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
Q26671 UniProt NPD GO	CDC2H_THEAN	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23)	0.04	-	cyt	0	Cytoplasm (By similarity)				298
P51958 UniProt NPD GO	CDC2_CARAU	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34 protein kinase) (Cyclin-d ...	0.04	-	cyt	0	Nucleus (By similarity)				302
P84578 UniProt NPD GO	FTSH_POPEU	Cell division protein ftsH homolog, chloroplast (EC 3.4.24.-) (Fragments)	0.04	-	cyt	0	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (By similarity)				47
Q5E9Y0 UniProt NPD GO	CDK2_BOVIN	Cell division protein kinase 2 (EC 2.7.11.22)	0.04	-	cyt	0					298
P97377 UniProt NPD GO	CDK2_MOUSE	Cell division protein kinase 2 (EC 2.7.11.22)	0.04	-	cyt	0		cyclin-dependent protein kinase holoenzyme ... [IPI] nucleus [IDA] transcription factor complex [IDA]			346
Q63699 UniProt NPD GO	CDK2_RAT	Cell division protein kinase 2 (EC 2.7.11.22)	0.04	-	cyt	0					298
P24941 UniProt NPD GO	CDK2_HUMAN	Cell division protein kinase 2 (EC 2.7.11.22) (p33 protein kinase)	0.04	-	cyt	0		cytoplasm [TAS] nucleus [TAS]	116953	2EXM	298
P48609 UniProt NPD GO	CDK5_DROME	Cell division protein kinase 5 homolog (EC 2.7.11.22)	0.04	-	cyt	0					294
P51083 UniProt NPD GO	CHS1_TRISU	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.04	-	cyt	0					389
P51084 UniProt NPD GO	CHS2_TRISU	Chalcone synthase 2 (EC 2.3.1.74) (Naringenin-chalcone synthase 2)	0.04	-	cyt	0					389
P51087 UniProt NPD GO	CHS5_TRISU	Chalcone synthase 5 (EC 2.3.1.74) (Naringenin-chalcone synthase 5)	0.04	-	nuc	0					389
P51088 UniProt NPD GO	CHS6_TRISU	Chalcone synthase 6 (EC 2.3.1.74) (Naringenin-chalcone synthase 6)	0.04	-	cyt	0					389
Q9SB26 UniProt NPD GO	CHS9_DAUCA	Chalcone synthase 9 (EC 2.3.1.74) (Naringenin-chalcone synthase 9)	0.04	-	cyt	0					389
Q9MB37 UniProt NPD GO	CHS7_IPOBA	Chalcone synthase DIII (EC 2.3.1.74) (Naringenin-chalcone synthase DIII)	0.04	-	cyt	0					393
P14298 UniProt NPD GO	CFI_PHAVU	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase)	0.04	-	cyt	0					221
Q43056 UniProt NPD GO	CFI_PUELO	Chalcone--flavonone isomerase (EC 5.5.1.6) (Chalcone isomerase)	0.04	-	cyt	0					224
P35480 UniProt NPD GO	CH60_BRANA	Chaperonin CPN60, mitochondrial precursor	0.04	-	mit	0	Mitochondrion				587
Q93ZM7 UniProt NPD GO	CH60C_ARATH	Chaperonin CPN60-like 2, mitochondrial precursor (HSP60-like 2)	0.04	-	mit	0	Mitochondrion				572
P50140 UniProt NPD GO	CH60_CAEEL	Chaperonin homolog HSP60, mitochondrial precursor (Heat shock protein 60) (HSP-60)	0.04	-	mit	0	Mitochondrion; mitochondrial matrix				568
Q53I51 UniProt NPD GO	CDA_CRYNE	Chitin deacetylase precursor (EC 3.5.1.41)	0.04	-	exc	0					410
P82476 UniProt NPD GO	CDA_CRYNV	Chitin deacetylase precursor (EC 3.5.1.41)	0.04	-	exc	0					410
P30576 UniProt NPD GO	CHS1_AJECA	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-I chitin synth ...	0.04	-	cyt	0	Cell membrane; multi-pass membrane protein				189
P30581 UniProt NPD GO	CHS1_ASPNG	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-I chitin synth ...	0.04	-	cyt	0	Cell membrane; multi-pass membrane protein				189
P30585 UniProt NPD GO	CHS1_EXOJE	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-I chitin synth ...	0.04	-	cyt	0	Cell membrane; multi-pass membrane protein				189
