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
Q9ZQV8 UniProt NPD GO	NAS3_HORVU	Probable nicotianamine synthase 3 (EC 2.5.1.43) (S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-a ...	0.03	-	cyt	0					335
Q876L4 UniProt NPD GO	AKR2_SACBA	Probable palmitoyltransferase AKR2 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR2)	0.03	-	end	7	Membrane; multi-pass membrane protein (Probable)				730
Q5NVB9 UniProt NPD GO	ZDH13_PONPY	Probable palmitoyltransferase ZDHHC13 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 13) ( ...	0.03	-	end	6	Membrane; multi-pass membrane protein (Potential)				622
Q5W0Z9 UniProt NPD GO	ZDH20_HUMAN	Probable palmitoyltransferase ZDHHC20 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 20) ( ...	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				365
Q66KD6 UniProt NPD GO	PHOP2_XENTR	Probable phosphatase phospho2 (EC 3.1.3.-)	0.03	-	nuc	0					238
O49299 UniProt NPD GO	PGMC1_ARATH	Probable phosphoglucomutase, cytoplasmic 1 (EC 5.4.2.2) (Glucose phosphomutase 1) (PGM 1)	0.03	-	cyt	0	Cytoplasm (By similarity)				582
Q9SGC1 UniProt NPD GO	PGMC2_ARATH	Probable phosphoglucomutase, cytoplasmic 2 (EC 5.4.2.2) (Glucose phosphomutase 2) (PGM 2)	0.03	-	cyt	0	Cytoplasm (By similarity)				585
Q2N2K3 UniProt NPD GO	PHYK_WHEAT	Probable phytol kinase, chloroplast precursor (EC 2.7.-.-)	0.03	-	end	8 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				300
Q9BAC0 UniProt NPD GO	RRP3_EUGST	Probable plastid-specific 30S ribosomal protein 3 (PSRP-3)	0.03	-	cyt	0	Plastid; chloroplast				101
O94517 UniProt NPD GO	PSA6_SCHPO	Probable proteasome subunit alpha type 6 (EC 3.4.25.1)	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				244
Q9USQ9 UniProt NPD GO	PSB4_SCHPO	Probable proteasome subunit beta type 4 (EC 3.4.25.1)	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				262
O22263 UniProt NPD GO	PDIA6_ARATH	Probable protein disulfide-isomerase A6 precursor (EC 5.3.4.1) (P5)	0.03	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				361
Q09827 UniProt NPD GO	SC61G_SCHPO	Probable protein transport protein SEC61 subunit gamma	0.03	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				70
Q8WPW2 UniProt NPD GO	PDX1_SUBDO	Probable pyridoxin biosynthesis SNZERR (PDX1 homolog) (Ethylene response protein)	0.03	-	cyt	0					306
Q9P7P6 UniProt NPD GO	PDC3_SCHPO	Probable pyruvate decarboxylase C186.09 (EC 4.1.1.1)	0.03	-	cyt	0					572
Q9SYM5 UniProt NPD GO	RHM1_ARATH	Probable rhamnose biosynthetic enzyme 1 (EC 4.2.1.-) (EC 1.1.1.-)	0.03	-	mit	0					669
Q6AWV1 UniProt NPD GO	RNP2_ARATH	Probable ribonuclease P protein subunit 2 (EC 3.1.26.5)	0.03	-	cyt	0	Nucleus (Potential)				151
Q5RFE4 UniProt NPD GO	CPVL_PONPY	Probable serine carboxypeptidase CPVL precursor (EC 3.4.16.-)	0.03	-	end	0					476
O18391 UniProt NPD GO	KRAK_DROME	Probable serine hydrolase (EC 3.1.-.-) (Kraken protein)	0.03	-	cyt	0					331
Q615A2 UniProt NPD GO	SPCS2_CAEBR	Probable signal peptidase complex subunit 2 (EC 3.4.-.-) (Microsomal signal peptidase 25 kDa subunit ...	0.03	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				180
Q5M8Y1 UniProt NPD GO	SPCS2_XENTR	Probable signal peptidase complex subunit 2 (EC 3.4.-.-) (Microsomal signal peptidase 25 kDa subunit ...	0.03	-	end	2	Membrane; multi-pass membrane protein (Potential)				201
O82221 UniProt NPD GO	RUXG_ARATH	Probable small nuclear ribonucleoprotein G (snRNP-G) (Sm protein G) (Sm-G) (SmG)	0.03	-	nuc	0	Nucleus (Potential)				80
