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
Q9TJ83 UniProt NPD GO	FTSH_CYAME	Cell division protein ftsH homolog (EC 3.4.24.-) (FtsHCP)	0.06	-	nuc	2 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				603
P79432 UniProt NPD GO	CDK4_PIG	Cell division protein kinase 4 (EC 2.7.11.22) (Cyclin-dependent kinase 4)	0.06	-	cyt	0					303
Q00535 UniProt NPD GO	CDK5_HUMAN	Cell division protein kinase 5 (EC 2.7.11.22) (Tau protein kinase II catalytic subunit) (TPKII catal ...	0.06	-	cyt	0	Cytoplasm. In axonal growth cone with extension to the peripheral lamellipodia (By similarity)	axon [ISS] cell soma [ISS] cytoplasm [ISS] dendrite [ISS] growth cone [ISS] membrane [ISS] neuromuscular junction [ISS] nucleus [ISS]	123831	1UNL	292
Q03114 UniProt NPD GO	CDK5_RAT	Cell division protein kinase 5 (EC 2.7.11.22) (Tau protein kinase II catalytic subunit) (TPKII catal ...	0.06	-	cyt	0	Cytoplasm. In axonal growth cone with extension to the peripheral lamellipodia (By similarity)	axon [IDA] cell junction [TAS] cell soma [IDA] cytoplasm [IDA] dendrite [IDA] growth cone [IDA] membrane [IDA] neuromuscular junction [IDA] nucleus [IDA]			292
P49615 UniProt NPD GO	CDK5_MOUSE	Cell division protein kinase 5 (EC 2.7.11.22) (Tau protein kinase II catalytic subunit) (TPKII catal ...	0.06	-	cyt	0	Cytoplasm. In axonal growth cone with extension to the peripheral lamellipodia	axon [ISS] cell soma [ISS] cytoplasm [ISS] cytosol [IDA] dendrite [ISS] filopodium [IDA] growth cone [ISS] lamellipodium [IDA] membrane [ISS] neuromuscular junction [ISS] nucleus [ISS]			292
Q01738 UniProt NPD GO	CDH_PHACH	Cellobiose dehydrogenase precursor (EC 1.1.99.18) (CDH) (Cellobiose-quinone oxidoreductase)	0.06	-	exc	0	Secreted protein			1PL3	773
Q00023 UniProt NPD GO	CEL1_AGABI	Cellulose-growth-specific protein precursor	0.06	-	exc	0	Secreted protein				320
O82144 UniProt NPD GO	CHSY_HYDMC	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.06	-	cyt	0					389
P51085 UniProt NPD GO	CHS3_TRISU	Chalcone synthase 3 (EC 2.3.1.74) (Naringenin-chalcone synthase 3)	0.06	-	nuc	0					389
Q9M5M0 UniProt NPD GO	CHS7_PICMA	Chalcone synthase 7 (EC 2.3.1.74) (Naregenin-chalcone synthase 7)	0.06	-	cyt	0					395
P29185 UniProt NPD GO	CH61_MAIZE	Chaperonin CPN60-1, mitochondrial precursor (HSP60-1)	0.06	-	mit	0	Mitochondrion				577
Q43298 UniProt NPD GO	CH62_MAIZE	Chaperonin CPN60-2, mitochondrial precursor (HSP60-2)	0.06	-	mit	0	Mitochondrion				576
P49603 UniProt NPD GO	CHS1_BOTCI	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-I chitin synth ...	0.06	-	cyt	0	Cell membrane; multi-pass membrane protein				189
P30603 UniProt NPD GO	CHS1_XYLBA	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Fragment)	0.06	-	cyt	0	Cell membrane; multi-pass membrane protein				189
Q9T2L0 UniProt NPD GO	CB2B_SPIOL	Chlorophyll a-b binding protein (LHCII type I CAB) (LHCP) (Fragment)	0.06	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein	thylakoid membrane (sensu Viridiplantae) [IDA]			9
P27522 UniProt NPD GO	CB13_LYCES	Chlorophyll a-b binding protein 8, chloroplast precursor (LHCI type III CAB-8)	0.06	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				273
Q93WD2 UniProt NPD GO	CB29_CHLRE	Chlorophyll a-b binding protein CP29	0.06	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein	light-harvesting complex (sensu Viridiplantae) [IDA]			279
Q07473 UniProt NPD GO	CB4A_ARATH	Chlorophyll a-b binding protein CP29.1, chloroplast precursor (LHCII protein 4.1) (LHCB4.1)	0.06	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein	thylakoid membrane (sensu Viridiplantae) [IDA]			290
Q4G357 UniProt NPD GO	RR17_EMIHU	Chloroplast 30S ribosomal protein S17	0.06	-	nuc	0	Plastid; chloroplast				82
Q7FNS1 UniProt NPD GO	RR19_ATRBE	Chloroplast 30S ribosomal protein S19	0.06	-	mit	0	Plastid; chloroplast				92
