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
Q9M7M9 UniProt NPD GO	PROF4_HEVBR	Profilin-4 (Pollen allergen Hev b 8.0202)	0.01	-	cyt	0					131
Q9M7M8 UniProt NPD GO	PROF5_HEVBR	Profilin-5 (Pollen allergen Hev b 8.0203)	0.01	-	cyt	0					131
Q9LEI8 UniProt NPD GO	PROF6_HEVBR	Profilin-6 (Pollen allergen Hev b 8.0204)	0.01	-	cyt	0				1G5U	131
P22271 UniProt NPD GO	PROF1_PHYPO	Profilin-A	0.01	-	cyt	0					124
Q9FUD1 UniProt NPD GO	PROFA_ORYSA	Profilin-A	0.01	-	cyt	0					131
P18322 UniProt NPD GO	PROF2_PHYPO	Profilin-P	0.01	-	cyt	0					124
Q9JJE4 UniProt NPD GO	PAQR4_MOUSE	Progestin and adipoQ receptor family member 4 (Progestin and adipoQ receptor family member IV)	0.01	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)				273
P33439 UniProt NPD GO	GON1_CLAGA	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.01	-	exc	0	Secreted protein				80
P45653 UniProt NPD GO	GON3_SALTR	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.01	-	exc	0	Secreted protein				82
P55246 UniProt NPD GO	GON3_ONCMY	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.01	-	vac	0	Secreted protein				74
Q92097 UniProt NPD GO	GON3_ONCTS	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.01	-	end	0	Secreted protein				74
P05805 UniProt NPD GO	CAC3_BOVIN	Proproteinase E precursor (Procarboxypeptidase A complex component III) (Procarboxypeptidase A-S6 su ...	0.01	-	mit	0	Secreted protein; extracellular space			1PYT	253
O43653 UniProt NPD GO	PSCA_HUMAN	Prostate stem cell antigen precursor	0.01	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	plasma membrane [TAS]	602470		123
P21242 UniProt NPD GO	PSA3_YEAST	Proteasome component C1 (EC 3.4.25.1) (Macropain subunit C1) (Proteinase YSCE subunit 1) (Multicatal ...	0.01	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex, alpha-subunit comp... [IPI]		2FNY	287
P92188 UniProt NPD GO	PSA1_TRYCR	Proteasome subunit alpha type 1 (EC 3.4.25.1) (Proteasome 29 kDa subunit) (TCPR29)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				265
Q27488 UniProt NPD GO	PSA2_CAEEL	Proteasome subunit alpha type 2 (EC 3.4.25.1) (Proteasome subunit alpha 2)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				231
Q58DU5 UniProt NPD GO	PSA3_BOVIN	Proteasome subunit alpha type 3 (EC 3.4.25.1)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				254
Q27563 UniProt NPD GO	PSA3_DICDI	Proteasome subunit alpha type 3 (EC 3.4.25.1)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				248
P90513 UniProt NPD GO	PSA3_ACACA	Proteasome subunit alpha type 3 (EC 3.4.25.1) (Fragment)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				252
P25788 UniProt NPD GO	PSA3_HUMAN	Proteasome subunit alpha type 3 (EC 3.4.25.1) (Proteasome component C8) (Macropain subunit C8) (Mult ...	0.01	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS] proteasome complex (sensu Eukaryota) [TAS]	176845		254
O70435 UniProt NPD GO	PSA3_MOUSE	Proteasome subunit alpha type 3 (EC 3.4.25.1) (Proteasome component C8) (Macropain subunit C8) (Mult ...	0.01	-	cyt	0	Cytoplasm. Nucleus				254
P18422 UniProt NPD GO	PSA3_RAT	Proteasome subunit alpha type 3 (EC 3.4.25.1) (Proteasome component C8) (Macropain subunit C8) (Mult ...	0.01	-	cyt	0	Cytoplasm. Nucleus				254
Q09583 UniProt NPD GO	PSA3_CAEEL	Proteasome subunit alpha type 3 (EC 3.4.25.1) (Proteasome subunit alpha 7)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				249
O23715 UniProt NPD GO	PSA3_ARATH	Proteasome subunit alpha type 3 (EC 3.4.25.1) (Proteasome subunit alpha type 7) (20S proteasome alph ...	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				249
Q9LSU1 UniProt NPD GO	PSA5_ORYSA	Proteasome subunit alpha type 5 (EC 3.4.25.1) (20S proteasome alpha subunit E) (20S proteasome subun ...	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				237
