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
Q8L850 UniProt NPD GO	PI5K9_ARATH	Phosphatidylinositol-4-phosphate 5-kinase 9 (EC 2.7.1.68) (AtPIP5K9) (1-phosphatidylinositol-4-phosp ...	0.48	+	cyt	0					815
O55012 UniProt NPD GO	PICA_RAT	Phosphatidylinositol-binding clathrin assembly protein (Clathrin assembly lymphoid myeloid leukemia ...	0.48	-	nuc	0	Cell membrane (By similarity). Clathrin-coated areas of the plasma membrane. Golgi apparatus (By sim ...	coated pit [ISS]		1HG5	640
Q75W16 UniProt NPD GO	AROG_ORYSA	Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplast precursor (EC 2.5.1.54) (Phospho-2-keto-3 ...	0.48	+	mit	0	Plastid; chloroplast (Potential)				539
Q05017 UniProt NPD GO	PHLX_RABIT	Phospholipase AdRab-B precursor (EC 3.1.-.-)	0.48	-	end	1	Cell membrane; single-pass type I membrane protein. Brush border				1458
Q40762 UniProt NPD GO	PHY_PICAB	Phytochrome	0.48	-	mit	0					1136
P42499 UniProt NPD GO	PHYB_SOYBN	Phytochrome B	0.48	-	nuc	0					1156
P30060 UniProt NPD GO	RR12_EPIVI	Plastid 30S ribosomal protein S12	0.48	-	mit	0	Plastid				124
Q05028 UniProt NPD GO	PDGFB_RAT	Platelet-derived growth factor B chain precursor (PDGF B-chain) (Platelet-derived growth factor beta ...	0.48	-	nuc	0					225
P31240 UniProt NPD GO	PDGFB_MOUSE	Platelet-derived growth factor B chain precursor (PDGF B-chain) (Platelet-derived growth factor beta ...	0.48	-	exc	0					241
P70207 UniProt NPD GO	PLXA2_MOUSE	Plexin-A2 precursor (Plexin-2) (Plex 2)	0.48	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1884
Q9HCM2 UniProt NPD GO	PLXA4_HUMAN	Plexin-A4 precursor	0.48	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)		604280		1894
Q80UG2 UniProt NPD GO	PLXA4_MOUSE	Plexin-A4 precursor	0.48	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				1893
Q9Z0T6 UniProt NPD GO	PKDRE_MOUSE	Polycystic kidney disease and receptor for egg jelly-related protein precursor (PKD and REJ homolog) ...	0.48	-	end	13	Membrane; multi-pass membrane protein (Potential)				2126
Q8R5I0 UniProt NPD GO	KCNKF_RAT	Potassium channel subfamily K member 15 (Acid-sensitive potassium channel protein TASK-5) (TWIK-rela ...	0.48	-	end	5 *	Membrane; multi-pass membrane protein				318
Q03719 UniProt NPD GO	KCND1_MOUSE	Potassium voltage-gated channel subfamily D member 1 (Voltage-gated potassium channel subunit Kv4.1) ...	0.48	-	end	5	Membrane; multi-pass membrane protein				651
Q03772 UniProt NPD GO	CWC15_YEAST	Pre-mRNA-splicing factor CWC15 (Complexed with CEF1 protein 15)	0.48	-	nuc	0	Nucleus (Probable)	spliceosome complex [IPI]			175
Q6FNR8 UniProt NPD GO	CWC2_CANGA	Pre-mRNA-splicing factor CWC2	0.48	-	nuc	0	Nucleus (By similarity)				306
Q5ACW2 UniProt NPD GO	CWC24_CANAL	Pre-mRNA-splicing factor CWC24	0.48	-	nuc	0	Nucleus (By similarity)				216
Q51LS1 UniProt NPD GO	ISY1_MAGGR	Pre-mRNA-splicing factor ISY1	0.48	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				246
Q9DC48 UniProt NPD GO	PRP17_MOUSE	Pre-mRNA-splicing factor PRP17 (Cell division cycle 40 homolog)	0.48	-	nuc	0	Nucleus (By similarity)				579
Q9P7R9 UniProt NPD GO	SYF1_SCHPO	Pre-mRNA-splicing factor syf1 (Complexed with cdc5 protein 3) (Cell cycle control protein cwf3)	0.48	-	cyt	0	Nucleus (By similarity)	spliceosome complex [IDA]			790
Q5RCG9 UniProt NPD GO	PFD3_PONPY	Prefoldin subunit 3 (Von Hippel-Lindau-binding protein 1) (VHL-binding protein 1) (VBP-1)	0.48	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). In complex with VHL can translocate to the nucle ...				197
P61758 UniProt NPD GO	PFD3_HUMAN	Prefoldin subunit 3 (Von Hippel-Lindau-binding protein 1) (VHL-binding protein 1) (VBP-1) (HIBBJ46)	0.48	+	nuc	0	Cytoplasm. Nucleus. In complex with VHL can translocate to the nucleus		300133		197
