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
Q8BMJ7 UniProt NPD GO	CGRF1_MOUSE	Cell growth regulator with RING finger domain 1 (Cell growth regulatory gene 19 protein)	0.26	-	cyt	1 *					332
O95813 UniProt NPD GO	CER1_HUMAN	Cerberus precursor (Cerberus-related protein)	0.26	-	nuc	0	Secreted protein (Probable)		603777		267
P00450 UniProt NPD GO	CERU_HUMAN	Ceruloplasmin precursor (EC 1.16.3.1) (Ferroxidase)	0.26	-	exc	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	117700	1KCW	1065
P48393 UniProt NPD GO	CHSA_IPOCO	Chalcone synthase A (EC 2.3.1.74) (Naringenin-chalcone synthase A) (CHS-A) (Fragment)	0.26	-	cyt	0					361
P48401 UniProt NPD GO	CHSA_IPOTF	Chalcone synthase A (EC 2.3.1.74) (Naringenin-chalcone synthase A) (CHS-A) (Fragment)	0.26	-	cyt	0					362
Q7LBR1 UniProt NPD GO	CHM1B_HUMAN	Charged multivesicular body protein 1b (Chromatin-modifying protein 1b) (CHMP1b) (CHMP1.5) (Vacuolar ...	0.26	-	nuc	0	Cytoplasm; cytosol. Endosome		606486		199
Q99LU0 UniProt NPD GO	CH1B1_MOUSE	Charged multivesicular body protein 1b-1 (Chromatin-modifying protein 1b-1) (CHMP1b-1)	0.26	-	nuc	0	Cytoplasm; cytosol (By similarity). Endosome (By similarity)				199
P23316 UniProt NPD GO	CHS1_CANAL	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1)	0.26	-	end	7	Cell membrane; multi-pass membrane protein				776
P30589 UniProt NPD GO	CHS2_NEUCR	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2)	0.26	-	end	7	Cell membrane; multi-pass membrane protein				944
Q96NY7 UniProt NPD GO	CLIC6_HUMAN	Chloride intracellular channel 6	0.26	-	cyt	0	Cytoplasm (By similarity). Predominantly. Cell membrane (By similarity). Upon chloride ion efflux fr ...				704
Q6ENC0 UniProt NPD GO	RR12_ORYNI	Chloroplast 30S ribosomal protein S12	0.26	-	mit	0	Plastid; chloroplast				124
P12149 UniProt NPD GO	RR12_ORYSA	Chloroplast 30S ribosomal protein S12	0.26	-	mit	0	Plastid; chloroplast				124
Q2VEC4 UniProt NPD GO	RR15_SOLTU	Chloroplast 30S ribosomal protein S15	0.26	-	nuc	0	Plastid; chloroplast				87
P28807 UniProt NPD GO	RR16_SPIOL	Chloroplast 30S ribosomal protein S16	0.26	-	mit	0	Plastid; chloroplast				88
P06356 UniProt NPD GO	RR3_MARPO	Chloroplast 30S ribosomal protein S3	0.26	-	mit	0	Plastid; chloroplast				217
Q9TLV7 UniProt NPD GO	RR7_CYACA	Chloroplast 30S ribosomal protein S7	0.26	-	nuc	0	Plastid; chloroplast				156
P05727 UniProt NPD GO	RK16_CHLSP	Chloroplast 50S ribosomal protein L16	0.26	-	mit	0	Plastid; chloroplast				136
P56364 UniProt NPD GO	RK16_CHLVU	Chloroplast 50S ribosomal protein L16	0.26	-	mit	0	Plastid; chloroplast				134
Q85AT7 UniProt NPD GO	RK21_ANTFO	Chloroplast 50S ribosomal protein L21	0.26	+	cyt	0	Plastid; chloroplast				118
Q6EW12 UniProt NPD GO	RK22_NYMAL	Chloroplast 50S ribosomal protein L22	0.26	-	nuc	0	Plastid; chloroplast				125
Q85FI0 UniProt NPD GO	RK23_ADICA	Chloroplast 50S ribosomal protein L23	0.26	-	mit	0	Plastid; chloroplast				93
O78430 UniProt NPD GO	RK27_GUITH	Chloroplast 50S ribosomal protein L27	0.26	+	nuc	0	Plastid; chloroplast				86
Q8M9Y6 UniProt NPD GO	RK33_CHAGL	Chloroplast 50S ribosomal protein L33	0.26	-	nuc	0	Plastid; chloroplast				65
P25461 UniProt NPD GO	RK33_MAIZE	Chloroplast 50S ribosomal protein L33	0.26	-	nuc	0	Plastid; chloroplast				65
Q8WI00 UniProt NPD GO	RK33_PSINU	Chloroplast 50S ribosomal protein L33	0.26	-	nuc	0	Plastid; chloroplast				65
Q6L380 UniProt NPD GO	RK33_SACHY	Chloroplast 50S ribosomal protein L33	0.26	-	nuc	0	Plastid; chloroplast				66
Q6ENU3 UniProt NPD GO	RK33_SACOF	Chloroplast 50S ribosomal protein L33	0.26	-	nuc	0	Plastid; chloroplast				66
