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
Q29RK9 UniProt NPD GO	MOL2B_BOVIN	Mps one binder kinase activator-like 2B (Mob1 homolog 2b)	0.29	-	nuc	0					216
Q86TA1 UniProt NPD GO	MOL2B_HUMAN	Mps one binder kinase activator-like 2B (Mob1 homolog 2b) (Protein Mob3B)	0.29	-	nuc	0					216
Q9H3R2 UniProt NPD GO	MUC13_HUMAN	Mucin-13 precursor (Down-regulated in colon cancer 1)	0.29	-	exc	1	Cell membrane; single-pass type I membrane protein (Potential). Secreted protein. Also exists as a s ...				512
P34713 UniProt NPD GO	MDR3_CAEEL	Multidrug resistance protein 3 (EC 3.6.3.44) (P-glycoprotein C)	0.29	-	end	12 *	Membrane; multi-pass membrane protein				1268
Q9M1C7 UniProt NPD GO	MRP9_ARATH	Multidrug resistance-associated protein 9 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPase ...	0.29	-	end	15 *	Membrane; multi-pass membrane protein (Potential)				1490
Q5B8Y4 UniProt NPD GO	MBF1_EMENI	Multiprotein-bridging factor 1	0.29	-	nuc	0					154
P34125 UniProt NPD GO	MHCK_DICDI	Myosin heavy chain kinase (EC 2.7.11.7) (MHCK)	0.29	-	end	0	Membrane; peripheral membrane protein				783
Q9UUG5 UniProt NPD GO	MLR1_SCHPO	Myosin regulatory light chain 1	0.29	-	nuc	0	Cytoplasm	contractile ring (sensu Fungi) [IDA]			184
Q5E9E2 UniProt NPD GO	MLRN_BOVIN	Myosin regulatory light chain 2, smooth muscle isoform (Myosin RLC) (Myosin regulatory light chain 9 ...	0.29	-	mit	0					171
P24032 UniProt NPD GO	MLRN_CHICK	Myosin regulatory light chain 2, smooth muscle minor isoform (G1) (DTNB) (MLC-2) (Isoform L20-B1)	0.29	-	mit	0					171
P13832 UniProt NPD GO	MLRA_RAT	Myosin regulatory light chain 2-A, smooth muscle isoform (Myosin RLC-A)	0.29	-	mit	0					171
P18666 UniProt NPD GO	MLRB_RAT	Myosin regulatory light chain 2-B, smooth muscle isoform (Myosin RLC-B)	0.29	-	mit	0					171
Q6S5C2 UniProt NPD GO	GNPTG_MOUSE	N-acetylglucosamine-1-phosphotransferase subunit gamma precursor (GlcNAc-1-phosphotransferase subuni ...	0.29	-	exc	0	Secreted protein. Golgi apparatus				307
Q2PMN6 UniProt NPD GO	NUIC_SOYBN	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.29	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				163
O95139 UniProt NPD GO	NDUB6_HUMAN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.29	-	nuc	1	Mitochondrion; mitochondrial inner membrane; matrix side		603322		127
O47950 UniProt NPD GO	NUKM_NEUCR	NADH-ubiquinone oxidoreductase 19.3 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) ...	0.29	-	mit	0					226
Q60HE3 UniProt NPD GO	NUIM_MACFA	NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.29	-	mit	0					210
O03197 UniProt NPD GO	NU2M_CERSI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.29	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P18937 UniProt NPD GO	NU2M_CHICK	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.29	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
P11662 UniProt NPD GO	NU2M_RAT	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.29	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	cytoplasm [TAS]			345
P41308 UniProt NPD GO	NU4M_DIDMA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.29	-	end	14 *					474
P03919 UniProt NPD GO	NU5M_HYLLA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.29	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				603
P06801 UniProt NPD GO	MAOX_MOUSE	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME) (Malic enzyme 1)	0.29	-	mit	0	Cytoplasm	cytosol [ISS] soluble fraction [IDA]			572
Q5R4A0 UniProt NPD GO	UBA3_PONPY	NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) (Ubiquitin-activating enzyme 3) (NEDD8-act ...	0.29	+	cyt	0					463
Q9Z1E3 UniProt NPD GO	IKBA_MOUSE	NF-kappa-B inhibitor alpha (I-kappa-B-alpha) (IkappaBalpha) (IKB-alpha)	0.29	-	nuc	0	Cytoplasm	cytoplasm [IDA] cytosol [IDA] nucleus [IDA]			314
P25963 UniProt NPD GO	IKBA_HUMAN	NF-kappa-B inhibitor alpha (Major histocompatibility complex enhancer-binding protein MAD3) (I-kappa ...	0.29	-	nuc	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]	164008	1NFI	317
Q61UX1 UniProt NPD GO	NACA_CAEBR	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC)	0.29	-	nuc	0					197
