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
P15600 UniProt NPD GO	NUGM_PARTE	NADH-ubiquinone oxidoreductase subunit 9 (EC 1.6.5.3) (EC 1.6.99.3) (Protein P1)	0.24	-	cyt	0	Mitochondrion; mitochondrial inner membrane				209
Q924V1 UniProt NPD GO	NOX4_RAT	NADPH oxidase 4 (EC 1.6.3.-) (Kidney superoxide-producing NADPH oxidase) (Kox-1)	0.24	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Cell membrane; m ...				578
Q9V3T9 UniProt NPD GO	ADRO_DROME	NADPH:adrenodoxin oxidoreductase, mitochondrial precursor (EC 1.18.1.2) (Adrenodoxin reductase) (AR) ...	0.24	-	nuc	0	Mitochondrion; mitochondrial matrix				466
Q7ZVX6 UniProt NPD GO	UBA3_BRARE	NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) (Ubiquitin-activating enzyme 3) (NEDD8-act ...	0.24	+	cyt	0					462
Q9VSF3 UniProt NPD GO	UBC12_DROME	NEDD8-conjugating enzyme Ubc12 (EC 6.3.2.-) (NEDD8 protein ligase) (NEDD8 carrier protein)	0.24	-	nuc	0					181
P56965 UniProt NPD GO	DDAH1_BOVIN	NG,NG-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18) (Dimethylargininase-1) (Dimethylargini ...	0.24	-	mit	0				2CI7	284
P61252 UniProt NPD GO	NKG2D_MACFA	NKG2-D type II integral membrane protein (NKG2-D-activating NK receptor) (NK cell receptor D) (Kille ...	0.24	-	nuc	1	Membrane; single-pass type II membrane protein (By similarity)				216
Q9MZJ7 UniProt NPD GO	NKG2D_MACMU	NKG2-D type II integral membrane protein (NKG2-D-activating NK receptor) (NK cell receptor D) (Kille ...	0.24	-	nuc	1	Membrane; single-pass type II membrane protein				216
Q60817 UniProt NPD GO	NACA_MOUSE	Nascent polypeptide-associated complex subunit alpha (Alpha-NAC) (Alpha-NAC/1.9.2)	0.24	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			215
Q5E9A1 UniProt NPD GO	NACA_BOVIN	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC)	0.24	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Also found in nucleus (By similar ...				215
Q5R9I9 UniProt NPD GO	NACA_PONPY	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC)	0.24	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Also found in nucleus (By similar ...				215
Q13765 UniProt NPD GO	NACA_HUMAN	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC) (Hom s 2.02)	0.24	-	nuc	0	Cytoplasm. Predominantly. Nucleus. Also found in nucleus	cytoplasm [TAS] nascent polypeptide-associated complex [TAS]	601234		215
P07634 UniProt NPD GO	ANFB_PIG	Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic pepti ...	0.24	-	exc	0	Secreted protein				131
Q8R4G0 UniProt NPD GO	NTNG1_MOUSE	Netrin G1 precursor (Laminet-1)	0.24	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [IDA] plasma membrane [IDA]			539
P13595 UniProt NPD GO	NCA11_MOUSE	Neural cell adhesion molecule 1, 180 kDa isoform precursor (N-CAM 180) (NCAM-180)	0.24	-	end	2	Membrane; single-pass type I membrane protein				1115
Q9DDD0 UniProt NPD GO	NRX1A_CHICK	Neurexin-1-alpha (Neurexin I-alpha) (Fragment)	0.24	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				1363
P30926 UniProt NPD GO	ACHB4_HUMAN	Neuronal acetylcholine receptor protein subunit beta-4 precursor	0.24	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]	118509		498
P70310 UniProt NPD GO	NTR2_MOUSE	Neurotensin receptor type 2 (NT-R-2) (Low-affinity levocabastine-sensitive neurotensin receptor) (NT ...	0.24	-	end	4 *	Membrane; multi-pass membrane protein				417
O42893 UniProt NPD GO	TREA_SCHPO	Neutral trehalase (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.24	-	cyt	0	Cytoplasm (By similarity)				735
P32356 UniProt NPD GO	TREA_YEAST	Neutral trehalase (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.24	-	cyt	0	Cytoplasm	cytoplasm [IDA] cytosol [TAS]			751
Q9BSH3 UniProt NPD GO	NICN1_HUMAN	Nicolin-1 (NPCEDRG)	0.24	-	mit	0	Nucleus				213
Q6T3U3 UniProt NPD GO	NPCL1_RAT	Niemann-Pick C1-like protein 1 precursor	0.24	-	end	13	Cell membrane; apical cell membrane; multi-pass membrane protein. Cell membrane; multi-pass membrane ...				1331
P39869 UniProt NPD GO	NIA_LOTJA	Nitrate reductase [NADH] (EC 1.7.1.1) (NR)	0.24	-	cyt	0					900
