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
Q01662 UniProt NPD GO	AMPM1_YEAST	Methionine aminopeptidase 1 precursor (EC 3.4.11.18) (MetAP 1) (MAP 1) (Peptidase M 1)	0.07	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [IDA]			387
Q6XMH7 UniProt NPD GO	AMPM2_ENCIN	Methionine aminopeptidase 2 (EC 3.4.11.18) (MetAP 2) (Peptidase M 2) (MetAP2) (MAP-2)	0.07	-	cyt	0					358
P00958 UniProt NPD GO	SYMC_YEAST	Methionyl-tRNA synthetase, cytoplasmic (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.07	-	nuc	0	Cytoplasm	cytoplasm [IDA] methionyl glutamyl tRNA synthetase complex [IDA]			750
Q5R719 UniProt NPD GO	ICLN_PONPY	Methylosome subunit pICln (Chloride conductance regulatory protein ICln) (I(Cln)) (Chloride channel, ...	0.07	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). A small fraction is also associated with the cyt ...				237
Q6AYP2 UniProt NPD GO	MFA3L_RAT	Microfibrillar-associated protein 3-like precursor	0.07	-	end	1	Membrane; single-pass type I membrane protein (Potential)				409
Q99735 UniProt NPD GO	MGST2_HUMAN	Microsomal glutathione S-transferase 2 (EC 2.5.1.18) (Microsomal GST-2) (Microsomal GST-II)	0.07	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	membrane fraction [TAS] microsome [TAS]	601733		147
Q6P848 UniProt NPD GO	MARE1_XENTR	Microtubule-associated protein RP/EB family member 1	0.07	-	cyt	0	Cytoplasm (By similarity). Associated with the microtubule network (By similarity)				269
P42059 UniProt NPD GO	CLAH7_CLAHE	Minor allergen Cla h 7 (Cla h 5) (Cla h V)	0.07	-	cyt	0	Cytoplasm (Probable)				204
P82670 UniProt NPD GO	RT10_BOVIN	Mitochondrial 28S ribosomal protein S10 (S10mt) (MRP-S10)	0.07	-	mit	0	Mitochondrion				201
P34829 UniProt NPD GO	RM14_ACAPO	Mitochondrial 60S ribosomal protein L14 (Fragment)	0.07	-	cyt	0	Mitochondrion				116
P19956 UniProt NPD GO	RM44_YEAST	Mitochondrial 60S ribosomal protein L44 (YmL44)	0.07	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			98
Q9D8K8 UniProt NPD GO	CG69_MOUSE	Mitochondrial carrier protein CGI-69 homolog	0.07	-	cyt	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				359
Q06143 UniProt NPD GO	DIC1_YEAST	Mitochondrial dicarboxylate transporter (Dicarboxylate carrier 1) (DTP)	0.07	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial envelope [IDA]			298
Q4PGT2 UniProt NPD GO	TIM13_USTMA	Mitochondrial import inner membrane translocase subunit TIM13	0.07	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				108
Q9VTJ8 UniProt NPD GO	TIM14_DROME	Mitochondrial import inner membrane translocase subunit TIM14	0.07	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)	presequence translocase-associated import m... [ISS]			118
Q4I375 UniProt NPD GO	TIM16_GIBZE	Mitochondrial import inner membrane translocase subunit TIM16 (Presequence translocated-associated m ...	0.07	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				138
Q4X0V2 UniProt NPD GO	TIM13_ASPFU	Mitochondrial import inner membrane translocase subunit tim13	0.07	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				113
P49334 UniProt NPD GO	TOM22_YEAST	Mitochondrial import receptor subunit TOM22 (Mitochondrial 22 kDa outer membrane protein) (Transloca ...	0.07	-	cyt	0	Mitochondrion; mitochondrial outer membrane; single-pass type II membrane protein	integral to mitochondrial outer membrane [IDA] mitochondrial outer membrane translocase co... [TAS]			151
Q8VEA4 UniProt NPD GO	MIA40_MOUSE	Mitochondrial intermembrane space import and assembly protein 40 (Coiled-coil-helix-coiled-coil-heli ...	0.07	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				139
Q3E7B2 UniProt NPD GO	YJ062_YEAST	Mitochondrial membrane protein YJL062W-A	0.07	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)	mitochondrion [IDA]			85
Q9Y619 UniProt NPD GO	ORNT1_HUMAN	Mitochondrial ornithine transporter 1 (Solute carrier family 25 member 15)	0.07	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to membrane [TAS] mitochondrial inner membrane [TAS]	603861		301
O08911 UniProt NPD GO	MK12_MOUSE	Mitogen-activated protein kinase 12 (EC 2.7.11.24) (Extracellular signal-regulated kinase 6) (ERK-6) ...	0.07	-	cyt	0	Cytoplasm. Mitochondrion. Mitochondrial when associated with SH3BP5 (By similarity)	cytoplasm [IEP]			367