Q9TLT6 UniProt NPD GO	RR19_CYACA	Chloroplast 30S ribosomal protein S19	0.06	-	mit	0	Plastid; chloroplast				92
P06377 UniProt NPD GO	RR19_MARPO	Chloroplast 30S ribosomal protein S19	0.06	-	nuc	0	Plastid; chloroplast				91
Q36570 UniProt NPD GO	RR19_NICBI	Chloroplast 30S ribosomal protein S19	0.06	-	mit	0	Plastid; chloroplast				91
O62953 UniProt NPD GO	RR19_PICAB	Chloroplast 30S ribosomal protein S19	0.06	-	mit	0	Plastid; chloroplast				92
P02376 UniProt NPD GO	RR19_TOBAC	Chloroplast 30S ribosomal protein S19	0.06	-	mit	0	Plastid; chloroplast				91
Q9TLU8 UniProt NPD GO	RR5_CYACA	Chloroplast 30S ribosomal protein S5	0.06	-	nuc	0	Plastid; chloroplast				168
Q85G12 UniProt NPD GO	RK11_CYAME	Chloroplast 50S ribosomal protein L11	0.06	-	cyt	0	Plastid; chloroplast				138
Q9TLZ9 UniProt NPD GO	RK12_CYACA	Chloroplast 50S ribosomal protein L12	0.06	-	cyt	0	Plastid; chloroplast				130
Q5SD20 UniProt NPD GO	RK22_HUPLU	Chloroplast 50S ribosomal protein L22	0.06	-	cyt	0	Plastid; chloroplast				125
P41549 UniProt NPD GO	RK27_CHRAL	Chloroplast 50S ribosomal protein L27 (Fragment)	0.06	-	mit	0	Plastid; chloroplast				73
Q6B8X7 UniProt NPD GO	RK31_GRATL	Chloroplast 50S ribosomal protein L31	0.06	-	cyt	0	Plastid; chloroplast				79
Q5MIM5 UniProt NPD GO	RK31_PALPL	Chloroplast 50S ribosomal protein L31	0.06	-	cyt	0	Plastid; chloroplast				73
Q7FNS6 UniProt NPD GO	RK33_ATRBE	Chloroplast 50S ribosomal protein L33	0.06	-	nuc	0	Plastid; chloroplast				66
Q9MTK2 UniProt NPD GO	RK33_OENHO	Chloroplast 50S ribosomal protein L33	0.06	-	nuc	0	Plastid; chloroplast				66
Q9TM16 UniProt NPD GO	CEMA_CYACA	Chloroplast envelope membrane protein	0.06	-	end	4	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				278
O78470 UniProt NPD GO	CEMA_GUITH	Chloroplast envelope membrane protein	0.06	-	end	4	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				278
Q20027 UniProt NPD GO	C25HL_CAEEL	Cholesterol 25-hydroxylase-like protein (EC 1.14.99.-)	0.06	-	nuc	4	Membrane; multi-pass membrane protein (Potential)				300
Q93XE1 UniProt NPD GO	CHMO_AMATR	Choline monooxygenase, chloroplast precursor (EC 1.14.15.7)	0.06	-	mit	0	Plastid; chloroplast; chloroplast stroma (By similarity)				442
O22553 UniProt NPD GO	CHMO_BETVU	Choline monooxygenase, chloroplast precursor (EC 1.14.15.7)	0.06	-	cyt	0	Plastid; chloroplast; chloroplast stroma (By similarity)				446
Q9I9B9 UniProt NPD GO	CTL1_TORMA	Choline transporter-like protein 1	0.06	-	end	10 *	Membrane; multi-pass membrane protein				646
P24516 UniProt NPD GO	CH19_DROVI	Chorion protein S19	0.06	-	end	0					198
O74413 UniProt NPD GO	AROC_SCHPO	Chorismate synthase (EC 4.2.3.5) (5-enolpyruvylshikimate-3-phosphate phospholyase)	0.06	-	cyt	0					395
P47796 UniProt NPD GO	CTRA_GADMO	Chymotrypsin A precursor (EC 3.4.21.1)	0.06	-	cyt	0	Secreted protein; extracellular space				263
O88507 UniProt NPD GO	CNTFR_MOUSE	Ciliary neurotrophic factor receptor alpha precursor (CNTFR alpha)	0.06	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				372
O82056 UniProt NPD GO	CADH_SACOF	Cinnamyl alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.06	-	mit	0					365
O24562 UniProt NPD GO	CADH_MAIZE	Cinnamyl alcohol dehydrogenase (EC 1.1.1.195) (CAD) (Brown-midrib 1 protein)	0.06	-	mit	0					367
O76879 UniProt NPD GO	CCCP_DROME	Circadian clock-controlled protein precursor	0.06	-	end	0					260
P51044 UniProt NPD GO	CISY_ASPNG	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.06	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				475
P24118 UniProt NPD GO	CISY_TETTH	Citrate synthase, mitochondrial precursor (EC 2.3.3.1) (14 NM filament-forming protein)	0.06	-	mit	0	Mitochondrion; mitochondrial matrix. Cytoplasm. Cytoplasmic cytoskeleton				462
Q6L708 UniProt NPD GO	CLD1_BOVIN	Claudin-1	0.06	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)				211

You are viewing entries 71751 to 71800 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.