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
P33270 UniProt NPD GO	CP6A2_DROME	Cytochrome P450 6a2 (EC 1.14.-.-) (CYPVIA2) (P450-B1)	0.19	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				506
Q27593 UniProt NPD GO	CP6A8_DROME	Cytochrome P450 6a8 (EC 1.14.-.-) (CYPVIA8)	0.19	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				506
Q964R0 UniProt NPD GO	CP6K1_BLAGE	Cytochrome P450 6k1 (EC 1.14.-.-) (CYPVIK1)	0.19	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				524
Q9STK7 UniProt NPD GO	C71AQ_ARATH	Cytochrome P450 71A26 (EC 1.14.-.-)	0.19	-	end	1 *					489
O65782 UniProt NPD GO	C83B1_ARATH	Cytochrome P450 83B1 (EC 1.14.-.-)	0.19	-	nuc	0					499
Q62737 UniProt NPD GO	CY24A_RAT	Cytochrome b-245 light chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 22 kDa polypeptid ...	0.19	-	end	3 *					191
P09437 UniProt NPD GO	CYB2_HANAN	Cytochrome b2, mitochondrial precursor (EC 1.1.2.3) (L-lactate dehydrogenase [Cytochrome]) (L-lactat ...	0.19	-	mit	0	Mitochondrion; mitochondrial intermembrane space				573
P14622 UniProt NPD GO	COX82_BOVIN	Cytochrome c oxidase polypeptide VIII-liver, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.19	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				69
Q7YRK7 UniProt NPD GO	COX6C_TARSY	Cytochrome c oxidase polypeptide VIc precursor (EC 1.9.3.1)	0.19	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				75
P20374 UniProt NPD GO	COX1_APILI	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.19	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				521
P00429 UniProt NPD GO	CX6B1_BOVIN	Cytochrome c oxidase subunit VIb isoform 1 (EC 1.9.3.1) (COX VIb-1) (Cytochrome c oxidase polypeptid ...	0.19	-	nuc	0	Mitochondrion; mitochondrial intermembrane space			2OCC	85
Q6BKY9 UniProt NPD GO	CCPR_DEBHA	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.19	-	mit	1 *					360
O75462 UniProt NPD GO	CRLF1_HUMAN	Cytokine receptor-like factor 1 precursor (Cytokine-like factor 1) (CLF-1) (ZcytoR5)	0.19	-	nuc	0	Secreted protein	extracellular space [TAS]	604237		422
Q9ZQ99 UniProt NPD GO	COGT1_ARATH	Cytokinin-O-glucosyltransferase 1 (EC 2.4.1.-) (Zeatin O-glucosyltransferase 1) (AtZOG1)	0.19	-	cyt	0					491
Q62698 UniProt NPD GO	DC1L2_RAT	Cytoplasmic dynein 1 light intermediate chain 2 (Dynein light intermediate chain 2, cytosolic) (LIC5 ...	0.19	-	cyt	0		cytoplasmic dynein complex [TAS]			497
P30729 UniProt NPD GO	DRD4_RAT	D(4) dopamine receptor (Dopamine D4 receptor) (D(2C) dopamine receptor)	0.19	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [NAS]			387
Q12743 UniProt NPD GO	DFM1_YEAST	DER1-like family member protein 1	0.19	-	mit	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			341
Q32001 UniProt NPD GO	DNE1_CHLHU	DNA endonuclease I-ChuI (EC 3.1.-.-)	0.19	-	cyt	0	Plastid; chloroplast				218
P46957 UniProt NPD GO	DPOD2_YEAST	DNA polymerase delta small subunit (EC 2.7.7.7) (Hydroxyurea sensitive protein HYS2)	0.19	-	cyt	0	Nucleus (By similarity)	delta DNA polymerase complex [TAS]			487
O46914 UniProt NPD GO	RPOA_GUITH	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.19	-	cyt	0	Plastid; chloroplast				318
P28000 UniProt NPD GO	RPC19_YEAST	DNA-directed RNA polymerases I and III 16 kDa polypeptide (EC 2.7.7.6) (AC19)	0.19	-	nuc	0	Nucleus	DNA-directed RNA polymerase I complex [TAS] DNA-directed RNA polymerase III complex [TAS]			142
P80154 UniProt NPD GO	DEFI_AESCY	Defensin	0.19	-	nuc	0	Secreted protein				38
Q5G861 UniProt NPD GO	DEF5_PANTR	Defensin 5 precursor (Defensin, alpha 5)	0.19	-	exc	0	Secreted protein				94
P81610 UniProt NPD GO	DEFA_MYTED	Defensin-A	0.19	-	nuc	0	Secreted protein				37
P28640 UniProt NPD GO	DHN2_PEA	Dehydrin DHN2	0.19	-	cyt	0					232
Q9LND9 UniProt NPD GO	ADSL1_ARATH	Delta-9 desaturase-like 1 protein (EC 1.14.19.-)	0.19	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				299
