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
Q06396 UniProt NPD GO	ARF1_ORYSA	ADP-ribosylation factor 1 (13 kDa cold-induced protein)	0.03	-	cyt	0					180
Q9SRC3 UniProt NPD GO	ARF2_ARATH	ADP-ribosylation factor 2 (AtARF2)	0.03	-	nuc	0					180
Q5E9I6 UniProt NPD GO	ARF3_BOVIN	ADP-ribosylation factor 3	0.03	-	cyt	0					180
P61207 UniProt NPD GO	ARF3_FUGRU	ADP-ribosylation factor 3	0.03	-	cyt	0					180
P61204 UniProt NPD GO	ARF3_HUMAN	ADP-ribosylation factor 3	0.03	-	cyt	0			103190		180
P61205 UniProt NPD GO	ARF3_MOUSE	ADP-ribosylation factor 3	0.03	-	cyt	0		Golgi apparatus [IDA]			180
Q5R5P7 UniProt NPD GO	ARF3_PONPY	ADP-ribosylation factor 3	0.03	-	cyt	0					180
P61206 UniProt NPD GO	ARF3_RAT	ADP-ribosylation factor 3 (Liver regeneration-related protein LRRG202)	0.03	-	cyt	0					180
Q6P3A9 UniProt NPD GO	ARL11_MOUSE	ADP-ribosylation factor-like protein 11	0.03	-	cyt	0					176
Q5BK71 UniProt NPD GO	ARL11_RAT	ADP-ribosylation factor-like protein 11	0.03	-	cyt	0					173
O43931 UniProt NPD GO	AFG31_HUMAN	AFG3-like protein 1 (EC 3.4.24.-) (Fragment)	0.03	-	cyt	0	Mitochondrion (Potential)	mitochondrion [NAS]	603020		69
Q4WS49 UniProt NPD GO	AP2S_ASPFU	AP-2 complex subunit sigma (Clathrin assembly protein 2 small chain) (Adaptin small chain)	0.03	-	cyt	0	Component of the coat surrounding the cytoplasmic face of the plasma membrane coated vesicles (By si ...				145
Q5BFF8 UniProt NPD GO	AP2S_EMENI	AP-2 complex subunit sigma (Clathrin assembly protein 2 small chain) (Adaptin small chain)	0.03	-	cyt	0	Component of the coat surrounding the cytoplasmic face of the plasma membrane coated vesicles (By si ...				145
Q96GX9 UniProt NPD GO	APIP_HUMAN	APAF1-interacting protein	0.03	-	cyt	0	Cytoplasm				242
Q5FW37 UniProt NPD GO	APIP_XENTR	APAF1-interacting protein homolog	0.03	-	cyt	0	Cytoplasm (By similarity)				239
Q63055 UniProt NPD GO	ARFRP_RAT	ARF-related protein (ARP)	0.03	-	nuc	0	Golgi apparatus (By similarity)				201
Q32LJ2 UniProt NPD GO	ARFRP_BOVIN	ARF-related protein 1	0.03	-	nuc	0	Golgi apparatus (By similarity)				201
Q8BXL7 UniProt NPD GO	ARFRP_MOUSE	ARF-related protein 1	0.03	-	nuc	0	Golgi apparatus (By similarity)	membrane fraction [IDA]			201
Q5R579 UniProt NPD GO	ARFRP_PONPY	ARF-related protein 1	0.03	-	nuc	0	Golgi apparatus (By similarity)				201
Q13795 UniProt NPD GO	ARFRP_HUMAN	ARF-related protein 1 (ARP)	0.03	-	nuc	0	Golgi apparatus	membrane fraction [TAS]	604699		201
Q9N3B0 UniProt NPD GO	ARMET_CAEEL	ARMET-like protein precursor	0.03	-	exc	0	Secreted protein (Potential)				168
Q75AK8 UniProt NPD GO	HIS1_ASHGO	ATP phosphoribosyltransferase (EC 2.4.2.17) (ATP-PRTase) (ATP-PRT)	0.03	-	cyt	0	Cytoplasm (By similarity)				297
P00498 UniProt NPD GO	HIS1_YEAST	ATP phosphoribosyltransferase (EC 2.4.2.17) (ATP-PRTase) (ATP-PRT)	0.03	-	cyt	0	Cytoplasm (By similarity)	intracellular [TAS]			297
P80088 UniProt NPD GO	ATP7_SPIOL	ATP synthase 28 kDa subunit, mitochondrial (EC 3.6.3.14) (Fragment)	0.03	-	cyt	0	Mitochondrion				32
O94390 UniProt NPD GO	ATP7_SCHPO	ATP synthase D chain, mitochondrial (EC 3.6.3.14)	0.03	-	cyt	0					174
O03200 UniProt NPD GO	ATP6_CERSI	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.03	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q2I3G9 UniProt NPD GO	ATP6_ELEMA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.03	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				222
P25005 UniProt NPD GO	ATP6_PISOC	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.03	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
