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
P15175 UniProt NPD GO	ICTL_PIG	Cathelin	0.25	-	nuc	0	Secreted protein				96
O35740 UniProt NPD GO	CITE2_MOUSE	Cbp/p300-interacting transactivator 2 (MSG-related protein 1) (MRG-1)	0.25	-	nuc	0	Nucleus	cytoplasm [ISS] nucleus [ISS]			269
Q9UQY9 UniProt NPD GO	SPO4_SCHPO	Cell cycle protein kinase spo4 (EC 2.7.11.1) (Sporulation-specific protein 4)	0.25	-	cyt	0	Nucleus				429
O60543 UniProt NPD GO	CIDEA_HUMAN	Cell death activator CIDE-A (Cell death-inducing DFFA-like effector A)	0.25	-	cyt	0			604440		219
P51327 UniProt NPD GO	FTSH_PORPU	Cell division protein ftsH homolog (EC 3.4.24.-)	0.25	-	end	2 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				628
Q39444 UniProt NPD GO	FTSH_CAPAN	Cell division protein ftsH homolog, chloroplast precursor (EC 3.4.24.-) (Fragment)	0.25	-	end	1	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				662
P41209 UniProt NPD GO	CETN1_MOUSE	Centrin-1 (Caltractin)	0.25	-	mit	0	Centrosome. Centrosome of interphase and mitotic cells	centrosome [IDA]			172
Q5EA18 UniProt NPD GO	CENPL_BOVIN	Centromere protein L (CENP-L)	0.25	-	cyt	0					346
P48398 UniProt NPD GO	CHSB_IPOPU	Chalcone synthase B (EC 2.3.1.74) (Naringenin-chalcone synthase B) (CHS-B)	0.25	-	mit	0					396
O80684 UniProt NPD GO	DNJ72_ARATH	Chaperone protein dnaJ 72 (AtJ72) (AtDjC72)	0.25	-	nuc	1	Membrane; single-pass membrane protein (Potential)				184
Q9SAG8 UniProt NPD GO	DNAJ8_ARATH	Chaperone protein dnaJ 8, chloroplast precursor (AtJ8) (AtDjC8)	0.25	-	mit	0	Plastid; chloroplast (Potential)				163
P48017 UniProt NPD GO	CHS_SAPMO	Chitin synthase (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase)	0.25	-	end	6	Cell membrane; multi-pass membrane protein				886
P30588 UniProt NPD GO	CHS3_NEUCR	Chitin synthase 3 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 3)	0.25	-	end	7	Cell membrane; multi-pass membrane protein				888
P40954 UniProt NPD GO	CHI3_CANAL	Chitinase 3 precursor (EC 3.2.1.14)	0.25	-	exc	0	Secreted protein (Probable)				567
P92942 UniProt NPD GO	CLCB_ARATH	Chloride channel protein CLC-b (AtCLC-b)	0.25	-	end	9	Membrane; multi-pass membrane protein				780
Q85FU4 UniProt NPD GO	RR11_CYAME	Chloroplast 30S ribosomal protein S11	0.25	+	mit	0	Plastid; chloroplast				121
Q85FN9 UniProt NPD GO	RR16_ADICA	Chloroplast 30S ribosomal protein S16	0.25	-	nuc	0	Plastid; chloroplast				78
Q7YJY6 UniProt NPD GO	RR16_CALFE	Chloroplast 30S ribosomal protein S16	0.25	-	mit	0	Plastid; chloroplast				88
Q6B8S1 UniProt NPD GO	RR18_GRATL	Chloroplast 30S ribosomal protein S18	0.25	-	nuc	0	Plastid; chloroplast				70
Q85AW7 UniProt NPD GO	RR2_ANTFO	Chloroplast 30S ribosomal protein S2	0.25	-	cyt	0	Plastid; chloroplast				235
O78482 UniProt NPD GO	RR2_GUITH	Chloroplast 30S ribosomal protein S2	0.25	-	nuc	0	Plastid; chloroplast				235
Q9MTM2 UniProt NPD GO	RR2_OENHO	Chloroplast 30S ribosomal protein S2	0.25	-	mit	0	Plastid; chloroplast				236
O78486 UniProt NPD GO	RR20_GUITH	Chloroplast 30S ribosomal protein S20	0.25	+	nuc	0	Plastid; chloroplast				95
Q3C1L6 UniProt NPD GO	RR3_NICSY	Chloroplast 30S ribosomal protein S3	0.25	-	cyt	0	Plastid; chloroplast				218
P51308 UniProt NPD GO	RR3_PORPU	Chloroplast 30S ribosomal protein S3	0.25	-	mit	0	Plastid; chloroplast				230
Q2MIE9 UniProt NPD GO	RR3_SOLBU	Chloroplast 30S ribosomal protein S3	0.25	-	cyt	0	Plastid; chloroplast				218
