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
P70584 UniProt NPD GO	ACDSB_RAT	Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.-) (SBCAD) ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]			432
Q5RFU0 UniProt NPD GO	SIAE_PONPY	Sialate O-acetylesterase precursor (EC 3.1.1.53) (Sialic acid-specific 9-O-acetylesterase)	0.07	-	vac	0	Lysosome (By similarity)				523
Q99519 UniProt NPD GO	NEUR1_HUMAN	Sialidase-1 precursor (EC 3.2.1.18) (Lysosomal sialidase) (N-acetyl-alpha-neuraminidase 1) (Acetylne ...	0.07	-	end	1 *	Lysosome; lysosomal membrane; peripheral membrane; lumenal side. Lysosome; lysosomal lumen. Cell mem ...	lysosome [TAS]	608272		415
P39980 UniProt NPD GO	SIT1_YEAST	Siderophore iron transporter 1 (Siderophore iron transporter ARN3) (Ferrioxamine B permease)	0.07	-	end	14	Endosome; endosomal membrane; multi-pass membrane protein	cytoplasmic membrane-bound vesicle [IDA] endosome [TAS]			628
Q9Y6A9 UniProt NPD GO	SPCS1_HUMAN	Signal peptidase complex subunit 1 (EC 3.4.-.-) (Microsomal signal peptidase 12 kDa subunit) (SPase ...	0.07	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	integral to endoplasmic reticulum membrane [IDA] signal peptidase complex [TAS]			102
Q5RF96 UniProt NPD GO	SPCS1_PONPY	Signal peptidase complex subunit 1 (EC 3.4.-.-) (Microsomal signal peptidase 12 kDa subunit) (SPase ...	0.07	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				102
Q9SMU7 UniProt NPD GO	SRP09_ARATH	Signal recognition particle 9 kDa protein (SRP9)	0.07	-	cyt	0	Cytoplasm (By similarity)				103
P49962 UniProt NPD GO	SRP09_MOUSE	Signal recognition particle 9 kDa protein (SRP9)	0.07	-	nuc	0	Cytoplasm			1914	85
Q9CYR0 UniProt NPD GO	SSB_MOUSE	Single-stranded DNA-binding protein, mitochondrial precursor (Mt-SSB) (MtSSB)	0.07	-	mit	0	Mitochondrion (By similarity)				152
Q92583 UniProt NPD GO	CCL17_HUMAN	Small inducible cytokine A17 precursor (CCL17) (Thymus and activation-regulated chemokine) (CC chemo ...	0.07	-	exc	0	Secreted protein		601520	1NR4	94
P55774 UniProt NPD GO	CCL18_HUMAN	Small inducible cytokine A18 precursor (CCL18) (Macrophage inflammatory protein 4) (MIP-4) (Pulmonar ...	0.07	-	exc	0	Secreted protein		603757		89
Q68A92 UniProt NPD GO	CCL3_CANFA	Small inducible cytokine A3 precursor (CCL3)	0.07	-	exc	0	Secreted protein (By similarity)				92
Q06217 UniProt NPD GO	SMD2_YEAST	Small nuclear ribonucleoprotein Sm D2 (snRNP core protein D2) (Sm-D2)	0.07	-	cyt	0	Nucleus	snRNP U1 [IDA] snRNP U5 [IPI] U4/U6 x U5 tri-snRNP complex [IDA]			110
Q64093 UniProt NPD GO	S6A20_RAT	Sodium- and chloride-dependent transporter XTRP3 (Solute carrier family 6 member 20) (Neurotransmitt ...	0.07	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				616
O00476 UniProt NPD GO	NPT4_HUMAN	Sodium-dependent phosphate transport protein 4 (Sodium/phosphate cotransporter 4) (Na(+)/PI cotransp ...	0.07	-	end	9 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	604216		401
Q9MYX0 UniProt NPD GO	SC6A4_MACMU	Sodium-dependent serotonin transporter (5HT transporter) (5HTT)	0.07	-	end	12	Membrane; multi-pass membrane protein				630
P26435 UniProt NPD GO	NTCP_RAT	Sodium/bile acid cotransporter (Na(+)/bile acid cotransporter) (Na(+)/taurocholate transport protein ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein				362
Q56XP4 UniProt NPD GO	NHX2_ARATH	Sodium/hydrogen exchanger 2 (Na(+)/H(+) exchanger 2) (NHE-2)	0.07	-	end	12 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				546
Q63377 UniProt NPD GO	AT1B3_RAT	Sodium/potassium-transporting ATPase subunit beta-3 (Sodium/potassium-dependent ATPase beta-3 subuni ...	0.07	-	mit	1 *	Membrane; single-pass type II membrane protein				279
Q9FNF2 UniProt NPD GO	SSY1_ARATH	Soluble starch synthase, chloroplast precursor (EC 2.4.1.21) (SSS)	0.07	-	mit	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast				652
Q9WTW7 UniProt NPD GO	S23A1_RAT	Solute carrier family 23 member 1 (Sodium-dependent vitamin C transporter 1) (Na(+)/L-ascorbic acid ...	0.07	-	end	10	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			604
Q96JT2 UniProt NPD GO	S45A3_HUMAN	Solute carrier family 45 member 3 (Prostate cancer-associated protein 6) (Prostein)	0.07	-	end	11 *	Membrane; multi-pass membrane protein (Potential)		605097		553
Q63673 UniProt NPD GO	SHH_RAT	Sonic hedgehog protein precursor (SHH) [Contains: Sonic hedgehog protein N-product; Sonic hedgehog p ...	0.07	-	cyt	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space. Sonic hedgehog protein N-pr ...	cell surface [ISS] extracellular space [ISS] lipid raft [ISS]			437
