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
O35147 UniProt NPD GO	BAD_RAT	Bcl2 antagonist of cell death (BAD) (Bcl-2-binding component 6) (Bcl-xL/Bcl-2-associated death promo ...	0.51	-	nuc	0	Mitochondrion; mitochondrial outer membrane (By similarity). Cytoplasm (By similarity). Upon phospho ...				205
Q9VCE1 UniProt NPD GO	BCN1_DROME	Beclin-1-like protein (Autophagy protein 6-like) (APG6-like)	0.51	-	cyt	0					422
O76090 UniProt NPD GO	VMD2_HUMAN	Bestrophin-1 (Vitelliform macular dystrophy protein 2) (TU15B)	0.51	-	end	4 *	Cell membrane; multi-pass membrane protein	basolateral plasma membrane [IDA] integral to membrane [TAS] membrane fraction [TAS]	608161		585
O12972 UniProt NPD GO	RFNG_CHICK	Beta-1,3-N-acetylglucosaminyltransferase radical fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-ac ...	0.51	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				372
Q96L58 UniProt NPD GO	B3GT6_HUMAN	Beta-1,3-galactosyltransferase 6 (EC 2.4.1.134) (beta 3GalT6) (Galactosylxylosylprotein 3-beta-galac ...	0.51	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein	Golgi medial cisterna [IDA]			329
P35223 UniProt NPD GO	CTNB_TRIGR	Beta-catenin	0.51	-	nuc	0					820
Q5IAB9 UniProt NPD GO	D104A_PANTR	Beta-defensin 104A precursor (Defensin, beta 104A) (Defensin, beta 104) (Beta-defensin 4) (DEFB-4) ( ...	0.51	-	exc	0	Secreted protein (By similarity)				72
Q29074 UniProt NPD GO	NGF_PIG	Beta-nerve growth factor precursor (Beta-NGF) (Fragment)	0.51	-	nuc	0	Secreted protein				229
Q9EQH7 UniProt NPD GO	NDST3_MOUSE	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.51	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				873
Q90751 UniProt NPD GO	BMP2_CHICK	Bone morphogenetic protein 2 precursor (BMP-2) (Fragment)	0.51	-	nuc	0	Secreted protein (By similarity)				353
Q29607 UniProt NPD GO	BMP4_DAMDA	Bone morphogenetic protein 4 precursor (BMP-4)	0.51	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				408
P49003 UniProt NPD GO	BMP5_MOUSE	Bone morphogenetic protein 5 precursor (BMP-5)	0.51	-	cyt	0	Secreted protein (By similarity)				452
P51908 UniProt NPD GO	ABEC1_MOUSE	C->U-editing enzyme APOBEC-1 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme 1)	0.51	-	mit	0					229
P27577 UniProt NPD GO	ETS1_MOUSE	C-ets-1 protein (p54)	0.51	+	nuc	0	Nucleus	nucleus [ISS]		1R36	440
O18906 UniProt NPD GO	CD226_MACMU	CD226 antigen precursor (Platelet and T-cell activation antigen 1)	0.51	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				336
P49593 UniProt NPD GO	PPM1F_HUMAN	Ca(2+)/calmodulin-dependent protein kinase phosphatase (EC 3.1.3.16) (CaM-kinase phosphatase) (CaMKP ...	0.51	-	cyt	0					454
P01263 UniProt NPD GO	CALC1_ONCKE	Calcitonin-1 precursor	0.51	-	nuc	0	Secreted protein			2GLH	136
P50477 UniProt NPD GO	CANA_CANEN	Canavalin precursor	0.51	-	exc	1 *				2CAV	445
O94168 UniProt NPD GO	SNF1_CANTR	Carbon catabolite derepressing protein kinase (EC 2.7.11.1)	0.51	-	nuc	0	Nucleus; nuclear membrane; peripheral membrane protein (By similarity)				619
P09620 UniProt NPD GO	KEX1_YEAST	Carboxypeptidase KEX1 precursor (EC 3.4.16.6) (Carboxypeptidase D)	0.51	-	nuc	1		Golgi trans face [IDA]		1AC5	729
P52826 UniProt NPD GO	CACP_COLLI	Carnitine O-acetyltransferase precursor (EC 2.3.1.7) (Carnitine acetylase) (CAT) (Carnitine acetyltr ...	0.51	-	pox	0	Endoplasmic reticulum (Potential). Peroxisome (Potential). Mitochondrion; mitochondrial inner membra ...				627
Q62761 UniProt NPD GO	KC1G1_RAT	Casein kinase I isoform gamma-1 (EC 2.7.11.1) (CKI-gamma 1)	0.51	-	nuc	0	Cytoplasm				390