P21532 UniProt NPD GO	RK36_EUGGR	Chloroplast 50S ribosomal protein L36	0.26	-	mit	0	Plastid; chloroplast				37
P41520 UniProt NPD GO	CCKN_BOVIN	Cholecystokinins precursor (CCK) [Contains: Cholecystokinin 58 (CCK58); Cholecystokinin 39 (CCK39); ...	0.26	-	nuc	0					58
Q9PUU8 UniProt NPD GO	LECT1_CHICK	Chondromodulin-1 precursor (Chondromodulin-I) (ChM-I) (Leukocyte cell-derived chemotaxin 1) [Contain ...	0.26	-	mit	1 *	Cytoplasm (By similarity). Secreted protein (By similarity). Accumulated in the inter-territorial ma ...				347
P07434 UniProt NPD GO	CGHB_PAPAN	Choriogonadotropin beta chain precursor (Chorionic gonadotrophin beta subunit) (CG-beta)	0.26	-	nuc	0	Secreted protein				165
P01233 UniProt NPD GO	CGHB_HUMAN	Choriogonadotropin beta chain precursor (Chorionic gonadotrophin subunit beta) (CG-beta)	0.26	-	nuc	0	Secreted protein	soluble fraction [TAS]	118860	1XUL	165
Q6BT38 UniProt NPD GO	EAF3_DEBHA	Chromatin modification-related protein EAF3	0.26	+	cyt	0	Nucleus (By similarity)				316
P08672 UniProt NPD GO	CSP_PLACB	Circumsporozoite protein precursor (CS)	0.26	-	mit	0					378
P08676 UniProt NPD GO	CSP_PLACM	Circumsporozoite protein precursor (CS)	0.26	-	nuc	0					419
Q8BH61 UniProt NPD GO	F13A_MOUSE	Coagulation factor XIII A chain precursor (EC 2.3.2.13) (Coagulation factor XIIIa) (Protein-glutamin ...	0.26	-	cyt	0	Cytoplasm (By similarity). Secreted protein (By similarity). Cytoplasmic in most tissues, but also s ...				731
Q9QXK3 UniProt NPD GO	COPG2_MOUSE	Coatomer subunit gamma-2 (Gamma-2 coat protein) (Gamma-2 COP)	0.26	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				871
P45592 UniProt NPD GO	COF1_RAT	Cofilin-1 (Cofilin, non-muscle isoform)	0.26	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				165
P23528 UniProt NPD GO	COF1_HUMAN	Cofilin-1 (Cofilin, non-muscle isoform) (18 kDa phosphoprotein) (p18)	0.26	+	cyt	0	Nucleus. Cytoplasm. Almost completely in nucleus in cells exposed to heat shock or 10% dimethyl sulf ...	cytoplasm [TAS] nucleus [TAS]	601442	1Q8X	165
Q5XHH8 UniProt NPD GO	COF2_XENLA	Cofilin-2	0.26	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				167
Q5U4Y2 UniProt NPD GO	COF2_XENTR	Cofilin-2	0.26	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				167
P20849 UniProt NPD GO	CO9A1_HUMAN	Collagen alpha-1(IX) chain precursor	0.26	-	nuc	0		collagen type IX [TAS]	120210		921
P12109 UniProt NPD GO	CO6A1_HUMAN	Collagen alpha-1(VI) chain precursor	0.26	-	mit	0		collagen type VI [NAS]	158810		1028
P25508 UniProt NPD GO	COCA1_BOVIN	Collagen alpha-1(XII) chain (Fragments)	0.26	-	nuc	0					86
Q01149 UniProt NPD GO	CO1A2_MOUSE	Collagen alpha-2(I) chain precursor	0.26	-	exc	0					1372
P55314 UniProt NPD GO	CO8B_RAT	Complement component C8 beta chain (Complement component 8 beta subunit) (Fragment)	0.26	-	nuc	0	Secreted protein				140
P06682 UniProt NPD GO	CO9_ONCMY	Complement component C9 (Fragment)	0.26	-	nuc	0	Secreted protein				574
Q9Y375 UniProt NPD GO	CIA30_HUMAN	Complex I intermediate-associated protein 30, mitochondrial precursor	0.26	-	mit	0	Mitochondrion (Probable)	respiratory chain complex I (sensu Eukaryota) [NAS]	606934		327
P16586 UniProt NPD GO	PDE6C_BOVIN	Cone cGMP-specific 3',5'-cyclic phosphodiesterase alpha'-subunit (EC 3.1.4.35) (cGMP phosphodiestera ...	0.26	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				855
P05545 UniProt NPD GO	CPI1_RAT	Contrapsin-like protease inhibitor 1 precursor (CPI-21) (Kallikrein-binding protein) (KBP) (Growth h ...	0.26	-	end	0	Secreted protein (By similarity)				416

You are viewing entries 44051 to 44100 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.