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
Q7L9L4 UniProt NPD GO	MOL1A_HUMAN	Mps one binder kinase activator-like 1A (Mob1 homolog 1A) (Mob1A) (Mob1B) (Protein Mob4A)	0.06	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			215
P56708 UniProt NPD GO	CXMA_CONMR	Mu-O-conotoxin MrVIA	0.06	-	mit	1 *	Secreted protein				31
P42866 UniProt NPD GO	OPRM_MOUSE	Mu-type opioid receptor (MOR-1)	0.06	-	end	7	Membrane; multi-pass membrane protein	membrane fraction [IDA]			398
P16877 UniProt NPD GO	MDR4_ENTHI	Multidrug resistance protein 4 (P-glycoprotein) (Fragment)	0.06	-	cyt	0	Membrane; multi-pass membrane protein				113
Q9I7S8 UniProt NPD GO	PUR6_DROME	Multifunctional protein ADE2 (Adenosine-5) [Includes: Phosphoribosylaminoimidazole-succinocarboxamid ...	0.06	-	mit	0					429
P22234 UniProt NPD GO	PUR6_HUMAN	Multifunctional protein ADE2 [Includes: Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC ...	0.06	-	nuc	0			172439		424
Q5R8Z6 UniProt NPD GO	MCFD2_PONPY	Multiple coagulation factor deficiency protein 2 homolog precursor	0.06	-	exc	0	Endoplasmic reticulum-Golgi intermediate compartment (By similarity)				146
Q8NI22 UniProt NPD GO	MCFD2_HUMAN	Multiple coagulation factor deficiency protein 2 precursor (Neural stem cell-derived neuronal surviv ...	0.06	-	exc	0	Endoplasmic reticulum-Golgi intermediate compartment		607788		146
Q871W6 UniProt NPD GO	MBF1_NEUCR	Multiprotein-bridging factor 1	0.06	-	nuc	0					160
P60235 UniProt NPD GO	NXM13_DENAN	Muscarinic m1-toxin3 (Fragment)	0.06	-	nuc	0	Secreted protein				40
P82463 UniProt NPD GO	TXML2_NAJKA	Muscarinic toxin-like protein 2 (MTLP-2)	0.06	-	nuc	0	Secreted protein				65
P02203 UniProt NPD GO	MYG_VARVA	Myoglobin	0.06	-	cyt	0					153
Q03459 UniProt NPD GO	GLB_TETTH	Myoglobin (Hemoglobin)	0.06	-	cyt	0					121
P22761 UniProt NPD GO	HEMTM_NERDI	Myohemerythrin (MHR)	0.06	-	cyt	0					120
P09541 UniProt NPD GO	MYL4_MOUSE	Myosin light polypeptide 4 (Myosin light chain 1, atrial/fetal isoform) (MLC1A) (MLC1EMB)	0.06	-	cyt	0					192
P13543 UniProt NPD GO	MLR_AEQIR	Myosin regulatory light chain, striated adductor muscle (R-LC)	0.06	-	nuc	0				1WDC	156
Q09013 UniProt NPD GO	DMPK_HUMAN	Myotonin-protein kinase (EC 2.7.11.1) (Myotonic dystrophy protein kinase) (MDPK) (DM-kinase) (DMK) ( ...	0.06	-	nuc	0			160900	1WT6	639
P01476 UniProt NPD GO	MYX1_CROVV	Myotoxin A (Myotoxin-1)	0.06	-	nuc	0	Secreted protein				42
P12028 UniProt NPD GO	MYX1_CROVC	Myotoxin I	0.06	-	nuc	0	Secreted protein				43
P63175 UniProt NPD GO	MYX2_CROVV	Myotoxin-2 [Contains: Myotoxin-4]	0.06	-	nuc	0	Secreted protein				45
P83179 UniProt NPD GO	MYRO_BREBR	Myrosinase (EC 3.2.1.147) (Sinigrinase) (Thioglucosidase) (Fragments)	0.06	-	cyt	0					140
Q9SAV0 UniProt NPD GO	MB12_ARATH	Myrosinase-binding protein-like At1g52040	0.06	-	cyt	0					462
O04309 UniProt NPD GO	MB31_ARATH	Myrosinase-binding protein-like At3g16470	0.06	-	nuc	0					451
Q68FH4 UniProt NPD GO	GALK2_MOUSE	N-acetylgalactosamine kinase (EC 2.7.1.157) (GalNAc kinase) (Galactokinase 2)	0.06	-	mit	0					458
P50127 UniProt NPD GO	GGTA1_PIG	N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.87) (Galactosyltransferase) (UDP-gal ...	0.06	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				371
Q13423 UniProt NPD GO	NNTM_HUMAN	NAD(P) transhydrogenase, mitochondrial precursor (EC 1.6.1.2) (Pyridine nucleotide transhydrogenase) ...	0.06	-	end	12	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (Potential)	mitochondrial electron transport chain [TAS]	607878	1U31	1086
Q8MA16 UniProt NPD GO	NU2C_CHAGL	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.06	-	end	13 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				500
Q9TKX9 UniProt NPD GO	NU3C_NEPOL	NAD(P)H-quinone oxidoreductase chain 3, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 3) (N ...	0.06	-	end	3 *	Plastid; chloroplast				120
