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
Q90830 UniProt NPD GO	CASP_CHICK	Cartilage-associated protein precursor (Dualin)	0.37	-	exc	0	Secreted protein; extracellular space; extracellular matrix				271
Q9MZV7 UniProt NPD GO	CASP1_CANFA	Caspase-1 precursor (EC 3.4.22.36) (CASP-1) (Interleukin-1 beta convertase) (IL-1BC) (IL-1 beta-conv ...	0.37	-	cyt	0	Cytoplasm				404
Q4R5X9 UniProt NPD GO	RAD9A_MACFA	Cell cycle checkpoint control protein RAD9A (EC 3.1.11.2) (DNA repair exonuclease rad9 homolog A)	0.37	-	nuc	0	Nucleus (By similarity)				379
P36589 UniProt NPD GO	CDC14_SCHPO	Cell division control protein 14	0.37	-	cyt	0	Spindle pole body. Localizes to the SPB prior to cytokinesis and leaves once septation is complete	spindle pole body [IDA]			240
P25656 UniProt NPD GO	CDC50_YEAST	Cell division control protein 50	0.37	-	mit	2 *	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein	Golgi trans face [IDA] integral to membrane of membrane fraction [IDA] late endosome [IDA]			391
Q15131 UniProt NPD GO	CDK10_HUMAN	Cell division protein kinase 10 (EC 2.7.11.22) (Serine/threonine-protein kinase PISSLRE)	0.37	-	cyt	0			603464		360
Q92357 UniProt NPD GO	CFR1_SCHPO	Cell fusion protein cfr1 (CHS5-related protein 1)	0.37	-	nuc	0	Golgi apparatus				620
O74452 UniProt NPD GO	SCW1_SCHPO	Cell wall integrity protein scw1 (Strong cell wall protein 1)	0.37	-	nuc	0	Cytoplasm	cytoplasm [IDA]			561
O48947 UniProt NPD GO	CESA2_ARATH	Cellulose synthase A catalytic subunit 2 [UDP-forming] (EC 2.4.1.12) (AtCesA-2) (Ath-A)	0.37	+	end	6	Cell membrane; multi-pass membrane protein (Probable)				1084
Q8TAP6 UniProt NPD GO	CEP76_HUMAN	Centrosomal protein of 76 kDa (Cep76 protein)	0.37	-	nuc	0	Centrosome				659
Q5JZQ8 UniProt NPD GO	CLN6_CANFA	Ceroid-lipofuscinosis neuronal protein 6 homolog (Protein CLN6)	0.37	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				312
P30597 UniProt NPD GO	CHS1_SCHPO	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1)	0.37	-	end	7	Cell membrane; multi-pass membrane protein				859
Q49KW5 UniProt NPD GO	RR11_EUCGG	Chloroplast 30S ribosomal protein S11	0.37	-	mit	0	Plastid; chloroplast				138
Q68RX4 UniProt NPD GO	RR11_PANGI	Chloroplast 30S ribosomal protein S11	0.37	-	mit	0	Plastid; chloroplast				138
P17703 UniProt NPD GO	RR15_MAIZE	Chloroplast 30S ribosomal protein S15	0.37	-	nuc	0	Plastid; chloroplast				90
Q3C1P7 UniProt NPD GO	RR15_NICSY	Chloroplast 30S ribosomal protein S15	0.37	-	nuc	0	Plastid; chloroplast				87
Q33BW5 UniProt NPD GO	RR15_NICTO	Chloroplast 30S ribosomal protein S15	0.37	-	nuc	0	Plastid; chloroplast				87
P06373 UniProt NPD GO	RR15_TOBAC	Chloroplast 30S ribosomal protein S15	0.37	-	nuc	0	Plastid; chloroplast				87
P06355 UniProt NPD GO	RR2_TOBAC	Chloroplast 30S ribosomal protein S2	0.37	-	mit	0	Plastid; chloroplast				236
Q9MUU2 UniProt NPD GO	RR3_MESVI	Chloroplast 30S ribosomal protein S3	0.37	-	cyt	0	Plastid; chloroplast				213
Q9M4B8 UniProt NPD GO	RR4_JAMAU	Chloroplast 30S ribosomal protein S4	0.37	-	mit	0	Plastid; chloroplast				202
Q9MUN0 UniProt NPD GO	RR4_MESVI	Chloroplast 30S ribosomal protein S4	0.37	-	mit	0	Plastid; chloroplast				205
Q9M4C1 UniProt NPD GO	RR4_MONFO	Chloroplast 30S ribosomal protein S4	0.37	-	mit	0	Plastid; chloroplast				202
Q6YXP3 UniProt NPD GO	RR4_PHYPA	Chloroplast 30S ribosomal protein S4	0.37	-	mit	0	Plastid; chloroplast				201
P59151 UniProt NPD GO	RR4_WOORA	Chloroplast 30S ribosomal protein S4	0.37	-	nuc	0	Plastid; chloroplast				185