P30592 UniProt NPD GO	CHS1_RHIAT	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-I chitin synth ...	0.04	-	cyt	0	Cell membrane; multi-pass membrane protein				189
P30596 UniProt NPD GO	CHS1_SCHCO	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Fragment)	0.04	-	cyt	0	Cell membrane; multi-pass membrane protein				189
Q9WTV1 UniProt NPD GO	CH3L1_RAT	Chitinase-3-like protein 1 precursor (Cartilage glycoprotein 39) (GP-39)	0.04	-	vac	0	Secreted protein; extracellular space (By similarity)				381
P92943 UniProt NPD GO	CLCD_ARATH	Chloride channel protein CLC-d (AtCLC-d)	0.04	-	end	8	Membrane; multi-pass membrane protein				792
P20865 UniProt NPD GO	CB2_DUNSA	Chlorophyll a-b binding protein of LHCII type I, chloroplast precursor (CAB) (LHCP)	0.04	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				273
Q9M7I7 UniProt NPD GO	CLH2_ARATH	Chlorophyllase-2, chloroplast precursor (EC 3.1.1.14) (AtCLH2) (Chlorophyll-chlorophyllido hydrolase ...	0.04	-	cyt	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (By similarity)				318
O78423 UniProt NPD GO	RR16_GUITH	Chloroplast 30S ribosomal protein S16	0.04	-	mit	0	Plastid; chloroplast				76
Q85BX6 UniProt NPD GO	RR19_ANTFO	Chloroplast 30S ribosomal protein S19	0.04	-	mit	0	Plastid; chloroplast				92
P56366 UniProt NPD GO	RR19_CHLVU	Chloroplast 30S ribosomal protein S19	0.04	-	mit	0	Plastid; chloroplast				92
P49506 UniProt NPD GO	RR19_ODOSI	Chloroplast 30S ribosomal protein S19	0.04	-	mit	0	Plastid; chloroplast				92
Q85WY8 UniProt NPD GO	RR19_PINKO	Chloroplast 30S ribosomal protein S19	0.04	-	mit	0	Plastid; chloroplast				92
P18550 UniProt NPD GO	RR19_PETHY	Chloroplast 30S ribosomal protein S19 (Fragment)	0.04	-	nuc	0	Plastid; chloroplast				23
O46910 UniProt NPD GO	RR5_GUITH	Chloroplast 30S ribosomal protein S5	0.04	-	nuc	0	Plastid; chloroplast				169
O46907 UniProt NPD GO	RR8_GUITH	Chloroplast 30S ribosomal protein S8	0.04	-	cyt	0	Plastid; chloroplast				132
P51301 UniProt NPD GO	RR8_PORPU	Chloroplast 30S ribosomal protein S8	0.04	-	cyt	0	Plastid; chloroplast				133
Q9TM01 UniProt NPD GO	RK11_CYACA	Chloroplast 50S ribosomal protein L11	0.04	-	nuc	0	Plastid; chloroplast				141
Q6B907 UniProt NPD GO	RK11_GRATL	Chloroplast 50S ribosomal protein L11	0.04	-	mit	0	Plastid; chloroplast				141
O78412 UniProt NPD GO	RK11_GUITH	Chloroplast 50S ribosomal protein L11	0.04	-	cyt	0	Plastid; chloroplast				141
Q85CT4 UniProt NPD GO	RK14_ANTFO	Chloroplast 50S ribosomal protein L14	0.04	-	cyt	0	Plastid; chloroplast				122
P06381 UniProt NPD GO	RK14_MARPO	Chloroplast 50S ribosomal protein L14	0.04	-	cyt	0	Plastid; chloroplast				122
Q9MUU4 UniProt NPD GO	RK14_MESVI	Chloroplast 50S ribosomal protein L14	0.04	-	cyt	0	Plastid; chloroplast				122
Q95H51 UniProt NPD GO	RK14_WHEAT	Chloroplast 50S ribosomal protein L14	0.04	-	cyt	0	Plastid; chloroplast				123
P26820 UniProt NPD GO	RK14_VIGUN	Chloroplast 50S ribosomal protein L14 (Fragment)	0.04	-	cyt	0	Plastid; chloroplast				47
P69668 UniProt NPD GO	RK23_HORVU	Chloroplast 50S ribosomal protein L23	0.04	-	cyt	0	Plastid; chloroplast				93
P09387 UniProt NPD GO	RK23_MAIZE	Chloroplast 50S ribosomal protein L23	0.04	-	cyt	0	Plastid; chloroplast				93
Q6ENC8 UniProt NPD GO	RK23_ORYNI	Chloroplast 50S ribosomal protein L23	0.04	-	cyt	0	Plastid; chloroplast				93

You are viewing entries 76501 to 76550 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.