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
Q2NKR1 UniProt NPD GO	TIM10_BOVIN	Mitochondrial import inner membrane translocase subunit Tim10	0.36	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				90
P62072 UniProt NPD GO	TIM10_HUMAN	Mitochondrial import inner membrane translocase subunit Tim10	0.36	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side	mitochondrial inner membrane presequence tr... [TAS]	602251	2BSK	90
P62073 UniProt NPD GO	TIM10_MOUSE	Mitochondrial import inner membrane translocase subunit Tim10	0.36	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				90
P62074 UniProt NPD GO	TIM10_RAT	Mitochondrial import inner membrane translocase subunit Tim10	0.36	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				90
Q6GR66 UniProt NPD GO	TIM9B_XENLA	Mitochondrial import inner membrane translocase subunit Tim9 B (TIMM10B) (Tim10b)	0.36	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				125
P36163 UniProt NPD GO	OMA1_YEAST	Mitochondrial metalloendopeptidase OMA1 (EC 3.4.24.-)	0.36	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			345
P26864 UniProt NPD GO	RT02_MARPO	Mitochondrial ribosomal protein S2	0.36	+	mit	0	Mitochondrion				237
Q6DN56 UniProt NPD GO	RMAR_KLULA	Mitochondrial ribosomal protein VAR1	0.36	-	nuc	0	Mitochondrion				388
Q90336 UniProt NPD GO	MK14A_CYPCA	Mitogen-activated protein kinase 14a (EC 2.7.11.24) (Mitogen-activated protein kinase p38a) (MAP kin ...	0.36	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			361
P16892 UniProt NPD GO	FUS3_YEAST	Mitogen-activated protein kinase FUS3 (EC 2.7.11.24) (MAP kinase FUS3)	0.36	-	cyt	0	Nucleus. Cytoplasm. Periplasm. FUS3 shuttles rapidly between the cytoplasm and the nucleus independe ...	cytoplasm [IDA] mating projection tip [IDA] mitochondrion [IDA] nucleus [IDA]		2FA2	353
Q9UI95 UniProt NPD GO	MD2L2_HUMAN	Mitotic spindle assembly checkpoint protein MAD2B (MAD2-like 2) (hREV7)	0.36	-	nuc	0			604094		211
Q39055 UniProt NPD GO	CNX2_ARATH	Molybdopterin biosynthesis protein CNX2 (Molybdenum cofactor biosynthesis enzyme CNX2)	0.36	-	mit	0					390
Q7DM58 UniProt NPD GO	MRP4_ARATH	Multidrug resistance-associated protein 4 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPase ...	0.36	-	end	15	Membrane; multi-pass membrane protein (Potential)				1516
O15146 UniProt NPD GO	MUSK_HUMAN	Muscle, skeletal receptor tyrosine protein kinase precursor (EC 2.7.10.1) (Muscle-specific tyrosine ...	0.36	-	end	2	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	601296		869
P20026 UniProt NPD GO	MYB1_HORVU	Myb-related protein Hv1	0.36	-	nuc	0	Nucleus (Probable)				267
P20939 UniProt NPD GO	MBP_HETFR	Myelin basic protein (MBP)	0.36	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				154
P83487 UniProt NPD GO	MBP_HORSE	Myelin basic protein (MBP)	0.36	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				172
P30605 UniProt NPD GO	ITR1_YEAST	Myo-inositol transporter 1	0.36	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [IDA]			584
P19625 UniProt NPD GO	MLR1_CAEEL	Myosin regulatory light chain 1	0.36	-	mit	0		muscle myosin [IDA]			170
Q9P804 UniProt NPD GO	TRM1_SCHPO	N(2),N(2)-dimethylguanosine tRNA methyltransferase (EC 2.1.1.32) (tRNA(guanine-26,N(2)-N(2)) methylt ...	0.36	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear/cytoplasmic compartments (By similarity) ...				548
Q9QY36 UniProt NPD GO	ARD1H_MOUSE	N-terminal acetyltransferase complex ARD1 subunit homolog A (EC 2.3.1.88) (EC 2.3.1.-)	0.36	-	nuc	0	Cytoplasm	cytoplasm [IDA]			235
P21373 UniProt NPD GO	UTR1_YEAST	NAD(+) kinase (EC 2.7.1.23) (Unknown transcript 1 protein)	0.36	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			530
Q8HVV8 UniProt NPD GO	NUIC_AMBTR	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.36	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				166
Q49KU4 UniProt NPD GO	NUIC_EUCGG	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.36	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				167
