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
P19984 UniProt NPD GO	PROF2_ACACA	Profilin-2 (Profilin II) (Basic profilin)	0.00	-	cyt	0				2ACG	125
P35082 UniProt NPD GO	PROF2_MAIZE	Profilin-2 (ZmPRO2)	0.00	-	cyt	0					131
O24650 UniProt NPD GO	PROF2_PHLPR	Profilin-2/4 (Pollen allergen Phl p 12) (Phl p 11)	0.00	-	cyt	0					131
Q38904 UniProt NPD GO	PROF3_ARATH	Profilin-3	0.00	-	cyt	0					134
Q21193 UniProt NPD GO	PROF3_CAEEL	Profilin-3	0.00	-	cyt	0					126
Q9XF42 UniProt NPD GO	PROF3_MALDO	Profilin-3 (GD4-5) (Pollen allergen Mal d 4.0101)	0.00	-	cyt	0					131
O24171 UniProt NPD GO	PROF3_OLEEU	Profilin-3 (Pollen allergen Ole e 2)	0.00	-	cyt	0					134
O24282 UniProt NPD GO	PROF3_PHLPR	Profilin-3 (Pollen allergen Phl p 12) (Phl p 11)	0.00	-	cyt	0					131
Q38905 UniProt NPD GO	PROF4_ARATH	Profilin-4	0.00	-	cyt	0					134
O22655 UniProt NPD GO	PROF4_MAIZE	Profilin-4 (ZmPRO4)	0.00	-	cyt	0					131
Q9FR39 UniProt NPD GO	PROF5_MAIZE	Profilin-5 (ZmPRO5)	0.00	-	cyt	0					131
Q28550 UniProt NPD GO	PE2R3_SHEEP	Prostaglandin E2 receptor, EP3 subtype (Prostanoid EP3 receptor) (PGE receptor, EP3 subtype) (Fragme ...	0.00	-	end	2 *	Membrane; multi-pass membrane protein				89
P36374 UniProt NPD GO	KLK8_RAT	Prostatic glandular kallikrein-8 precursor (EC 3.4.21.35) (Tissue kallikrein) (P1 kallikrein) (RGK-8 ...	0.00	-	exc	0					261
P01095 UniProt NPD GO	IPB2_YEAST	Protease B inhibitors 2 and 1 (Proteinase inhibitor I(B)2)	0.00	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [TAS] vacuole (sensu Fungi) [IPI]			74
Q8T0W4 UniProt NPD GO	CVP2_PIMHY	Protease inhibitor cvp2 precursor (Cysteine-rich venom protein 2)	0.00	-	mit	1 *	Secreted protein				77
P38624 UniProt NPD GO	PSB6_YEAST	Proteasome component PRE3 precursor (EC 3.4.25.1) (Macropain subunit PRE3) (Proteinase YSCE subunit ...	0.00	-	mit	0	Cytoplasm. Nucleus	proteasome core complex, beta-subunit compl... [IPI]		2FNY	215
Q9LSU0 UniProt NPD GO	PSA3_ORYSA	Proteasome subunit alpha type 3 (EC 3.4.25.1) (20S proteasome alpha subunit G) (20S proteasome subun ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				249
O24362 UniProt NPD GO	PSA3_SPIOL	Proteasome subunit alpha type 3 (EC 3.4.25.1) (20S proteasome alpha subunit G) (20S proteasome subun ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				249
Q9LSU3 UniProt NPD GO	PSA6_ORYSA	Proteasome subunit alpha type 6 (EC 3.4.25.1) (20S proteasome alpha subunit A) (20S proteasome subun ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				246
Q9XG77 UniProt NPD GO	PSA6_TOBAC	Proteasome subunit alpha type 6 (EC 3.4.25.1) (20S proteasome alpha subunit A) (20S proteasome subun ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				246
O48551 UniProt NPD GO	PSA6_SOYBN	Proteasome subunit alpha type 6 (EC 3.4.25.1) (20S proteasome alpha subunit A) (20S proteasome subun ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				246
O81146 UniProt NPD GO	PSA6A_ARATH	Proteasome subunit alpha type 6-A (EC 3.4.25.1) (Proteasome subunit alpha type 1) (20S proteasome al ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				246
Q9NHC6 UniProt NPD GO	PSB2_TRYBB	Proteasome subunit beta type 2 (EC 3.4.25.1) (20S proteasome subunit beta-4)	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				206
O23714 UniProt NPD GO	PSB2A_ARATH	Proteasome subunit beta type 2-A (EC 3.4.25.1) (Proteasome subunit beta type 4) (20S proteasome beta ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				204
O24633 UniProt NPD GO	PSB2B_ARATH	Proteasome subunit beta type 2-B (EC 3.4.25.1) (Proteasome subunit beta type 4) (20S proteasome beta ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				199
Q9LST7 UniProt NPD GO	PSB3_ORYSA	Proteasome subunit beta type 3 (EC 3.4.25.1) (20S proteasome alpha subunit C) (20S proteasome subuni ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				204
