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
Q9BXW7 UniProt NPD GO	CECR5_HUMAN	Cat eye syndrome critical region protein 5 precursor	0.18	-	nuc	0					423
P25379 UniProt NPD GO	STDH_YEAST	Catabolic L-serine/threonine dehydratase [Includes: L-serine dehydratase (EC 4.3.1.17) (L-serine dea ...	0.18	-	mit	0	Mitochondrion	mitochondrial nucleoid [IDA] mitochondrion [IDA]			360
P07145 UniProt NPD GO	CATA_IPOBA	Catalase (EC 1.11.1.6)	0.18	-	cyt	0	Peroxisome				492
P49318 UniProt NPD GO	CATA2_RICCO	Catalase isozyme 2 (EC 1.11.1.6)	0.18	-	cyt	0	Peroxisome (Potential). Glyoxysome (Potential)				492
Q6TPH3 UniProt NPD GO	HKT1_ORYSA	Cation transporter HKT1 (OsHKT1) (Ni-OsHKT1) (Po-OsHKT1)	0.18	-	end	11 *	Membrane; multi-pass membrane protein (Probable)				530
Q93XI5 UniProt NPD GO	HKT2_ORYSA	Cation transporter HKT2 (OsHKT2) (Po-OsHKT2)	0.18	-	end	9 *	Membrane; multi-pass membrane protein (Probable)				530
Q9Z0X0 UniProt NPD GO	BORG3_MOUSE	Cdc42 effector protein 5 (Binder of Rho GTPases 3)	0.18	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein	cytoplasm [IDA] plasma membrane [IDA]			150
Q07730 UniProt NPD GO	ECE1_CANAL	Cell elongation protein 1	0.18	-	end	1					271
P34116 UniProt NPD GO	G13B_DICDI	Cell surface glycoprotein gp138B precursor	0.18	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				734
Q9ZU06 UniProt NPD GO	CHSY_PERAE	Chalcone synthase (EC 2.3.1.74) (Naregenin-chalcone synthase)	0.18	-	nuc	0					392
Q9ZRR8 UniProt NPD GO	CHS1_CASGL	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.18	-	cyt	0					389
Q06703 UniProt NPD GO	CDA2_YEAST	Chitin deacetylase 2 precursor (EC 3.5.1.41)	0.18	-	exc	0					312
Q29411 UniProt NPD GO	CH3L1_PIG	Chitinase-3-like protein 1 precursor (38 kDa heparin-binding glycoprotein) (gp38k) (Signal-processin ...	0.18	-	vac	0	Secreted protein; extracellular space			1ZBC	383
Q8MX40 UniProt NPD GO	IDGF1_DROYA	Chitinase-like protein Idgf1 precursor (Imaginal disk growth factor protein 1)	0.18	-	exc	0	Secreted protein (By similarity). Secreted in hemolymph (By similarity). It is probably transported ...	extracellular region [ISS]			439
Q9QYB1 UniProt NPD GO	CLIC4_MOUSE	Chloride intracellular channel protein 4 (mc3s5/mtCLIC)	0.18	-	mit	0	Cytoplasm. Mitochondrion	actin cytoskeleton [ISS] cytoplasm [ISS] microvillus [ISS] mitochondrion [IDA] soluble fraction [ISS]			252
Q9MBA1 UniProt NPD GO	CAO_ARATH	Chlorophyllide a oxygenase, chloroplast precursor (EC 1.-.-.-) (Chlorophyll a oxygenase) (Chlorophyl ...	0.18	-	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chlor ...				536
Q70Y15 UniProt NPD GO	RR16_AMBTC	Chloroplast 30S ribosomal protein S16	0.18	-	mit	0	Plastid; chloroplast				78
Q6B8V7 UniProt NPD GO	RR19_GRATL	Chloroplast 30S ribosomal protein S19	0.18	+	nuc	0	Plastid; chloroplast				92
Q3BAJ8 UniProt NPD GO	RR3_PHAAO	Chloroplast 30S ribosomal protein S3	0.18	-	mit	0	Plastid; chloroplast				218
Q4G354 UniProt NPD GO	RR8_EMIHU	Chloroplast 30S ribosomal protein S8	0.18	-	nuc	0	Plastid; chloroplast				132
P51292 UniProt NPD GO	RK13_PORPU	Chloroplast 50S ribosomal protein L13	0.18	-	nuc	0	Plastid; chloroplast				142
Q9TL22 UniProt NPD GO	RK14_NEPOL	Chloroplast 50S ribosomal protein L14	0.18	-	cyt	0	Plastid; chloroplast				121
Q3ZJ84 UniProt NPD GO	RK16_PSEAK	Chloroplast 50S ribosomal protein L16	0.18	-	mit	0	Plastid; chloroplast				137
Q6B8W8 UniProt NPD GO	RK18_GRATL	Chloroplast 50S ribosomal protein L18	0.18	-	mit	0	Plastid; chloroplast				105
O46899 UniProt NPD GO	RK22_GUITH	Chloroplast 50S ribosomal protein L22	0.18	-	mit	0	Plastid; chloroplast				121
P51224 UniProt NPD GO	RK28_PORPU	Chloroplast 50S ribosomal protein L28	0.18	-	nuc	0	Plastid; chloroplast				63
P59774 UniProt NPD GO	RK36_CHLRE	Chloroplast 50S ribosomal protein L36	0.18	-	nuc	0	Plastid; chloroplast				37
O98460 UniProt NPD GO	RK36_SPIMX	Chloroplast 50S ribosomal protein L36	0.18	-	mit	0	Plastid; chloroplast				37
O46895 UniProt NPD GO	RK4_GUITH	Chloroplast 50S ribosomal protein L4	0.18	-	nuc	0	Plastid; chloroplast				223
