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
Q62070 UniProt NPD GO	PIM2_MOUSE	Serine/threonine-protein kinase Pim-2 (EC 2.7.11.1)	0.12	-	nuc	0					370
Q75V57 UniProt NPD GO	SAPK9_ORYSA	Serine/threonine-protein kinase SAPK9 (EC 2.7.11.1) (Osmotic stress/abscisic acid-activated protein ...	0.12	-	cyt	0					361
Q52WX2 UniProt NPD GO	SBK1_HUMAN	Serine/threonine-protein kinase SBK1 (EC 2.7.11.1) (SH3-binding kinase 1)	0.12	+	mit	0	Cytoplasm (By similarity)				424
Q8QZX0 UniProt NPD GO	SBK1_MOUSE	Serine/threonine-protein kinase SBK1 (EC 2.7.11.1) (SH3-binding kinase 1)	0.12	+	cyt	0	Cytoplasm (By similarity)				417
Q9Z335 UniProt NPD GO	SBK1_RAT	Serine/threonine-protein kinase SBK1 (EC 2.7.11.1) (SH3-binding kinase 1)	0.12	+	cyt	0	Cytoplasm				417
P30154 UniProt NPD GO	2AAB_HUMAN	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform (PP2A, subunit A, P ...	0.12	-	cyt	0		cytosol [ISS] membrane [ISS] microtubule cytoskeleton [ISS] mitochondrion [ISS] nucleus [ISS] protein phosphatase type 2A complex [ISS] soluble fraction [ISS]	603113		601
P67774 UniProt NPD GO	PP2AA_BOVIN	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) (PP2A-alpha)	0.12	-	cyt	0	Cytoplasm	cytosol [ISS] membrane [ISS] microtubule cytoskeleton [ISS] mitochondrion [ISS] nucleus [ISS] protein phosphatase type 2A complex [ISS] soluble fraction [ISS]			309
P67776 UniProt NPD GO	PP2AA_PIG	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) (PP2A-alpha)	0.12	-	cyt	0	Cytoplasm	cytosol [ISS] membrane [ISS] microtubule cytoskeleton [ISS] mitochondrion [ISS] nucleus [ISS] protein phosphatase type 2A complex [ISS] soluble fraction [ISS]			309
P67777 UniProt NPD GO	PP2AA_RABIT	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) (PP2A-alpha)	0.12	-	cyt	0	Cytoplasm	cytosol [ISS] membrane [ISS] microtubule cytoskeleton [ISS] mitochondrion [ISS] nucleus [ISS] protein phosphatase type 2A complex [ISS] soluble fraction [ISS]			309
P67775 UniProt NPD GO	PP2AA_HUMAN	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) (PP2A-alpha) ( ...	0.12	-	cyt	0	Cytoplasm	cytosol [TAS] membrane [NAS] microtubule cytoskeleton [NAS] mitochondrion [NAS] nucleus [NAS] protein phosphatase type 2A complex [TAS] soluble fraction [NAS]	176915		309
P62714 UniProt NPD GO	PP2AB_HUMAN	Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform (EC 3.1.3.16) (PP2A-beta)	0.12	-	cyt	0	Cytoplasm	protein phosphatase type 2A complex [TAS]	176916		309
P62715 UniProt NPD GO	PP2AB_MOUSE	Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform (EC 3.1.3.16) (PP2A-beta)	0.12	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [TAS]			309
P11611 UniProt NPD GO	PP2AB_RABIT	Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform (EC 3.1.3.16) (PP2A-beta)	0.12	-	cyt	0	Cytoplasm				309
P62716 UniProt NPD GO	PP2AB_RAT	Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform (EC 3.1.3.16) (PP2A-beta)	0.12	-	cyt	0	Cytoplasm (By similarity)	cytosol [ISS] membrane [ISS] microtubule cytoskeleton [ISS] mitochondrion [ISS] nucleus [ISS] protein phosphatase type 2A complex [ISS] soluble fraction [ISS]			309
P36179 UniProt NPD GO	2AAA_DROME	Serine/threonine-protein phosphatase PP2A 65 kDa regulatory subunit (Protein phosphatase PP2A regula ...	0.12	-	cyt	0					590
