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
Q96PG2 UniProt NPD GO	M4A10_HUMAN	Membrane-spanning 4-domains subfamily A member 10	0.16	-	end	3	Membrane; multi-pass membrane protein (By similarity)		608403		267
P80291 UniProt NPD GO	MT2D_RABIT	Metallothionein-2D (MT-2D) (Metallothionein-IID) (MT-IID)	0.16	-	nuc	0					61
Q9TUI5 UniProt NPD GO	MT4_CANFA	Metallothionein-4 (MT-4) (Metallothionein-IV) (MT-IV)	0.16	-	nuc	0					62
Q96GW9 UniProt NPD GO	SYMM_HUMAN	Methionyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.10) (Methionine--tRNA ligase 2) (Mitoch ...	0.16	-	mit	0	Mitochondrion; mitochondrial matrix (Probable)	mitochondrial matrix [IDA]	609728		593
Q00650 UniProt NPD GO	I3MS_BRANA	Microspore-specific protein I3	0.16	-	end	2 *					156
Q6P7D5 UniProt NPD GO	M1IP1_RAT	Mid1-interacting protein 1 (Gastrulation-specific G12-like protein) (Mid1-interacting G12-like prote ...	0.16	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Associated with microtubules (By similarity)	microtubule cytoskeleton [ISS]			183
Q9Y2Q9 UniProt NPD GO	RT28_HUMAN	Mitochondrial 28S ribosomal protein S28 (S28mt) (MRP-S28) (MRP-S35)	0.16	-	cyt	0	Mitochondrion	mitochondrial small ribosomal subunit [TAS]			187
Q9CQP0 UniProt NPD GO	RM33_MOUSE	Mitochondrial 39S ribosomal protein L33 (L33mt) (MRP-L33)	0.16	-	mit	0	Mitochondrion	mitochondrion [IDA]			65
Q298L5 UniProt NPD GO	MIRO_DROPS	Mitochondrial Rho GTPase (EC 3.6.5.-) (Miro)	0.16	-	cyt	0	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				649
P46750 UniProt NPD GO	RT19_PROWI	Mitochondrial ribosomal protein S19	0.16	-	mit	0	Mitochondrion				78
P48938 UniProt NPD GO	RT03_CHOCR	Mitochondrial ribosomal protein S3	0.16	-	mit	0	Mitochondrion				240
Q5QN75 UniProt NPD GO	M2K1_ORYSA	Mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) (MAP kinase kinase 1) (MAPKK1) (OsMEK1)	0.16	-	cyt	0					355
Q6DH44 UniProt NPD GO	MORG1_BRARE	Mitogen-activated protein kinase organizer 1 (MAPK organizer 1)	0.16	-	mit	0	Cytoplasm (By similarity)				315
P55322 UniProt NPD GO	MIH_PENVA	Molt-inhibiting hormone-like precursor (MIH-like) (Fragment)	0.16	-	nuc	0	Secreted protein				102
Q9ZNW0 UniProt NPD GO	MOC3_ARATH	Molybdenum cofactor synthesis protein 3 (Molybdopterin synthase sulfurylase) (MPT synthase sulfuryla ...	0.16	-	nuc	0					464
O18811 UniProt NPD GO	MOTI_MACMU	Motilin precursor [Contains: Motilin; Motilin-associated peptide (MAP)]	0.16	-	mit	0	Secreted protein				115
P11058 UniProt NPD GO	TXMG2_AGEAP	Mu-agatoxin-2	0.16	-	nuc	0	Secreted protein				37
P60178 UniProt NPD GO	TXMG3_AGEAP	Mu-agatoxin-3	0.16	-	nuc	0	Secreted protein				38
Q91511 UniProt NPD GO	VSP5_TRIMU	Mucrofibrase-5 precursor (EC 3.4.21.-)	0.16	-	exc	0	Secreted protein				257
Q9FWX7 UniProt NPD GO	MDR8_ARATH	Multidrug resistance protein 8 (P-glycoprotein 11)	0.16	-	end	10	Membrane; multi-pass membrane protein (Potential)				1278
Q864R9 UniProt NPD GO	MRP1_MACFA	Multidrug resistance-associated protein 1 (ATP-binding cassette sub-family C member 1) (Leukotriene ...	0.16	-	end	16 *	Membrane; multi-pass membrane protein				1531
Q5KAR7 UniProt NPD GO	MBF1_CRYNE	Multiprotein-bridging factor 1	0.16	-	nuc	0					150
P30372 UniProt NPD GO	ACM2_CHICK	Muscarinic acetylcholine receptor M2	0.16	-	end	7 *	Membrane; multi-pass membrane protein				466
P08172 UniProt NPD GO	ACM2_HUMAN	Muscarinic acetylcholine receptor M2	0.16	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	118493	1LUB	466
P06199 UniProt NPD GO	ACM2_PIG	Muscarinic acetylcholine receptor M2	0.16	-	end	7 *	Membrane; multi-pass membrane protein				466
Q9N2A7 UniProt NPD GO	ACM2_PANTR	Muscarinic acetylcholine receptor M2 (Fragment)	0.16	-	end	7 *	Membrane; multi-pass membrane protein				440