P29452 UniProt NPD GO	CASP1_MOUSE	Caspase-1 precursor (EC 3.4.22.36) (CASP-1) (Interleukin-1 beta convertase) (IL-1BC) (IL-1 beta-conv ...	0.51	-	cyt	0	Cytoplasm	cytoplasm [TAS] extracellular region [IDA]			402
Q4V862 UniProt NPD GO	CDK9A_XENLA	Cell division protein kinase 9-A (EC 2.7.11.22) (EC 2.7.11.23) (Cyclin-dependent kinase 9-A)	0.51	-	cyt	0	Nucleus (By similarity)				376
O43264 UniProt NPD GO	ZW10_HUMAN	Centromere/kinetochore protein zw10 homolog	0.51	-	nuc	0	Cytoplasm. Dynamic pattern of localization during the cell cycle. In most cells at interphase, prese ...	endoplasmic reticulum [IDA] kinetochore [TAS] kinetochore microtubule [IDA] nucleus [NAS] spindle pole [IDA]	603954		778
Q9ZSY2 UniProt NPD GO	DNJ15_ARATH	Chaperone protein dnaJ 15 (Protein ALTERED RESPONSE TO GRAVITY) (AtARG1) (AtJ15) (AtDjB15)	0.51	-	nuc	0	Membrane; peripheral membrane protein. Found in endoplasmic reticulum, Golgi, vesicles near the plas ...				410
Q6B8X2 UniProt NPD GO	RR13_GRATL	Chloroplast 30S ribosomal protein S13	0.51	-	nuc	0	Plastid; chloroplast				126
P49501 UniProt NPD GO	RR13_ODOSI	Chloroplast 30S ribosomal protein S13	0.51	-	nuc	0	Plastid; chloroplast				123
P49502 UniProt NPD GO	RR14_ODOSI	Chloroplast 30S ribosomal protein S14	0.51	-	nuc	0	Plastid; chloroplast				100
P56805 UniProt NPD GO	RR15_ARATH	Chloroplast 30S ribosomal protein S15	0.51	-	nuc	0	Plastid; chloroplast				88
Q9BBS6 UniProt NPD GO	RR2_LOTJA	Chloroplast 30S ribosomal protein S2	0.51	-	cyt	0	Plastid; chloroplast				236
Q85AX4 UniProt NPD GO	RR4_ANTFO	Chloroplast 30S ribosomal protein S4	0.51	-	mit	0	Plastid; chloroplast				202
Q7YJX0 UniProt NPD GO	RR4_CALFE	Chloroplast 30S ribosomal protein S4	0.51	-	mit	0	Plastid; chloroplast				201
P59137 UniProt NPD GO	RR4_CATCI	Chloroplast 30S ribosomal protein S4	0.51	-	mit	0	Plastid; chloroplast				202
Q4VZH3 UniProt NPD GO	RR4_CUCSA	Chloroplast 30S ribosomal protein S4	0.51	-	mit	0	Plastid; chloroplast				201
Q6H9K4 UniProt NPD GO	RR4_EQUSY	Chloroplast 30S ribosomal protein S4	0.51	-	nuc	0	Plastid; chloroplast				207
Q49KZ6 UniProt NPD GO	RR4_EUCGG	Chloroplast 30S ribosomal protein S4	0.51	-	mit	0	Plastid; chloroplast				201
P59145 UniProt NPD GO	RR4_HYPLA	Chloroplast 30S ribosomal protein S4	0.51	-	mit	0	Plastid; chloroplast				202
Q2PMU5 UniProt NPD GO	RR4_SOYBN	Chloroplast 30S ribosomal protein S4	0.51	-	mit	0	Plastid; chloroplast				201
O20254 UniProt NPD GO	RR4_LIBFO	Chloroplast 30S ribosomal protein S4 (Fragment)	0.51	-	nuc	0	Plastid; chloroplast				182
Q67IL8 UniProt NPD GO	RR7_ANACO	Chloroplast 30S ribosomal protein S7	0.51	-	nuc	0	Plastid; chloroplast				155
Q7HKW9 UniProt NPD GO	RR7_CALFE	Chloroplast 30S ribosomal protein S7	0.51	-	nuc	0	Plastid; chloroplast				155
Q9GFM6 UniProt NPD GO	RR7_CALFL	Chloroplast 30S ribosomal protein S7	0.51	-	nuc	0	Plastid; chloroplast				155
Q67IG9 UniProt NPD GO	RR7_COECR	Chloroplast 30S ribosomal protein S7	0.51	-	nuc	0	Plastid; chloroplast				155
Q6EM99 UniProt NPD GO	RR7_EUOAL	Chloroplast 30S ribosomal protein S7	0.51	-	nuc	0	Plastid; chloroplast				155
Q9B1A1 UniProt NPD GO	RR7_LOTJA	Chloroplast 30S ribosomal protein S7	0.51	-	nuc	0	Plastid; chloroplast				155
P51331 UniProt NPD GO	RK19_PORPU	Chloroplast 50S ribosomal protein L19	0.51	-	cyt	0	Plastid; chloroplast				123
Q8M9U7 UniProt NPD GO	RK2_CHAGL	Chloroplast 50S ribosomal protein L2	0.51	-	nuc	0	Plastid; chloroplast				275
P49545 UniProt NPD GO	RK2_ODOSI	Chloroplast 50S ribosomal protein L2	0.51	+	mit	0	Plastid; chloroplast				275
Q6END4 UniProt NPD GO	RK22_ORYNI	Chloroplast 50S ribosomal protein L22	0.51	-	nuc	0	Plastid; chloroplast				149

You are viewing entries 24201 to 24250 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.