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
O64847 UniProt NPD GO	U136_ARATH	UPF0136 protein At2g26240	0.02	-	cyt	3 *	Membrane; multi-pass membrane protein (Potential)				108
Q9SD88 UniProt NPD GO	U139_ARATH	UPF0139 protein At5g07960	0.02	-	nuc	2 *					107
Q9Y3B6 UniProt NPD GO	CN122_HUMAN	UPF0172 protein C14orf122	0.02	-	mit	0					208
Q9DB76 UniProt NPD GO	CN122_MOUSE	UPF0172 protein C14orf122 homolog	0.02	-	cyt	0					206
Q8WUR7 UniProt NPD GO	U235_HUMAN	UPF0235 protein C15orf40	0.02	-	nuc	0					126
Q9CRC3 UniProt NPD GO	U235_MOUSE	UPF0235 protein C15orf40 homolog	0.02	-	nuc	0					126
Q9D291 UniProt NPD GO	CG146_MOUSE	UPF0326 protein CGI-146 homolog	0.02	-	cyt	0					194
Q08971 UniProt NPD GO	YP225_YEAST	UPF0368 protein YPL225W	0.02	-	cyt	0	Cytoplasm	cytoplasm [IDA]			146
Q8TGJ3 UniProt NPD GO	U373_YEAST	UPF0373 protein YNL024C-A precursor	0.02	-	exc	0	Secreted protein (Potential)				72
Q9VWH8 UniProt NPD GO	U373_DROME	UPF0373 protein precursor	0.02	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				74
Q8TBQ9 UniProt NPD GO	U373_HUMAN	UPF0373 protein precursor	0.02	-	exc	2 *	Membrane; single-pass type I membrane protein				72
Q9CR64 UniProt NPD GO	U373_MOUSE	UPF0373 protein precursor	0.02	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				72
Q5RAL1 UniProt NPD GO	U373_PONPY	UPF0373 protein precursor	0.02	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				72
O64459 UniProt NPD GO	UGPA_PYRPY	UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (UDP-glucose pyrophosphorylase) (UDPGP) (U ...	0.02	-	cyt	0	Cytoplasm				471
P22289 UniProt NPD GO	UCR9_YEAST	Ubiquinol-cytochrome c reductase complex 7.3 kDa protein (Complex III subunit 9) (Cytochrome b-c1 co ...	0.02	-	mit	1 *	Mitochondrion; mitochondrial inner membrane	respiratory chain complex III (sensu Eukary... [IDA]		1P84	65
Q69BK4 UniProt NPD GO	UCRI_GORGO	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				274
P47985 UniProt NPD GO	UCRI_HUMAN	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane	respiratory chain complex III (sensu Eukary... [NAS]	191327		274
Q69BK6 UniProt NPD GO	UCRI_PANPA	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				274
Q69BK5 UniProt NPD GO	UCRI_PANTR	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				274
Q69BK2 UniProt NPD GO	UCRI_THEGE	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				274
Q75CW5 UniProt NPD GO	UQCR2_ASHGO	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2)	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				366
P43265 UniProt NPD GO	UQCR2_EUGGR	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2)	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				474
Q6CWJ6 UniProt NPD GO	UQCR2_KLULA	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2)	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				360
P60604 UniProt NPD GO	UB2G2_HUMAN	Ubiquitin-conjugating enzyme E2 G2 (EC 6.3.2.19) (Ubiquitin-protein ligase G2) (Ubiquitin carrier pr ...	0.02	-	nuc	0			603124	2CYX	165
P60605 UniProt NPD GO	UB2G2_MOUSE	Ubiquitin-conjugating enzyme E2 G2 (EC 6.3.2.19) (Ubiquitin-protein ligase G2) (Ubiquitin carrier pr ...	0.02	-	nuc	0		cytosol [IDA] endoplasmic reticulum [IDA]			165
