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
O15439 UniProt NPD GO	MRP4_HUMAN	Multidrug resistance-associated protein 4 (MRP/cMOAT-related ABC transporter) (Multi-specific organi ...	0.31	-	end	11	Membrane; multi-pass membrane protein	membrane fraction [IDA] plasma membrane [IDA] platelet dense granule membrane [IDA]	605250		1325
Q9H1U4 UniProt NPD GO	MEGF9_HUMAN	Multiple epidermal growth factor-like domains 9 precursor (EGF-like domain-containing protein 5) (Mu ...	0.31	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)		604268		600
O14467 UniProt NPD GO	MBF1_YEAST	Multiprotein-bridging factor 1 (Suppressor of frameshift mutations protein 13)	0.31	-	nuc	0	Cytoplasm. Nucleus	mitochondrion [IDA] nucleus [IC]			151
O94321 UniProt NPD GO	MPR1_SCHPO	Multistep phosphorelay regulator 1	0.31	-	nuc	0					295
Q24400 UniProt NPD GO	MLP2_DROME	Muscle LIM protein Mlp84B	0.31	-	nuc	0	Cytoplasm. Nucleus				495
P13854 UniProt NPD GO	MGF_CHICK	Myelomonocytic growth factor precursor (MGF)	0.31	-	end	0	Secreted protein				201
Q13203 UniProt NPD GO	MYBPH_HUMAN	Myosin-binding protein H (MyBP-H) (H-protein)	0.31	-	nuc	0			160795		477
Q8R4E4 UniProt NPD GO	MYOZ3_MOUSE	Myozenin-3 (Calsarcin-3) (FATZ-related protein 3)	0.31	-	nuc	0	Localized at the Z-line of skeletal muscle	Z disc [IDA]			245
Q757N6 UniProt NPD GO	ECO1_ASHGO	N-acetyltransferase ECO1 (EC 2.3.1.-) (Establishment of cohesion protein 1)	0.31	-	mit	0	Nucleus (By similarity)				266
Q7ZVK3 UniProt NPD GO	SIRT2_BRARE	NAD-dependent deacetylase sirtuin-2 (EC 3.5.1.-)	0.31	-	cyt	0					379
P27443 UniProt NPD GO	MAOM_ASCSU	NAD-dependent malic enzyme, mitochondrial precursor (EC 1.1.1.38) (NAD-ME) (Fragment)	0.31	-	mit	0	Mitochondrion; mitochondrial matrix			1O0S	643
Q02367 UniProt NPD GO	NDUB6_BOVIN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.31	-	nuc	1	Mitochondrion; mitochondrial inner membrane; matrix side				127
P03905 UniProt NPD GO	NU4M_HUMAN	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.31	-	end	10 *		respiratory chain complex I (sensu Eukaryota) [NAS]	540000		459
Q9JHI8 UniProt NPD GO	NOX4_MOUSE	NADPH oxidase 4 (EC 1.6.3.-) (Kidney superoxide-producing NADPH oxidase) (Kox-1) (Renal NAD(P)H-oxid ...	0.31	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				578
O54709 UniProt NPD GO	NKG2D_MOUSE	NKG2-D type II integral membrane protein (NKG2-D-activating NK receptor) (NK cell receptor D) (Kille ...	0.31	-	nuc	1	Membrane; single-pass type II membrane protein (By similarity)			1JSK	232
O00634 UniProt NPD GO	NET2_HUMAN	Netrin-2-like protein precursor	0.31	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		602349		580
Q9HCJ2 UniProt NPD GO	NGL1_HUMAN	Netrin-G1 ligand precursor (NGL-1) (Leucine-rich repeat-containing protein 4C)	0.31	-	nuc	2 *	Membrane; single-pass type I membrane protein	integral to membrane [NAS] membrane [IDA]	608817		640
Q9UHF0 UniProt NPD GO	TKNK_HUMAN	Neurokinin-B precursor (NKB) (Neuromedin-K) (Tachykinin-3) (ZNEUROK1)	0.31	-	exc	0	Secreted protein	extracellular space [TAS] soluble fraction [TAS]	162330	1P9F	121
Q69ZK9 UniProt NPD GO	NGLN2_MOUSE	Neuroligin-2 precursor	0.31	-	end	1	Membrane; single-pass type I membrane protein (Potential)	synapse [IDA]			836
Q62888 UniProt NPD GO	NLGN2_RAT	Neuroligin-2 precursor	0.31	-	end	1	Membrane; single-pass type I membrane protein (Potential)				836
P09484 UniProt NPD GO	ACHB2_CHICK	Neuronal acetylcholine receptor protein subunit beta-2 precursor (Neuronal acetylcholine receptor no ...	0.31	-	end	4	Membrane; multi-pass membrane protein				491
Q8K4P2 UniProt NPD GO	NPB_RAT	Neuropeptide B precursor (Preproprotein L7) (rPPL7) [Contains: Neuropeptide B-29 (NPB29) (L7C)]	0.31	-	mit	0	Secreted protein				119
P41321 UniProt NPD GO	NPF_HELAS	Neuropeptide F (NPF)	0.31	-	nuc	0	Secreted protein				39
Q5G271 UniProt NPD GO	NETR_PANTR	Neurotrypsin precursor (EC 3.4.21.-)	0.31	-	end	0	Secreted protein				875
