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
P93472 UniProt NPD GO	DIM_PEA	Cell elongation protein diminuto	0.30	-	mit	1 *					567
Q9NVX0 UniProt NPD GO	CEP27_HUMAN	Centrosomal protein of 27 kDa (Cep27 protein)	0.30	-	cyt	0	Centrosome	centrosome [IDA]			235
Q6B8V2 UniProt NPD GO	DNAK_GRATL	Chaperone protein dnaK (Heat shock protein 70) (Heat shock 70 kDa protein) (HSP70)	0.30	-	cyt	0	Plastid; chloroplast				621
Q58CS7 UniProt NPD GO	CHMP3_BOVIN	Charged multivesicular body protein 3 (Chromatin-modifying protein 3) (Vacuolar protein sorting 24)	0.30	-	nuc	0	Cytoplasm; cytosol. Membrane; lipid-anchor				221
Q5BKM3 UniProt NPD GO	CHMP3_XENTR	Charged multivesicular body protein 3 (Chromatin-modifying protein 3) (Vacuolar protein sorting 24)	0.30	-	nuc	0	Intracytoplasmic membrane; lipid-anchor (By similarity)				219
Q12632 UniProt NPD GO	CHS1_RHIRA	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-II chitin synt ...	0.30	-	end	7	Cell membrane; multi-pass membrane protein				852
Q8GVE1 UniProt NPD GO	CIGR2_ORYSA	Chitin-inducible gibberellin-responsive protein 2	0.30	-	nuc	0	Nucleus				544
Q9R279 UniProt NPD GO	CLCN3_CAVPO	Chloride channel protein 3 (ClC-3)	0.30	-	end	11	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein (By similarity). End ...	cell surface [ISS] early endosome [ISS] Golgi apparatus [ISS] integral to membrane [ISS] late endosome [ISS] vesicle membrane [ISS]			760
Q9TLV9 UniProt NPD GO	RR10_CYACA	Chloroplast 30S ribosomal protein S10	0.30	-	nuc	0	Plastid; chloroplast				109
Q8M9V6 UniProt NPD GO	RR11_CHAGL	Chloroplast 30S ribosomal protein S11	0.30	-	nuc	0	Plastid; chloroplast				130
Q2L937 UniProt NPD GO	RR11_GOSHI	Chloroplast 30S ribosomal protein S11	0.30	-	nuc	0	Plastid; chloroplast				138
Q332U4 UniProt NPD GO	RR11_LACSA	Chloroplast 30S ribosomal protein S11	0.30	-	mit	0	Plastid; chloroplast				136
Q6EW19 UniProt NPD GO	RR11_NYMAL	Chloroplast 30S ribosomal protein S11	0.30	-	mit	0	Plastid; chloroplast				138
P51294 UniProt NPD GO	RR11_PORPU	Chloroplast 30S ribosomal protein S11	0.30	-	nuc	0	Plastid; chloroplast				130
Q85FG4 UniProt NPD GO	RR12_ADICA	Chloroplast 30S ribosomal protein S12	0.30	-	nuc	0	Plastid; chloroplast				135
P06368 UniProt NPD GO	RR12_MARPO	Chloroplast 30S ribosomal protein S12	0.30	-	nuc	0	Plastid; chloroplast				123
Q589B0 UniProt NPD GO	RR16_SILLA	Chloroplast 30S ribosomal protein S16	0.30	-	mit	0	Plastid; chloroplast				88
P06354 UniProt NPD GO	RR2_MARPO	Chloroplast 30S ribosomal protein S2	0.30	-	mit	0	Plastid; chloroplast				235
P51249 UniProt NPD GO	RR2_PORPU	Chloroplast 30S ribosomal protein S2	0.30	-	cyt	0	Plastid; chloroplast				241
Q9MUV1 UniProt NPD GO	RR9_MESVI	Chloroplast 30S ribosomal protein S9	0.30	-	mit	0	Plastid; chloroplast				137
Q85FV6 UniProt NPD GO	RK16_CYAME	Chloroplast 50S ribosomal protein L16	0.30	-	nuc	0	Plastid; chloroplast				143
P06391 UniProt NPD GO	RK23_TOBAC	Chloroplast 50S ribosomal protein L23	0.30	-	nuc	0	Plastid; chloroplast				93
Q9TLU3 UniProt NPD GO	RK24_CYACA	Chloroplast 50S ribosomal protein L24	0.30	-	nuc	0	Plastid; chloroplast				94
Q85FU5 UniProt NPD GO	RK36_CYAME	Chloroplast 50S ribosomal protein L36	0.30	-	mit	0	Plastid; chloroplast				37
Q6B8X1 UniProt NPD GO	RK36_GRATL	Chloroplast 50S ribosomal protein L36	0.30	-	nuc	0	Plastid; chloroplast				37
Q8MCA1 UniProt NPD GO	RK36_PHAAN	Chloroplast 50S ribosomal protein L36	0.30	-	mit	0	Plastid; chloroplast				37