P24715 UniProt NPD GO	RUXG_MEDSA	Probable small nuclear ribonucleoprotein G (snRNP-G) (Sm protein G) (Sm-G) (SmG)	0.03	-	nuc	0	Nucleus (Potential)				81
Q38944 UniProt NPD GO	DET2_ARATH	Probable steroid reductase DET2 (EC 1.3.99.-)	0.03	-	nuc	6 *	Membrane; multi-pass membrane protein (By similarity)				262
Q9SXS2 UniProt NPD GO	SUT33_ARATH	Probable sulfate transporter 3.3 (AST91)	0.03	-	end	9	Membrane; multi-pass membrane protein (Potential)				631
P40386 UniProt NPD GO	THI4_SCHPO	Probable thiamine biosynthetic bifunctional enzyme [Includes: Thiamine-phosphate pyrophosphorylase ( ...	0.03	-	mit	0					518
P13865 UniProt NPD GO	PRO1_LEIEN	Probable transport protein (LTP)	0.03	-	end	12 *	Membrane; multi-pass membrane protein				567
Q08268 UniProt NPD GO	MCH4_YEAST	Probable transporter MCH4	0.03	-	end	12	Membrane; multi-pass membrane protein (Probable)	vacuolar membrane (sensu Fungi) [IDA]			501
O01884 UniProt NPD GO	COQ6_CAEEL	Probable ubiquinone biosynthesis monooxygenase coq-6 (EC 1.14.13.-)	0.03	-	cyt	0					451
O13843 UniProt NPD GO	ALLA_SCHPO	Probable ureidoglycolate hydrolase (EC 3.5.3.19)	0.03	-	cyt	0					191
Q9LJR7 UniProt NPD GO	XTH3_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 3 precursor (EC 2.4.1.207) (At-XTH3) (XTH ...	0.03	-	end	0	Secreted protein; extracellular space; apoplast (Probable)				290
Q8W245 UniProt NPD GO	ZIP10_ARATH	Probable zinc transporter 10 precursor (ZRT/IRT-like protein 10)	0.03	-	end	9 *	Cell membrane; multi-pass membrane protein (Potential)				364
P53696 UniProt NPD GO	PROF_CANAL	Profilin	0.03	-	cyt	0					126
Q9XF39 UniProt NPD GO	PROF_PRUAV	Profilin (Allergen Pru av 4) (Pru a 3)	0.03	-	cyt	0					131
Q941H7 UniProt NPD GO	PROF_LITCN	Profilin (Minor allergen Lit c 1)	0.03	-	cyt	0					131
Q5EF31 UniProt NPD GO	PROF_CROSA	Profilin (Pollen allergen Cro s 1)	0.03	-	cyt	0					131
P25843 UniProt NPD GO	PROF_DROME	Profilin (Protein chickadee)	0.03	-	cyt	0					126
P49231 UniProt NPD GO	PROF1_PHAVU	Profilin-1	0.03	-	cyt	0					131
O82572 UniProt NPD GO	PROF1_RICCO	Profilin-1	0.03	-	cyt	0					131
Q64LH1 UniProt NPD GO	PROF1_AMBAR	Profilin-1 (Pollen allergen Amb a 8)	0.03	-	cyt	0					131
P60673 UniProt NPD GO	PROF3_HUMAN	Profilin-3 (Profilin III)	0.03	-	cyt	0					137
Q9FE63 UniProt NPD GO	PROF5_ARATH	Profilin-5	0.03	-	cyt	0					131
Q6TCH7 UniProt NPD GO	PAQR3_HUMAN	Progestin and adipoQ receptor family member 3 (Progestin and adipoQ receptor family member III)	0.03	-	end	7	Membrane; multi-pass membrane protein (Potential)				311
Q6ZVX9 UniProt NPD GO	PAQR9_HUMAN	Progestin and adipoQ receptor family member 9 (Progestin and adipoQ receptor family member IX)	0.03	-	end	6	Membrane; multi-pass membrane protein (Potential)				377
P60989 UniProt NPD GO	PIP_PANTR	Prolactin-inducible protein homolog precursor	0.03	-	end	0	Secreted protein (By similarity)				146
Q9DEA3 UniProt NPD GO	PCNA_CHICK	Proliferating cell nuclear antigen (PCNA)	0.03	-	cyt	0	Nucleus (By similarity)				262
Q9DDF1 UniProt NPD GO	PCNA_COTJA	Proliferating cell nuclear antigen (PCNA)	0.03	-	cyt	0	Nucleus (By similarity)				262
P61258 UniProt NPD GO	PCNA_MACFA	Proliferating cell nuclear antigen (PCNA)	0.03	-	cyt	0	Nucleus (By similarity)				261
Q9MAY3 UniProt NPD GO	PCNA_POPNI	Proliferating cell nuclear antigen (PCNA)	0.03	-	mit	0	Nucleus				264
Q00268 UniProt NPD GO	PCNA1_DAUCA	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.03	-	mit	0	Nucleus				264

You are viewing entries 81251 to 81300 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.