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
Q05791 UniProt NPD GO	CD123_YEAST	Cell division cycle protein 123	0.20	-	cyt	0	Cytoplasm	cytoplasm [IDA]			360
Q9BXL8 UniProt NPD GO	CDCA4_HUMAN	Cell division cycle-associated protein 4 (Hematopoietic progenitor protein)	0.20	-	nuc	0					241
Q00526 UniProt NPD GO	CDK3_HUMAN	Cell division protein kinase 3 (EC 2.7.11.22)	0.20	-	cyt	0			123828	1LFN	305
P34115 UniProt NPD GO	G13A_DICDI	Cell surface glycoprotein gp138A precursor	0.20	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				730
Q9SEP2 UniProt NPD GO	CHSY_CARAN	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.20	-	cyt	0					395
O04220 UniProt NPD GO	CHSY_CHRAE	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.20	-	cyt	0					396
O22652 UniProt NPD GO	CHSY_RAPSA	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.20	-	cyt	0					394
Q9SBL7 UniProt NPD GO	CHS2_SORBI	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2)	0.20	-	cyt	0					401
O23729 UniProt NPD GO	CHS3_BROFI	Chalcone synthase 3 (EC 2.3.1.74) (Naringenin-chalcone synthase 3)	0.20	-	cyt	0					394
Q9XGX1 UniProt NPD GO	CHS7_SORBI	Chalcone synthase 7 (EC 2.3.1.74) (Naringenin-chalcone synthase 7)	0.20	-	cyt	0					400
Q8BQY8 UniProt NPD GO	HUS1_MOUSE	Checkpoint protein HUS1 (mHUS1)	0.20	-	nuc	0	Nucleus. In discrete nuclear foci upon DNA damage. DNA damage induces its nuclear translocation. Shu ...	nucleus [ISS]			280
Q9XSA7 UniProt NPD GO	CLIC4_BOVIN	Chloride intracellular channel protein 4 (Intracellular chloride ion channel protein p64H1)	0.20	-	mit	0					252
Q9BBP7 UniProt NPD GO	RR19_LOTJA	Chloroplast 30S ribosomal protein S19	0.20	-	mit	0	Plastid; chloroplast				92
Q68RW6 UniProt NPD GO	RR19_PANGI	Chloroplast 30S ribosomal protein S19	0.20	-	mit	0	Plastid; chloroplast				92
Q8M9V0 UniProt NPD GO	RR3_CHAGL	Chloroplast 30S ribosomal protein S3	0.20	-	nuc	0	Plastid; chloroplast				255
Q4VZN0 UniProt NPD GO	RR3_CUCSA	Chloroplast 30S ribosomal protein S3	0.20	-	mit	0	Plastid; chloroplast				218
Q9TL20 UniProt NPD GO	RR3_NEPOL	Chloroplast 30S ribosomal protein S3	0.20	-	mit	0	Plastid; chloroplast				221
Q8MCA5 UniProt NPD GO	RR3_PHAAN	Chloroplast 30S ribosomal protein S3	0.20	-	mit	0	Plastid; chloroplast				216
P51359 UniProt NPD GO	RR6_PORPU	Chloroplast 30S ribosomal protein S6	0.20	-	nuc	0	Plastid; chloroplast				112
Q6B906 UniProt NPD GO	RK1_GRATL	Chloroplast 50S ribosomal protein L1	0.20	-	mit	0	Plastid; chloroplast				235
Q4G358 UniProt NPD GO	RK16_EMIHU	Chloroplast 50S ribosomal protein L16	0.20	-	mit	0	Plastid; chloroplast				138
Q9TM06 UniProt NPD GO	RK19_CYACA	Chloroplast 50S ribosomal protein L19	0.20	-	nuc	0	Plastid; chloroplast				116
Q6B8Z3 UniProt NPD GO	RK19_GRATL	Chloroplast 50S ribosomal protein L19	0.20	-	nuc	0	Plastid; chloroplast				122
Q6B8P2 UniProt NPD GO	RK28_GRATL	Chloroplast 50S ribosomal protein L28	0.20	-	nuc	0	Plastid; chloroplast				64
Q6ENF2 UniProt NPD GO	RK33_ORYNI	Chloroplast 50S ribosomal protein L33	0.20	-	nuc	0	Plastid; chloroplast				66
P12141 UniProt NPD GO	RK33_ORYSA	Chloroplast 50S ribosomal protein L33	0.20	-	nuc	0	Plastid; chloroplast				65
P51232 UniProt NPD GO	CEMA_PORPU	Chloroplast envelope membrane protein	0.20	-	mit	2	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				278
Q65ZA6 UniProt NPD GO	CTF8_SCHPO	Chromosome transmission fidelity protein 8	0.20	-	nuc	0	Nucleus (By similarity)	Ctf18 RFC-like complex [TAS] DNA replication factor C complex [TAS]			109