Q9TKZ2 UniProt NPD GO	CEMA_NEPOL	Chloroplast envelope membrane protein	0.30	-	end	4	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				392
Q42885 UniProt NPD GO	AROC2_LYCES	Chorismate synthase 2, chloroplast precursor (EC 4.2.3.5) (5-enolpyruvylshikimate-3-phosphate phosph ...	0.30	-	nuc	0	Plastid; chloroplast				431
P14593 UniProt NPD GO	CSP_PLABR	Circumsporozoite protein precursor (CS)	0.30	-	mit	0					485
P16211 UniProt NPD GO	1A01_PONPY	Class I histocompatibility antigen, A-1 alpha chain precursor	0.30	-	end	1	Membrane; single-pass type I membrane protein				365
Q8BIQ5 UniProt NPD GO	CSTF2_MOUSE	Cleavage stimulation factor 64 kDa subunit (CSTF 64 kDa subunit) (CF-1 64 kDa subunit) (CstF-64)	0.30	-	nuc	0	Nucleus				580
O96005 UniProt NPD GO	CLPT1_HUMAN	Cleft lip and palate transmembrane protein 1	0.30	-	end	5	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS]	604783		669
P98139 UniProt NPD GO	FA7_RABIT	Coagulation factor VII precursor (EC 3.4.21.21) (Serum prothrombin conversion accelerator) [Contains ...	0.30	-	exc	0					444
O89079 UniProt NPD GO	COPE_MOUSE	Coatomer subunit epsilon (Epsilon-coat protein) (Epsilon-COP)	0.30	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI-coated vesicle [IDA]			307
Q6NX11 UniProt NPD GO	COF1_XENTR	Cofilin-1	0.30	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				167
Q9Y281 UniProt NPD GO	COF2_HUMAN	Cofilin-2 (Cofilin, muscle isoform)	0.30	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)		601443		166
Q5G6V9 UniProt NPD GO	COF2_PIG	Cofilin-2 (Cofilin, muscle isoform)	0.30	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				166
Q4VC31 UniProt NPD GO	CCD58_HUMAN	Coiled-coil domain-containing protein 58	0.30	-	nuc	0					144
P11087 UniProt NPD GO	CO1A1_MOUSE	Collagen alpha-1(I) chain precursor	0.30	-	exc	0					1453
Q96A83 UniProt NPD GO	EMID2_HUMAN	Collagen alpha-1(XXVI) chain precursor (EMI domain-containing protein 2) (Protein Emu2) (Emilin and ...	0.30	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix		608927		441
P19070 UniProt NPD GO	CR2_MOUSE	Complement receptor type 2 precursor (Cr2) (Complement C3d receptor) (CD21 antigen)	0.30	-	cyt	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			1025
Q8R1B5 UniProt NPD GO	CPLX3_MOUSE	Complexin-3 (Complexin III) (CPX III)	0.30	-	nuc	0	Membrane; lipid-anchor. Enriched at the synaptic terminal	cytosol [IDA] plasma membrane [IDA] synapse [IDA]			158
Q8BT60 UniProt NPD GO	CPNE3_MOUSE	Copine-3 (Copine III)	0.30	-	nuc	0		cytoplasm [ISS] cytosol [ISS]			533
O77220 UniProt NPD GO	CHH_MACLE	Crustacean hyperglycemic hormones precursor [Contains: CHH precursor-related peptide (CPRP); Crustac ...	0.30	-	exc	0	Secreted protein				135
Q26181 UniProt NPD GO	CHH_PENVA	Crustacean hyperglycemic hormones precursor [Contains: CHH precursor-related peptide (CPRP); Crustac ...	0.30	-	nuc	0	Secreted protein				80
P30274 UniProt NPD GO	CCNA2_BOVIN	Cyclin-A2 (Cyclin-A) (Fragment)	0.30	-	nuc	0				1VIN	406
P39947 UniProt NPD GO	CCNC_RAT	Cyclin-C	0.30	-	nuc	0	Nucleus (By similarity)				298
Q16589 UniProt NPD GO	CCNG2_HUMAN	Cyclin-G2	0.30	-	nuc	0	Cytoplasm (By similarity)		603203		344
O08918 UniProt NPD GO	CCNG2_MOUSE	Cyclin-G2	0.30	-	cyt	0	Cytoplasm. Primarily. Nucleus. A minor portion can be detected in some cells in the nucleus				344
P09228 UniProt NPD GO	CYTT_HUMAN	Cystatin SA precursor (Cystatin S5)	0.30	-	exc	0	Secreted protein		123856		141

You are viewing entries 40201 to 40250 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.