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
O04151 UniProt NPD GO	CALR1_ARATH	Calreticulin-1 precursor	0.13	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				425
P0C092 UniProt NPD GO	CSEN4_MOUSE	Calsenilin isoform 4	0.13	-	mit	0					89
P32950 UniProt NPD GO	CARP2_CANPA	Candidapepsin-2 precursor (EC 3.4.23.24) (Aspartate protease 2) (ACP 2)	0.13	-	exc	0	Secreted protein				412
P43093 UniProt NPD GO	CARP4_CANAL	Candidapepsin-4 precursor (EC 3.4.23.24) (Aspartate protease 4) (ACP 4) (Secreted aspartic protease ...	0.13	-	exc	0	Secreted protein				417
P15169 UniProt NPD GO	CBPN_HUMAN	Carboxypeptidase N catalytic chain precursor (EC 3.4.17.3) (CPN) (Carboxypeptidase N polypeptide 1) ...	0.13	-	nuc	0	Secreted protein; extracellular space	extracellular space [TAS]	603103		458
Q00614 UniProt NPD GO	CACP_CANTR	Carnitine O-acetyltransferase, mitochondrial precursor (EC 2.3.1.7) (Carnitine acetylase)	0.13	-	cyt	0	Peroxisome (By similarity). Mitochondrion; mitochondrial inner membrane; matrix side (By similarity) ...				627
P35445 UniProt NPD GO	COMP_BOVIN	Cartilage oligomeric matrix protein (COMP) (Fragment)	0.13	-	cyt	0	Secreted protein				439
P55303 UniProt NPD GO	CATR_ASPNG	Catalase R (EC 1.11.1.6)	0.13	-	exc	0					730
P18123 UniProt NPD GO	CATA3_MAIZE	Catalase isozyme 3 (EC 1.11.1.6)	0.13	-	cyt	0	Mitochondrion				496
P55309 UniProt NPD GO	CATA2_ORYSA	Catalase isozyme B (EC 1.11.1.6) (CAT-B)	0.13	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
O61235 UniProt NPD GO	CATA2_CAEEL	Catalase-2 (EC 1.11.1.6)	0.13	-	cyt	0	Cytoplasm	cytoplasm [IEP]			497
Q42547 UniProt NPD GO	CATA3_ARATH	Catalase-3 (EC 1.11.1.6)	0.13	-	nuc	0	Peroxisome (Potential)				492
Q7XPF8 UniProt NPD GO	HKT4_ORYSA	Cation transporter HKT4 (OsHKT4)	0.13	-	end	9	Membrane; multi-pass membrane protein (Probable)				552
Q3YAF4 UniProt NPD GO	HKT8_ORYSA	Cation transporter HKT8 (OsHKT8)	0.13	-	end	10 *	Membrane; multi-pass membrane protein (Probable)				554
Q3MIR4 UniProt NPD GO	CC50B_HUMAN	Cell cycle control protein 50B (Transmembrane protein 30B)	0.13	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				351
Q38774 UniProt NPD GO	CDC2C_ANTMA	Cell division control protein 2 homolog C (EC 2.7.11.22) (EC 2.7.11.23)	0.13	-	cyt	0					305
Q9BAE0 UniProt NPD GO	FTSH_MEDSA	Cell division protein ftsH homolog, chloroplast precursor (EC 3.4.24.-)	0.13	-	nuc	1	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				706
Q04770 UniProt NPD GO	CDK2_ENTHI	Cell division protein kinase 2 homolog (EC 2.7.11.22)	0.13	+	cyt	0					291
P53694 UniProt NPD GO	CWL1_SCHPO	Cell lysis protein cwl1	0.13	+	vac	3					308
P48397 UniProt NPD GO	CHSA_IPOPU	Chalcone synthase A (EC 2.3.1.74) (Naringenin-chalcone synthase A) (CHS-A)	0.13	-	cyt	0					396
P48403 UniProt NPD GO	CHSA_IPOTR	Chalcone synthase A (EC 2.3.1.74) (Naringenin-chalcone synthase A) (CHS-A) (Fragment)	0.13	-	cyt	0					362
P24824 UniProt NPD GO	CHS1_MAIZE	Chalcone synthase WHP1 (EC 2.3.1.74) (Naringenin-chalcone synthase WHP1) (White pollen)	0.13	-	cyt	0					400
P50325 UniProt NPD GO	CDA_MUCRO	Chitin deacetylase precursor (EC 3.5.1.41)	0.13	-	nuc	0					421
P30598 UniProt NPD GO	CHS1_USTMA	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Fragment)	0.13	-	mit	0	Cell membrane; multi-pass membrane protein				198
Q91Z98 UniProt NPD GO	CH3L4_MOUSE	Chitinase 3-like protein 4 precursor (Secreted protein Ym2)	0.13	-	mit	0	Secreted protein				402
Q6TMG6 UniProt NPD GO	CH3L1_SHEEP	Chitinase-3-like protein 1 (Signal-processing protein) (Secretory glycoprotein of 40 kDa)	0.13	-	cyt	0	Secreted protein; extracellular space (By similarity)			2G8Z	361