P91536 UniProt NPD GO	SRH72_CAEEL	Serpentine receptor class H-72 (Protein srh-72)	0.12	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				344
O17842 UniProt NPD GO	SRA17_CAEEL	Serpentine receptor class alpha-17 (Protein sra-17)	0.12	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				337
O62368 UniProt NPD GO	SRA24_CAEEL	Serpentine receptor class alpha-24 (Protein sra-24)	0.12	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				339
Q19508 UniProt NPD GO	SRD46_CAEEL	Serpentine receptor class delta-46 (Protein srd-46)	0.12	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				317
O62267 UniProt NPD GO	SRE30_CAEEL	Serpentine receptor class epsilon-30 (Protein sre-30)	0.12	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				357
Q18428 UniProt NPD GO	SRG15_CAEEL	Serpentine receptor class gamma-15 (Protein srg-15)	0.12	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				320
Q96P15 UniProt NPD GO	SPB11_HUMAN	Serpin B11	0.12	-	nuc	0	Cytoplasm (By similarity)				392
Q9UIV8 UniProt NPD GO	SPB13_HUMAN	Serpin B13 (Hurpin) (HaCaT UV-repressible serpin) (Protease inhibitor 13) (Headpin)	0.12	-	mit	1 *	Cytoplasm		604445		391
P14639 UniProt NPD GO	ALBU_SHEEP	Serum albumin precursor	0.12	-	exc	0	Secreted protein				607
P35747 UniProt NPD GO	ALBU_HORSE	Serum albumin precursor (Allergen Equ c 3)	0.12	-	cyt	0	Secreted protein	extracellular region [ISS] protein complex [ISS]			607
P20726 UniProt NPD GO	SAA1_MESAU	Serum amyloid A-1 protein precursor	0.12	-	exc	0					122
P09179 UniProt NPD GO	SSP1_BOMMO	Sex-specific storage-protein 1 precursor (SP 1) (Methionine-rich storage protein)	0.12	-	exc	1 *	Secreted protein; extracellular space				747
Q00497 UniProt NPD GO	AROK_LYCES	Shikimate kinase, chloroplast precursor (EC 2.7.1.71)	0.12	-	cyt	0	Plastid; chloroplast				300
P79273 UniProt NPD GO	ACADS_PIG	Short-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.2) (SCAD) (Butyryl-C ...	0.12	-	mit	0	Mitochondrion; mitochondrial matrix				413
Q5RD16 UniProt NPD GO	SFXN3_PONPY	Sideroflexin-3	0.12	-	cyt	1	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				321
P83362 UniProt NPD GO	SPCS1_CANFA	Signal peptidase complex subunit 1 (EC 3.4.-.-) (Microsomal signal peptidase 12 kDa subunit) (SPase ...	0.12	-	nuc	0	Membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [ISS] signal peptidase complex [ISS]			39
Q28250 UniProt NPD GO	SPCS2_CANFA	Signal peptidase complex subunit 2 (EC 3.4.-.-) (Microsomal signal peptidase 25 kDa subunit) (SPase ...	0.12	+	end	2	Membrane; multi-pass membrane protein (Potential)				226
Q15005 UniProt NPD GO	SPCS2_HUMAN	Signal peptidase complex subunit 2 (EC 3.4.-.-) (Microsomal signal peptidase 25 kDa subunit) (SPase ...	0.12	-	end	2	Membrane; multi-pass membrane protein (Potential)				226
Q5RAY6 UniProt NPD GO	SPCS2_PONPY	Signal peptidase complex subunit 2 (EC 3.4.-.-) (Microsomal signal peptidase 25 kDa subunit) (SPase ...	0.12	-	end	2	Membrane; multi-pass membrane protein (Potential)				226
Q8NFT2 UniProt NPD GO	STEA2_HUMAN	Six-transmembrane epithelial antigen of prostate 2 (SixTransMembrane protein of prostate 1) (Prostat ...	0.12	-	end	6	Cell membrane; multi-pass membrane protein	cytosol [IDA] early endosome [IDA] integral to Golgi membrane [IDA] plasma membrane [IDA] trans-Golgi network transport vesicle [IDA] vesicular fraction [IDA]	605094		490