Q29S22 UniProt NPD GO	DDX47_BOVIN	Probable ATP-dependent RNA helicase DDX47 (EC 3.6.1.-) (DEAD box protein 47)	0.48	+	cyt	0	Nucleus; nucleolus (By similarity)				457
Q96C10 UniProt NPD GO	LGP2_HUMAN	Probable ATP-dependent helicase LGP2 (EC 3.6.1.-) (Protein D11Lgp2 homolog)	0.48	-	cyt	0	Cytoplasm (By similarity)		608588		678
Q9LYJ9 UniProt NPD GO	RH46_ARATH	Probable DEAD-box ATP-dependent RNA helicase 46 (EC 3.6.1.-)	0.48	-	nuc	0					645
P22373 UniProt NPD GO	DPOM_CLAPU	Probable DNA polymerase (EC 2.7.7.7)	0.48	-	cyt	0					1063
Q9M8Y0 UniProt NPD GO	SEC_ARATH	Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SEC (EC 2.4.1.-) (Protein ...	0.48	-	nuc	0					977
Q84WF5 UniProt NPD GO	VAMPL_ARATH	Probable VAMP-like protein At1g33485	0.48	-	nuc	1					255
Q93WV4 UniProt NPD GO	WRK71_ARATH	Probable WRKY transcription factor 71 (WRKY DNA-binding protein 71)	0.48	-	nuc	0	Nucleus (Probable)				282
Q8GYY0 UniProt NPD GO	1A112_ARATH	Probable aminotransferase ACS12 (EC 2.6.1.-)	0.48	-	mit	1 *				2GEA	495
Q8IIJ9 UniProt NPD GO	CATC_PLAF7	Probable cathepsin C precursor (EC 3.4.22.-)	0.48	-	mit	1 *	Lysosome				700
Q9V6H1 UniProt NPD GO	CP9H1_DROME	Probable cytochrome P450 9h1 (EC 1.14.-.-) (CYPIXH1)	0.48	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				518
Q04647 UniProt NPD GO	CCBS_DAUCA	Probable cytochrome c biosynthesis protein	0.48	-	end	3 *					579
Q19000 UniProt NPD GO	BODG_CAEEL	Probable gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine,2-oxoglutarate dioxygen ...	0.48	-	mit	0					421
Q751Z6 UniProt NPD GO	SPC25_ASHGO	Probable kinetochore protein SPC25	0.48	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				231
P91869 UniProt NPD GO	MED31_CAEEL	Probable mediator of RNA polymerase II transcription subunit 31 (Mediator complex subunit 31) (Media ...	0.48	-	nuc	0					163
Q9VZD5 UniProt NPD GO	RT06_DROME	Probable mitochondrial 28S ribosomal protein S6 (MRP-S6)	0.48	-	cyt	0	Mitochondrion				147
Q93Z25 UniProt NPD GO	PEL22_ARATH	Probable pectate lyase 22 precursor (EC 4.2.2.2)	0.48	-	mit	1 *					432
Q03533 UniProt NPD GO	KM8S_YEAST	Probable serine/threonine-protein kinase YMR291W (EC 2.7.11.1)	0.48	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			586
Q09738 UniProt NPD GO	UBP8_SCHPO	Probable ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) (Ubiquitin thioesterase 8) (Ubiquitin ...	0.48	-	cyt	0					449
Q91094 UniProt NPD GO	PRLR_MELGA	Prolactin receptor precursor (PRL-R) (TPRLR)	0.48	-	exc	1 *	Membrane; single-pass type I membrane protein				831
P09319 UniProt NPD GO	PRL1_OREMO	Prolactin-1 precursor (Prolactin I) (PRL-188)	0.48	-	exc	0	Secreted protein				212
Q99935 UniProt NPD GO	PROL1_HUMAN	Proline-rich protein 1 precursor (PRL1) (Basic proline-rich lacrimal protein)	0.48	-	exc	0	Secreted protein		608936		201
Q8N7Y1 UniProt NPD GO	PRR10_HUMAN	Proline-rich protein 10	0.48	-	nuc	0					241
P43116 UniProt NPD GO	PE2R2_HUMAN	Prostaglandin E2 receptor, EP2 subtype (Prostanoid EP2 receptor) (PGE receptor, EP2 subtype)	0.48	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	176804		358
Q8K3A6 UniProt NPD GO	ARMX6_MOUSE	Protein ARMCX6	0.48	-	exc	0					301
O80931 UniProt NPD GO	ASL1_ARATH	Protein ASYMMETRIC LEAVES1 (Myb-related protein 91) (AtMYB91) (Protein PHANTASTICA)	0.48	-	nuc	0	Nucleus (By similarity)				367
P34730 UniProt NPD GO	BMH2_YEAST	Protein BMH2	0.48	-	nuc	0		nucleus [IDA]			272
Q9NZ38 UniProt NPD GO	CJ110_HUMAN	Protein C10orf110	0.48	-	nuc	0					188

You are viewing entries 26451 to 26500 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.