P30922 UniProt NPD GO	CH3L1_BOVIN	Chitinase-3-like protein 1 precursor (Cartilage glycoprotein 39) (GP-39) (39 kDa whey protein) (Sign ...	0.13	-	exc	0	Secreted protein; extracellular space			2ESC	383
Q23997 UniProt NPD GO	CH47_DROME	Chitinase-like protein DS47 precursor	0.13	-	exc	0	Secreted protein. It is transported to target tissues via hemolymph				452
P40879 UniProt NPD GO	S26A3_HUMAN	Chloride anion exchanger (Protein DRA) (Down-regulated in adenoma) (Solute carrier family 26 member ...	0.13	-	end	11	Membrane; multi-pass membrane protein (Probable)	membrane fraction [TAS]	214700		764
P35522 UniProt NPD GO	CICH_TORCA	Chloride channel protein (ClC-0)	0.13	-	end	10 *	Membrane; multi-pass membrane protein				809
Q7YJT8 UniProt NPD GO	RR19_CALFE	Chloroplast 30S ribosomal protein S19	0.13	-	mit	0	Plastid; chloroplast				92
P06588 UniProt NPD GO	RR19_MAIZE	Chloroplast 30S ribosomal protein S19	0.13	-	mit	0	Plastid; chloroplast				92
P49491 UniProt NPD GO	RR3_ODOSI	Chloroplast 30S ribosomal protein S3	0.13	-	mit	0	Plastid; chloroplast				214
P51304 UniProt NPD GO	RK14_PORPU	Chloroplast 50S ribosomal protein L14	0.13	-	mit	0	Plastid; chloroplast				122
P09596 UniProt NPD GO	RK14_SPIOL	Chloroplast 50S ribosomal protein L14 (Ribosomal protein CS-L29)	0.13	-	cyt	0	Plastid; chloroplast				121
Q3BAJ7 UniProt NPD GO	RK22_PHAAO	Chloroplast 50S ribosomal protein L22	0.13	-	nuc	0	Plastid; chloroplast				119
Q70XY5 UniProt NPD GO	RK33_AMBTC	Chloroplast 50S ribosomal protein L33	0.13	-	nuc	0	Plastid; chloroplast				68
Q3ZJ82 UniProt NPD GO	RK5_PSEAK	Chloroplast 50S ribosomal protein L5	0.13	-	cyt	0	Plastid; chloroplast				180
Q70XZ1 UniProt NPD GO	CEMA_AMBTC	Chloroplast envelope membrane protein	0.13	-	cyt	0	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				229
P69374 UniProt NPD GO	CEMA_AEGCR	Chloroplast envelope membrane protein (Fragment)	0.13	-	end	2 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				151
P69375 UniProt NPD GO	CEMA_AEGTA	Chloroplast envelope membrane protein (Fragment)	0.13	-	end	2 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				151
Q9H9P2 UniProt NPD GO	CHODL_HUMAN	Chondrolectin precursor (Transmembrane protein MT75)	0.13	-	end	1	Membrane; single-pass type I membrane protein (Potential)	perinuclear region [IDA]	607247		273
P14059 UniProt NPD GO	CSH2_MESAU	Chorionic somatomammotropin hormone 2 precursor (Placental lactogen II) (PL-II)	0.13	-	nuc	0	Secreted protein				221
P31656 UniProt NPD GO	CADH_MEDSA	Cinnamyl alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.13	-	cyt	0					358
O08585 UniProt NPD GO	CLCA_MOUSE	Clathrin light chain A (Lca)	0.13	-	cyt	0	Cytoplasmic face of coated pits and vesicles				235
Q9NGJ7 UniProt NPD GO	CLC5_CAEEL	Clc-like protein 5	0.13	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	membrane [NAS]			281
Q9QXK7 UniProt NPD GO	CPSF3_MOUSE	Cleavage and polyadenylation specificity factor 73 kDa subunit (CPSF 73 kDa subunit)	0.13	-	cyt	0	Nucleus (By similarity)				684
Q9CQI6 UniProt NPD GO	COTL1_MOUSE	Coactosin-like protein	0.13	-	cyt	0				1WM4	141
P25155 UniProt NPD GO	FA10_CHICK	Coagulation factor X precursor (EC 3.4.21.6) (Stuart factor) (Virus-activating protease) (VAP) [Cont ...	0.13	-	exc	0					475
Q96EY8 UniProt NPD GO	MMAB_HUMAN	Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial precursor (EC 2.5.1.17) (Cob(I)alam ...	0.13	-	mit	0	Mitochondrion (Probable)		607568		250

You are viewing entries 59501 to 59550 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.