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
Q95YL7 UniProt NPD GO	HSP70_ENCHE	Mitochondrial-type heat shock protein 70 (mit-hsp70)	0.27	-	nuc	0	Nucleus (Potential)				593
Q3ZBJ8 UniProt NPD GO	MFRN1_BOVIN	Mitoferrin-1 (Mitochondrial iron transporter 1) (Solute carrier family 25 member 37)	0.27	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				171
O23236 UniProt NPD GO	MPK14_ARATH	Mitogen-activated protein kinase 14 (EC 2.7.11.24) (MAP kinase 14) (AtMPK14)	0.27	-	cyt	0					361
Q9DGD9 UniProt NPD GO	MK08_BRARE	Mitogen-activated protein kinase 8 (EC 2.7.11.24) (Stress-activated protein kinase JNK1) (c-Jun N-te ...	0.27	-	cyt	0					384
Q04669 UniProt NPD GO	MOUB_ORNMO	Moubatin precursor	0.27	-	exc	0					171
P39552 UniProt NPD GO	MST28_YEAST	Multicopy suppressor of SEC21 protein 28 (DUP240 protein MST28)	0.27	-	end	2 *	Membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum, endoplasmic reticulum to G ...	endoplasmic reticulum [IPI] Golgi apparatus [IPI] integral to membrane [IDA]			234
Q9LSJ8 UniProt NPD GO	MDR18_ARATH	Multidrug resistance protein 18 (P-glycoprotein 16)	0.27	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				1228
Q8LGU1 UniProt NPD GO	MRP6_ARATH	Multidrug resistance-associated protein 6 precursor (EC 3.6.3.44) (Glutathione S-conjugate-transport ...	0.27	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				1295
Q80V70 UniProt NPD GO	MEGF6_MOUSE	Multiple epidermal growth factor-like domains 6 (EGF-like domain-containing protein 3) (Multiple EGF ...	0.27	-	nuc	0					656
O54873 UniProt NPD GO	MCA1_CRIGR	Multisynthetase complex auxiliary component p43 [Contains: Endothelial monocyte-activating polypepti ...	0.27	-	mit	0					359
Q12904 UniProt NPD GO	MCA1_HUMAN	Multisynthetase complex auxiliary component p43 [Contains: Endothelial monocyte-activating polypepti ...	0.27	-	nuc	0		extracellular space [TAS]	603605	1FL0	312
Q7XBH4 UniProt NPD GO	MYB4_ORYSA	Myb-related protein Myb4 (OsMyb4) (Transcription factor RLTR1)	0.27	-	nuc	0	Nucleus (Probable)				257
P07722 UniProt NPD GO	MAG_RAT	Myelin-associated glycoprotein precursor (Siglec-4a) (Brain neuron cytoplasmic protein 3)	0.27	-	end	1	Membrane; single-pass type I membrane protein				626
Q64122 UniProt NPD GO	MLRN_RAT	Myosin regulatory light chain 2, smooth muscle isoform (Myosin RLC) (Myosin regulatory light chain 9 ...	0.27	-	mit	0					170
Q9R0C5 UniProt NPD GO	GALT7_RAT	N-acetylgalactosaminyltransferase 7 (EC 2.4.1.-) (Protein-UDP acetylgalactosaminyltransferase 7) (UD ...	0.27	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				657
P15882 UniProt NPD GO	CHIN_HUMAN	N-chimaerin (NC) (N-chimerin) (Alpha chimerin) (A-chimaerin) (Rho-GTPase-activating protein 2)	0.27	-	nuc	0			118423		459
Q13287 UniProt NPD GO	NMI_HUMAN	N-myc-interactor (Nmi) (N-myc and STAT interactor)	0.27	-	cyt	0	Cytoplasm	cytoplasm [IDA]	603525		307
Q9MTI4 UniProt NPD GO	NU5C_OENHO	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.27	-	end	15 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				736
Q3V4Y0 UniProt NPD GO	NUIC_ACOCL	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.27	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				179
P36013 UniProt NPD GO	MAOX_YEAST	NAD-dependent malic enzyme (EC 1.1.1.38) (NAD-ME)	0.27	-	mit	0		mitochondrion [IDA]			669
P91929 UniProt NPD GO	NDUAA_DROME	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial precursor (EC 1.6.5.3) ...	0.27	-	mit	0	Mitochondrion; mitochondrial matrix				407
P51970 UniProt NPD GO	NDUA8_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.27	-	nuc	0	Mitochondrion	mitochondrion [TAS]	603359		171
Q03015 UniProt NPD GO	NUMM_NEUCR	NADH-ubiquinone oxidoreductase 12 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.27	-	nuc	0					104
Q94VJ5 UniProt NPD GO	NU2M_VARBN	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.27	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				345
Q00506 UniProt NPD GO	NU4M_PHOVI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.27	-	end	12 *					459
