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
Q76LN6 UniProt NPD GO	CYB_CYNVO	Cytochrome b	0.07	-	end	9 *					379
Q34341 UniProt NPD GO	CYB_DAUMA	Cytochrome b	0.07	-	end	9 *					379
Q8SJL1 UniProt NPD GO	CYB_EMYBL	Cytochrome b	0.07	-	end	9 *					379
Q9T9V5 UniProt NPD GO	CYB_PANTR	Cytochrome b	0.07	-	end	9 *					380
Q8SJK6 UniProt NPD GO	CYB_TEROR	Cytochrome b	0.07	-	end	9 *					379
P52649 UniProt NPD GO	CY24B_PIG	Cytochrome b-245 heavy chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 91 kDa polypeptid ...	0.07	-	end	3 *	Membrane; multi-pass membrane protein				484
Q9BBR5 UniProt NPD GO	PSBE_LOTJA	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.07	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P13554 UniProt NPD GO	PSBE_PEA	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.07	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q2PMR7 UniProt NPD GO	PSBE_SOYBN	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.07	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83
Q6B8K5 UniProt NPD GO	PSBF_GRATL	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.07	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
P49447 UniProt NPD GO	CY561_HUMAN	Cytochrome b561 (Cytochrome b-561)	0.07	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600019		251
Q95245 UniProt NPD GO	CY561_PIG	Cytochrome b561 (Cytochrome b-561)	0.07	-	end	6 *	Secretory vesicle; secretory vesicle membrane; multi-pass membrane protein (By similarity). Secretor ...				252
Q5RCZ2 UniProt NPD GO	CY561_PONPY	Cytochrome b561 (Cytochrome b-561)	0.07	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				251
O14569 UniProt NPD GO	C56D2_HUMAN	Cytochrome b561 domain-containing protein 2 (Putative tumor suppressor protein 101F6)	0.07	-	end	6 *	Membrane; multi-pass membrane protein (Probable)		607068		222
Q9LLC6 UniProt NPD GO	PETO_CHLRE	Cytochrome b6-f complex subunit petO, chloroplast precursor (Cytochrome b6-f-associated phosphoprote ...	0.07	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane	cytochrome b6f complex [IDA] thylakoid membrane (sensu Viridiplantae) [IDA]			198
P81280 UniProt NPD GO	CYC_ALLMI	Cytochrome c	0.07	-	nuc	0	Mitochondrion; mitochondrial matrix				104
P00038 UniProt NPD GO	CYC_APIME	Cytochrome c	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix				107
P53698 UniProt NPD GO	CYC_CANAL	Cytochrome c	0.07	-	nuc	0	Mitochondrion; mitochondrial matrix				109
P00022 UniProt NPD GO	CYC_CHESE	Cytochrome c	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00051 UniProt NPD GO	CYC_CUCMA	Cytochrome c	0.07	-	nuc	0	Mitochondrion; mitochondrial matrix				111
Q4HVX7 UniProt NPD GO	CYC_GIBZE	Cytochrome c	0.07	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				109
P00074 UniProt NPD GO	CYC_GINBI	Cytochrome c	0.07	-	nuc	0	Mitochondrion; mitochondrial matrix				113
Q6WUX8 UniProt NPD GO	CYC_GORGO	Cytochrome c	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
P99999 UniProt NPD GO	CYC_HUMAN	Cytochrome c	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [IMP] mitochondrial intermembrane space [TAS]	123970	1J3S	104
P00028 UniProt NPD GO	CYC_LAMTR	Cytochrome c	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00002 UniProt NPD GO	CYC_MACMU	Cytochrome c	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
Q52V08 UniProt NPD GO	CYC_MACSY	Cytochrome c	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				104
P99998 UniProt NPD GO	CYC_PANTR	Cytochrome c	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
P00052 UniProt NPD GO	CYC_PHAAU	Cytochrome c	0.07	-	nuc	0	Mitochondrion; mitochondrial matrix				111
O13393 UniProt NPD GO	CYC_PICST	Cytochrome c	0.07	-	nuc	0	Mitochondrion; mitochondrial matrix				109
Q5RFH4 UniProt NPD GO	CYC_PONPY	Cytochrome c	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				104
P00024 UniProt NPD GO	CYC_RANCA	Cytochrome c	0.07	-	nuc	0	Mitochondrion; mitochondrial matrix				104
P00067 UniProt NPD GO	CYC_TROMA	Cytochrome c	0.07	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P00068 UniProt NPD GO	CYC_WHEAT	Cytochrome c	0.07	-	nuc	0	Mitochondrion; mitochondrial matrix				112
P12216 UniProt NPD GO	CCSA_TOBAC	Cytochrome c biogenesis protein ccsA	0.07	-	end	8 *	Plastid; chloroplast				313
P00044 UniProt NPD GO	CYC1_YEAST	Cytochrome c iso-1	0.07	-	nuc	0	Mitochondrion; mitochondrial intermembrane space	mitochondrial intermembrane space [IDA]		2YCC	108
P56394 UniProt NPD GO	COX17_MOUSE	Cytochrome c oxidase copper chaperone	0.07	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				62
P81045 UniProt NPD GO	COX17_PIG	Cytochrome c oxidase copper chaperone (Dopuin)	0.07	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				62
P80433 UniProt NPD GO	COX82_RAT	Cytochrome c oxidase polypeptide VIII-liver (EC 1.9.3.1) (Cytochrome c oxidase subunit 8-2)	0.07	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				44
P07470 UniProt NPD GO	CX7A1_BOVIN	Cytochrome c oxidase polypeptide VIIa-heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.07	-	mit	1	Mitochondrion; mitochondrial inner membrane			2OCC	80
O74471 UniProt NPD GO	COX13_SCHPO	Cytochrome c oxidase polypeptide VIa, mitochondrial precursor (EC 1.9.3.1)	0.07	-	mit	0	Mitochondrion; mitochondrial inner membrane				130
P07471 UniProt NPD GO	CX6A2_BOVIN	Cytochrome c oxidase polypeptide VIa-heart, mitochondrial precursor (EC 1.9.3.1) (COXVIAH) (Polypept ...	0.07	-	mit	0	Mitochondrion; mitochondrial inner membrane			2OCC	97
P20674 UniProt NPD GO	COX5A_HUMAN	Cytochrome c oxidase polypeptide Va, mitochondrial precursor (EC 1.9.3.1)	0.07	-	mit	0	Mitochondrion; mitochondrial inner membrane		603773		150
Q9LZQ0 UniProt NPD GO	CX5C2_ARATH	Cytochrome c oxidase polypeptide Vc-2 (EC 1.9.3.1) (Cytochrome c oxidase subunit 5c-2)	0.07	-	mit	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				64
P62514 UniProt NPD GO	COX1_ASHGO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.07	-	end	11 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				535
P24984 UniProt NPD GO	COX1_COTJA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.07	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
Q9ZXY2 UniProt NPD GO	COX1_PAPHA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.07	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				513
O47670 UniProt NPD GO	COX2_CHRBR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.07	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50687 UniProt NPD GO	COX2_DASNO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.07	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98032 UniProt NPD GO	COX2_DAUMA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.07	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227

You are viewing entries 69801 to 69850 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.