P59152 UniProt NPD GO	RR4_WOOUN	Chloroplast 30S ribosomal protein S4	0.37	-	nuc	0	Plastid; chloroplast				185
Q85AM2 UniProt NPD GO	RR8_ANTFO	Chloroplast 30S ribosomal protein S8	0.37	+	cyt	0	Plastid; chloroplast				132
Q7YJU3 UniProt NPD GO	RR8_CALFE	Chloroplast 30S ribosomal protein S8	0.37	-	nuc	0	Plastid; chloroplast				132
Q7YJU1 UniProt NPD GO	RK16_CALFE	Chloroplast 50S ribosomal protein L16	0.37	-	mit	0	Plastid; chloroplast				135
Q332T9 UniProt NPD GO	RK16_LACSA	Chloroplast 50S ribosomal protein L16	0.37	-	mit	0	Plastid; chloroplast				135
Q8WHZ8 UniProt NPD GO	RK20_PSINU	Chloroplast 50S ribosomal protein L20	0.37	-	nuc	0	Plastid; chloroplast				114
Q8WHY3 UniProt NPD GO	RK22_PSINU	Chloroplast 50S ribosomal protein L22	0.37	-	nuc	0	Plastid; chloroplast				116
Q9TM38 UniProt NPD GO	RK33_CYACA	Chloroplast 50S ribosomal protein L33	0.37	-	nuc	0	Plastid; chloroplast				64
P49565 UniProt NPD GO	RK33_ODOSI	Chloroplast 50S ribosomal protein L33	0.37	-	nuc	0	Plastid; chloroplast				64
Q95GN4 UniProt NPD GO	RK36_MESCR	Chloroplast 50S ribosomal protein L36	0.37	-	mit	0	Plastid; chloroplast				37
Q6EW18 UniProt NPD GO	RK36_NYMAL	Chloroplast 50S ribosomal protein L36	0.37	-	mit	0	Plastid; chloroplast				37
P56349 UniProt NPD GO	CEMA_CHLVU	Chloroplast envelope membrane protein	0.37	-	mit	1 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				266
P50145 UniProt NPD GO	CCKN2_XENLA	Cholecystokinin type 2 precursor [Contains: Cholecystokinin (CCK)]	0.37	-	exc	0					128
O93464 UniProt NPD GO	CCKN_CARAU	Cholecystokinins precursor (CCK8) [Contains: Cholecystokinin 8 (CCK8); Cholecystokinin 12 (CCK12); C ...	0.37	-	exc	0	Secreted protein (Potential)	extracellular space [ISS]			123
Q9EPU4 UniProt NPD GO	CPSF1_MOUSE	Cleavage and polyadenylation specificity factor 160 kDa subunit (CPSF 160 kDa subunit)	0.37	-	nuc	0	Nucleus; nucleoplasm (By similarity)				1441
Q99LC2 UniProt NPD GO	CSTF1_MOUSE	Cleavage stimulation factor 50 kDa subunit (CSTF 50 kDa subunit) (CF-1 50 kDa subunit) (CstF-50)	0.37	-	nuc	0	Nucleus (By similarity)				431
Q5BJQ6 UniProt NPD GO	CSTF1_RAT	Cleavage stimulation factor 50 kDa subunit (CSTF 50 kDa subunit) (CF-1 50 kDa subunit) (CstF-50)	0.37	-	nuc	0	Nucleus (By similarity)				431
Q2NL17 UniProt NPD GO	CLPT1_BOVIN	Cleft lip and palate transmembrane protein 1 homolog	0.37	-	end	5	Membrane; multi-pass membrane protein (Potential)				670
P08709 UniProt NPD GO	FA7_HUMAN	Coagulation factor VII precursor (EC 3.4.21.21) (Serum prothrombin conversion accelerator) (SPCA) (P ...	0.37	-	exc	0		extracellular region [TAS]	227500	2FLB	466
Q2F9P4 UniProt NPD GO	FA7_PANPA	Coagulation factor VII precursor (EC 3.4.21.21) (Serum prothrombin conversion accelerator) [Contains ...	0.37	-	vac	0					466
Q8N300 UniProt NPD GO	CCD23_HUMAN	Coiled-coil domain-containing protein 23	0.37	-	nuc	0					66
Q8BH35 UniProt NPD GO	CO8B_MOUSE	Complement component C8 beta chain precursor (Complement component 8 subunit beta)	0.37	-	mit	0	Secreted protein				589
P09930 UniProt NPD GO	CGD2S_LUPAN	Conglutin delta-2 small chain	0.37	-	nuc	0					37
O94779 UniProt NPD GO	CNTN5_HUMAN	Contactin-5 precursor (Neural recognition molecule NB-2) (hNB-2)	0.37	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)		607219		1100
Q96FN4 UniProt NPD GO	CPNE2_HUMAN	Copine-2 (Copine II)	0.37	-	cyt	0			604206		548

You are viewing entries 34051 to 34100 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.