Q8R4F1 UniProt NPD GO	NTNG2_MOUSE	Netrin G2 precursor (Laminet-2)	0.29	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [IDA] plasma membrane [IDA]			589
P33147 UniProt NPD GO	CADHO_XENLA	Neural-cadherin 2 precursor (N-cadherin 2)	0.29	-	end	1 *	Membrane; single-pass type I membrane protein				906
P54866 UniProt NPD GO	NEUG_SERCA	Neurogranin (NG) (Canarigranin)	0.29	-	nuc	0					73
Q9JJI5 UniProt NPD GO	NMUR1_RAT	Neuromedin U receptor 1 (NMU-R1) (G-protein coupled receptor 66) (G-protein coupled receptor FM-3)	0.29	+	end	7 *	Membrane; multi-pass membrane protein				412
Q8BZ39 UniProt NPD GO	NMUR2_MOUSE	Neuromedin U receptor 2 (NMU-R2)	0.29	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]			395
Q92823 UniProt NPD GO	NRCAM_HUMAN	Neuronal cell adhesion molecule precursor (Nr-CAM) (NgCAM-related cell adhesion molecule) (Ng-CAM-re ...	0.29	-	nuc	1 *	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [NAS] integral to plasma membrane [NAS] neuron projection [NAS]	601581	1UEY	1304
P47971 UniProt NPD GO	NPTX1_RAT	Neuronal pentraxin-1 precursor (NP1) (Neuronal pentraxin I) (NP-I) (47 kDa taipoxin-binding protein) ...	0.29	-	exc	0	Secretory vesicle (Potential)				432
Q8NG41 UniProt NPD GO	NPB_HUMAN	Neuropeptide B precursor (Preproprotein L7) (hPPL7) [Contains: Neuropeptide B-23 (NPB23) (hL7); Neur ...	0.29	-	mit	1 *	Secreted protein		607996		125
P33689 UniProt NPD GO	NEUY_XENLA	Neuropeptide Y precursor [Contains: Neuropeptide Y (Neuropeptide tyrosine) (NPY); C-flanking peptide ...	0.29	-	exc	1 *	Secreted protein				97
P79217 UniProt NPD GO	NPY6R_RABIT	Neuropeptide Y receptor type 6 (NPY6-R)	0.29	-	end	7 *	Membrane; multi-pass membrane protein				371
Q8MJV3 UniProt NPD GO	NPBW1_BOVIN	Neuropeptides B/W receptor type 1 (G-protein coupled receptor 7)	0.29	-	end	5 *	Membrane; multi-pass membrane protein				331
P23654 UniProt NPD GO	NRT_DROME	Neurotactin	0.29	-	cyt	1	Membrane; single-pass type II membrane protein	basolateral plasma membrane [NAS] plasma membrane [IDA]			846
Q64319 UniProt NPD GO	SLC31_RAT	Neutral and basic amino acid transport protein rBAT (B(0,+)-type amino acid transport protein) (NAA- ...	0.29	-	mit	1	Membrane; single-pass type II membrane protein (Potential)				683
P10493 UniProt NPD GO	NID1_MOUSE	Nidogen-1 precursor (Entactin)	0.29	-	cyt	0	Secreted protein; extracellular space; extracellular matrix; basement membrane	basement membrane [IDA]		1NPE	1245
Q19127 UniProt NPD GO	NPC1_CAEEL	Niemann-Pick C1 protein homolog 1 precursor	0.29	-	end	13	Membrane; multi-pass membrane protein				1383
P29597 UniProt NPD GO	TYK2_HUMAN	Non-receptor tyrosine-protein kinase TYK2 (EC 2.7.10.2)	0.29	-	cyt	0			176941		1187
Q05541 UniProt NPD GO	NSE3_YEAST	Non-structural maintenance of chromosome element 3 (Non-SMC element 3)	0.29	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA] Smc5-Smc6 complex [IPI]			303
P39946 UniProt NPD GO	NUDF_YEAST	Nuclear distribution protein PAC1 (nudF homolog)	0.29	-	cyt	0	Cytoplasm. Nucleus. Localizes to the plus ends of cytoplasmic microtubules	cytoplasm [IDA] cytoplasmic microtubule [IDA]			494
Q2UGU1 UniProt NPD GO	NUDF_ASPOR	Nuclear distribution protein nudF homolog	0.29	-	cyt	0	Cytoplasm. Localizes to the plus ends of microtubules and the mitotic spindle poles (By similarity)				455
Q9UKX7 UniProt NPD GO	NUP50_HUMAN	Nucleoporin 50 kDa (Nuclear pore-associated protein 60 kDa-like)	0.29	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; nucleoplasmic side (By similarity). Localizes to th ...	nuclear pore [TAS]	604646		468
Q78ZA7 UniProt NPD GO	NP1L4_MOUSE	Nucleosome assembly protein 1-like 4	0.29	+	cyt	0	Nucleus (By similarity)				375
Q5W9T5 UniProt NPD GO	OPR_OCTVU	Octopressin receptor	0.29	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [IC]			419
Q8NGE3 UniProt NPD GO	O10P1_HUMAN	Olfactory receptor 10P1 (Olfactory receptor OR12-7)	0.29	-	end	6 *	Membrane; multi-pass membrane protein				313

You are viewing entries 41501 to 41550 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.