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
P49558 UniProt NPD GO	RK22_ODOSI	Chloroplast 50S ribosomal protein L22	0.10	-	mit	0	Plastid; chloroplast				115
Q85FW3 UniProt NPD GO	RK3_CYAME	Chloroplast 50S ribosomal protein L3	0.10	-	cyt	0	Plastid; chloroplast				203
P56796 UniProt NPD GO	RK33_ARATH	Chloroplast 50S ribosomal protein L33	0.10	-	nuc	0	Plastid; chloroplast				66
P21510 UniProt NPD GO	RK5_EUGGR	Chloroplast 50S ribosomal protein L5	0.10	-	cyt	0	Plastid; chloroplast				179
Q1KVR2 UniProt NPD GO	RK5_SCEOB	Chloroplast 50S ribosomal protein L5	0.10	-	cyt	0	Plastid; chloroplast				180
P51300 UniProt NPD GO	RK6_PORPU	Chloroplast 50S ribosomal protein L6	0.10	-	mit	0	Plastid; chloroplast				180
Q8NCS7 UniProt NPD GO	CTL5_HUMAN	Choline transporter-like protein 5 (Solute carrier family 44 member 5)	0.10	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				719
O62760 UniProt NPD GO	CHLE_FELCA	Cholinesterase precursor (EC 3.1.1.8) (Acylcholine acylhydrolase) (Choline esterase II) (Butyrylchol ...	0.10	+	vac	0					602
P24514 UniProt NPD GO	CH18_DROSU	Chorion protein S18	0.10	-	exc	0					174
P83546 UniProt NPD GO	CHY2_PAGMA	Chrysophsin-2	0.10	-	mit	0	Secreted protein				25
P84347 UniProt NPD GO	MEX2_JACME	Chymomexicain (EC 3.4.22.-)	0.10	-	nuc	0					215
P10831 UniProt NPD GO	ISC1_BOMMO	Chymotrypsin inhibitor SCI-I	0.10	-	nuc	0					62
P00768 UniProt NPD GO	CTR2_VESOR	Chymotrypsin-2 (EC 3.4.21.1) (Chymotrypsin II)	0.10	-	cyt	0	Secreted protein; extracellular space				216
P30360 UniProt NPD GO	CADH9_TOBAC	Cinnamyl alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.10	-	cyt	0					357
P49298 UniProt NPD GO	CISY_CITMA	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.10	-	mit	0	Mitochondrion; mitochondrial matrix				471
Q9P4A2 UniProt NPD GO	CLIT_CLINE	Clitocypin	0.10	-	cyt	0	Secreted protein				150
P34121 UniProt NPD GO	COAC_DICDI	Coactosin (Cytoskeletal p17 protein) (Cyclic AMP-regulated protein p16)	0.10	-	cyt	0	Cytoplasm				146
P19540 UniProt NPD GO	FA9_CANFA	Coagulation factor IX precursor (EC 3.4.21.22) (Christmas factor) [Contains: Coagulation factor IXa ...	0.10	-	mit	0	Secreted protein				452
P00743 UniProt NPD GO	FA10_BOVIN	Coagulation factor X precursor (EC 3.4.21.6) (Stuart factor) [Contains: Factor X light chain; Factor ...	0.10	-	exc	0				1WHF	492
O62621 UniProt NPD GO	COPB2_DROME	Coatomer subunit beta' (Beta'-coat protein) (Beta'-COP)	0.10	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [NAS]			914
P40509 UniProt NPD GO	COPE_YEAST	Coatomer subunit epsilon (Epsilon-coat protein) (Epsilon-COP)	0.10	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IMP]			296
P80958 UniProt NPD GO	NSXB_NAJAT	Cobrotoxin b precursor (CBT b) (Short neurotoxin)	0.10	-	nuc	0	Secreted protein			1VB0	82
P04118 UniProt NPD GO	COL_HUMAN	Colipase precursor	0.10	-	exc	1 *	Secreted protein		120105		112
Q03692 UniProt NPD GO	COAA1_HUMAN	Collagen alpha-1(X) chain precursor	0.10	-	nuc	0		collagen [TAS]	120110	1GR3	680
Q7SIB3 UniProt NPD GO	CO4A2_BOVIN	Collagen alpha-2(IV) chain (Fragment)	0.10	-	nuc	0				1M3D	227
P25067 UniProt NPD GO	CO8A2_HUMAN	Collagen alpha-2(VIII) chain precursor (Endothelial collagen)	0.10	-	exc	0		basement membrane [NAS]	609140		703