Q5RF84 UniProt NPD GO	UB2G2_PONPY	Ubiquitin-conjugating enzyme E2 G2 (EC 6.3.2.19) (Ubiquitin-protein ligase G2) (Ubiquitin carrier pr ...	0.02	-	nuc	0					165
P52486 UniProt NPD GO	UBCD4_DROME	Ubiquitin-conjugating enzyme E2-22 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.02	-	cyt	0					199
Q8CFI2 UniProt NPD GO	UB2R1_MOUSE	Ubiquitin-conjugating enzyme E2-32 kDa complementing (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiqu ...	0.02	-	cyt	0					235
P91302 UniProt NPD GO	UBL5_CAEEL	Ubiquitin-like protein 5	0.02	-	cyt	0	Cytoplasm (By similarity)				73
Q5E953 UniProt NPD GO	UFC1_BOVIN	Ufm1-conjugating enzyme 1 (Ubiquitin-fold modifier-conjugating enzyme 1)	0.02	-	cyt	0					167
Q9Y3C8 UniProt NPD GO	UFC1_HUMAN	Ufm1-conjugating enzyme 1 (Ubiquitin-fold modifier-conjugating enzyme 1)	0.02	-	cyt	0				1YWZ	167
Q6BBI8 UniProt NPD GO	UFC1_RAT	Ufm1-conjugating enzyme 1 (Ubiquitin-fold modifier-conjugating enzyme 1)	0.02	-	cyt	0					167
P42849 UniProt NPD GO	UMEC_ARMRU	Umecyanin (UMC)	0.02	-	cyt	0				1X9U	115
P59833 UniProt NPD GO	UGPI3_ARATH	Uncharacterized GPI-anchored protein At5g19250 precursor	0.02	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor				196
P40363 UniProt NPD GO	YJG8_YEAST	Uncharacterized esterase YJL068C (EC 3.1.1.-)	0.02	-	cyt	0		cytosol [IDA]		1PV1	299
Q9JIS3 UniProt NPD GO	CK075_MOUSE	Uncharacterized protein C11orf75 homolog (Protein FN5)	0.02	-	nuc	1 *					59
Q96IT6 UniProt NPD GO	CN128_HUMAN	Uncharacterized protein C14orf128	0.02	-	nuc	0					56
Q4R5V2 UniProt NPD GO	CO024_MACFA	Uncharacterized protein C15orf24 homolog precursor	0.02	-	end	1	Membrane; single-pass type I membrane protein (Potential)				242
Q9EP72 UniProt NPD GO	CO024_MOUSE	Uncharacterized protein C15orf24 homolog precursor	0.02	-	end	1	Membrane; single-pass type I membrane protein (Potential)				241
Q9NPA0 UniProt NPD GO	CO024_HUMAN	Uncharacterized protein C15orf24 precursor	0.02	-	end	1	Membrane; single-pass type I membrane protein (Potential)	cytoplasm [NAS]			242
Q9CPT4 UniProt NPD GO	CS010_MOUSE	Uncharacterized protein C19orf10 homolog precursor (Stromal cell-derived growth factor SF20) (Interl ...	0.02	-	cyt	0	Secreted protein				166
Q9D1K7 UniProt NPD GO	CT027_MOUSE	Uncharacterized protein C20orf27 homolog	0.02	-	mit	0					173
Q9Y3B1 UniProt NPD GO	CT045_HUMAN	Uncharacterized protein C20orf45	0.02	-	cyt	0					194
Q58DB0 UniProt NPD GO	CT045_BOVIN	Uncharacterized protein C20orf45 homolog	0.02	-	cyt	0					194
Q9UJQ7 UniProt NPD GO	CT079_HUMAN	Uncharacterized protein C20orf79	0.02	-	cyt	0					156
Q5RFT1 UniProt NPD GO	CB018_PONPY	Uncharacterized protein C2orf18 homolog precursor	0.02	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				371
Q8N357 UniProt NPD GO	CB018_HUMAN	Uncharacterized protein C2orf18 precursor	0.02	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				371
Q5M828 UniProt NPD GO	CF105_RAT	Uncharacterized protein C6orf105 homolog (Liver regeneration-related protein LRRG140)	0.02	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				230
P18411 UniProt NPD GO	YAA8_YEAST	Uncharacterized protein YAL008W	0.02	-	mit	2 *		mitochondrial outer membrane [IDA] mitochondrion [IDA]			198
P25347 UniProt NPD GO	YCP2_YEAST	Uncharacterized protein YCR001W	0.02	-	mit	1					104

You are viewing entries 86101 to 86150 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.