Q96068 UniProt NPD GO	NU4M_RHIUN	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.27	-	end	13 *					459
Q9G2W8 UniProt NPD GO	NU5M_MYXGL	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.27	-	end	17 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				601
P92699 UniProt NPD GO	NU5M_PONPA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.27	-	end	17 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				603
P03918 UniProt NPD GO	NU5M_PONPY	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.27	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				603
P15601 UniProt NPD GO	NUGM_PARPR	NADH-ubiquinone oxidoreductase subunit 9 (EC 1.6.5.3) (EC 1.6.99.3) (Protein P1)	0.27	-	cyt	0	Mitochondrion; mitochondrial inner membrane				209
P37039 UniProt NPD GO	NCPR_CAVPO	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.27	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Anchored to the ...				677
Q9NV92 UniProt NPD GO	NFIP2_HUMAN	NEDD4 family-interacting protein 2 (NEDD4 WW domain-binding protein 5A) (Putative MAPK-activating pr ...	0.27	-	end	3	Golgi apparatus; Golgi membrane; multi-pass membrane protein. Endosome; endosomal membrane; multi-pa ...		610041		336
Q99MI7 UniProt NPD GO	UBA3_RAT	NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) (Ubiquitin-activating enzyme 3) (NEDD8-act ...	0.27	+	cyt	0					462
P24565 UniProt NPD GO	2SSI_BRANA	Napin-1A (Napin BnIa) [Contains: Napin-1A small chain; Napin-1A large chain]	0.27	-	nuc	0				1PNB	110
P84782 UniProt NPD GO	2SS1_BRAOA	Napin-like polypeptide [Contains: Napin-like polypeptide small chain; Napin-like polypeptide large c ...	0.27	-		0					17
P16859 UniProt NPD GO	ANFB_CANFA	Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic pepti ...	0.27	-	exc	0	Secreted protein				140
Q9MZ41 UniProt NPD GO	KLRD1_PANTR	Natural killer cells antigen CD94 (NK cell receptor) (Killer cell lectin-like receptor subfamily D m ...	0.27	-	nuc	1 *	Membrane; single-pass type II membrane protein				179
Q15491 UniProt NPD GO	SMDF_HUMAN	Neuregulin-1, sensory and motor neuron-derived factor isoform	0.27	-	nuc	1	Secreted protein. May possess an internal uncleaved signal sequence	membrane [NAS]	142445		296
Q28143 UniProt NPD GO	NRX3B_BOVIN	Neurexin-3-beta precursor (Neurexin III-beta)	0.27	-	nuc	1	Isoform 1, isoform 2: Cell membrane; single-pass type I membrane protein (Potential). Isoform 3, iso ...				456
Q61199 UniProt NPD GO	NXPH2_MOUSE	Neurexophilin-2 precursor	0.27	-	exc	0	Secreted protein (Potential)				261
Q16982 UniProt NPD GO	NECX_APLCA	Neurocalcin	0.27	-	nuc	0					192
Q8NFZ4 UniProt NPD GO	NLGN2_HUMAN	Neuroligin-2 precursor	0.27	-	end	1	Membrane; single-pass type I membrane protein (Potential)	postsynaptic membrane [NAS]	606479		835
Q2T9U8 UniProt NPD GO	NEUB_BOVIN	Neuromedin B-32 precursor [Contains: Neuromedin B]	0.27	-	exc	1 *	Secreted protein (By similarity)				121
Q9ERK7 UniProt NPD GO	ACHB2_MOUSE	Neuronal acetylcholine receptor protein subunit beta-2 precursor	0.27	+	end	4 *	Membrane; multi-pass membrane protein				501
Q99J85 UniProt NPD GO	NPTXR_MOUSE	Neuronal pentraxin receptor	0.27	-	end	1 *	Membrane; single-pass type II membrane protein (Potential)				493
O35375 UniProt NPD GO	NRP2_MOUSE	Neuropilin-2 precursor (Vascular endothelial cell growth factor 165 receptor 2)	0.27	-	nuc	1	Membrane; single-pass type I membrane protein	plasma membrane [IC]			931
O35276 UniProt NPD GO	NRP2_RAT	Neuropilin-2 precursor (Vascular endothelial cell growth factor 165 receptor 2)	0.27	-	nuc	1	Membrane; single-pass type I membrane protein				925
Q61955 UniProt NPD GO	NRPN_MOUSE	Neuropsin precursor (EC 3.4.21.-) (NP) (Kallikrein-8)	0.27	-	exc	0	Secreted protein			1NPM	260
Q5G266 UniProt NPD GO	NETR_TRAPH	Neurotrypsin precursor (EC 3.4.21.-)	0.27	-	end	0	Secreted protein				875
Q9CQM0 UniProt NPD GO	NICN1_MOUSE	Nicolin-1	0.27	-	mit	0	Nucleus (By similarity)				213

You are viewing entries 43401 to 43450 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.