Q23237 UniProt NPD GO	PSB3_CAEEL	Proteasome subunit beta type 3 (EC 3.4.25.1) (Proteasome subunit beta 3)	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				204
P33672 UniProt NPD GO	PSB3_BOVIN	Proteasome subunit beta type 3 (EC 3.4.25.1) (Proteasome theta chain) (Proteasome chain 13) (Proteas ...	0.00	-	cyt	0	Cytoplasm. Nucleus			1IRU	205
P49720 UniProt NPD GO	PSB3_HUMAN	Proteasome subunit beta type 3 (EC 3.4.25.1) (Proteasome theta chain) (Proteasome chain 13) (Proteas ...	0.00	-	cyt	0	Cytoplasm. Nucleus	proteasome complex (sensu Eukaryota) [TAS]	602176		205
Q9R1P1 UniProt NPD GO	PSB3_MOUSE	Proteasome subunit beta type 3 (EC 3.4.25.1) (Proteasome theta chain) (Proteasome chain 13) (Proteas ...	0.00	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex (sensu Eukaryota) [IDA]			205
P40112 UniProt NPD GO	PSB3_RAT	Proteasome subunit beta type 3 (EC 3.4.25.1) (Proteasome theta chain) (Proteasome chain 13) (Proteas ...	0.00	-	cyt	0	Cytoplasm. Nucleus				205
O81153 UniProt NPD GO	PSB3B_ARATH	Proteasome subunit beta type 3-B (EC 3.4.25.1) (20S proteasome beta subunit C-2)	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				204
Q3MHN0 UniProt NPD GO	PSB6_BOVIN	Proteasome subunit beta type 6 precursor (EC 3.4.25.1)	0.00	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				239
P28072 UniProt NPD GO	PSB6_HUMAN	Proteasome subunit beta type 6 precursor (EC 3.4.25.1) (Proteasome delta chain) (Macropain delta cha ...	0.00	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex (sensu Eukaryota) [NAS]	600307		239
Q60692 UniProt NPD GO	PSB6_MOUSE	Proteasome subunit beta type 6 precursor (EC 3.4.25.1) (Proteasome delta chain) (Macropain delta cha ...	0.00	-	cyt	0	Cytoplasm. Nucleus				238
P28073 UniProt NPD GO	PSB6_RAT	Proteasome subunit beta type 6 precursor (EC 3.4.25.1) (Proteasome delta chain) (Macropain delta cha ...	0.00	-	cyt	0	Cytoplasm. Nucleus				238
Q9PT26 UniProt NPD GO	PSB9_ONCMY	Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Low molecular mass protein 2)	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				217
Q8UW64 UniProt NPD GO	PSB9_ORYLA	Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Low molecular mass protein 2)	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				217
Q9DD33 UniProt NPD GO	PSB9_SALSA	Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Low molecular mass protein 2)	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				217
Q93118 UniProt NPD GO	A16_ANOGA	Protein A16 precursor	0.00	-	exc	1 *					192
Q9FNG3 UniProt NPD GO	Y5645_ARATH	Protein At5g06450	0.00	-	cyt	0				1VK0	206
Q5R9A6 UniProt NPD GO	CJ057_PONPY	Protein C10orf57 homolog	0.00	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				123
Q9NQ40 UniProt NPD GO	CT054_HUMAN	Protein C20orf54 precursor	0.00	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				469
P59043 UniProt NPD GO	CU100_HUMAN	Protein C21orf100	0.00	-	cyt	0					55
P59042 UniProt NPD GO	CU089_HUMAN	Protein C21orf89	0.00	-	cyt	0					33
Q7TNE1 UniProt NPD GO	CG010_MOUSE	Protein C7orf10 homolog	0.00	-	mit	0					436
Q9CQ00 UniProt NPD GO	CI123_MOUSE	Protein C9orf123 homolog	0.00	-	gol	2	Membrane; multi-pass membrane protein (Potential)				111
O75629 UniProt NPD GO	CREG1_HUMAN	Protein CREG1 precursor (Cellular repressor of E1A-stimulated genes 1)	0.00	-	exc	1 *	Secreted protein			1XHN	220
Q7T3C3 UniProt NPD GO	CUTA_BRARE	Protein CutA homolog precursor	0.00	-	exc	1 *					150
Q96BM0 UniProt NPD GO	FM14B_HUMAN	Protein FAM14B (ISG12(c) protein)	0.00	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				104

You are viewing entries 97251 to 97300 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.