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
Q9SXB0 UniProt NPD GO	SY125_ARATH	Putative syntaxin-125 (AtSYP125)	0.25	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				298
Q18600 UniProt NPD GO	YTV2_CAEEL	Putative zinc metalloprotease C44B7.11 (EC 3.4.-.-)	0.25	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				824
Q8LF65 UniProt NPD GO	ATL4G_ARATH	RING-H2 finger protein ATL4G (RING-H2 finger protein ATL17)	0.25	-	end	1 *					235
Q9FGJ6 UniProt NPD GO	ATL5M_ARATH	RING-H2 finger protein ATL5M precursor	0.25	-	exc	1 *					166
Q12343 UniProt NPD GO	MED4_YEAST	RNA polymerase II mediator complex subunit 4	0.25	-	nuc	0	Nucleus	mediator complex [IDA]			284
Q3MHX3 UniProt NPD GO	RBM4_BOVIN	RNA-binding protein 4 (RNA-binding motif protein 4) (RNA-binding motif protein 4a)	0.25	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Cytoplasm (By similarity). May undergo ...				362
Q62176 UniProt NPD GO	RNPC1_MOUSE	RNA-binding region-containing protein 1 (ssDNA-binding protein SEB4)	0.25	-	nuc	0					237
Q6Z808 UniProt NPD GO	RAC3_ORYSA	Rac-like GTP-binding protein 3 (OsRac3)	0.25	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				214
Q41254 UniProt NPD GO	RAC9_GOSHI	Rac-like GTP-binding protein RAC9	0.25	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				196
P34726 UniProt NPD GO	RAS2_PHYPO	Ras-like protein 2	0.25	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side. Inner surface of plasma membrane				193
P62823 UniProt NPD GO	RAB3C_MOUSE	Ras-related protein Rab-3C	0.25	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	synaptic vesicle [IDA]			227
P62824 UniProt NPD GO	RAB3C_RAT	Ras-related protein Rab-3C	0.25	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				227
Q9H0N0 UniProt NPD GO	RAB6C_HUMAN	Ras-related protein Rab-6C (Rab6-like protein WTH3)	0.25	-	cyt	0		intracellular [IC]			254
P18754 UniProt NPD GO	RCC1_HUMAN	Regulator of chromosome condensation (Chromosome condensation protein 1) (Cell cycle regulatory prot ...	0.25	-	mit	0	Nucleus. Cytoplasm. Becomes dispersed throughout the cytoplasm during mitosis	condensed nuclear chromosome [IDA] nuclear chromatin [IDA]	179710	1I2M	421
Q8BHD7 UniProt NPD GO	ROD1_MOUSE	Regulator of differentiation 1 (Rod1)	0.25	-	nuc	0					523
Q6DLS0 UniProt NPD GO	RENI_MACFA	Renin precursor (EC 3.4.23.15) (Angiotensinogenase)	0.25	-	end	0	Secreted protein (By similarity). Membrane (By similarity). Associated to membranes via binding to A ...				406
Q6DLW5 UniProt NPD GO	RENI_MACMU	Renin precursor (EC 3.4.23.15) (Angiotensinogenase)	0.25	-	end	0	Secreted protein (By similarity). Membrane (By similarity). Associated to membranes via binding to A ...				406
P82271 UniProt NPD GO	RTD1B_MACMU	Rhesus theta defensin-1/2, subunit B precursor (RTD-1b) (RTD-1 subunit B) (RTD-2) (Demidefensin-1)	0.25	-	exc	0					76
P10281 UniProt NPD GO	RNT2_ASPOR	Ribonuclease T2 precursor (EC 3.1.27.1) (RNase T2)	0.25	-	exc	0					276
P00685 UniProt NPD GO	RNAS1_CHOHO	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.25	-	nuc	0	Secreted protein				128
P00686 UniProt NPD GO	RNAS1_MACRU	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.25	-	nuc	0	Secreted protein				122
Q8VD90 UniProt NPD GO	RNS1G_RATFU	Ribonuclease pancreatic gamma-type precursor (EC 3.1.27.5) (RNase 1 gamma)	0.25	-	nuc	0	Secreted protein (By similarity)				152
Q7YRG8 UniProt NPD GO	RNAS9_CEBAL	Ribonuclease-like protein 9 precursor	0.25	-	exc	0	Secreted protein (Probable)				205
Q863J8 UniProt NPD GO	RNAS9_PAPAN	Ribonuclease-like protein 9 precursor	0.25	-	exc	0	Secreted protein (Probable)				204
P48592 UniProt NPD GO	RIR2_DROME	Ribonucleoside-diphosphate reductase M2 chain (EC 1.17.4.1) (Ribonucleotide reductase small subunit) ...	0.25	-	cyt	1	Cytoplasm				393