Q9MUK8 UniProt NPD GO	NU5C_MESVI	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.06	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				652
Q85FL7 UniProt NPD GO	NUGC_ADICA	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.06	-	cyt	0	Plastid; chloroplast				170
P19124 UniProt NPD GO	NUGC_MAIZE	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.06	-	cyt	0	Plastid; chloroplast				159
Q6L396 UniProt NPD GO	NUGC_SACHY	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.06	-	cyt	0	Plastid; chloroplast				159
Q6ENW0 UniProt NPD GO	NUGC_SACOF	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.06	-	cyt	0	Plastid; chloroplast				159
Q63362 UniProt NPD GO	NDUA5_RAT	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.06	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side				115
Q9DC69 UniProt NPD GO	NDUA9_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial precursor (EC 1.6.5.3) ( ...	0.06	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			377
Q02380 UniProt NPD GO	NDUB5_BOVIN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial precursor (EC 1.6.5.3) (E ...	0.06	-	mit	1	Mitochondrion; mitochondrial inner membrane; matrix side				189
P83686 UniProt NPD GO	NCB5R_PIG	NADH-cytochrome b5 reductase (EC 1.6.2.2) (B5R) (Diaphorase-1) (Cytochrome b5 reductase 3) (Fragment ...	0.06	-	cyt	0	NADH-cytochrome b5 reductase membrane-bound form: Endoplasmic reticulum; endoplasmic reticulum membr ...			1NDH	272
P07514 UniProt NPD GO	NCB5R_BOVIN	NADH-cytochrome b5 reductase (EC 1.6.2.2) (B5R) (Diaphorase-1) (Cytochrome b5 reductase 3) [Contains ...	0.06	-	mit	0	NADH-cytochrome b5 reductase membrane-bound form: Endoplasmic reticulum; endoplasmic reticulum membr ...				300
P36060 UniProt NPD GO	MCR1_YEAST	NADH-cytochrome b5 reductase precursor (EC 1.6.2.2) (p34/p32) [Contains: NADH-cytochrome b5 reductas ...	0.06	-	mit	1 *	NADH-cytochrome b5 reductase p34 form: Mitochondrion; mitochondrial outer membrane; single-pass memb ...	integral to mitochondrial outer membrane [IDA] mitochondrial intermembrane space [IDA] mitochondrial outer membrane [IDA]			302
Q07842 UniProt NPD GO	NDUA2_NEUCR	NADH-ubiquinone oxidoreductase 10.5 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I) (CI)	0.06	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side				94
P80267 UniProt NPD GO	NUO1_SOLTU	NADH-ubiquinone oxidoreductase 14 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-14KD) (CI-14KD) ...	0.06	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				29
Q8HXQ9 UniProt NPD GO	NUBM_MACFA	NADH-ubiquinone oxidoreductase 51 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side (By similarity ...				464
Q9CQY9 UniProt NPD GO	NIKM_MOUSE	NADH-ubiquinone oxidoreductase KFYI subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (Com ...	0.06	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				76
Q8M889 UniProt NPD GO	NU1M_DIAYO	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.06	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
O78696 UniProt NPD GO	NU1M_LEMCA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.06	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
O78704 UniProt NPD GO	NU1M_MACEU	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.06	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
O21077 UniProt NPD GO	NU1M_MYXGL	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.06	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
O79427 UniProt NPD GO	NU1M_RABIT	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.06	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q34799 UniProt NPD GO	NU2M_HYLSY	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.06	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P18938 UniProt NPD GO	NU3M_CHICK	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.06	-	end	3 *					116

You are viewing entries 72551 to 72600 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.