P32321 UniProt NPD GO	DCTD_HUMAN	Deoxycytidylate deaminase (EC 3.5.4.12) (dCMP deaminase)	0.19	-	nuc	0			607638		178
Q5RC69 UniProt NPD GO	DCTD_PONPY	Deoxycytidylate deaminase (EC 3.5.4.12) (dCMP deaminase)	0.19	-	nuc	0					178
Q9QZZ6 UniProt NPD GO	DERM_MOUSE	Dermatopontin precursor (Tyrosine-rich acidic matrix protein) (TRAMP) (Early quiescence protein 1) ( ...	0.19	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				201
O74850 UniProt NPD GO	DGA1_SCHPO	Diacylglycerol O-acyltransferase 1 (EC 2.3.1.20) (Diglyceride acyltransferase)	0.19	-	cyt	1 *	Membrane; multi-pass membrane protein. Localized to lipid particles				345
P52429 UniProt NPD GO	DGKE_HUMAN	Diacylglycerol kinase epsilon (EC 2.7.1.107) (Diglyceride kinase epsilon) (DGK-epsilon) (DAG kinase ...	0.19	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)		601440		567
Q09175 UniProt NPD GO	KRP1_SCHPO	Dibasic-processing endoprotease precursor (EC 3.4.21.-) (KEX2-related protease)	0.19	-	end	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type I membrane prot ...				709
P07807 UniProt NPD GO	DYR_YEAST	Dihydrofolate reductase (EC 1.5.1.3)	0.19	-	cyt	0		cytosol [TAS]			211
Q19749 UniProt NPD GO	ODP2_CAEEL	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochond ...	0.19	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				507
P17347 UniProt NPD GO	DISI_ECHCA	Disintegrin echistatin (Platelet aggregation activation inhibitor) (Carinatin) [Contains: Echistatin ...	0.19	-	nuc	0	Secreted protein			2ECH	49
P31989 UniProt NPD GO	DISI_BOTJA	Disintegrin jararacin (Platelet aggregation activation inhibitor)	0.19	-	nuc	0	Secreted protein				73
Q9QYJ0 UniProt NPD GO	DNJA2_MOUSE	DnaJ homolog subfamily A member 2 (mDj3)	0.19	-	cyt	0	Membrane; lipid-anchor (Potential)				412
Q05052 UniProt NPD GO	OST48_CANFA	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit precursor (EC 2.4.1.11 ...	0.19	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				445
P01002 UniProt NPD GO	IPSG_CANFA	Double-headed protease inhibitor, submandibular gland	0.19	-	nuc	0	Secreted protein				115
Q96T75 UniProt NPD GO	DSCR8_HUMAN	Down syndrome critical region protein 8 (Malignant melanoma-associated protein 1) (MMA-1) (MTAG2 pro ...	0.19	-	nuc	0					97
Q2NKU6 UniProt NPD GO	DPY30_BOVIN	Dpy-30-like protein	0.19	-	nuc	0	Nucleus (By similarity)				99
Q9C005 UniProt NPD GO	DPY30_HUMAN	Dpy-30-like protein	0.19	-	nuc	0	Nucleus (By similarity)				99
Q9UNI6 UniProt NPD GO	DUS12_HUMAN	Dual specificity protein phosphatase 12 (EC 3.1.3.48) (EC 3.1.3.16) (Dual specificity tyrosine phosp ...	0.19	-	cyt	0	Nucleus		604835		340
Q8WTR2 UniProt NPD GO	DUS19_HUMAN	Dual specificity protein phosphatase 19 (EC 3.1.3.48) (EC 3.1.3.16) (Stress-activated protein kinase ...	0.19	-	nuc	0					217
P62627 UniProt NPD GO	DLC2A_MOUSE	Dynein light chain 2A, cytoplasmic	0.19	-	nuc	0	Cytoplasm	cytoplasm [ISS]		1Y4O	95
P62628 UniProt NPD GO	DLC2A_RAT	Dynein light chain 2A, cytoplasmic (Dynein-associated protein Km23) (Bithoraxoid-like protein) (BLP) ...	0.19	-	nuc	0	Cytoplasm	cytoplasm [IDA]			95
Q9LRB7 UniProt NPD GO	EL5_ORYSA	E3 ubiquitin ligase EL5 (EC 6.3.2.-)	0.19	-	nuc	1 *				1IYM	325
Q9UHX3 UniProt NPD GO	EMR2_HUMAN	EGF-like module-containing mucin-like hormone receptor-like 2 precursor (EGF-like module EMR2) (CD31 ...	0.19	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]	606100		823
Q91ZE5 UniProt NPD GO	EMR4_MOUSE	EGF-like module-containing mucin-like hormone receptor-like 4 precursor (EGF-like module-containing ...	0.19	-	end	7	Membrane; multi-pass membrane protein	cell surface [IDA]			689
Q60899 UniProt NPD GO	ELAV2_MOUSE	ELAV-like protein 2 (Hu-antigen B) (HuB) (ELAV-like neuronal protein 1) (Nervous system-specific RNA ...	0.19	-	nuc	0					360

You are viewing entries 51751 to 51800 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.