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
Q99LB7 UniProt NPD GO	SARDH_MOUSE	Sarcosine dehydrogenase, mitochondrial precursor (EC 1.5.99.1) (SarDH)	0.09	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			919
Q64380 UniProt NPD GO	SARDH_RAT	Sarcosine dehydrogenase, mitochondrial precursor (EC 1.5.99.1) (SarDH)	0.09	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA] mitochondrion [ISS]			919
P14667 UniProt NPD GO	SRX2A_SARPE	Sarcotoxin-2A precursor (Sarcotoxin IIA)	0.09	-	exc	0	Secreted protein				294
P23811 UniProt NPD GO	SCTR_RAT	Secretin receptor precursor (SCT-R)	0.09	-	end	7	Membrane; multi-pass membrane protein				449
O15126 UniProt NPD GO	SCAM1_HUMAN	Secretory carrier-associated membrane protein 1 (Secretory carrier membrane protein 1)	0.09	-	end	4	Membrane; multi-pass membrane protein		606911		338
Q9CQJ7 UniProt NPD GO	PTTG1_MOUSE	Securin (Pituitary tumor-transforming protein 1)	0.09	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				199
P97613 UniProt NPD GO	PTTG1_RAT	Securin (Pituitary tumor-transforming protein 1)	0.09	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				199
Q63836 UniProt NPD GO	SBP2_MOUSE	Selenium-binding protein 2 (56 kDa acetaminophen-binding protein) (AP56)	0.09	-	cyt	0	Cytoplasm				472
Q26473 UniProt NPD GO	SEM1A_SCHAM	Semaphorin-1A precursor (Semaphorin-I) (Sema I) (Fasciclin IV)	0.09	-	end	2 *	Membrane; single-pass type I membrane protein				730
P35270 UniProt NPD GO	SPRE_HUMAN	Sepiapterin reductase (EC 1.1.1.153) (SPR)	0.09	-	end	0	Cytoplasm		182125	1Z6Z	261
O96614 UniProt NPD GO	SER1_GALME	Sericin-1 (Silk gum protein 1) (Fragment)	0.09	-	mit	0	Secreted protein				115
Q75BQ6 UniProt NPD GO	GLYC_ASHGO	Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltra ...	0.09	-	cyt	0	Cytoplasm				469
P58514 UniProt NPD GO	SPI1_SOLTU	Serine protease inhibitor 1 precursor (PSPI-21) (PSPI-21-6.3) [Contains: Serine protease inhibitor 1 ...	0.09	-	exc	0	Vacuole (By similarity)				221
Q91822 UniProt NPD GO	PIM3_XENLA	Serine/threonine-protein kinase Pim-3 (EC 2.7.11.1) (Pim-1)	0.09	-	nuc	0					323
Q75LR7 UniProt NPD GO	SAPK1_ORYSA	Serine/threonine-protein kinase SAPK1 (EC 2.7.11.1) (Osmotic stress/abscisic acid-activated protein ...	0.09	-	cyt	0					342
Q9P7H4 UniProt NPD GO	PTPA2_SCHPO	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.09	-	cyt	0	Cytoplasm (By similarity)				352
Q15257 UniProt NPD GO	PTPA_HUMAN	Serine/threonine-protein phosphatase 2A regulatory subunit B' (PP2A, subunit B', PR53 isoform) (Phos ...	0.09	-	nuc	0		protein phosphatase type 2A complex [TAS] soluble fraction [TAS]	600756	2G62	358
P11612 UniProt NPD GO	PPY_DROME	Serine/threonine-protein phosphatase PP-Y (EC 3.1.3.16)	0.09	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			314
O76192 UniProt NPD GO	SERO_GALME	Seroin precursor (Silk 23 kDa glycoprotein)	0.09	-	exc	1 *	Secreted protein				167
P27425 UniProt NPD GO	TRFE_HORSE	Serotransferrin precursor (Transferrin) (Siderophilin) (Beta-1 metal-binding globulin)	0.09	-	exc	0	Secreted protein				706
O17819 UniProt NPD GO	SRG16_CAEEL	Serpentine receptor class gamma-16 (Protein srg-16)	0.09	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				325
O01538 UniProt NPD GO	SRG33_CAEEL	Serpentine receptor class gamma-33 (Protein srg-33)	0.09	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				321
P21848 UniProt NPD GO	ALBU1_SALSA	Serum albumin 1 precursor	0.09	-	exc	0	Secreted protein				608
P49822 UniProt NPD GO	ALBU_CANFA	Serum albumin precursor (Allergen Can f 3)	0.09	-	exc	0	Secreted protein	extracellular region [ISS] protein complex [ISS]			608
P42819 UniProt NPD GO	SAA_SHEEP	Serum amyloid A protein (SAA)	0.09	-	cyt	0					112
P02740 UniProt NPD GO	SAA_ANAPL	Serum amyloid A protein precursor (SAA)	0.09	-	exc	0					127
P35542 UniProt NPD GO	SAA4_HUMAN	Serum amyloid A-4 protein precursor (Constitutively expressed serum amyloid A protein) (C-SAA)	0.09	-	end	0		extracellular region [NAS]	104752		130
P43289 UniProt NPD GO	KSG3_ARATH	Shaggy-related protein kinase gamma (EC 2.7.11.1) (ASK-gamma)	0.09	-	cyt	0					409
Q8WWR8 UniProt NPD GO	NEUR4_HUMAN	Sialidase-4 (EC 3.2.1.18) (N-acetyl-alpha-neuraminidase 4)	0.09	-	nuc	0	Membrane; peripheral membrane protein	lysosome [IDA] organelle inner membrane [IDA]	608527		484