Q6B8W5 UniProt NPD GO	RK5_GRATL	Chloroplast 50S ribosomal protein L5	0.18	-	cyt	0	Plastid; chloroplast				179
Q8NE62 UniProt NPD GO	CHDH_HUMAN	Choline dehydrogenase, mitochondrial precursor (EC 1.1.99.1) (CHD) (CDH)	0.18	-	mit	0	Mitochondrion (Potential)				594
Q6X893 UniProt NPD GO	CTL1_MOUSE	Choline transporter-like protein 1 (Solute carrier family 44 member 1) (CD92 antigen) (CDw92)	0.18	-	end	9 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]			653
Q9CXM0 UniProt NPD GO	CHODL_MOUSE	Chondrolectin precursor (Transmembrane protein MT75)	0.18	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	perinuclear region [ISS]			273
P38877 UniProt NPD GO	CTF8_YEAST	Chromosome transmission fidelity protein 8	0.18	-	cyt	0	Nucleus. Associates with chromatin	DNA replication factor C complex [IPI]			133
Q9D7D7 UniProt NPD GO	CLD23_MOUSE	Claudin-23	0.18	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			296
O43809 UniProt NPD GO	CPSF5_HUMAN	Cleavage and polyadenylation specificity factor 5 (Cleavage and polyadenylation specificity factor 2 ...	0.18	-	mit	0	Nucleus. In punctate subnuclear structures localized adjacent to nuclear speckles, called paraspeckl ...	paraspeckles [IDA]	604978	2CL3	227
Q3ZCA2 UniProt NPD GO	CPSF5_BOVIN	Cleavage and polyadenylation specificity factor 5 (Nucleoside diphosphate-linked moiety X motif 21) ...	0.18	-	mit	0	Nucleus (By similarity). In punctate subnuclear structures localized adjacent to nuclear speckles, c ...	paraspeckles [ISS]			227
Q9CQF3 UniProt NPD GO	CPSF5_MOUSE	Cleavage and polyadenylation specificity factor 5 (Nucleoside diphosphate-linked moiety X motif 21) ...	0.18	-	mit	0	Nucleus (By similarity). In punctate subnuclear structures localized adjacent to nuclear speckles, c ...	paraspeckles [ISS]			227
Q5RAI8 UniProt NPD GO	CPSF5_PONPY	Cleavage and polyadenylation specificity factor 5 (Nucleoside diphosphate-linked moiety X motif 21) ...	0.18	-	mit	0	Nucleus (By similarity). In punctate subnuclear structures localized adjacent to nuclear speckles, c ...	paraspeckles [ISS]			227
Q4KM65 UniProt NPD GO	CPSF5_RAT	Cleavage and polyadenylation specificity factor 5 (Nucleoside diphosphate-linked moiety X motif 21) ...	0.18	-	mit	0	Nucleus (By similarity). In punctate subnuclear structures localized adjacent to nuclear speckles, c ...	paraspeckles [ISS]			227
Q04341 UniProt NPD GO	YD031_YEAST	Coiled-coil-helix-coiled-coil-helix domain-containing protein YDR031W	0.18	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			121
Q91W50 UniProt NPD GO	CSDE1_MOUSE	Cold shock domain-containing protein E1	0.18	-	cyt	0	Cytoplasm (By similarity)				798
O75534 UniProt NPD GO	CSDE1_HUMAN	Cold shock domain-containing protein E1 (UNR protein) (N-ras upstream gene protein)	0.18	-	cyt	0	Cytoplasm		191510	1X65	798
P10863 UniProt NPD GO	TIR1_YEAST	Cold shock-induced protein TIR1 precursor (Serine-rich protein 1)	0.18	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			254
P20850 UniProt NPD GO	CO9A1_RAT	Collagen alpha-1(IX) chain (Fragment)	0.18	-	nuc	0					325
Q69DL0 UniProt NPD GO	C1QA_PIG	Complement C1q subcomponent subunit A precursor	0.18	-	exc	0	Secreted protein				247
Q9BXJ1 UniProt NPD GO	C1QT1_HUMAN	Complement C1q tumor necrosis factor-related protein 1 precursor (G protein-coupled receptor-interac ...	0.18	-	exc	1 *	Secreted protein (Potential)				281
Q60401 UniProt NPD GO	DAF_CAVPO	Complement decay-accelerating factor precursor (CD55 antigen) [Contains: Complement decay-accelerati ...	0.18	-	mit	1	Isoform 3: Cell membrane; lipid-anchor; GPI-anchor. Isoform 4: Secreted protein (Probable)				507
P81475 UniProt NPD GO	CFBL_CHICK	Complement factor B-like protease (EC 3.4.21.-) [Contains: Complement factor B-like protease Ba frag ...	0.18	-	cyt	0	Secreted protein				250
O14810 UniProt NPD GO	CPLX1_HUMAN	Complexin-1 (Complexin I) (CPX I) (Synaphin-2)	0.18	-	nuc	0	Cytoplasm; cytosol. Enriched at synaptic-releasing sites in mature neurons (By similarity)		605032		134

You are viewing entries 52851 to 52900 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.