O81149 UniProt NPD GO	PSA5A_ARATH	Proteasome subunit alpha type 5-A (EC 3.4.25.1) (20S proteasome alpha subunit E-1)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				237
Q42134 UniProt NPD GO	PSA5B_ARATH	Proteasome subunit alpha type 5-B (EC 3.4.25.1) (20S proteasome alpha subunit E-2) (Proteasome compo ...	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				237
Q9SXU1 UniProt NPD GO	PSA7_CICAR	Proteasome subunit alpha type 7 (EC 3.4.25.1) (20S proteasome alpha subunit D) (20S proteasome subun ...	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				249
Q9NDA1 UniProt NPD GO	PSB3_TRYBB	Proteasome subunit beta type 3 (EC 3.4.25.1) (20S proteasome subunit beta-3)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				205
O73817 UniProt NPD GO	PSB3_ONCMY	Proteasome subunit beta type 3 (EC 3.4.25.1) (Proteasome theta chain) (Proteasome chain 13) (Proteas ...	0.01	-	cyt	0	Cytoplasm. Nucleus				205
O55234 UniProt NPD GO	PSB5_MOUSE	Proteasome subunit beta type 5 precursor (EC 3.4.25.1) (Proteasome epsilon chain) (Macropain epsilon ...	0.01	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex (sensu Eukaryota) [IDA]			209
P28075 UniProt NPD GO	PSB5_RAT	Proteasome subunit beta type 5 precursor (EC 3.4.25.1) (Proteasome epsilon chain) (Macropain epsilon ...	0.01	-	cyt	0	Cytoplasm. Nucleus				208
P28074 UniProt NPD GO	PSB5_HUMAN	Proteasome subunit beta type 5 precursor (EC 3.4.25.1) (Proteasome epsilon chain) (Macropain epsilon ...	0.01	-	cyt	0	Cytoplasm. Nucleus	proteasome complex (sensu Eukaryota) [TAS]	600306		208
O23710 UniProt NPD GO	PSB7A_ARATH	Proteasome subunit beta type 7-A precursor (EC 3.4.25.1) (Proteasome subunit beta type 2) (20S prote ...	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				273
Q7DLS1 UniProt NPD GO	PSB7B_ARATH	Proteasome subunit beta type 7-B precursor (EC 3.4.25.1) (Proteasome subunit beta type 2) (20S prote ...	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				274
Q3SZC2 UniProt NPD GO	PSB9_BOVIN	Proteasome subunit beta type 9 precursor (EC 3.4.25.1)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				219
P28065 UniProt NPD GO	PSB9_HUMAN	Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Proteasome chain 7) (Macropain chain 7) (Mul ...	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	proteasome complex (sensu Eukaryota) [TAS]	177045		219
O35523 UniProt NPD GO	PSB9_MUSPL	Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Proteasome chain 7) (Macropain chain 7) (Mul ...	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				219
Q8NFR3 UniProt NPD GO	ADMP_HUMAN	Protein ADMP	0.01	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				76
Q9FK81 UniProt NPD GO	Y5258_ARATH	Protein At5g22580	0.01	-	cyt	0				1RJJ	111
P47040 UniProt NPD GO	BTN1_YEAST	Protein BTN1 precursor	0.01	-	end	11 *	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuole (sensu Fungi) [IDA]			408
Q9PW66 UniProt NPD GO	BV8_BOMVA	Protein Bv8 precursor	0.01	-	exc	1 *	Secreted protein				96
Q969W0 UniProt NPD GO	CN147_HUMAN	Protein C14orf147	0.01	-	cyt	1 *					68
Q5E978 UniProt NPD GO	CN147_BOVIN	Protein C14orf147 homolog	0.01	-	cyt	1 *					68
Q8R207 UniProt NPD GO	CN147_MOUSE	Protein C14orf147 homolog	0.01	-	cyt	2 *					68
Q9D6X5 UniProt NPD GO	CT054_MOUSE	Protein C20orf54 homolog precursor	0.01	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				460
Q9BT51 UniProt NPD GO	CU122_HUMAN	Protein C21orf122	0.01	-	nuc	0					43
P59092 UniProt NPD GO	CU094_HUMAN	Protein C21orf94	0.01	-	mit	0					62
Q9HAC7 UniProt NPD GO	CG010_HUMAN	Protein C7orf10 (Dermal papilla-derived protein 13)	0.01	-	mit	0			609187		445
Q9BU79 UniProt NPD GO	CG023_HUMAN	Protein C7orf23	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				118

You are viewing entries 90851 to 90900 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.