P14188 UniProt NPD GO	CNTF_RABIT	Ciliary neurotrophic factor (CNTF)	0.20	-	cyt	0	Cytoplasm				199
P13824 UniProt NPD GO	ARP2_PLAFA	Clustered-asparagine-rich protein (CARP)	0.20	-	nuc	0					443
P70375 UniProt NPD GO	FA7_MOUSE	Coagulation factor VII precursor (EC 3.4.21.21) (Serum prothrombin conversion accelerator) [Contains ...	0.20	-	exc	0					446
P53619 UniProt NPD GO	COPD_BOVIN	Coatomer subunit delta (Delta-coat protein) (Delta-COP) (Archain)	0.20	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IDA]			511
Q5XJY5 UniProt NPD GO	COPD_MOUSE	Coatomer subunit delta (Delta-coat protein) (Delta-COP) (Archain)	0.20	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				511
Q66H80 UniProt NPD GO	COPD_RAT	Coatomer subunit delta (Delta-coat protein) (Delta-COP) (Archain)	0.20	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				511
Q9CR27 UniProt NPD GO	CCD53_MOUSE	Coiled-coil domain-containing protein 53	0.20	-	nuc	0					194
Q9Y2S6 UniProt NPD GO	CCD72_HUMAN	Coiled-coil domain-containing protein 72	0.20	-	nuc	0					64
Q8K003 UniProt NPD GO	CCD72_MOUSE	Coiled-coil domain-containing protein 72	0.20	-	nuc	0					64
P60826 UniProt NPD GO	CIRBP_CRIGR	Cold-inducible RNA-binding protein (Glycine-rich RNA-binding protein CIRP) (A18 hnRNP)	0.20	-	nuc	0	Nucleus; nucleoplasm (By similarity)				172
P60824 UniProt NPD GO	CIRBP_MOUSE	Cold-inducible RNA-binding protein (Glycine-rich RNA-binding protein CIRP) (A18 hnRNP)	0.20	-	nuc	0	Nucleus; nucleoplasm				172
P60825 UniProt NPD GO	CIRBP_RAT	Cold-inducible RNA-binding protein (Glycine-rich RNA-binding protein CIRP) (A18 hnRNP)	0.20	-	nuc	0	Nucleus; nucleoplasm (By similarity)				172
P20785 UniProt NPD GO	CO6A1_CHICK	Collagen alpha-1(VI) chain precursor	0.20	-	nuc	0					1019
P42916 UniProt NPD GO	CL43_BOVIN	Collectin-43 precursor (CL-43) (43 kDa collectin)	0.20	-	exc	0	Secreted protein				321
Q8MHZ9 UniProt NPD GO	CL46_BOVIN	Collectin-46 precursor (CL-46) (46 kDa collectin)	0.20	-	exc	0	Secreted protein				371
Q8CFG9 UniProt NPD GO	C1RB_MOUSE	Complement C1r-B subcomponent precursor (EC 3.4.21.41) (Complement component 1, r-B subcomponent) [C ...	0.20	-	cyt	0					706
Q4R4N1 UniProt NPD GO	CPLX1_MACFA	Complexin-1	0.20	-	nuc	0	Cytoplasm; cytosol. Enriched at synaptic-releasing sites in mature neurons (By similarity)				134
P63041 UniProt NPD GO	CPLX1_RAT	Complexin-1 (Complexin I) (CPX I) (Synaphin-2)	0.20	-	nuc	0	Cytoplasm; cytosol. Enriched at synaptic-releasing sites in mature neurons			1KIL	134
P63040 UniProt NPD GO	CPLX1_MOUSE	Complexin-1 (Complexin I) (CPX I) (Synaphin-2) (921-S)	0.20	-	nuc	0	Cytoplasm; cytosol. Enriched at synaptic-releasing sites in mature neurons				134
Q5K0C4 UniProt NPD GO	CXO10_CONCE	Conotoxin-10 precursor	0.20	-	exc	1 *	Secreted protein (By similarity)				80
P22063 UniProt NPD GO	CNTN2_RAT	Contactin-2 precursor (Axonin-1) (Axonal glycoprotein TAG-1) (Transient axonal glycoprotein 1) (TAX- ...	0.20	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor. Attached to the neuronal membrane by a GPI-anchor and is al ...	cell surface [TAS]			1040
O54991 UniProt NPD GO	CNTP1_MOUSE	Contactin-associated protein 1 precursor (Caspr) (Caspr1) (Neurexin 4) (Neurexin IV) (Paranodin) (NC ...	0.20	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1385

You are viewing entries 50451 to 50500 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.