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
Q9CPX8 UniProt NPD GO	UCR11_MOUSE	Ubiquinol-cytochrome c reductase complex 6.4 kDa protein (EC 1.10.2.2) (Complex III subunit XI)	0.00	-	mit	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)	mitochondrion [IDA]			56
P49346 UniProt NPD GO	UCRQ_KLULA	Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C (EC 1.10.2.2) (Ubiquinol-cy ...	0.00	-	cyt	1	Mitochondrion; mitochondrial inner membrane				94
P48376 UniProt NPD GO	COQ7_CAEEL	Ubiquinone biosynthesis protein COQ7 homolog (Clock abnormal protein 1) (Protein clk-1)	0.00	-	mit	0		mitochondrion [IDA]			187
O01391 UniProt NPD GO	UCHL_APLCA	Ubiquitin carboxyl-terminal hydrolase (EC 3.4.19.12) (Ubiquitin thioesterase)	0.00	-	mit	0	Cytoplasm				214
P50103 UniProt NPD GO	UCHL1_MONDO	Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12) (EC 6.-.-.-) (UCH-L1) (Ubiquitin thi ...	0.00	-		0	Cytoplasm				15
Q2TBG8 UniProt NPD GO	UCHL3_BOVIN	Ubiquitin carboxyl-terminal hydrolase isozyme L3 (EC 3.4.19.12) (UCH-L3) (Ubiquitin thioesterase L3) ...	0.00	-	mit	0	Cytoplasm (By similarity)				230
P15374 UniProt NPD GO	UCHL3_HUMAN	Ubiquitin carboxyl-terminal hydrolase isozyme L3 (EC 3.4.19.12) (UCH-L3) (Ubiquitin thioesterase L3) ...	0.00	-	mit	0	Cytoplasm	cytoplasm [NAS]	603090	1XD3	230
Q9JKB1 UniProt NPD GO	UCHL3_MOUSE	Ubiquitin carboxyl-terminal hydrolase isozyme L3 (EC 3.4.19.12) (UCH-L3) (Ubiquitin thioesterase L3) ...	0.00	-	mit	0	Cytoplasm				230
Q91Y78 UniProt NPD GO	UCHL3_RAT	Ubiquitin carboxyl-terminal hydrolase isozyme L3 (EC 3.4.19.12) (UCH-L3) (Ubiquitin thioesterase L3) ...	0.00	-	mit	0	Cytoplasm (By similarity)				230
P58321 UniProt NPD GO	UCHL4_MOUSE	Ubiquitin carboxyl-terminal hydrolase isozyme L4 (EC 3.4.19.12) (UCH-L4) (Ubiquitin thioesterase L4) ...	0.00	-	mit	0	Cytoplasm (By similarity)				233
Q9P6I1 UniProt NPD GO	UBC16_SCHPO	Ubiquitin-conjugating enzyme E2 16 (EC 6.3.2.19) (Ubiquitin-protein ligase 16) (Ubiquitin carrier pr ...	0.00	-	cyt	0					160
Q2KJG2 UniProt NPD GO	UFM1_BOVIN	Ubiquitin-fold modifier 1 precursor	0.00	-	mit	0	Nucleus. Predominantly. Cytoplasm. Also expressed diffusely in the cytoplasm (By similarity)				85
Q5ZMK7 UniProt NPD GO	UFM1_CHICK	Ubiquitin-fold modifier 1 precursor	0.00	-	mit	0	Nucleus (By similarity). Predominantly. Cytoplasm (By similarity). Also expressed diffusely in the c ...				85
P61960 UniProt NPD GO	UFM1_HUMAN	Ubiquitin-fold modifier 1 precursor	0.00	-	mit	0	Nucleus. Predominantly. Cytoplasm. Also expressed diffusely in the cytoplasm			1WXS	85
Q4R4I2 UniProt NPD GO	UFM1_MACFA	Ubiquitin-fold modifier 1 precursor	0.00	-	mit	0	Nucleus (By similarity). Predominantly. Cytoplasm (By similarity). Also expressed diffusely in the c ...				85
P61961 UniProt NPD GO	UFM1_MOUSE	Ubiquitin-fold modifier 1 precursor	0.00	-	mit	0	Nucleus (By similarity). Predominantly. Cytoplasm (By similarity). Also expressed diffusely in the c ...			1J0G	85
Q5R4N5 UniProt NPD GO	UFM1_PONPY	Ubiquitin-fold modifier 1 precursor	0.00	-	mit	0	Nucleus (By similarity). Predominantly. Cytoplasm (By similarity). Also expressed diffusely in the c ...				85
Q5BJP3 UniProt NPD GO	UFM1_RAT	Ubiquitin-fold modifier 1 precursor	0.00	-	mit	0	Nucleus (By similarity). Predominantly. Cytoplasm (By similarity). Also expressed diffusely in the c ...				85
Q5RJW4 UniProt NPD GO	UFM1_XENLA	Ubiquitin-fold modifier 1 precursor	0.00	-	cyt	0	Nucleus (By similarity). Predominantly. Cytoplasm (By similarity). Also expressed diffusely in the c ...				85