Q23498 UniProt NPD GO	ASM2_CAEEL	Sphingomyelin phosphodiesterase 2 precursor (EC 3.1.4.12) (Acid sphingomyelinase 2)	0.07	-	vac	0	Secreted protein	extracellular region [IDA]			618
Q9Y194 UniProt NPD GO	SGPL_CAEEL	Sphingosine-1-phosphate lyase (EC 4.1.2.27) (SP-lyase) (SPL) (Sphingosine-1-phosphate aldolase)	0.07	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				552
Q52RG7 UniProt NPD GO	SGPL_ORYSA	Sphingosine-1-phosphate lyase precursor (EC 4.1.2.27) (SP-lyase) (SPL) (Sphingosine-1-phosphate aldo ...	0.07	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				539
Q15743 UniProt NPD GO	SPR1_HUMAN	Sphingosylphosphorylcholine receptor (Ovarian cancer G-protein coupled receptor 1) (OGR-1) (G-protei ...	0.07	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601404		365
P04815 UniProt NPD GO	BPT2_BOVIN	Spleen trypsin inhibitor I precursor (SI-I) [Contains: Spleen trypsin inhibitor II (SI-II); Spleen t ...	0.07	-	exc	0	Secreted protein				100
Q9HGZ6 UniProt NPD GO	FDFT_CANGA	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.07	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				443
Q99JV5 UniProt NPD GO	STAR4_MOUSE	StAR-related lipid transfer protein 4 (StARD4) (START domain-containing protein 4)	0.07	-	cyt	0		mitochondrion [TAS]		1JSS	224
Q08080 UniProt NPD GO	HSP7S_SPIOL	Stromal 70 kDa heat shock-related protein, chloroplast (Fragment)	0.07	-	cyt	0	Plastid; chloroplast; chloroplast stroma				599
O18494 UniProt NPD GO	STYC_STYCL	Styelin-C precursor	0.07	-	vac	0	Secreted protein				80
P79218 UniProt NPD GO	NK2R_RABIT	Substance-K receptor (SKR) (Neurokinin A receptor) (NK-2 receptor) (NK-2R) (Tachykinin receptor 2)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				384
P16610 UniProt NPD GO	NK2R_RAT	Substance-K receptor (SKR) (Neurokinin A receptor) (NK-2 receptor) (NK-2R) (Tachykinin receptor 2)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				390
P08626 UniProt NPD GO	ICI3_HORVU	Subtilisin-chymotrypsin inhibitor-2B (CI-2B) (Fragment)	0.07	-	cyt	0					72
Q42652 UniProt NPD GO	SUSY_BETVU	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase) (Fragment)	0.07	-	cyt	0					766
Q9FG00 UniProt NPD GO	SUC9_ARATH	Sucrose transport protein SUC9 (Sucrose permease 9) (Sucrose-proton symporter 9)	0.07	-	end	11 *	Cell membrane; multi-pass membrane protein (Probable)				491
Q8NBJ7 UniProt NPD GO	SUMF2_HUMAN	Sulfatase-modifying factor 2 precursor (C-alpha-formyglycine-generating enzyme 2)	0.07	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen		607940	1Y4J	301
Q5RCR5 UniProt NPD GO	SUMF2_PONPY	Sulfatase-modifying factor 2 precursor (C-alpha-formyglycine-generating enzyme 2)	0.07	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				301
O04289 UniProt NPD GO	SUT32_ARATH	Sulfate transporter 3.2 (AST77)	0.07	-	end	10	Membrane; multi-pass membrane protein (Potential)				646
Q9FY46 UniProt NPD GO	SUT41_ARATH	Sulfate transporter 4.1, chloroplast precursor (AST82)	0.07	-	end	12	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				685
P17988 UniProt NPD GO	ST1A1_RAT	Sulfotransferase 1A1 (EC 2.8.2.1) (Aryl sulfotransferase) (Phenol sulfotransferase) (PST-1) (Sulfoki ...	0.07	-	cyt	0	Cytoplasm	cytosol [TAS]			291
Q8JG30 UniProt NPD GO	ST1B1_CHICK	Sulfotransferase family cytosolic 1B member 1 (EC 2.8.2.-) (Sulfotransferase 1B1)	0.07	-	nuc	0	Cytoplasm (By similarity)				296
P41976 UniProt NPD GO	SODM_BOVIN	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.07	-	mit	0	Mitochondrion; mitochondrial matrix				222
O49066 UniProt NPD GO	SODM_CAPAN	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.07	-	mit	0	Mitochondrion; mitochondrial matrix				228
Q8HXP3 UniProt NPD GO	SODM_MACFA	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				222
Q5FB30 UniProt NPD GO	SODM_MACNE	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				222
Q8HXP6 UniProt NPD GO	SODM_PONPY	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.07	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				222
Q9SM64 UniProt NPD GO	SODM_PRUPE	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.07	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial matrix [ISS]			228
Q92450 UniProt NPD GO	SODM_ASPFU	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1) (Allergen Asp f 6)	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix			1KKC	210

You are viewing entries 71051 to 71100 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.