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
P35181 UniProt NPD GO	AP1T1_YEAST	AP-1 complex subunit theta-1 (Theta(1)-adaptin) (Clathrin coat assembly protein AP19) (Clathrin coat ...	0.01	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	AP-1 adaptor complex [IPI]			156
Q4ICG5 UniProt NPD GO	AP2S_GIBZE	AP-2 complex subunit sigma (Clathrin assembly protein 2 small chain) (Adaptin small chain)	0.01	-	cyt	0	Component of the coat surrounding the cytoplasmic face of the plasma membrane coated vesicles (By si ...				143
Q7SAQ1 UniProt NPD GO	AP2S_NEUCR	AP-2 complex subunit sigma (Clathrin assembly protein 2 small chain) (Adaptin small chain)	0.01	-	cyt	0	Component of the coat surrounding the cytoplasmic face of the plasma membrane coated vesicles (By si ...				143
Q750L8 UniProt NPD GO	AP3M_ASHGO	AP-3 complex subunit mu (Adapter-related protein complex 3 mu subunit) (Mu-adaptin 3A) (AP-3 adapter ...	0.01	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				411
Q9WVQ5 UniProt NPD GO	APIP_MOUSE	APAF1-interacting protein (Monocyte/macrophage protein 19)	0.01	-	cyt	0	Cytoplasm (By similarity)				241
P80513 UniProt NPD GO	ARMET_BOVIN	ARMET protein (Arginine-rich protein) (Fragment)	0.01	-	cyt	0	Secreted protein (Potential)				39
P35013 UniProt NPD GO	ATPH_GALSU	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.01	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				83
P81450 UniProt NPD GO	ATP18_YEAST	ATP synthase J chain, mitochondrial (EC 3.6.3.14) (ATPase synthase I subunit)	0.01	-	cyt	0		proton-transporting ATP synthase complex, c... [IMP]			59
P33507 UniProt NPD GO	ATP6_ANOQU	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P48878 UniProt NPD GO	ATP6_CHOCR	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				253
P14862 UniProt NPD GO	ATP6_COCHE	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				257
Q8W9N1 UniProt NPD GO	ATP6_DUGDU	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
P12696 UniProt NPD GO	ATP6_PARLI	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				232
P48879 UniProt NPD GO	ATP6_PICCA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				256
P15994 UniProt NPD GO	ATP6_PODAN	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				264
P15995 UniProt NPD GO	ATP6_STRPU	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P68526 UniProt NPD GO	ATP6_TRITI	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	4	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				386
P24499 UniProt NPD GO	ATP6_TRYBB	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
Q04654 UniProt NPD GO	ATP6_VICFA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				291
P68527 UniProt NPD GO	ATP6_WHEAT	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	4	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				386
P22067 UniProt NPD GO	ATP6_NAEFO	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6) (Fragment)	0.01	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				119
Q36967 UniProt NPD GO	ATP6_SALTR	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6) (Fragment)	0.01	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				105
P80086 UniProt NPD GO	ATP6_SPIOL	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6) (Fragment)	0.01	-		0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				14
Q75G39 UniProt NPD GO	ATP6_ASHGO	ATP synthase a chain precursor (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				263
P21535 UniProt NPD GO	ATP6_SCHPO	ATP synthase a chain precursor (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				257
P00854 UniProt NPD GO	ATP6_YEAST	ATP synthase a chain precursor (EC 3.6.3.14) (ATPase protein 6)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	proton-transporting ATP synthase complex, c... [TAS]			259
P80504 UniProt NPD GO	ATPO_SOLTU	ATP synthase delta chain, mitochondrial (EC 3.6.3.14) (Oligomycin sensitivity conferral protein) (OS ...	0.01	-	cyt	0	Mitochondrion				37
P80087 UniProt NPD GO	ATPO_SPIOL	ATP synthase delta chain, mitochondrial (EC 3.6.3.14) (Oligomycin sensitivity conferral protein) (OS ...	0.01	-	cyt	0	Mitochondrion				32
Q92196 UniProt NPD GO	ATPD_AGABI	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)	0.01	-	mit	0	Mitochondrion				162
P30049 UniProt NPD GO	ATPD_HUMAN	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)	0.01	-	mit	0	Mitochondrion	proton-transporting ATP synthase complex (s... [TAS]	603150		168
Q40089 UniProt NPD GO	ATP4_IPOBA	ATP synthase delta' chain, mitochondrial precursor (EC 3.6.3.14)	0.01	-	mit	0	Mitochondrion				200
P49648 UniProt NPD GO	ATPE_ODOSI	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				133
P05632 UniProt NPD GO	ATP5E_BOVIN	ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14)	0.01	-	mit	0	Mitochondrion			2CK3	50
P56381 UniProt NPD GO	ATP5E_HUMAN	ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14)	0.01	-	mit	0	Mitochondrion	proton-transporting ATP synthase complex (s... [TAS]	606153		50
P56382 UniProt NPD GO	ATP5E_MOUSE	ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14)	0.01	-	nuc	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrion [IDA]			51
P56134 UniProt NPD GO	ATPK_HUMAN	ATP synthase f chain, mitochondrial (EC 3.6.3.14)	0.01	-	mit	1		proton-transporting ATP synthase complex (s... [NAS]			93
Q5R6T5 UniProt NPD GO	ATPK_PONPY	ATP synthase f chain, mitochondrial (EC 3.6.3.14)	0.01	-	cyt	1					93
P80084 UniProt NPD GO	ATPG3_SPIOL	ATP synthase gamma chain, mitochondrial (EC 3.6.3.14) (Fragment)	0.01	-	nuc	0	Mitochondrion				26
Q9U505 UniProt NPD GO	ATP9_MANSE	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATPase protein 9) (ATPase ...	0.01	-	cyt	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				131
P48895 UniProt NPD GO	ATP8_ALBCO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.01	-	cyt	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q37707 UniProt NPD GO	ATP8_ARTSF	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.01	-	end	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
O78683 UniProt NPD GO	ATP8_CARAU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.01	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54
O47493 UniProt NPD GO	ATP8_METSE	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.01	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				72
P25004 UniProt NPD GO	ATP8_PISOC	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.01	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q36257 UniProt NPD GO	ATP8_YARLI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.01	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				48
Q75G38 UniProt NPD GO	ATP9_ASHGO	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.01	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				76
Q85Q98 UniProt NPD GO	ATP9_CANGA	ATP synthase protein 9, mitochondrial (EC 3.6.3.14) (Lipid-binding protein)	0.01	-	end	2 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				76
P09457 UniProt NPD GO	ATPO_YEAST	ATP synthase subunit 5, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.01	-	mit	0	Mitochondrion	proton-transporting ATP synthase, stator st... [IMP]			212
P80021 UniProt NPD GO	ATPA1_PIG	ATP synthase subunit alpha heart isoform, mitochondrial (EC 3.6.3.14) (Fragments)	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane				32
O03062 UniProt NPD GO	ATPB_ADICA	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				493

You are viewing entries 86451 to 86500 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.