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
O64636 UniProt NPD GO	C76C1_ARATH	Cytochrome P450 76C1 (EC 1.14.-.-)	0.11	-	end	1 *					512
O48922 UniProt NPD GO	C98A2_SOYBN	Cytochrome P450 98A2 (EC 1.14.-.-)	0.11	-	nuc	1 *					509
Q94ZD1 UniProt NPD GO	CYB_EPTBU	Cytochrome b	0.11	-	end	9 *					385
Q35930 UniProt NPD GO	CYB_SAISC	Cytochrome b	0.11	-	end	9 *					379
P04839 UniProt NPD GO	CY24B_HUMAN	Cytochrome b-245 heavy chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 91 kDa polypeptid ...	0.11	-	end	5 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]	306400		569
P25400 UniProt NPD GO	CYC_CANGA	Cytochrome c	0.11	-	nuc	0	Mitochondrion; mitochondrial matrix				104
P67881 UniProt NPD GO	CYC_CHICK	Cytochrome c	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00021 UniProt NPD GO	CYC_COLLI	Cytochrome c	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]		1KTD	104
P00018 UniProt NPD GO	CYC_DRONO	Cytochrome c	0.11	-	nuc	0	Mitochondrion; mitochondrial matrix				104
P00004 UniProt NPD GO	CYC_HORSE	Cytochrome c	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]		2PCB	104
P67882 UniProt NPD GO	CYC_MELGA	Cytochrome c	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix				104
Q52V10 UniProt NPD GO	CYC_SAISC	Cytochrome c	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				104
P00019 UniProt NPD GO	CYC_STRCA	Cytochrome c	0.11	-	nuc	0	Mitochondrion; mitochondrial matrix				104
Q8BJ03 UniProt NPD GO	COX15_MOUSE	Cytochrome c oxidase assembly protein COX15 homolog	0.11	-	end	7	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA]			413
Q9P7Z7 UniProt NPD GO	COX17_SCHPO	Cytochrome c oxidase copper chaperone	0.11	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				70
P04039 UniProt NPD GO	COX8_YEAST	Cytochrome c oxidase polypeptide VIII, mitochondrial precursor (EC 1.9.3.1)	0.11	-	mit	1 *	Mitochondrion; mitochondrial inner membrane	respiratory chain complex IV (sensu Eukaryota) [IPI]			78
Q863F8 UniProt NPD GO	COX81_EULFU	Cytochrome c oxidase polypeptide VIII-heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.11	-	mit	0	Mitochondrion; mitochondrial inner membrane				70
P14406 UniProt NPD GO	CX7A2_HUMAN	Cytochrome c oxidase polypeptide VIIa-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.11	-	mit	1	Mitochondrion; mitochondrial inner membrane		123996		83
P80431 UniProt NPD GO	COX7B_RAT	Cytochrome c oxidase polypeptide VIIb, mitochondrial precursor (EC 1.9.3.1)	0.11	-	mit	0					80
P11951 UniProt NPD GO	CX6C2_RAT	Cytochrome c oxidase polypeptide VIc-2 (EC 1.9.3.1)	0.11	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane				75
Q94514 UniProt NPD GO	COX5A_DROME	Cytochrome c oxidase polypeptide Va, mitochondrial precursor (EC 1.9.3.1)	0.11	-	mit	0	Mitochondrion; mitochondrial inner membrane				149
P00425 UniProt NPD GO	COX5B_YEAST	Cytochrome c oxidase polypeptide Vb, mitochondrial precursor (EC 1.9.3.1)	0.11	-	mit	1	Mitochondrion; mitochondrial inner membrane	respiratory chain complex IV (sensu Eukaryota) [IDA]			151
P19173 UniProt NPD GO	COX5C_IPOBA	Cytochrome c oxidase polypeptide Vc (EC 1.9.3.1) (Cytochrome c oxidase subunit 5c)	0.11	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				63
Q7IC90 UniProt NPD GO	COX2_AOTNI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				231
P68296 UniProt NPD GO	COX2_BISBO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P68295 UniProt NPD GO	COX2_BOSGA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P68294 UniProt NPD GO	COX2_BOSJA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q37430 UniProt NPD GO	COX2_CAPHI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50683 UniProt NPD GO	COX2_CAVAP	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P41311 UniProt NPD GO	COX2_DIDMA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				235
P92478 UniProt NPD GO	COX2_EQUAS	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P48660 UniProt NPD GO	COX2_HORSE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q9G2X2 UniProt NPD GO	COX2_MYXGL	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P29876 UniProt NPD GO	COX2_ONCFA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
Q37718 UniProt NPD GO	COX2_ORNAN	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
P98049 UniProt NPD GO	COX2_RABIT	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q37643 UniProt NPD GO	COX2_RHIDA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q37649 UniProt NPD GO	COX2_ROULE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O78750 UniProt NPD GO	COX2_SHEEP	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P29881 UniProt NPD GO	COX2_ZOOAN	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.11	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
P32646 UniProt NPD GO	COX2_VIGUN	Cytochrome c oxidase subunit 2, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase polypepti ...	0.11	-	end	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				376
O46581 UniProt NPD GO	COX41_THEGE	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.11	-	mit	1	Mitochondrion; mitochondrial inner membrane				144
P41996 UniProt NPD GO	B028_CAEEL	Cytokinesis protein B0280.5 precursor	0.11	-	exc	0					524
Q9FUJ3 UniProt NPD GO	CKX2_ARATH	Cytokinin dehydrogenase 2 precursor (EC 1.5.99.12) (Cytokinin oxidase 2) (CKO 2) (AtCKX2)	0.11	-	mit	0	Endoplasmic reticulum. Secreted protein; extracellular space				501
Q5RE09 UniProt NPD GO	DC1L2_PONPY	Cytoplasmic dynein 1 light intermediate chain 2 (Dynein light intermediate chain 2, cytosolic)	0.11	-	cyt	0					492
P16333 UniProt NPD GO	NCK1_HUMAN	Cytoplasmic protein NCK1 (NCK adaptor protein 1) (SH2/SH3 adaptor protein NCK-alpha)	0.11	-	cyt	0	Cytoplasm	cytoplasm [NAS]	600508	2CUB	377
P00727 UniProt NPD GO	AMPL_BOVIN	Cytosol aminopeptidase (EC 3.4.11.1) (Leucine aminopeptidase) (LAP) (Leucyl aminopeptidase) (Proline ...	0.11	-	nuc	0	Cytoplasm			2EWB	487
P53452 UniProt NPD GO	DRD1L_FUGRU	D(1)-like dopamine receptor	0.11	-	end	7 *	Membrane; multi-pass membrane protein				459
Q75E22 UniProt NPD GO	DTD_ASHGO	D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-)	0.11	-	mit	0	Cytoplasm (By similarity)				150
Q8W127 UniProt NPD GO	SLN1_HORVU	DELLA protein SLN1 (Slender protein 1)	0.11	-	mit	0	Nucleus				618

You are viewing entries 62551 to 62600 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.