P82462 UniProt NPD GO	TXML1_NAJKA	Muscarinic toxin-like protein 1 (MTLP-1)	0.16	-	nuc	0	Secreted protein				65
P82464 UniProt NPD GO	TXML3_NAJKA	Muscarinic toxin-like protein 3 (MTLP-3)	0.16	-	nuc	0	Secreted protein				65
P02690 UniProt NPD GO	MYP2_BOVIN	Myelin P2 protein	0.16	-	cyt	0				1PMP	131
Q32PI9 UniProt NPD GO	MPZL1_BOVIN	Myelin protein zero-like protein 1 precursor	0.16	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				269
Q24654 UniProt NPD GO	MLC1_DROSI	Myosin light chain alkali	0.16	+	cyt	0		muscle myosin [ISS]			155
P08733 UniProt NPD GO	MLRV_RAT	Myosin regulatory light chain 2, ventricular/cardiac muscle isoform (MLC-2) (MLC-2v)	0.16	+	cyt	0					165
P50857 UniProt NPD GO	TRPF_CANGA	N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI)	0.16	-	cyt	0					217
P23797 UniProt NPD GO	GPI12_YEAST	N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase (EC 3.5.1.89)	0.16	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane				304
Q8W848 UniProt NPD GO	NU2C_PSINU	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.16	-	end	13 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				496
P51096 UniProt NPD GO	NU5C_ANIIN	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.16	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				741
Q8S8V0 UniProt NPD GO	NU5C_ATRBE	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.16	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				740
P06265 UniProt NPD GO	NU5C_TOBAC	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.16	-	end	16 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				740
Q31952 UniProt NPD GO	NU5C_CAPBA	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.16	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				695
Q32440 UniProt NPD GO	NU5C_HORVU	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.16	-	end	13 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				705
Q9MUR0 UniProt NPD GO	NUKC_MESVI	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.16	-	nuc	0	Plastid; chloroplast				247
Q5SCZ1 UniProt NPD GO	NUIC_HUPLU	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.16	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				183
Q8R104 UniProt NPD GO	SIRT3_MOUSE	NAD-dependent deacetylase sirtuin-3 (EC 3.5.1.-) (SIR2-like protein 3) (mSIR2L3)	0.16	-	cyt	0	Cytoplasm	cytoplasm [IDA] membrane [IDA]			257
P40375 UniProt NPD GO	MAOX_SCHPO	NAD-dependent malic enzyme (EC 1.1.1.38) (NAD-ME)	0.16	-	cyt	0					565
Q7TMF3 UniProt NPD GO	NDUAC_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqu ...	0.16	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)	mitochondrion [IDA]			145
Q3SZ44 UniProt NPD GO	NUA4L_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4-like 2	0.16	-	nuc	1 *					87
Q60HG4 UniProt NPD GO	NCB5R_MACFA	NADH-cytochrome b5 reductase (EC 1.6.2.2) (B5R) (Diaphorase-1) (Cytochrome b5 reductase 3) [Contains ...	0.16	-	cyt	0	Isoform 1: Endoplasmic reticulum; endoplasmic reticulum membrane; lipid-anchor; cytoplasmic side (By ...				300
P40915 UniProt NPD GO	NUHM_NEUCR	NADH-ubiquinone oxidoreductase 24 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3)	0.16	-	mit	0	Mitochondrion; mitochondrial inner membrane				263
P24917 UniProt NPD GO	NUBM_NEUCR	NADH-ubiquinone oxidoreductase 51 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.16	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				493
P28331 UniProt NPD GO	NUAM_HUMAN	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.16	-	mit	0	Mitochondrion; mitochondrial inner membrane		252010		727

You are viewing entries 55901 to 55950 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.