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
Q43206 UniProt NPD GO	CATA1_WHEAT	Catalase-1 (EC 1.11.1.6)	0.16	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
P80529 UniProt NPD GO	CYSB_FASHE	Cathepsin B-like cysteine proteinase precursor (EC 3.4.22.-) (Newly excysted juvenile proteins 5 and ...	0.16	-	nuc	0					32
Q800A0 UniProt NPD GO	CATE_RANCA	Cathepsin E precursor (EC 3.4.23.34)	0.16	-	vac	1 *	Endosome (By similarity). The proenzyme is localized to the endoplasmic reticulum and Golgi apparatu ...	endosome [ISS]			397
P43235 UniProt NPD GO	CATK_HUMAN	Cathepsin K precursor (EC 3.4.22.38) (Cathepsin O) (Cathepsin X) (Cathepsin O2)	0.16	-	end	0	Lysosome		265800	7PCK	329
Q9UBR2 UniProt NPD GO	CATZ_HUMAN	Cathepsin Z precursor (EC 3.4.22.-) (Cathepsin X) (Cathepsin P)	0.16	-	end	1 *	Lysosome		603169	1EF7	303
Q96RK1 UniProt NPD GO	CITE4_HUMAN	Cbp/p300-interacting transactivator 4 (MSG1-related protein 2) (MRG-2)	0.16	-	nuc	0	Nucleus. Cytoplasm		606815		184
P14661 UniProt NPD GO	CECP1_PIG	Cecropin-P1	0.16	-	nuc	0	Secreted protein				31
Q29026 UniProt NPD GO	CEND_PIG	Cell cycle exit and neuronal differentiation protein 1 (BM88 antigen)	0.16	-	nuc	1	Cell membrane; single-pass type IV membrane protein (Potential). Intracellular membrane; single-pass ...				140
P34508 UniProt NPD GO	CRN6_CAEEL	Cell death-related nuclease 6 precursor (EC 3.1.-.-)	0.16	-	end	0					378
P23573 UniProt NPD GO	CDC2C_DROME	Cell division control protein 2 cognate (EC 2.7.11.22) (EC 2.7.11.23)	0.16	-	cyt	0					314
P29618 UniProt NPD GO	CDC21_ORYSA	Cell division control protein 2 homolog 1 (EC 2.7.11.22)	0.16	-	cyt	0					294
O19922 UniProt NPD GO	FTSH_CYACA	Cell division protein ftsH homolog (EC 3.4.24.-)	0.16	-	end	2 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				614
P40552 UniProt NPD GO	TIR3_YEAST	Cell wall protein TIR3 precursor	0.16	-	exc	0		cell wall (sensu Fungi) [IDA]			269
Q07990 UniProt NPD GO	YL042_YEAST	Cell wall protein YLR042C precursor	0.16	-	exc	0	Cell wall; lipid-anchor; GPI-anchor. GPI-anchored cell wall protein (GPI-CWP)	cell wall (sensu Fungi) [IDA]			161
Q9XT27 UniProt NPD GO	CERU_SHEEP	Ceruloplasmin precursor (EC 1.16.3.1) (Ferroxidase)	0.16	-	exc	0	Secreted protein				1048
Q9FUB7 UniProt NPD GO	CHSY_HYPAN	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.16	-	cyt	0					390
P23569 UniProt NPD GO	CHSY_PUELO	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.16	-	nuc	0					389
P48388 UniProt NPD GO	CHS3_CAMSI	Chalcone synthase 3 (EC 2.3.1.74) (Naringenin-chalcone synthase 3)	0.16	-	cyt	0					389
P22924 UniProt NPD GO	CHSB_PETHY	Chalcone synthase B (EC 2.3.1.74) (Naringenin-chalcone synthase B)	0.16	-	cyt	0					392
P49463 UniProt NPD GO	DNAK_ODOSI	Chaperone protein dnaK (Heat shock protein 70) (Heat shock 70 kDa protein) (HSP70)	0.16	-	cyt	0	Plastid; chloroplast				614
Q94596 UniProt NPD GO	CH60_LEIMA	Chaperonin HSP60, mitochondrial precursor (Protein Cpn60) (groEL protein) (Heat shock protein 60)	0.16	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				589
Q9R0M1 UniProt NPD GO	XCR1_MOUSE	Chemokine XC receptor 1 (XC chemokine receptor 1) (Lymphotactin receptor) (SCM1 receptor) (mXCR1)	0.16	-	end	7 *	Membrane; multi-pass membrane protein				322
P29026 UniProt NPD GO	CHI1_RHIOL	Chitinase 1 precursor (EC 3.2.1.14)	0.16	-	exc	0	Secreted protein (Probable)				540
Q5RBP6 UniProt NPD GO	CH3L1_PONPY	Chitinase-3-like protein 1 precursor	0.16	-	cyt	0	Secreted protein; extracellular space (By similarity)				410
