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
P97364 UniProt NPD GO	SPS2_MOUSE	Selenide, water dikinase 2 (EC 2.7.9.3) (Selenophosphate synthetase 2) (Selenium donor protein 2)	0.04	-	cyt	0					452
Q9C0D9 UniProt NPD GO	SELI_HUMAN	Selenoprotein I	0.04	-	end	10 *	Membrane; multi-pass membrane protein (Potential)		607915		397
Q80TA1 UniProt NPD GO	SELI_MOUSE	Selenoprotein I	0.04	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				398
Q5NV96 UniProt NPD GO	SELI_PONPY	Selenoprotein I	0.04	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				397
P87027 UniProt NPD GO	SPG1_SCHPO	Septum-promoting GTP-binding protein 1 (GTPase spg1) (Sid3 protein)	0.04	-	cyt	0					198
P52712 UniProt NPD GO	CBPX_ORYSA	Serine carboxypeptidase-like precursor (EC 3.4.16.-)	0.04	-	mit	0		endoplasmic reticulum membrane [IEP] peroxisome [IEP]			429
Q5E9P9 UniProt NPD GO	GLYC_BOVIN	Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltra ...	0.04	-	cyt	0	Cytoplasm (By similarity)				483
P35623 UniProt NPD GO	GLYC_SHEEP	Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltra ...	0.04	-	cyt	0	Cytoplasm				483
Q8K0E7 UniProt NPD GO	SERC2_MOUSE	Serine incorporator 2 (Tumor differentially expressed 2-like)	0.04	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				450
O54695 UniProt NPD GO	LCB1_CRIGR	Serine palmitoyltransferase 1 (EC 2.3.1.50) (Long chain base biosynthesis protein 1) (LCB 1) (Serine ...	0.04	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				473
O35704 UniProt NPD GO	LCB1_MOUSE	Serine palmitoyltransferase 1 (EC 2.3.1.50) (Long chain base biosynthesis protein 1) (LCB 1) (Serine ...	0.04	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				473
O35679 UniProt NPD GO	ISK4_MOUSE	Serine protease inhibitor Kazal-type 4 precursor (Peptide PEC-60 homolog) (MPGC60 protein)	0.04	-	exc	0	Secreted protein (By similarity)				86
P22323 UniProt NPD GO	COTR_CAVPO	Serine proteinase inhibitor A3K precursor (Contrapsin) (CP) (Serpin A3K)	0.04	-	end	0	Secreted protein; extracellular space				410
Q56YA5 UniProt NPD GO	SGAT_ARATH	Serine--glyoxylate aminotransferase (EC 2.6.1.45) (Alanine--glyoxylate aminotransferase) (EC 2.6.1.4 ...	0.04	-	cyt	0	Peroxisome				401
Q9Z1Z2 UniProt NPD GO	STRAP_MOUSE	Serine-threonine kinase receptor-associated protein (UNR-interacting protein)	0.04	-	cyt	0					351
P97343 UniProt NPD GO	UHMK1_MOUSE	Serine/threonine-protein kinase Kist (EC 2.7.11.1) (Kinase interacting with stathmin) (U2AF homology ...	0.04	-	cyt	0	Nucleus. Mostly nuclear	cytoplasm [ISS] nucleus [ISS]			419
P58750 UniProt NPD GO	PIM3_MOUSE	Serine/threonine-protein kinase Pim-3 (EC 2.7.11.1)	0.04	-	cyt	0					326
O70444 UniProt NPD GO	PIM3_RAT	Serine/threonine-protein kinase Pim-3 (EC 2.7.11.1) (Protein kinase Kid-1) (Kinase induced by depola ...	0.04	-	cyt	0					326
P87347 UniProt NPD GO	MOS_APTAU	Serine/threonine-protein kinase mos (EC 2.7.11.1) (Oocyte maturation factor mos) (Fragment)	0.04	-	mit	0					200
Q8QHF0 UniProt NPD GO	MOS_ATHNI	Serine/threonine-protein kinase mos (EC 2.7.11.1) (Oocyte maturation factor mos) (Fragment)	0.04	-	cyt	0					189
Q6CKF0 UniProt NPD GO	PTPA2_KLULA	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.04	-	mit	0	Cytoplasm (By similarity)				360
P48577 UniProt NPD GO	PP2A_ACECL	Serine/threonine-protein phosphatase PP2A-1 catalytic subunit (EC 3.1.3.16)	0.04	-	nuc	0					307
Q95ZY2 UniProt NPD GO	SRB3_CAEEL	Serpentine receptor class beta-3 (Protein srb-3)	0.04	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				341
Q19992 UniProt NPD GO	SRD1_CAEEL	Serpentine receptor class delta-1 (Protein srd-1)	0.04	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				371