P33435 UniProt NPD GO	MMP13_MOUSE	Collagenase 3 precursor (EC 3.4.24.-) (Matrix metalloproteinase-13) (MMP-13)	0.10	-	exc	0				1CXV	472
O18739 UniProt NPD GO	CTGF_BOVIN	Connective tissue growth factor precursor	0.10	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity). Secreted protein (By si ...				349
P15472 UniProt NPD GO	CXGS_CONGE	Conotoxin GS (CGS)	0.10	-	nuc	0	Secreted protein			1AG7	34
Q8BLR2 UniProt NPD GO	CPNE4_MOUSE	Copine-4 (Copine IV)	0.10	-	cyt	0					557
Q96A23 UniProt NPD GO	CPNE4_HUMAN	Copine-4 (Copine IV) (Copine-8)	0.10	-	cyt	0			604208		557
Q6PWT7 UniProt NPD GO	CCS_PIG	Copper chaperone for superoxide dismutase (Superoxide dismutase copper chaperone)	0.10	-	cyt	0	Cytoplasm (By similarity)				274
P84155 UniProt NPD GO	HEM6_LEIMA	Coproporphyrinogen III oxidase (EC 1.3.3.3) (Coproporphyrinogenase) (Coprogen oxidase)	0.10	-	cyt	0	Cytoplasm (By similarity)			1VJU	301
P27133 UniProt NPD GO	CORO_DICDI	Coronin (p55)	0.10	-	mit	0	On crown-like cell surface projections				445
Q9WUM3 UniProt NPD GO	COR1B_MOUSE	Coronin-1B (Coronin-2)	0.10	-	nuc	0	Localized to the leading edge in fibroblasts, as well as weakly along actin stress fibers (By simila ...				484
Q04447 UniProt NPD GO	KCRB_MOUSE	Creatine kinase B-type (EC 2.7.3.2) (Creatine kinase B chain) (B-CK)	0.10	-	nuc	0	Cytoplasm	mitochondrion [IDA]			381
P07335 UniProt NPD GO	KCRB_RAT	Creatine kinase B-type (EC 2.7.3.2) (Creatine kinase B chain) (B-CK)	0.10	-	nuc	0	Cytoplasm	plasma membrane [TAS]			381
Q4KML2 UniProt NPD GO	CRYD_BRARE	Cryptochrome DASH (Protein CRY-DASH) (zCRY-DASH)	0.10	-	mit	0					520
P18835 UniProt NPD GO	COL19_CAEEL	Cuticle collagen 19 precursor	0.10	-	nuc	1 *		extracellular region [NAS]			289
P18831 UniProt NPD GO	COL6_CAEEL	Cuticle collagen 6 (Protein roller-8)	0.10	-	nuc	1 *					329
P55271 UniProt NPD GO	CDN2B_MOUSE	Cyclin-dependent kinase 4 inhibitor B (p14-INK4b) (p15-INK4b)	0.10	-	cyt	0				1D9S	130
P42772 UniProt NPD GO	CDN2B_HUMAN	Cyclin-dependent kinase 4 inhibitor B (p14-INK4b) (p15-INK4b) (Multiple tumor suppressor 2) (MTS2)	0.10	-	cyt	0			600431		138
Q60773 UniProt NPD GO	CDN2D_MOUSE	Cyclin-dependent kinase 4 inhibitor D (p19-INK4d)	0.10	-	cyt	0				1BLX	166
P42773 UniProt NPD GO	CDN2C_HUMAN	Cyclin-dependent kinase 6 inhibitor (p18-INK6) (Cyclin-dependent kinase 4 inhibitor C) (p18-INK4c)	0.10	-	cyt	0		cytoplasm [TAS]	603369	1MX6	168
Q16878 UniProt NPD GO	CDO1_HUMAN	Cysteine dioxygenase type 1 (EC 1.13.11.20) (Cysteine dioxygenase type I) (CDO) (CDO-I)	0.10	-	nuc	0		cytosol [TAS]	603943		200
Q5RBQ7 UniProt NPD GO	CDO1_PONPY	Cysteine dioxygenase type 1 (EC 1.13.11.20) (Cysteine dioxygenase type I) (CDO) (CDO-I)	0.10	-	nuc	0					200
Q01958 UniProt NPD GO	CPP2_ENTHI	Cysteine proteinase 2 precursor (EC 3.4.22.-)	0.10	-	vac	0					315
P36185 UniProt NPD GO	ACP2_ENTHI	Cysteine proteinase ACP2 precursor (EC 3.4.22.-) (Fragment)	0.10	-	cyt	0	Secreted protein; extracellular space				310
P91758 UniProt NPD GO	CRNF_LYMST	Cysteine-rich neurotrophic factor precursor (CRNF)	0.10	-	exc	0	Secreted protein				121
Q9NS75 UniProt NPD GO	CLTR2_HUMAN	Cysteinyl leukotriene receptor 2 (CysLTR2) (HG57) (HPN321) (hGPCR21)	0.10	-	end	7 *	Membrane; multi-pass membrane protein		605666		346

You are viewing entries 64151 to 64200 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.