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
P15086 UniProt NPD GO	CBPB1_HUMAN	Carboxypeptidase B precursor (EC 3.4.17.2) (Pancreas-specific protein) (PASP)	0.10	-	exc	0	Secreted protein		114852	1ZLI	417
Q63111 UniProt NPD GO	CEAM3_RAT	Carcinoembryonic antigen-related cell adhesion molecule 3 precursor (Carcinoembryonic antigen CGM1)	0.10	-	mit	0					709
Q9NIP6 UniProt NPD GO	CP2B_DROME	Cardio acceleratory peptide 2b precursor (Myotropin-CAP2b-like protein) [Contains: CAP-1 (Capa-1) (C ...	0.10	-	mit	0	Secreted protein	extracellular region [NAS]			151
Q6ITB0 UniProt NPD GO	IVBI_TROCA	Carinatin precursor	0.10	-	vac	0	Secreted protein (By similarity)				83
P81123 UniProt NPD GO	KC1D_RABIT	Casein kinase I isoform delta (EC 2.7.11.1) (CKI-delta) (CKId) (Fragment)	0.10	-	cyt	0	Cytoplasm				81
P28548 UniProt NPD GO	CSK2B_CAEEL	Casein kinase II subunit beta (CK II beta)	0.10	-	cyt	0					234
Q9Y2G2 UniProt NPD GO	CARD8_HUMAN	Caspase recruitment domain-containing protein 8 (Apoptotic protein NDPP1) (DACAR) (CARD-inhibitor of ...	0.10	-	end	0	Cytoplasm. Nucleus	cytoplasm [IDA]	609051		431
P55313 UniProt NPD GO	CATA2_WHEAT	Catalase (EC 1.11.1.6)	0.10	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
P32290 UniProt NPD GO	CATA_PHAAU	Catalase (EC 1.11.1.6)	0.10	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
Q99028 UniProt NPD GO	COMT_PIG	Catechol O-methyltransferase (EC 2.1.1.6) (Fragment)	0.10	-	cyt	0	Isoform S-COMT: Cytoplasm. Isoform MB-COMT: Cell membrane; single-pass type II membrane protein; ext ...				186
Q26563 UniProt NPD GO	CATC_SCHMA	Cathepsin C precursor (EC 3.4.22.-)	0.10	-	exc	0	Lysosome				454
P16228 UniProt NPD GO	CATE_RAT	Cathepsin E precursor (EC 3.4.23.34)	0.10	-	exc	0	Endosome. The proenzyme is localized to the endoplasmic reticulum and Golgi apparatus, while the mat ...	endosome [IDA]			398
Q9JL96 UniProt NPD GO	CATM_MOUSE	Cathepsin M precursor (EC 3.4.22.-)	0.10	-	end	0	Lysosome (Potential)				333
Q8HY81 UniProt NPD GO	CATS_CANFA	Cathepsin S precursor (EC 3.4.22.27)	0.10	-	exc	0	Lysosome (By similarity)				331
Q5SPB6 UniProt NPD GO	CHAC1_BRARE	Cation transport regulator-like protein 1	0.10	-	cyt	0					196
Q9BUX1 UniProt NPD GO	CHAC1_HUMAN	Cation transport regulator-like protein 1	0.10	-	cyt	0					222
Q8R3J5 UniProt NPD GO	CHAC1_MOUSE	Cation transport regulator-like protein 1	0.10	-	cyt	0					223
Q8BHG3 UniProt NPD GO	CC50B_MOUSE	Cell cycle control protein 50B (Transmembrane protein 30B)	0.10	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				353
Q5FVI4 UniProt NPD GO	CEND_RAT	Cell cycle exit and neuronal differentiation protein 1	0.10	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				149
Q8N111 UniProt NPD GO	CEND_HUMAN	Cell cycle exit and neuronal differentiation protein 1 (BM88 antigen)	0.10	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)		608213		149
Q9JKC6 UniProt NPD GO	CEND_MOUSE	Cell cycle exit and neuronal differentiation protein 1 (BM88 antigen)	0.10	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				149
O70302 UniProt NPD GO	CIDEA_MOUSE	Cell death activator CIDE-A (Cell death-inducing DFFA-like effector A)	0.10	-	mit	0		mitochondrial envelope [IDA] mitochondrion [IDA]			217
Q00646 UniProt NPD GO	CDC2_EMENI	Cell division control protein 2 (EC 2.7.11.22) (EC 2.7.11.23) (Cyclin-dependent protein kinase)	0.10	-	cyt	0					323
Q4Y4B1 UniProt NPD GO	CDC2H_PLACH	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23)	0.10	-	nuc	0	Cytoplasm (By similarity)				288
Q9XZD6 UniProt NPD GO	CDC2H_PLAVI	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (Pvcrk2)	0.10	-	cyt	0	Cytoplasm (By similarity)				288