Q6AY91 UniProt NPD GO	NRK1_RAT	Nicotinamide riboside kinase 1 (EC 2.7.1.-)	0.31	-	cyt	0					195
Q14112 UniProt NPD GO	NID2_HUMAN	Nidogen-2 precursor (NID-2) (Osteonidogen)	0.31	-	exc	0	Secreted protein; extracellular space; extracellular matrix	basement membrane [TAS]	605399		1375
P22945 UniProt NPD GO	NIA_EMENI	Nitrate reductase [NADPH] (EC 1.7.1.3) (NR)	0.31	-	mit	1					873
Q711A6 UniProt NPD GO	HMGN2_CANFA	Nonhistone chromosomal protein HMG-17 (High-mobility group nucleosome-binding domain-containing prot ...	0.31	+	nuc	0	Nucleus				89
Q64FT8 UniProt NPD GO	HMGN2_GECJA	Nonhistone chromosomal protein HMG-17 (High-mobility group nucleosome-binding domain-containing prot ...	0.31	+	nuc	0	Nucleus (By similarity)				89
P80272 UniProt NPD GO	HMGN2_PIG	Nonhistone chromosomal protein HMG-17 (High-mobility group nucleosome-binding domain-containing prot ...	0.31	+	nuc	0	Nucleus				89
Q5RAA0 UniProt NPD GO	HMGN2_PONPY	Nonhistone chromosomal protein HMG-17 (High-mobility group nucleosome-binding domain-containing prot ...	0.31	+	nuc	0	Nucleus (By similarity)				89
Q9XVS7 UniProt NPD GO	NXF1_CAEEL	Nuclear RNA export factor 1	0.31	-	cyt	0	Nucleus. Shuttle protein that accumulates in the nucleoplasm and at the nuclear rim				628
Q15466 UniProt NPD GO	SHP_HUMAN	Nuclear receptor 0B2 (Orphan nuclear receptor SHP) (Small heterodimer partner)	0.31	-	mit	0	Nucleus		601665	1YUC	257
Q91V36 UniProt NPD GO	NRBP2_MOUSE	Nuclear receptor-binding protein 2	0.31	-	cyt	0					258
P79084 UniProt NPD GO	ORDA_ASPFL	O-methylsterigmatocystin oxidoreductase (EC 1.14.-.-) (OMST oxidoreductase) (Cytochrome P450 64)	0.31	-	cyt	0					528
Q96R27 UniProt NPD GO	OR2M4_HUMAN	Olfactory receptor 2M4 (Olfactory receptor TPCR100) (OST710) (HTPCRX18) (Olfactory receptor OR1-55)	0.31	+	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			311
P28881 UniProt NPD GO	CXO6B_CONST	Omega-conotoxin SVIB precursor (SNX-183)	0.31	-	exc	1 *	Secreted protein			1MVJ	72
P05483 UniProt NPD GO	CXO7_CONGE	Omega-conotoxins GVIIA/GVIIB (Shaker peptides GVIIA/GVIIB) (SNX-178)	0.31	-	nuc	0	Secreted protein				29
Q9NL82 UniProt NPD GO	ORCKB_PROCL	Orcokinin peptides type B precursor [Contains: Orcomyotropin-like peptide; Orcokinin; Orcokinin-like ...	0.31	-	vac	0	Secreted protein	extracellular region [IC]			266
Q62052 UniProt NPD GO	P_MOUSE	P protein (Melanocyte-specific transporter protein) (Pink-eyed dilution protein)	0.31	-	end	11	Melanosome; melanosomal membrane; multi-pass membrane protein				833
Q96RG2 UniProt NPD GO	PASK_HUMAN	PAS domain-containing serine/threonine-protein kinase (EC 2.7.11.1) (PAS-kinase) (PASKIN) (hPASK)	0.31	-	cyt	0	Cytoplasm		607505	1LL8	1323
O76818 UniProt NPD GO	PBAN_AGRIP	PBAN-type neuropeptides precursor [Contains: Diapause hormone homolog (DH); Alpha-SG neuropeptide; B ...	0.31	-	nuc	0	Secreted protein				193
Q5U3P0 UniProt NPD GO	PCID2_BRARE	PCI domain-containing protein 2 (CSN12-like protein)	0.31	-	cyt	0					399
Q5AL27 UniProt NPD GO	AKR1_CANAL	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.31	-	end	6	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				813
Q6FMP5 UniProt NPD GO	PFA5_CANGA	Palmitoyltransferase PFA5 (EC 2.3.1.-) (Protein fatty acyltransferase 5)	0.31	+	end	4 *	Membrane; multi-pass membrane protein (Potential)				352
Q8C1C8 UniProt NPD GO	PNMA1_MOUSE	Paraneoplastic antigen Ma1 homolog	0.31	+	cyt	0	Nucleus; nucleolus (By similarity)				353
Q9XT35 UniProt NPD GO	PTHY_MACFA	Parathyroid hormone precursor (Parathyrin) (PTH)	0.31	-	nuc	0	Secreted protein				115
Q63425 UniProt NPD GO	PRAX_RAT	Periaxin	0.31	-	nuc	0					1383
Q9LHA7 UniProt NPD GO	PER31_ARATH	Peroxidase 31 precursor (EC 1.11.1.7) (Atperox P31) (ATP41)	0.31	-	exc	0	Secreted protein (By similarity)				316
Q756Q3 UniProt NPD GO	NPC2_ASHGO	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.31	+	mit	0					213

You are viewing entries 39651 to 39700 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.