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
Q9C8H1 UniProt NPD GO	MRP12_ARATH	Multidrug resistance-associated protein 12 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPas ...	0.25	-	end	13 *	Membrane; multi-pass membrane protein (Potential)				1495
P20027 UniProt NPD GO	MYB3_HORVU	Myb-related protein Hv33	0.25	-	nuc	0	Nucleus (Probable)				302
P20025 UniProt NPD GO	MYB38_MAIZE	Myb-related protein Zm38	0.25	-	nuc	0	Nucleus (Probable)				255
P20938 UniProt NPD GO	MYP0_HETFR	Myelin P0 protein precursor (Myelin protein zero) (Myelin peripheral protein) (MPP)	0.25	-	end	1	Membrane; single-pass type I membrane protein				246
P20917 UniProt NPD GO	MAG_MOUSE	Myelin-associated glycoprotein precursor (Siglec-4a)	0.25	-	end	1	Membrane; single-pass type I membrane protein				626
Q7RQ71 UniProt NPD GO	MYOA_PLAYO	Myosin A	0.25	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Tightly associated wit ...				817
P07347 UniProt NPD GO	ARD1_YEAST	N-terminal acetyltransferase A complex catalytic subunit ARD1 (EC 2.3.1.88) (NatA complex subunit AR ...	0.25	-	mit	0	Cytoplasm	NatA complex [IDA]			238
Q5Z6B6 UniProt NPD GO	NAC76_ORYSA	NAC domain-containing protein 76 (ONAC076)	0.25	-	cyt	0	Nucleus (Probable)				276
Q32126 UniProt NPD GO	NU5C_DAMDI	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.25	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				744
Q32238 UniProt NPD GO	NU5C_FLARA	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.25	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				741
Q32384 UniProt NPD GO	NU5C_HELAN	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.25	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				741
Q9BBP6 UniProt NPD GO	NU5C_LOTJA	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.25	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				747
Q9TLC2 UniProt NPD GO	NU5C_TECST	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.25	-	end	14 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				750
P56753 UniProt NPD GO	NUCC_ARATH	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.25	-	cyt	0	Plastid; chloroplast				393
Q9MUL2 UniProt NPD GO	NUIC_MESVI	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.25	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				176
Q32S03 UniProt NPD GO	NUIC_STAPU	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.25	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				181
P23710 UniProt NPD GO	NUGM_NEUCR	NADH-ubiquinone oxidoreductase 30.4 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) ...	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane				283
O21241 UniProt NPD GO	NUAM_RECAM	NADH-ubiquinone oxidoreductase 75 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-75KD) (CI-75KD) ...	0.25	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...				691
P25712 UniProt NPD GO	NUOM_BOVIN	NADH-ubiquinone oxidoreductase 9 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (Co ...	0.25	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side				109
P03911 UniProt NPD GO	NU4M_MOUSE	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.25	-	end	12 *					459
O78755 UniProt NPD GO	NU4M_SHEEP	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.25	-	end	12 *					459
P18940 UniProt NPD GO	NU5M_CHICK	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.25	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				605
Q9TA19 UniProt NPD GO	NU5M_LOXAF	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.25	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				606
P03916 UniProt NPD GO	NU5M_PANPA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.25	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				603
P34857 UniProt NPD GO	NU6M_APILI	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.25	-	end	4 *					167
Q3SYT8 UniProt NPD GO	NCPR_BOVIN	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.25	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...				677
P04175 UniProt NPD GO	NCPR_PIG	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.25	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...				677
Q8JIU7 UniProt NPD GO	NACA_BRARE	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC)	0.25	-	nuc	0					215
Q86S66 UniProt NPD GO	NACA_CAEEL	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC)	0.25	-	nuc	0					197
Q6QN10 UniProt NPD GO	NACA_CHILA	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC)	0.25	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Also found in nucleus (By similar ...				215
Q6IP73 UniProt NPD GO	NACA_XENLA	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC)	0.25	-	nuc	0					213
Q68F90 UniProt NPD GO	NACA_XENTR	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC)	0.25	-	nuc	0					214
P27471 UniProt NPD GO	KLRBB_RAT	Natural killer cell surface protein P1-3.2.3 (NKR-P1 3.2.3) (Antigen 3.2.3)	0.25	-	nuc	1 *	Membrane; single-pass type II membrane protein				223
Q63376 UniProt NPD GO	NRX2B_RAT	Neurexin-2-beta precursor (Neurexin II-beta)	0.25	-	end	1	Membrane; single-pass type I membrane protein (Potential)				662
P54877 UniProt NPD GO	NEUG_CAPHI	Neurogranin (NG) (Protein kinase C substrate 7.5 kDa protein) (RC3)	0.25	-	nuc	0					78
P35722 UniProt NPD GO	NEUG_BOVIN	Neurogranin (NG) (p17) (B-50 immunoreactive C-kinase substrate) (BICKS)	0.25	-	nuc	0					78
P97459 UniProt NPD GO	NPAS1_MOUSE	Neuronal PAS domain-containing protein 1 (Neuronal PAS1)	0.25	-	cyt	0	Nucleus	nucleus [IDA]			594
Q8JFN7 UniProt NPD GO	ACH91_ONCMY	Neuronal acetylcholine receptor protein subunit alpha-9-I precursor (Nicotinic acetylcholine recepto ...	0.25	-	end	4	Membrane; multi-pass membrane protein (Probable)				572
Q62443 UniProt NPD GO	NPTX1_MOUSE	Neuronal pentraxin-1 precursor (NP1) (Neuronal pentraxin I) (NP-I)	0.25	-	exc	0	Secretory vesicle (Potential)				432
P01525 UniProt NPD GO	NXB4_CERLA	Neurotoxin B-IV	0.25	-	nuc	0	Secreted protein			1VIB	55
P24727 UniProt NPD GO	NT4_XENLA	Neurotrophin-4 precursor (NT-4)	0.25	-	mit	0					236
Q5G268 UniProt NPD GO	NETR_HYLLE	Neurotrypsin precursor (EC 3.4.21.-)	0.25	-	end	0	Secreted protein				875
P60031 UniProt NPD GO	DEF3_MACMU	Neutrophil defensin 3 precursor (RMAD-3)	0.25	-	exc	0	Secreted protein				96
Q8VCM8 UniProt NPD GO	NCLN_MOUSE	Nicalin precursor (Nicastrin-like protein)	0.25	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				563
Q5XIA1 UniProt NPD GO	NCLN_RAT	Nicalin precursor (Nicastrin-like protein)	0.25	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				563
P17570 UniProt NPD GO	NIA_LYCES	Nitrate reductase [NADH] (EC 1.7.1.1) (NR)	0.25	-	nuc	0					911
P36859 UniProt NPD GO	NIA_PETHY	Nitrate reductase [NADH] (EC 1.7.1.1) (NR)	0.25	-	nuc	0					909
Q8VDK1 UniProt NPD GO	NIT1_MOUSE	Nitrilase homolog 1 (EC 3.5.-.-)	0.25	-	mit	0					323
Q810Q5 UniProt NPD GO	NMES1_MOUSE	Normal mucosa of esophagus-specific gene 1 protein	0.25	-	mit	1 *	Nucleus (By similarity)	nucleus [ISS]			83
Q10902 UniProt NPD GO	NHR2_CAEEL	Nuclear hormone receptor family member nhr-2	0.25	-	nuc	0	Nucleus (Potential)				359

You are viewing entries 45451 to 45500 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.