Q5RCH1 UniProt NPD GO	CDC2_PONPY	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase) (Cyclin-d ...	0.10	-	cyt	0	Nucleus (By similarity)				297
Q01112 UniProt NPD GO	CDC42_SCHPO	Cell division control protein 42 homolog (CDC42Sp)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				192
Q5Z974 UniProt NPD GO	FTSH_ORYSA	Cell division protein ftsH homolog, chloroplast precursor (EC 3.4.24.-)	0.10	-	end	1	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				686
Q8TD46 UniProt NPD GO	MOX2R_HUMAN	Cell surface glycoprotein OX2 receptor precursor (CD200 cell surface glycoprotein receptor)	0.10	-	end	2 *	Isoform 1, isoform 4: Cell membrane; single-pass type I membrane protein. Isoform 2, isoform 3: Secr ...		607546		325
P51861 UniProt NPD GO	CDR1_HUMAN	Cerebellar degeneration-related antigen 1 (CDR34)	0.10	-	cyt	0			302650		223
Q9SML4 UniProt NPD GO	CHS1_CICAR	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.10	-	cyt	0					389
P48392 UniProt NPD GO	CHS3_GERHY	Chalcone synthase 3 (EC 2.3.1.74) (Naringenin-chalcone synthase 3)	0.10	-	cyt	0					403
O23882 UniProt NPD GO	CHS4_PEA	Chalcone synthase 4 (EC 2.3.1.74) (Naregenin-chalcone synthase 4)	0.10	-	mit	0					389
P30081 UniProt NPD GO	CHS7_SOYBN	Chalcone synthase 7 (EC 2.3.1.74) (Naringenin-chalcone synthase 7)	0.10	-	nuc	0					389
P08894 UniProt NPD GO	CHSA_PETHY	Chalcone synthase A (EC 2.3.1.74) (Naringenin-chalcone synthase A)	0.10	-	mit	0					389
O22046 UniProt NPD GO	CHSE_IPONI	Chalcone synthase E (EC 2.3.1.74) (Naringenin-chalcone synthase E) (CHS-E)	0.10	-	cyt	0					389
O22047 UniProt NPD GO	CHSE_IPOPU	Chalcone synthase E (EC 2.3.1.74) (Naringenin-chalcone synthase E) (CHS-E)	0.10	-	cyt	0					389
P41089 UniProt NPD GO	CFI_PEA	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase)	0.10	-	nuc	0					223
O60921 UniProt NPD GO	HUS1_HUMAN	Checkpoint protein HUS1 (hHUS1)	0.10	-	cyt	0	Nucleus. In discrete nuclear foci upon DNA damage. According to Ref.12, localized also in the cytopl ...	nucleus [IDA]	603760		280
Q61362 UniProt NPD GO	CH3L1_MOUSE	Chitinase-3-like protein 1 precursor (Cartilage glycoprotein 39) (GP-39) (BRP39 protein)	0.10	-	exc	0	Secreted protein; extracellular space (By similarity)				381
Q75BA5 UniProt NPD GO	ALG1_ASHGO	Chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) (GDP-mannose-dolichol diphospho ...	0.10	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				471
Q96282 UniProt NPD GO	CLCC_ARATH	Chloride channel protein CLC-c (AtCLC-c)	0.10	-	end	10	Membrane; multi-pass membrane protein				779
Q9TLU1 UniProt NPD GO	RR17_CYACA	Chloroplast 30S ribosomal protein S17	0.10	-	nuc	0	Plastid; chloroplast				77
P56808 UniProt NPD GO	RR19_ARATH	Chloroplast 30S ribosomal protein S19	0.10	-	mit	0	Plastid; chloroplast				92
P12153 UniProt NPD GO	RR19_ORYSA	Chloroplast 30S ribosomal protein S19	0.10	-	nuc	0	Plastid; chloroplast				92
Q6YXK6 UniProt NPD GO	RR19_PHYPA	Chloroplast 30S ribosomal protein S19	0.10	-	nuc	0	Plastid; chloroplast				92
P06508 UniProt NPD GO	RR19_SPIOL	Chloroplast 30S ribosomal protein S19 alpha (CS-S23)	0.10	-	mit	0	Plastid; chloroplast				91
Q85G29 UniProt NPD GO	RR6_CYAME	Chloroplast 30S ribosomal protein S6	0.10	-	cyt	0	Plastid; chloroplast				99
P56792 UniProt NPD GO	RK14_ARATH	Chloroplast 50S ribosomal protein L14	0.10	-	cyt	0	Plastid; chloroplast				122
P51311 UniProt NPD GO	RK2_PORPU	Chloroplast 50S ribosomal protein L2	0.10	-	mit	0	Plastid; chloroplast				294

You are viewing entries 64101 to 64150 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.