_RABIT	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.06	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P05504 UniProt NPD GO	ATP6_RAT	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.06	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein			1ED3	226
O99821 UniProt NPD GO	ATP6_RHISA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.06	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				221
Q96064 UniProt NPD GO	ATP6_RHIUN	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.06	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q36835 UniProt NPD GO	ATP6_TRIRU	ATP synthase a chain precursor (EC 3.6.3.14) (ATPase protein 6)	0.06	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				255
P48082 UniProt NPD GO	ATPD_CYAPA	ATP synthase delta chain (EC 3.6.3.14)	0.06	-	cyt	0	Plastid; cyanelle; cyanelle thylakoid membrane (By similarity)				186
P11402 UniProt NPD GO	ATPD_SPIOL	ATP synthase delta chain, chloroplast precursor (EC 3.6.3.14)	0.06	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				257
P78700 UniProt NPD GO	ATPD_KLULA	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)	0.06	-	mit	0	Mitochondrion				159
P81449 UniProt NPD GO	ATPJ_YEAST	ATP synthase e chain, mitochondrial (EC 3.6.3.14) (Translocase of the inner membrane protein 11)	0.06	-	cyt	0		proton-transporting ATP synthase complex, c... [IMP]			95
Q85X21 UniProt NPD GO	ATPE_PINKO	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.06	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
P51260 UniProt NPD GO	ATPE_PORPU	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.06	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				134
Q96250 UniProt NPD GO	ATPG3_ARATH	ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)	0.06	-	mit	0	Mitochondrion				325
P48201 UniProt NPD GO	AT5G3_HUMAN	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.06	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	proton-transporting ATP synthase complex (s... [TAS]	602736		142
Q5RFL2 UniProt NPD GO	AT5G3_PONPY	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.06	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				142
Q71S46 UniProt NPD GO	AT5G3_RAT	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.06	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				142
P15996 UniProt NPD GO	ATP8_GADMO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.06	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q08656 UniProt NPD GO	ATP8_NEUCR	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.06	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54
P12697 UniProt NPD GO	ATP8_PARLI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.06	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54
Q4JQI3 UniProt NPD GO	ATP8_TETNG	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.06	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q36838 UniProt NPD GO	ATP8_TRIRU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.06	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				48
Q01859 UniProt NPD GO	ATPBM_ORYSA	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.06	-	mit	0	Mitochondrion				552
Q9MTJ8 UniProt NPD GO	CLPP_OENHO	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.06	-	nuc	3 *	Plastid; chloroplast				249
P08910 UniProt NPD GO	LBH2_HUMAN	Abhydrolase domain-containing protein 2 (Protein PHPS1-2)	0.06	-	nuc	0		integral to membrane [NAS]			425
Q6BKW1 UniProt NPD GO	ACH1_DEBHA	Acetyl-CoA hydrolase (EC 3.1.2.1) (Acetyl-CoA deacylase) (Acetyl-CoA acylase)	0.06	-	mit	0	Cytoplasm (By similarity)				523
Q6C3Z9 UniProt NPD GO	ACH1_YARLI	Acetyl-CoA hydrolase (EC 3.1.2.1) (Acetyl-CoA deacylase) (Acetyl-CoA acylase)	0.06	-	cyt	0	Cytoplasm (By similarity)				524
P16928 UniProt NPD GO	ACSA_EMENI	Acetyl-coenzyme A synthetase (EC 6.2.1.1) (Acetate--CoA ligase) (Acyl-activating enzyme)	0.06	-	mit	0					670
P02715 UniProt NPD GO	ACHE_BOVIN	Acetylcholine receptor protein subunit epsilon precursor	0.06	-	end	4	Membrane; multi-pass membrane protein				491
Q04844 UniProt NPD GO	ACHE_HUMAN	Acetylcholine receptor protein subunit epsilon precursor	0.06	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]	608931		493
P07140 UniProt NPD GO	ACES_DROME	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.06	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Attached to the membrane of the neuronal cholinergic synaps ...	cytoplasm [IDA] plasma membrane [IDA]		1QON	649
P56271 UniProt NPD GO	AMYA_ASPNG	Acid alpha-amylase (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.06	-	mit	0				2AAA	484

You are viewing entries 71401 to 71450 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.