Q2KJD7 UniProt NPD GO	UBCP1_BOVIN	Ubiquitin-like domain-containing CTD phosphatase 1 (EC 3.1.3.16)	0.00	-	cyt	0	Nucleus (By similarity)				318
Q8WVY7 UniProt NPD GO	UBCP1_HUMAN	Ubiquitin-like domain-containing CTD phosphatase 1 (EC 3.1.3.16)	0.00	-	cyt	0	Nucleus		609867		318
Q8BGR9 UniProt NPD GO	UBCP1_MOUSE	Ubiquitin-like domain-containing CTD phosphatase 1 (EC 3.1.3.16)	0.00	-	cyt	0	Nucleus (By similarity)				318
Q5R4C4 UniProt NPD GO	UBCP1_PONPY	Ubiquitin-like domain-containing CTD phosphatase 1 (EC 3.1.3.16)	0.00	-	cyt	0	Nucleus (By similarity)				318
Q5FWT7 UniProt NPD GO	UBCP1_RAT	Ubiquitin-like domain-containing CTD phosphatase 1 (EC 3.1.3.16)	0.00	-	cyt	0	Nucleus (By similarity)				318
Q756X3 UniProt NPD GO	HUB1_ASHGO	Ubiquitin-like modifier HUB1	0.00	-	cyt	0					73
Q6BUP7 UniProt NPD GO	HUB1_DEBHA	Ubiquitin-like modifier HUB1	0.00	-	cyt	0					73
Q6CU12 UniProt NPD GO	HUB1_KLULA	Ubiquitin-like modifier HUB1	0.00	-	cyt	0					74
Q07371 UniProt NPD GO	UBL1_CAEBR	Ubiquitin-like protein 1	0.00	-	nuc	0					70
Q07372 UniProt NPD GO	UBL1_CAEEL	Ubiquitin-like protein 1	0.00	-	cyt	0					70
Q7SXF2 UniProt NPD GO	UBL5_BRARE	Ubiquitin-like protein 5	0.00	-	cyt	0	Cytoplasm (By similarity)				73
Q9BZL1 UniProt NPD GO	UBL5_HUMAN	Ubiquitin-like protein 5	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA]	606849	1P0R	73
Q9EPV8 UniProt NPD GO	UBL5_MOUSE	Ubiquitin-like protein 5	0.00	-	cyt	0	Cytoplasm (By similarity)			1UH6	73
Q6EGX7 UniProt NPD GO	UBL5_MESAU	Ubiquitin-like protein 5 (Beacon protein)	0.00	-	cyt	0	Cytoplasm (By similarity)				73
Q791B0 UniProt NPD GO	UBL5_PSAOB	Ubiquitin-like protein 5 (Beacon protein)	0.00	-	cyt	0	Cytoplasm (By similarity)				73
P62865 UniProt NPD GO	UBIM_BOVIN	Ubiquitin-like protein FUBI	0.00	-	cyt	0					74
P35544 UniProt NPD GO	UBIM_HUMAN	Ubiquitin-like protein FUBI	0.00	-	cyt	0			134690		74
P62868 UniProt NPD GO	UBIM_MUSSI	Ubiquitin-like protein FUBI	0.00	-	cyt	0					74
P55812 UniProt NPD GO	UBIM_PIG	Ubiquitin-like protein FUBI	0.00	-	cyt	0					74
Q05474 UniProt NPD GO	UBIM_RAT	Ubiquitin-like protein FUBI	0.00	-	cyt	0					74
P35545 UniProt NPD GO	UBIM_MOUSE	Ubiquitin-like protein FUBI (Monoclonal nonspecific suppressor factor beta) (MNSF-beta)	0.00	-	cyt	0					74
P55853 UniProt NPD GO	SMT3_CAEEL	Ubiquitin-like protein SMT3	0.00	-	cyt	0					91
Q90309 UniProt NPD GO	OPSUV_CARAU	Ultraviolet-sensitive opsin (Ultraviolet cone photoreceptor pigment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				336
Q8GUL8 UniProt NPD GO	UGPI1_ARATH	Uncharacterized GPI-anchored protein At5g19230 precursor	0.00	-	end	1	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			189
P53750 UniProt NPD GO	YN93_YEAST	Uncharacterized hydrolase YNR064C (EC 3.1.-.-)	0.00	-	cyt	0		soluble fraction [IDA]			290
P38765 UniProt NPD GO	YHI9_YEAST	Uncharacterized isomerase YHR029C (EC 5.1.-.-)	0.00	-	cyt	0				1YM5	294
P53757 UniProt NPD GO	YN9A_YEAST	Uncharacterized isomerase YNR071C (EC 5.-.-.-)	0.00	-	cyt	0				1YGA	342
P39941 UniProt NPD GO	YEI0_YEAST	Uncharacterized oxidoreductase YEL070W/YNR073C (EC 1.1.-.-)	0.00	-	cyt	0					502
Q9H0R3 UniProt NPD GO	CA160_HUMAN	Uncharacterized protein C1orf160	0.00	-	cyt	3	Membrane; multi-pass membrane protein (Potential)				208
Q8BVA2 UniProt NPD GO	CA160_MOUSE	Uncharacterized protein C1orf160 homolog	0.00	-	cyt	3	Membrane; multi-pass membrane protein (Potential)				208
Q9D8B6 UniProt NPD GO	CT108_MOUSE	Uncharacterized protein C20orf108 homolog	0.00	-	end	0	Membrane; multi-pass membrane protein (Potential)				190

You are viewing entries 98501 to 98550 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.