P36222 UniProt NPD GO	CH3L1_HUMAN	Chitinase-3-like protein 1 precursor (Cartilage glycoprotein 39) (GP-39) (39 kDa synovial protein) ( ...	0.16	-	vac	0	Secreted protein; extracellular space	extracellular matrix (sensu Metazoa) [TAS] extracellular space [TAS]	601525	1NWU	383
P49010 UniProt NPD GO	HEXC_BOMMO	Chitooligosaccharidolytic beta-N-acetylglucosaminidase precursor (EC 3.2.1.52) (Beta-GlcNAcase) (Bet ...	0.16	-	cyt	0					596
Q13231 UniProt NPD GO	CHIT1_HUMAN	Chitotriosidase-1 precursor (EC 3.2.1.14) (Chitinase-1)	0.16	-	end	1 *	Secreted protein. Lysosome. A small proportion is lysosomal	extracellular space [IC]	600031	1WB0	466
Q8LUX2 UniProt NPD GO	RR19_PHAAN	Chloroplast 30S ribosomal protein S19	0.16	-	mit	0	Plastid; chloroplast				92
P07816 UniProt NPD GO	RR19_SOYBN	Chloroplast 30S ribosomal protein S19	0.16	-	mit	0	Plastid; chloroplast				91
Q85FN0 UniProt NPD GO	RR2_ADICA	Chloroplast 30S ribosomal protein S2	0.16	-	cyt	0	Plastid; chloroplast				235
Q8WHY4 UniProt NPD GO	RR3_PSINU	Chloroplast 30S ribosomal protein S3	0.16	-	mit	0	Plastid; chloroplast				220
O98455 UniProt NPD GO	RR3_SPIMX	Chloroplast 30S ribosomal protein S3	0.16	-	nuc	0	Plastid; chloroplast				218
O78447 UniProt NPD GO	RR6_GUITH	Chloroplast 30S ribosomal protein S6	0.16	-	cyt	0	Plastid; chloroplast				96
P52772 UniProt NPD GO	RK23_PINTH	Chloroplast 50S ribosomal protein L23	0.16	-	nuc	0	Plastid; chloroplast				91
P49561 UniProt NPD GO	RK27_ODOSI	Chloroplast 50S ribosomal protein L27	0.16	-	nuc	0	Plastid; chloroplast				83
Q9TLU9 UniProt NPD GO	RK36_CYACA	Chloroplast 50S ribosomal protein L36	0.16	-	mit	0	Plastid; chloroplast				37
O46906 UniProt NPD GO	RK5_GUITH	Chloroplast 50S ribosomal protein L5	0.16	-	cyt	0	Plastid; chloroplast				181
P11597 UniProt NPD GO	CETP_HUMAN	Cholesteryl ester transfer protein precursor (Lipid transfer protein I)	0.16	-	exc	0	Secreted protein; extracellular space		607322		493
Q8VII6 UniProt NPD GO	CTL1_RAT	Choline transporter-like protein 1 (Solute carrier family 44 member 1) (CD92 antigen) (CDw92)	0.16	-	end	9 *	Membrane; multi-pass membrane protein (By similarity)				656
Q63148 UniProt NPD GO	CHRD_RAT	Chordin (Fragment)	0.16	-	nuc	0	Secreted protein (By similarity)				176
P13426 UniProt NPD GO	CH15_DROSU	Chorion protein S15	0.16	-	mit	0					121
P17110 UniProt NPD GO	CH36_CERCA	Chorion protein S36	0.16	-	nuc	0					320
Q9JKP8 UniProt NPD GO	CHRC1_MOUSE	Chromatin accessibility complex protein 1 (CHRAC-1) (DNA polymerase epsilon subunit p15) (YC-like pr ...	0.16	-	nuc	0	Nucleus (Potential)	chromatin accessibility complex [ISS] epsilon DNA polymerase complex [ISS]			129
P19597 UniProt NPD GO	CSP_PLAFO	Circumsporozoite protein precursor (CS)	0.16	-	mit	1					397
P26694 UniProt NPD GO	CSP_PLARE	Circumsporozoite protein precursor (CS)	0.16	-	mit	0					388
P09496 UniProt NPD GO	CLCA_HUMAN	Clathrin light chain A (Lca)	0.16	-	nuc	0	Cytoplasmic face of coated pits and vesicles	clathrin coat [NAS]	118960		248
Q9UKF6 UniProt NPD GO	CPSF3_HUMAN	Cleavage and polyadenylation specificity factor 73 kDa subunit (CPSF 73 kDa subunit)	0.16	-	cyt	0	Nucleus (By similarity)	nucleoplasm [TAS]	606029		684
Q9BSH4 UniProt NPD GO	CCD44_HUMAN	Coiled-coil domain-containing protein 44	0.16	-	nuc	0					297
Q9Y534 UniProt NPD GO	CSDC2_HUMAN	Cold shock domain-containing protein C2 (RNA-binding protein PIPPin)	0.16	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). PIPPin-RNA complexes are located to the nucleus ...	cytoplasm [NAS] nucleus [NAS]			153
P33890 UniProt NPD GO	TIR2_YEAST	Cold shock-induced protein TIR2 precursor (Serine-rich protein 2)	0.16	-	exc	0	Secreted protein (Probable)				251

You are viewing entries 55451 to 55500 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.