Q2VEE2 UniProt NPD GO	RR3_SOLTU	Chloroplast 30S ribosomal protein S3	0.25	-	cyt	0	Plastid; chloroplast				218
P06357 UniProt NPD GO	RR3_TOBAC	Chloroplast 30S ribosomal protein S3	0.25	-	cyt	0	Plastid; chloroplast				218
P49553 UniProt NPD GO	RK16_ODOSI	Chloroplast 50S ribosomal protein L16	0.25	-	mit	0	Plastid; chloroplast				137
P56356 UniProt NPD GO	RK19_CHLVU	Chloroplast 50S ribosomal protein L19	0.25	-	cyt	0	Plastid; chloroplast				130
O98454 UniProt NPD GO	RK22_SPIMX	Chloroplast 50S ribosomal protein L22	0.25	-	nuc	0	Plastid; chloroplast				119
Q6B931 UniProt NPD GO	RK27_GRATL	Chloroplast 50S ribosomal protein L27	0.25	-	nuc	0	Plastid; chloroplast				87
P51416 UniProt NPD GO	RK33_PEA	Chloroplast 50S ribosomal protein L33 (Fragment)	0.25	-	nuc	0	Plastid; chloroplast				40
P49568 UniProt NPD GO	RK36_ODOSI	Chloroplast 50S ribosomal protein L36	0.25	-	nuc	0	Plastid; chloroplast				37
P25914 UniProt NPD GO	CETP_MESAU	Cholesteryl ester transfer protein (Lipid transfer protein I) (Fragment)	0.25	-	cyt	0	Secreted protein				289
Q8C1F4 UniProt NPD GO	CGAT2_MOUSE	Chondroitin beta-1,4-N-acetylgalactosaminyltransferase 2 (EC 2.4.1.174) (GalNAcT-2) (beta4GalNAcT-2) ...	0.25	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...	integral to Golgi membrane [ISS]			542
Q9DF69 UniProt NPD GO	CSPG5_CHICK	Chondroitin sulfate proteoglycan 5 precursor (Acidic leucine-rich EGF-like domain-containing brain p ...	0.25	-	cyt	1	Cell membrane; single-pass type I membrane protein				594
P51500 UniProt NPD GO	CGHB_CALJA	Choriogonadotropin beta chain precursor (Chorionic gonadotrophin beta subunit) (CG-beta)	0.25	-	nuc	0	Secreted protein				164
P47128 UniProt NPD GO	EAF6_YEAST	Chromatin modification-related protein EAF6 (ESA1-associated factor 6)	0.25	-	nuc	0	Nucleus	H4/H2A histone acetyltransferase complex [IPI] nucleus [IDA]			113
P51642 UniProt NPD GO	CNTF_MOUSE	Ciliary neurotrophic factor (CNTF)	0.25	-	cyt	0	Cytoplasm	extracellular space [IDA]			198
Q02011 UniProt NPD GO	CNTF_CHICK	Ciliary neurotrophic factor (CNTF) (Growth-promoting activity) (GPA)	0.25	-	cyt	0	Cytoplasm				195
P08307 UniProt NPD GO	CSP_PLAFW	Circumsporozoite protein precursor (CS)	0.25	-	mit	0					442
P04922 UniProt NPD GO	CSP_PLAKU	Circumsporozoite protein precursor (CS)	0.25	-	end	1					351
Q8BQZ5 UniProt NPD GO	CPSF4_MOUSE	Cleavage and polyadenylation specificity factor 30 kDa subunit (CPSF 30 kDa subunit) (Clipper homolo ...	0.25	-	nuc	0	Nucleus (By similarity)				211
Q63207 UniProt NPD GO	FA10_RAT	Coagulation factor X precursor (EC 3.4.21.6) (Stuart factor) [Contains: Factor X light chain; Factor ...	0.25	-	nuc	1 *					482
P98140 UniProt NPD GO	FA12_BOVIN	Coagulation factor XII precursor (EC 3.4.21.38) (Hageman factor) (HAF) [Contains: Coagulation factor ...	0.25	-	nuc	0	Secreted protein				593
O93235 UniProt NPD GO	CIRBP_XENLA	Cold-inducible RNA-binding protein (Glycine-rich RNA-binding protein CIRP) (xCIRP)	0.25	+	nuc	0	Nucleus; nucleoplasm (By similarity)				163
P08120 UniProt NPD GO	CO4A1_DROME	Collagen alpha-1(IV) chain precursor	0.25	-	nuc	0		collagen type IV [TAS]			1775
P02462 UniProt NPD GO	CO4A1_HUMAN	Collagen alpha-1(IV) chain precursor	0.25	-	exc	0		extracellular region [NAS]	120130	1LI1	1669
P02463 UniProt NPD GO	CO4A1_MOUSE	Collagen alpha-1(IV) chain precursor	0.25	-	exc	0		collagen type IV [IDA]			1669

You are viewing entries 45051 to 45100 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.