Q8BWB6 UniProt NPD GO	STEA2_MOUSE	Six-transmembrane epithelial antigen of prostate 2	0.09	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)	cytosol [ISS] early endosome [ISS] integral to Golgi membrane [ISS] plasma membrane [ISS] trans-Golgi network transport vesicle [ISS] vesicular fraction [ISS]			489
P80952 UniProt NPD GO	SPYY_PHYBI	Skin peptide tyrosine-tyrosine (Skin-PYY) (SPYY)	0.09	-	nuc	0	Secreted protein				36
P04930 UniProt NPD GO	HRP_PLAFF	Small histidine-alanine-rich protein precursor (SHARP) (Antigen 57)	0.09	-	nuc	0					221
O15444 UniProt NPD GO	CCL25_HUMAN	Small inducible cytokine A25 precursor (CCL25) (Chemokine TECK) (Thymus expressed chemokine)	0.09	-	exc	0	Secreted protein	soluble fraction [TAS]	602565		150
Q8HYQ1 UniProt NPD GO	CCL5_MACMU	Small inducible cytokine A5 precursor (CCL5) (T-cell-specific RANTES protein)	0.09	-	exc	0	Secreted protein (By similarity)				91
P97272 UniProt NPD GO	CCL5_CAVPO	Small inducible cytokine A5 precursor (CCL5) (T-cell-specific RANTES protein) (SIS-delta)	0.09	-	exc	0	Secreted protein				91
Q60825 UniProt NPD GO	NPT2A_MOUSE	Sodium-dependent phosphate transport protein 2A (Sodium/phosphate cotransporter 2A) (Na(+)/Pi cotran ...	0.09	-	end	11	Membrane; multi-pass membrane protein				637
Q6PFM1 UniProt NPD GO	S20AA_BRARE	Sodium-dependent phosphate transporter 1-A (Solute carrier family 20 member 1-A)	0.09	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				665
Q9XT49 UniProt NPD GO	SC6A4_BOVIN	Sodium-dependent serotonin transporter (5HT transporter) (5HTT)	0.09	-	end	12	Membrane; multi-pass membrane protein				630
P13866 UniProt NPD GO	SC5A1_HUMAN	Sodium/glucose cotransporter 1 (Na(+)/glucose cotransporter 1) (High affinity sodium-glucose cotrans ...	0.09	-	end	14 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	606824		664
P53790 UniProt NPD GO	SC5A1_RAT	Sodium/glucose cotransporter 1 (Na(+)/glucose cotransporter 1) (High affinity sodium-glucose cotrans ...	0.09	-	end	14 *	Membrane; multi-pass membrane protein	apical plasma membrane [IDA]			665
P53791 UniProt NPD GO	SC5A1_SHEEP	Sodium/glucose cotransporter 1 (Na(+)/glucose cotransporter 1) (High affinity sodium-glucose cotrans ...	0.09	-	end	14 *	Membrane; multi-pass membrane protein				664
P31639 UniProt NPD GO	SC5A2_HUMAN	Sodium/glucose cotransporter 2 (Na(+)/glucose cotransporter 2) (Low affinity sodium-glucose cotransp ...	0.09	-	end	14 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	233100		672
Q923I7 UniProt NPD GO	SC5A2_MOUSE	Sodium/glucose cotransporter 2 (Na(+)/glucose cotransporter 2) (Low affinity sodium-glucose cotransp ...	0.09	-	end	14 *	Membrane; multi-pass membrane protein				670
P53792 UniProt NPD GO	SC5A2_RAT	Sodium/glucose cotransporter 2 (Na(+)/glucose cotransporter 2) (Low affinity sodium-glucose cotransp ...	0.09	-	end	14 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]			670
Q3YL57 UniProt NPD GO	NHX8_ARATH	Sodium/hydrogen exchanger 8 (Na(+)/H(+) exchanger 8) (NHE-8) (Protein SALT OVERLY SENSITIVE 1B)	0.09	-	end	12 *	Cell membrane; multi-pass membrane protein (By similarity)				756
P26430 UniProt NPD GO	SC5A2_RABIT	Sodium/nucleoside cotransporter (Na(+)/nucleoside cotransporter)	0.09	-	end	14 *	Membrane; multi-pass membrane protein				672
P05026 UniProt NPD GO	AT1B1_HUMAN	Sodium/potassium-transporting ATPase subunit beta-1 (Sodium/potassium-dependent ATPase beta-1 subuni ...	0.09	-	mit	1 *	Membrane; single-pass type II membrane protein	sodium:potassium-exchanging ATPase complex [TAS]	182330		303
P97370 UniProt NPD GO	AT1B3_MOUSE	Sodium/potassium-transporting ATPase subunit beta-3 (Sodium/potassium-dependent ATPase beta-3 subuni ...	0.09	-	mit	1 *	Membrane; single-pass type II membrane protein	cytoplasm [IDA]			278
Q9JIS8 UniProt NPD GO	S12A4_MOUSE	Solute carrier family 12 member 4 (Electroneutral potassium-chloride cotransporter 1) (Erythroid K-C ...	0.09	-	end	12	Membrane; multi-pass membrane protein	integral to membrane [ISS]			1085
Q63ZE4 UniProt NPD GO	OAT5_HUMAN	Solute carrier family 22 member 10 (Organic anion transporter 5)	0.09	-	end	10 *	Membrane; multi-pass membrane protein (Potential)		607580		531

You are viewing entries 67051 to 67100 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.