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
P29163 UniProt NPD GO	COX2_PNECA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				243
Q37677 UniProt NPD GO	COX2_SALSA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
P21534 UniProt NPD GO	COX2_SCHPO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				248
P00413 UniProt NPD GO	COX2_WHEAT	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				260
Q36952 UniProt NPD GO	COX3_AEGCO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.02	-	end	5 *					265
Q8SEW8 UniProt NPD GO	COX3_COTJA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.02	-	end	7 *					261
Q8LX26 UniProt NPD GO	COX3_LEMCA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.02	-	end	6 *					274
P09138 UniProt NPD GO	COX3_MAIZE	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.02	-	end	5 *					265
P14852 UniProt NPD GO	COX3_ORYSA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.02	-	end	5 *					265
O79433 UniProt NPD GO	COX3_RABIT	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.02	-	end	6 *					261
O21403 UniProt NPD GO	COX3_STRCA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.02	-	end	7 *					261
Q36098 UniProt NPD GO	COX3_THEPA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.02	-	end	6 *					255
Q9I8U0 UniProt NPD GO	COX41_THUOB	Cytochrome c oxidase subunit 4 isoform 1, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase ...	0.02	-	mit	1	Mitochondrion; mitochondrial inner membrane				169
Q5AEN1 UniProt NPD GO	CCPR_CANAL	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				366
P51199 UniProt NPD GO	CY550_PORPU	Cytochrome c-550 precursor (Cytochrome c550)	0.02	-	gol	1 *	Plastid; chloroplast				163
P00110 UniProt NPD GO	CYC6_BUMFI	Cytochrome c6 (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				86
Q17802 UniProt NPD GO	CEJ1_CAEEL	Cytokinesis protein cej-1 precursor (Cell junction protein 1)	0.02	-	exc	0					584
Q9T0N8 UniProt NPD GO	CKX1_MAIZE	Cytokinin dehydrogenase 1 precursor (EC 1.5.99.12) (Cytokinin oxidase 1) (CKO 1) (COX 1) (ZmCKX1)	0.02	-	end	1 *	Secreted protein; extracellular space			1W1S	534
Q67YU0 UniProt NPD GO	CKX5_ARATH	Cytokinin dehydrogenase 5 precursor (EC 1.5.99.12) (Cytokinin oxidase 5) (CKO5) (AtCKX5) (AtCKX6)	0.02	-	mit	1 *	Secreted protein; extracellular space (By similarity)				540
Q9SK82 UniProt NPD GO	COGT2_ARATH	Cytokinin-O-glucosyltransferase 2 (EC 2.4.1.-) (Zeatin O-glucosyltransferase 2)	0.02	-	mit	0					489
P83782 UniProt NPD GO	CAP5_CANAL	Cytoplasmic antigenic protein 5 (Fragment)	0.02	-		0	Cytoplasm				11
Q9D1A2 UniProt NPD GO	CNDP2_MOUSE	Cytosolic nonspecific dipeptidase (Glutamate carboxypeptidase-like protein 1) (CNDP dipeptidase 2)	0.02	-	cyt	0					475
P60305 UniProt NPD GO	CTX1_NAJKA	Cytotoxin 1 (CTX1) (Cardiotoxin F8) (Cytotoxin CM-6)	0.02	-	nuc	0	Secreted protein				60
P01447 UniProt NPD GO	CX1_NAJNA	Cytotoxin 1 (Cytotoxin XI) (Cytotoxin-like basic protein) (CLBP)	0.02	-	nuc	0	Secreted protein				60
P24776 UniProt NPD GO	CX2_HEMHA	Cytotoxin 2 (Toxin 12A)	0.02	-	nuc	0	Secreted protein				61
P01463 UniProt NPD GO	CX2_NAJNI	Cytotoxin 2 (Toxin V-II-2)	0.02	-	nuc	0	Secreted protein				60
P01446 UniProt NPD GO	CX3_NAJKA	Cytotoxin 3 (CX3) (Cytotoxin CM-7)	0.02	-	nuc	0	Secreted protein	extracellular region [IDA]			60