P78556 UniProt NPD GO	CCL20_HUMAN	Small inducible cytokine A20 precursor (CCL20) (Macrophage inflammatory protein 3 alpha) (MIP-3-alph ...	0.12	-	exc	0	Secreted protein	extracellular space [TAS]	601960	1M8A	96
P14097 UniProt NPD GO	CCL4_MOUSE	Small inducible cytokine A4 precursor (CCL4) (Macrophage inflammatory protein 1-beta) (MIP-1-beta) ( ...	0.12	-	exc	1 *	Secreted protein				92
Q9QXY8 UniProt NPD GO	CCL7_RAT	Small inducible cytokine A7 precursor (CCL7) (Monocyte chemotactic protein 3) (MCP-3) (Monocyte chem ...	0.12	-	exc	0	Secreted protein				97
Q9WVL7 UniProt NPD GO	SCYBF_MOUSE	Small inducible cytokine B15 precursor (CXCL15) (Lungkine)	0.12	-	mit	0	Secreted protein	extracellular region [IDA]			167
Q17348 UniProt NPD GO	SMD3_CAEEL	Small nuclear ribonucleoprotein Sm D3 (snRNP core protein D3) (Sm-D3)	0.12	-	cyt	0	Nucleus (By similarity)				136
Q7Z1K8 UniProt NPD GO	SCX4_CENLL	Sodium-channel modifier toxin Cll4 precursor	0.12	-	exc	1 *	Secreted protein (By similarity)				87
Q5RE87 UniProt NPD GO	S38A4_PONPY	Sodium-coupled neutral amino acid transporter 4 (Na(+)-coupled neutral amino acid transporter 4) (Am ...	0.12	-	end	11	Cell membrane; multi-pass membrane protein (By similarity)				547
Q6PB26 UniProt NPD GO	S20AB_XENLA	Sodium-dependent phosphate transporter 1-B (Solute carrier family 20 member 1-B)	0.12	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				685
Q92911 UniProt NPD GO	SC5A5_HUMAN	Sodium/iodide cotransporter (Na(+)/I(-) cotransporter) (Sodium-iodide symporter) (Na(+)/I(-)-symport ...	0.12	-	end	13 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	601843		643
Q99PN0 UniProt NPD GO	SC5A5_MOUSE	Sodium/iodide cotransporter (Na(+)/I(-) cotransporter) (Sodium-iodide symporter) (Na(+)/I(-)-symport ...	0.12	-	end	13 *	Membrane; multi-pass membrane protein				618
O00337 UniProt NPD GO	S28A1_HUMAN	Sodium/nucleoside cotransporter 1 (Na(+)/nucleoside cotransporter 1) (Sodium-coupled nucleoside tran ...	0.12	-	end	12	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	606207		649
O43868 UniProt NPD GO	S28A2_HUMAN	Sodium/nucleoside cotransporter 2 (Na(+)/nucleoside cotransporter 2) (Sodium-coupled nucleoside tran ...	0.12	-	end	12	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	606208		658
P06583 UniProt NPD GO	AT1B1_CANFA	Sodium/potassium-transporting ATPase subunit beta-1 (Sodium/potassium-dependent ATPase beta-1 subuni ...	0.12	-	mit	1 *	Membrane; single-pass type II membrane protein				303
P14094 UniProt NPD GO	AT1B1_MOUSE	Sodium/potassium-transporting ATPase subunit beta-1 (Sodium/potassium-dependent ATPase beta-1 subuni ...	0.12	-	mit	1 *	Membrane; single-pass type II membrane protein	basolateral plasma membrane [IDA] plasma membrane [IDA]			304
P05028 UniProt NPD GO	AT1B1_SHEEP	Sodium/potassium-transporting ATPase subunit beta-1 (Sodium/potassium-dependent ATPase beta-1 subuni ...	0.12	-	mit	1 *	Membrane; single-pass type II membrane protein				303

You are viewing entries 61901 to 61950 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.