Q95A26 UniProt NPD GO	ATP6_PONPY	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.03	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q8W9G8 UniProt NPD GO	ATP6_TACAC	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.03	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q4JQI2 UniProt NPD GO	ATP6_TETNG	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.03	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P00853 UniProt NPD GO	ATP6_ASPAM	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6) (Fragment)	0.03	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				78
Q36964 UniProt NPD GO	ATP6_ONCMA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6) (Fragment)	0.03	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				219
Q36090 UniProt NPD GO	ATP6_THUOB	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6) (Fragment)	0.03	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				133
Q03671 UniProt NPD GO	ATP6_CANPA	ATP synthase a chain precursor (EC 3.6.3.14) (ATPase protein 6) (ATP synthase subunit 6)	0.03	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				246
P05630 UniProt NPD GO	ATPD_BOVIN	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)	0.03	-	mit	0	Mitochondrion	mitochondrial envelope [IDA] proton-transporting ATP synthase complex [IDA]		2CK3	168
Q9D3D9 UniProt NPD GO	ATPD_MOUSE	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)	0.03	-	mit	0	Mitochondrion	mitochondrial inner membrane [IDA]			168
P35434 UniProt NPD GO	ATPD_RAT	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)	0.03	-	mit	0	Mitochondrion	proton-transporting ATP synthase complex, c... [IDA]			168
Q9P6R6 UniProt NPD GO	ATPD_SCHPO	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)	0.03	-	cyt	0	Mitochondrion				160
Q31793 UniProt NPD GO	ATPE_ANTFO	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.03	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				138
Q06450 UniProt NPD GO	ATP5E_IPOBA	ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14)	0.03	-	nuc	0	Mitochondrion				69
Q06405 UniProt NPD GO	ATPK_YEAST	ATP synthase f chain, mitochondrial precursor (EC 3.6.3.14)	0.03	-	mit	0		proton-transporting ATP synthase complex, c... [IMP]			101
P05496 UniProt NPD GO	AT5G1_HUMAN	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.03	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	proton-transporting ATP synthase complex (s... [TAS]	603192		136
P34190 UniProt NPD GO	ATP8_CROLA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.03	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
P00857 UniProt NPD GO	ATP8_EMENI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.03	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				48
Q9MGD7 UniProt NPD GO	ATP8_PENMO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.03	-	cyt	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				52
O79405 UniProt NPD GO	ATP8_SCYCA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.03	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q9P602 UniProt NPD GO	ATPO_NEUCR	ATP synthase subunit 5, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.03	-	mit	0	Mitochondrion				220
Q29596 UniProt NPD GO	ATPA2_PIG	ATP synthase subunit alpha liver isoform, mitochondrial precursor (EC 3.6.3.14) (Fragment)	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				148
P48081 UniProt NPD GO	ATPB_CYAPA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.03	-	cyt	0	Plastid; cyanelle; cyanelle thylakoid membrane; peripheral membrane protein (By similarity)				485

You are viewing entries 78951 to 79000 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.