P24777 UniProt NPD GO	CX3_HEMHA	Cytotoxin 3 (Toxin 11/11A)	0.02	-	nuc	0	Secreted protein				61
P01452 UniProt NPD GO	CX4_NAJMO	Cytotoxin 4 (Cardiotoxin V-II-4)	0.02	-	nuc	0	Secreted protein			1CDT	60
P60306 UniProt NPD GO	CTX3B_NAJAT	Cytotoxin SP13b	0.02	-	nuc	0	Secreted protein				60
Q9PS34 UniProt NPD GO	CTX5_NAJOX	Cytotoxin Vc-5	0.02	-	nuc	0	Secreted protein				60
Q95136 UniProt NPD GO	DRD1_BOVIN	D(1A) dopamine receptor	0.02	-	end	7 *	Cell membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; m ...				446
P43066 UniProt NPD GO	ARDH_CANAL	D-arabinitol 2-dehydrogenase [ribulose-forming] (EC 1.1.1.250) (ARDH)	0.02	-	mit	0					281
P31228 UniProt NPD GO	OXDD_BOVIN	D-aspartate oxidase (EC 1.4.3.1) (DASOX) (DDO)	0.02	-	mit	0	Peroxisome				341
Q15038 UniProt NPD GO	DAZP2_HUMAN	DAZ-associated protein 2 (Deleted in azoospermia-associated protein 2)	0.02	-	cyt	0			607431		168
Q757G7 UniProt NPD GO	RAD59_ASHGO	DNA repair protein RAD59	0.02	-	cyt	0	Nucleus (By similarity)				204
P29214 UniProt NPD GO	DBH_GUITH	DNA-binding protein HU homolog (Histone-like protein)	0.02	-	cyt	0	Plastid; chloroplast				93
P32529 UniProt NPD GO	RPA9_YEAST	DNA-directed RNA polymerase I 13.7 kDa polypeptide (EC 2.7.7.6) (A12.2)	0.02	-	nuc	0	Nucleus	DNA-directed RNA polymerase I complex [TAS]			125
P34087 UniProt NPD GO	RPB7_YEAST	DNA-directed RNA polymerase II 19 kDa polypeptide (EC 2.7.7.6) (B16)	0.02	-	cyt	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]		2B8K	171
Q12091 UniProt NPD GO	DAP1_YEAST	Damage response protein 1	0.02	-	cyt	0					152
Q9M3T9 UniProt NPD GO	DAD1_BETVE	Defender against cell death 1 (DAD-1)	0.02	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				115
P81929 UniProt NPD GO	PSD1_PEA	Defense-related peptide 1 (Defensin-1) (Antifungal protein Psd1)	0.02	-	nuc	0				1JKZ	46
P80407 UniProt NPD GO	DEFI_PALPR	Defensin	0.02	-	nuc	0	Secreted protein				43
P80033 UniProt NPD GO	DEFA_ZOPAT	Defensin, isoforms B and C	0.02	-	cyt	0	Secreted protein				43
P91793 UniProt NPD GO	DEFA_AEDAE	Defensin-A precursor (AaDef)	0.02	-	exc	0	Secreted protein				98
P83668 UniProt NPD GO	DEFB_ANOCP	Defensin-B	0.02	-	cyt	0	Secreted protein				43
Q9BPX1 UniProt NPD GO	DHR10_HUMAN	Dehydrogenase/reductase SDR family member 10 (EC 1.1.-.-) (Retinal short-chain dehydrogenase/reducta ...	0.02	-	cyt	0				1YDE	270
Q9BPW9 UniProt NPD GO	DHRS9_HUMAN	Dehydrogenase/reductase SDR family member 9 precursor (EC 1.1.-.-) (3-alpha hydroxysteroid dehydroge ...	0.02	-	mit	0	Microsome; microsomal membrane. Asociated with microsomal membranes	integral to endoplasmic reticulum membrane [IDA] microsome [IDA]			319
Q58NB6 UniProt NPD GO	DHRS9_MOUSE	Dehydrogenase/reductase SDR family member 9 precursor (EC 1.1.-.-) (3-alpha hydroxysteroid dehydroge ...	0.02	+	mit	0	Cytoplasm (By similarity). Microsome; microsomal membrane (By similarity). Associated with microsoma ...				319
Q8VD48 UniProt NPD GO	DHRS9_RAT	Dehydrogenase/reductase SDR family member 9 precursor (EC 1.1.-.-) (3-alpha hydroxysteroid dehydroge ...	0.02	+	mit	0	Cytoplasm (By similarity). Microsome; microsomal membrane (By similarity). Associated with microsoma ...	integral to endoplasmic reticulum membrane [ISS] microsome [ISS]			319

You are viewing entries 83251 to 83300 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.