P92002 UniProt NPD GO	SRD19_CAEEL	Serpentine receptor class delta-19 (Protein srd-19)	0.04	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				339
Q9CQV3 UniProt NPD GO	SPB11_MOUSE	Serpin B11	0.04	-	mit	0	Cytoplasm (By similarity)				388
O08800 UniProt NPD GO	SPB8_MOUSE	Serpin B8	0.04	-	mit	0	Cytoplasm (By similarity)				374
P50452 UniProt NPD GO	SPB8_HUMAN	Serpin B8 (Cytoplasmic antiproteinase 2) (CAP-2) (CAP2) (Protease inhibitor 8)	0.04	-	mit	0	Cytoplasm	cytosol [TAS]	601697		374
P23680 UniProt NPD GO	SAMP_RAT	Serum amyloid P-component precursor (SAP)	0.04	-	exc	0	Secreted protein				228
Q24800 UniProt NPD GO	SEVE_ECHGR	Severin	0.04	-	cyt	0					374
P29355 UniProt NPD GO	SEM5_CAEEL	Sex muscle abnormal protein 5	0.04	-	cyt	0				3SEM	228
Q9BM98 UniProt NPD GO	JANA_DROMA	Sex-regulated protein janus-A	0.04	-	mit	0					135
Q9BM99 UniProt NPD GO	JANA_DROSI	Sex-regulated protein janus-A	0.04	-	mit	0					135
Q9BM93 UniProt NPD GO	JANB_DROMA	Sex-regulated protein janus-B	0.04	-	mit	0					140
Q9BM94 UniProt NPD GO	JANB_DROSE	Sex-regulated protein janus-B	0.04	-	mit	0					140
Q9BM95 UniProt NPD GO	JANB_DROSI	Sex-regulated protein janus-B	0.04	-	mit	0					140
Q9BM91 UniProt NPD GO	JANB_DROTE	Sex-regulated protein janus-B	0.04	-	mit	0					140
P40901 UniProt NPD GO	ISP5_SCHPO	Sexual differentiation process putative amino-acid permease isp5	0.04	-	end	12	Membrane; multi-pass membrane protein (Probable)				580
Q9W7J7 UniProt NPD GO	NXS6_PSETE	Short neurotoxin 6 precursor (Alpha neurotoxin 6)	0.04	-	nuc	0	Secreted protein (By similarity)				79
Q9YGI0 UniProt NPD GO	NXSH1_BUNMU	Short neurotoxin homolog NTL1 precursor	0.04	-	nuc	0	Secreted protein				86
O77769 UniProt NPD GO	DHRS3_BOVIN	Short-chain dehydrogenase/reductase 3 (EC 1.1.-.-) (Retinal short-chain dehydrogenase/reductase 1) ( ...	0.04	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				302
O75911 UniProt NPD GO	DHRS3_HUMAN	Short-chain dehydrogenase/reductase 3 (EC 1.1.-.-) (Retinal short-chain dehydrogenase/reductase 1) ( ...	0.04	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				302
P18269 UniProt NPD GO	8511_TRYCR	Sialidase 85-1.1 precursor (EC 3.2.1.18) (Neuraminidase) (NA) (Major 85 kDa surface antigen) (SA85-1 ...	0.04	-	end	1 *					752
Q96NB2 UniProt NPD GO	SFXN2_HUMAN	Sideroflexin-2	0.04	-	cyt	5	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				322
Q3T134 UniProt NPD GO	SPCS1_BOVIN	Signal peptidase complex subunit 1 (EC 3.4.-.-) (Microsomal signal peptidase 12 kDa subunit) (SPase ...	0.04	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				102
Q9D958 UniProt NPD GO	SPCS1_MOUSE	Signal peptidase complex subunit 1 (EC 3.4.-.-) (Microsomal signal peptidase 12 kDa subunit) (SPase ...	0.04	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	integral to endoplasmic reticulum membrane [ISS] signal peptidase complex [ISS]			102
O00241 UniProt NPD GO	SIRB1_HUMAN	Signal-regulatory protein beta-1 precursor (SIRP-beta-1) (CD172b antigen)	0.04	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	603889		398
Q84J78 UniProt NPD GO	SSB_ARATH	Single-stranded DNA-binding protein, mitochondrial precursor	0.04	-	mit	0	Mitochondrion (Potential)				201
Q96DR8 UniProt NPD GO	MUCL_HUMAN	Small breast epithelial mucin precursor (Protein BS106)	0.04	-	exc	0	Secreted protein (Probable). Membrane (Probable)				90
P50231 UniProt NPD GO	CCL5_RAT	Small inducible cytokine A5 precursor (CCL5) (T-cell-specific RANTES protein) (SIS-delta)	0.04	-	exc	0	Secreted protein				92

You are viewing entries 78401 to 78450 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.