Q9I9M2 UniProt NPD GO	NOS_SQUAC	Nitric-oxide synthase (EC 1.14.13.39) (NOS) (Fragment)	0.24	-	cyt	0					212
P46011 UniProt NPD GO	NRL4_ARATH	Nitrilase 4 (EC 3.5.5.1)	0.24	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Tightly associated with the plasma mem ...				355
Q7YS54 UniProt NPD GO	DFNA5_HORSE	Non-syndromic hearing impairment protein 5 homolog	0.24	+	nuc	0					497
P18437 UniProt NPD GO	HMGN2_RAT	Nonhistone chromosomal protein HMG-17 (High-mobility group nucleosome-binding domain-containing prot ...	0.24	+	nuc	0	Nucleus				89
Q9XVS8 UniProt NPD GO	NXF2_CAEEL	Nuclear RNA export factor 2	0.24	-	nuc	0	Nucleus. Not localized at the nuclear rim				421
P97947 UniProt NPD GO	SHP_RAT	Nuclear receptor 0B2 (Orphan nuclear receptor SHP) (Small heterodimer partner)	0.24	-	mit	0	Nucleus (Probable)			1ZH7	260
Q75AA5 UniProt NPD GO	NTF2_ASHGO	Nuclear transport factor 2 (NTF-2)	0.24	-	cyt	0	Cytoplasm (By similarity)				125
P33331 UniProt NPD GO	NTF2_YEAST	Nuclear transport factor 2 (NTF-2) (Nuclear transport factor P10)	0.24	-	cyt	0	Cytoplasm	nuclear envelope [IDA]		1GYB	125
P81204 UniProt NPD GO	NUC1_SYNRA	Nuclease precursor (EC 3.1.30.-) (Sr-nuclease)	0.24	-	nuc	1 *	Secreted protein				320
P05221 UniProt NPD GO	NUPL_XENLA	Nucleoplasmin	0.24	+	nuc	0	Nucleus			1K5J	200
O75414 UniProt NPD GO	NDK6_HUMAN	Nucleoside diphosphate kinase 6 (EC 2.7.4.6) (NDK 6) (NDP kinase 6) (nm23-H6) (Inhibitor of p53-indu ...	0.24	-	cyt	0			608294		186
Q9CWD3 UniProt NPD GO	NUD17_MOUSE	Nucleoside diphosphate-linked moiety X motif 17, mitochondrial precursor (EC 3.6.1.-) (Nudix motif 1 ...	0.24	-	cyt	0	Mitochondrion (Potential)				296
Q8CH40 UniProt NPD GO	NUDT6_MOUSE	Nucleoside diphosphate-linked moiety X motif 6 (Nudix motif 6) (Antisense basic fibroblast growth fa ...	0.24	-	mit	0					313
Q9ULW6 UniProt NPD GO	NP1L2_HUMAN	Nucleosome assembly protein 1-like 2 (Brain-specific protein, X-linked)	0.24	-	cyt	0	Nucleus (Probable)	chromatin assembly complex [TAS] nucleus [TAS]	300026		460
P51860 UniProt NPD GO	NP1L2_MOUSE	Nucleosome assembly protein 1-like 2 (Brain-specific protein, X-linked)	0.24	-	nuc	0	Nucleus (Probable)				460
P93740 UniProt NPD GO	NUD23_ARATH	Nudix hydrolase 23, chloroplast precursor (EC 3.6.1.-) (AtNUDT23)	0.24	-	mit	0	Plastid; chloroplast (Potential)				280
P41217 UniProt NPD GO	OX2G_HUMAN	OX-2 membrane glycoprotein precursor (CD200 antigen)	0.24	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	155970		278
O54901 UniProt NPD GO	OX2G_MOUSE	OX-2 membrane glycoprotein precursor (MRC OX-2 antigen) (CD200 antigen)	0.24	-	end	1	Membrane; single-pass type I membrane protein				278
P04218 UniProt NPD GO	OX2G_RAT	OX-2 membrane glycoprotein precursor (MRC OX-2 antigen) (CD200 antigen)	0.24	-	end	1	Membrane; single-pass type I membrane protein				278
P81910 UniProt NPD GO	OR22B_DROME	Odorant receptor 22b	0.24	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	dendrite [IDA] integral to membrane [NAS]			397
P47887 UniProt NPD GO	OR1E2_HUMAN	Olfactory receptor 1E2 (Olfactory receptor 17-93/17-135/17-136) (OR17-93) (OR17-135) (OR17-136)	0.24	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			323
Q8NGG4 UniProt NPD GO	OR8H1_HUMAN	Olfactory receptor 8H1	0.24	-	end	6 *	Membrane; multi-pass membrane protein				311
Q21219 UniProt NPD GO	OPT2_CAEEL	Oligopeptide transporter 2 (Di-/tri-peptide transporter CPTB)	0.24	-	end	10	Membrane; multi-pass membrane protein (Potential)	apical plasma membrane [IDA]			835
P02865 UniProt NPD GO	GDO_TRIMO	Omega-gliadin (Fragment)	0.24	-	nuc	0					28
Q9XZK2 UniProt NPD GO	CXSO3_CONST	Omega-type conotoxin SO3 precursor (SO-3)	0.24	-	nuc	0	Secreted protein (By similarity)			1FYG	71
Q9UMX2 UniProt NPD GO	OAZ3_HUMAN	Ornithine decarboxylase antizyme 3 (ODC-Az 3) (AZ3)	0.24	-	nuc	0	Nucleus. Cytoplasm (By similarity)		605138		187
P04641 UniProt NPD GO	OSTC_MOUSE	Osteocalcin precursor (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.24	-	exc	0	Secreted protein				95

You are viewing entries 46551 to 46600 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.