Q9Z223 UniProt NPD GO	MOS2L_MOUSE	Molybdenum cofactor synthesis protein 2 large subunit (Molybdopterin synthase large subunit) (MPT sy ...	0.07	-	nuc	0					189
Q03064 UniProt NPD GO	MOT1_CRILO	Monocarboxylate transporter 1 (MCT 1)	0.07	-	end	11 *	Cell membrane; multi-pass membrane protein (By similarity)				494
O70461 UniProt NPD GO	MOT3_RAT	Monocarboxylate transporter 3 (MCT 3)	0.07	-	end	12 *	Cell membrane; multi-pass membrane protein	basal plasma membrane [IDA]			492
O74790 UniProt NPD GO	GLRX5_SCHPO	Monothiol glutaredoxin-5	0.07	-	mit	0		cytoplasm [IDA] nucleus [IDA]			244
Q5IS39 UniProt NPD GO	OPRM_PANTR	Mu-type opioid receptor (MOR-1)	0.07	-	end	7	Membrane; multi-pass membrane protein (By similarity)				401
P09177 UniProt NPD GO	CARP_RHIPU	Mucorpepsin precursor (EC 3.4.23.23) (Mucor rennin)	0.07	-	exc	0				1MPP	427
P38024 UniProt NPD GO	PUR6_CHICK	Multifunctional protein ADE2 [Includes: Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC ...	0.07	-	nuc	0					426
Q5RB59 UniProt NPD GO	PUR6_PONPY	Multifunctional protein ADE2 [Includes: Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC ...	0.07	-	nuc	0					424
P51583 UniProt NPD GO	PUR6_RAT	Multifunctional protein ADE2 [Includes: Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC ...	0.07	-	nuc	0					424
Q5A940 UniProt NPD GO	MBF1_CANAL	Multiprotein-bridging factor 1	0.07	-	nuc	0					151
P81031 UniProt NPD GO	TXM3_DENAN	Muscarinic toxin 3 (MT3)	0.07	-	nuc	0	Secreted protein				65
P27573 UniProt NPD GO	MYP0_MOUSE	Myelin P0 protein precursor (Myelin protein zero) (Myelin peripheral protein) (MPP)	0.07	-	end	2 *	Membrane; single-pass type I membrane protein				248
P80164 UniProt NPD GO	MLR_LUMTE	Myosin regulatory light chain, striated muscle, 25 kDa isoform (LC25)	0.07	-	cyt	0					195
P01477 UniProt NPD GO	MYXC_CROVH	Myotoxin (Toxic peptide C)	0.07	-	nuc	0	Secreted protein				43
P69438 UniProt NPD GO	TMC47_THAMA	Myotoxin TmC4-47.2 (Fragment)	0.07	-	nuc	0	Secreted protein				24
P63176 UniProt NPD GO	MYX3_CROVV	Myotoxin-3	0.07	-	nuc	0	Secreted protein				45
Q5XIG6 UniProt NPD GO	GALK2_RAT	N-acetylgalactosamine kinase (EC 2.7.1.157) (GalNAc kinase) (Galactokinase 2)	0.07	-	nuc	0					458
P51606 UniProt NPD GO	RENBP_HUMAN	N-acylglucosamine 2-epimerase (EC 5.1.3.8) (GlcNAc 2-epimerase) (N-acetyl-D-glucosamine 2-epimerase) ...	0.07	-	cyt	0			312420		417
Q8TBE9 UniProt NPD GO	NANP_HUMAN	N-acylneuraminate-9-phosphatase (EC 3.1.3.29) (Neu5Ac-9-Pase) (Haloacid dehalogenase-like hydrolase ...	0.07	-	cyt	0					248
Q5M969 UniProt NPD GO	NANP_RAT	N-acylneuraminate-9-phosphatase (EC 3.1.3.29) (Neu5Ac-9-Pase) (Haloacid dehalogenase-like hydrolase ...	0.07	-	cyt	0					248
Q53NF7 UniProt NPD GO	NAC71_ORYSA	NAC domain-containing protein 71 (ONAC071)	0.07	+	cyt	0	Nucleus (Probable)				329
Q9FMR3 UniProt NPD GO	NAC90_ARATH	NAC domain-containing protein 90 (ANAC090)	0.07	-	cyt	0	Nucleus (Potential)				235
Q5RD31 UniProt NPD GO	NQO1_PONPY	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) (Quinone reductase 1) (NAD(P)H:quinone oxidoreductase ...	0.07	-	mit	0	Cytoplasm (By similarity)				274
Q9TKV8 UniProt NPD GO	NU4C_NEPOL	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.07	-	end	14 *	Plastid; chloroplast				500
Q5R9E8 UniProt NPD GO	NDUAA_PONPY	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial precursor (EC 1.6.5.3) ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				355
Q8HXG6 UniProt NPD GO	NDUAB_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.07	-	cyt	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...	mitochondrion [ISS]			140
Q6PBH5 UniProt NPD GO	NDUA4_BRARE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4 (EC 1.6.5.3) (EC 1.6.99.3)	0.07	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				82
Q01321 UniProt NPD GO	NDUA4_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.07	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; matrix side				82

You are viewing entries 70451 to 70500 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.