P48306 UniProt NPD GO	NDUB4_CHICK	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.36	-	nuc	1	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				133
P80269 UniProt NPD GO	NUIM_SOLTU	NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.36	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				229
O21334 UniProt NPD GO	NU4M_DASNO	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.36	-	end	13 *					459
Q9XVK5 UniProt NPD GO	UBC12_CAEEL	NEDD8-conjugating enzyme ubc-12 (EC 6.3.2.-) (NEDD8 protein ligase) (NEDD8 carrier protein) (Ubiquit ...	0.36	-	nuc	0					180
Q91974 UniProt NPD GO	IKBA_CHICK	NF-kappa-B inhibitor alpha (I-kappa-B-alpha) (IkappaBalpha) (IKB-alpha) (REL-associated protein pp40 ...	0.36	-	nuc	0	Cytoplasm				318
P60324 UniProt NPD GO	NANO3_MOUSE	Nanos homolog 3	0.36	-	nuc	0					178
Q9GLK4 UniProt NPD GO	ANFB_FELCA	Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic pepti ...	0.36	-	exc	0	Secreted protein (By similarity)				132
Q9PVD5 UniProt NPD GO	UNC5_PETMA	Netrin receptor unc-5 homolog (Fragment)	0.36	-	cyt	0	Membrane; single-pass type I membrane protein (By similarity)				199
Q90479 UniProt NPD GO	L1CA2_BRARE	Neural cell adhesion molecule L1.2 (N-CAM L1.2) (Fragment)	0.36	-	nuc	1	Membrane; single-pass type I membrane protein				216
Q56H79 UniProt NPD GO	NPSR1_MACMU	Neuropeptide S receptor (G-protein coupled receptor 154)	0.36	-	end	6	Membrane; multi-pass membrane protein (By similarity)				371
Q27995 UniProt NPD GO	NOS2_BOVIN	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.36	-	cyt	0					246
P02314 UniProt NPD GO	HMGN2_CHICK	Nonhistone chromosomal protein HMG-17 (High-mobility group nucleosome-binding domain-containing prot ...	0.36	+	nuc	0	Nucleus				89
Q6CVZ8 UniProt NPD GO	NMD4_KLULA	Nonsense-mediated decay protein 4	0.36	-	nuc	0	Cytoplasm (By similarity)				244
Q754W7 UniProt NPD GO	NCBP2_ASHGO	Nuclear cap-binding protein subunit 2	0.36	-	cyt	0	Nucleus (By similarity)				218
Q5RDG8 UniProt NPD GO	NFHEV_PONPY	Nuclear factor from high endothelial venules (NF-HEV)	0.36	-	nuc	0	Nucleus (By similarity)				270
O16391 UniProt NPD GO	NH124_CAEEL	Nuclear hormone receptor family member nhr-124	0.36	-	nuc	0	Nucleus (Potential)				376
O17573 UniProt NPD GO	NH150_CAEEL	Nuclear hormone receptor family member nhr-150	0.36	-	pox	0	Nucleus (Potential)				342
O45907 UniProt NPD GO	NHR65_CAEEL	Nuclear hormone receptor family member nhr-65	0.36	-	cyt	0	Nucleus (Potential)				401
Q20745 UniProt NPD GO	UNC84_CAEEL	Nuclear migration and anchoring protein unc-84 (Uncoordinated protein 84)	0.36	-	end	7	Nucleus; nuclear inner membrane; single-pass membrane protein; nucleoplasmic side (Probable). Associ ...	nuclear envelope [IDA]			1111
Q5RF26 UniProt NPD GO	NUCL_PONPY	Nucleolin	0.36	+	nuc	0	Nucleus; nucleolus (By similarity)				711
P13383 UniProt NPD GO	NUCL_RAT	Nucleolin (Protein C23)	0.36	+	nuc	0	Nucleus; nucleolus				712
O08587 UniProt NPD GO	NUP50_RAT	Nucleoporin 50 kDa (Nuclear pore-associated protein 60 kDa-like)	0.36	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; nucleoplasmic side. Localizes to the nucleoplasmic ...	nuclear pore [IDA]			467
P40066 UniProt NPD GO	GLE2_YEAST	Nucleoporin GLE2 (Nuclear pore protein GLE2) (poly(A) RNA export protein RAE1)	0.36	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			365
O13838 UniProt NPD GO	NUP40_SCHPO	Nucleoporin nup40 (Nuclear pore protein nup40)	0.36	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Biased toward ...	nuclear pore [TAS]			371
Q5FVW4 UniProt NPD GO	NUPL2_XENTR	Nucleoporin-like 2	0.36	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side (By similarity)				449
Q50EX6 UniProt NPD GO	ODO1_PETHY	ODORANT1 protein (MYB-like protein ODO1)	0.36	-	nuc	0	Nucleus (Probable)				294

You are viewing entries 35151 to 35200 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.