Q75F02 UniProt NPD GO	RRF1_ASHGO	Ribosomal recycling factor, mitochondrial precursor	0.25	-	mit	0	Mitochondrion (By similarity)				226
P33726 UniProt NPD GO	PDE6B_CANFA	Rod cGMP-specific 3',5'-cyclic phosphodiesterase beta-subunit precursor (EC 3.1.4.35) (GMP-PDE beta) ...	0.25	-	cyt	0	Membrane; lipid-anchor				856
Q42679 UniProt NPD GO	DCAM_CATRO	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.25	-	nuc	0					357
Q27883 UniProt NPD GO	DCAM_ONCVO	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.25	-	cyt	0					365
Q851W1 UniProt NPD GO	SLY1_ORYSA	SEC1-family transport protein SLY1	0.25	-	nuc	0					623
Q75DK1 UniProt NPD GO	SEC14_ASHGO	SEC14 cytosolic factor (Phosphatidylinositol/phosphatidylcholine transfer protein) (PI/PC TP)	0.25	-	mit	0	Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity)				311
P24859 UniProt NPD GO	SEC14_KLULA	SEC14 cytosolic factor (Phosphatidylinositol/phosphatidylcholine transfer protein) (PI/PC TP)	0.25	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity)				301
Q9JJU8 UniProt NPD GO	SH3L1_MOUSE	SH3 domain-binding glutamic acid-rich-like protein	0.25	-	nuc	0					114
P98077 UniProt NPD GO	SHC2_HUMAN	SHC-transforming protein 2 (SH2 domain protein C2) (Src homology 2 domain-containing-transforming pr ...	0.25	-	nuc	0			605217		551
Q6CPF9 UniProt NPD GO	SWC7_KLULA	SWR1-complex protein 7	0.25	-	nuc	0	Nucleus (By similarity)				125
P98119 UniProt NPD GO	URT1_DESRO	Salivary plasminogen activator alpha 1 precursor (EC 3.4.21.68) (DSPA alpha-1)	0.25	-	exc	0				1A5I	477
P49150 UniProt NPD GO	URTG_DESRO	Salivary plasminogen activator gamma precursor (EC 3.4.21.68) (DSPA gamma)	0.25	-	exc	0					394
P31529 UniProt NPD GO	SAPB_SARPE	Sapecin-B precursor	0.25	-	exc	1 *	Secreted protein				88
P31226 UniProt NPD GO	SAX_RANCA	Saxiphilin precursor (SAX)	0.25	-	nuc	0	Secreted protein				844
Q92765 UniProt NPD GO	SFRP3_HUMAN	Secreted frizzled-related protein 3 precursor (sFRP-3) (Frizzled-related protein 1) (FrzB-1) (Frezzl ...	0.25	-	exc	0	Secreted protein (Probable)	extracellular region [ISS] membrane [TAS]	605083		325
Q5RF67 UniProt NPD GO	SFRP3_PONPY	Secreted frizzled-related protein 3 precursor (sFRP-3) (Frizzled-related protein) (FrzB)	0.25	-	exc	0	Secreted protein (Probable)				325
Q710A0 UniProt NPD GO	SPP24_CHICK	Secreted phosphoprotein 24 precursor (Spp-24) (Secreted phosphoprotein 2)	0.25	-	nuc	0	Secreted protein (By similarity)				192
Q58DR5 UniProt NPD GO	SCAM3_BOVIN	Secretory carrier-associated membrane protein 3 (Secretory carrier membrane protein 3)	0.25	-	end	4	Membrane; multi-pass membrane protein (By similarity)				347
Q92743 UniProt NPD GO	HTRA1_HUMAN	Serine protease HTRA1 precursor (EC 3.4.21.-) (L56)	0.25	-	exc	0	Secreted protein	extracellular space [TAS]	602194		480
Q758T2 UniProt NPD GO	ISR1_ASHGO	Serine/threonine-protein kinase ISR1 (EC 2.7.11.1)	0.25	-	nuc	0					342
P59895 UniProt NPD GO	NEK6_RAT	Serine/threonine-protein kinase Nek6 (EC 2.7.11.1) (NimA-related protein kinase 6)	0.25	-	cyt	0	Cytoplasm (By similarity)				313
Q8R4U9 UniProt NPD GO	SGK2_RAT	Serine/threonine-protein kinase Sgk2 (EC 2.7.11.1) (Serum/glucocorticoid-regulated kinase 2) (Fragme ...	0.25	-	cyt	0					302
Q10364 UniProt NPD GO	SCK2_SCHPO	Serine/threonine-protein kinase sck2 (EC 2.7.11.1)	0.25	-	mit	0					646
P48486 UniProt NPD GO	PP16_ARATH	Serine/threonine-protein phosphatase PP1 isozyme 6 (EC 3.1.3.16)	0.25	-	cyt	0					322
Q3T0E7 UniProt NPD GO	PP1A_BOVIN	Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) (PP-1A)	0.25	-	mit	0	Cytoplasm (By similarity)				330

You are viewing entries 45701 to 45750 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.