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
P68217 UniProt NPD GO	FIBA_CEREN	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				19
P14447 UniProt NPD GO	FIBA_CERNI	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				19
P14453 UniProt NPD GO	FIBA_HYLLA	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				16
P68218 UniProt NPD GO	FIBA_LAMGL	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				18
P68219 UniProt NPD GO	FIBA_LAMVI	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				18
P14457 UniProt NPD GO	FIBA_MUNMU	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				19
P14459 UniProt NPD GO	FIBA_ODOHE	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				16
P14460 UniProt NPD GO	FIBA_PIG	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				17
P14462 UniProt NPD GO	FIBA_RANTA	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				19
P68214 UniProt NPD GO	FIBA_SHEEP	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				19
P14463 UniProt NPD GO	FIBA_SYNCA	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.00	-		0	Secreted protein				15
P14472 UniProt NPD GO	FIBB_HYLLA	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.00	-		0	Secreted protein				13
Q61077 UniProt NPD GO	FIN14_MOUSE	Fibroblast growth factor-inducible protein 14 (FIN14)	0.00	-	cyt	1 *					61
P54680 UniProt NPD GO	FIMB_DICDI	Fimbrin	0.00	-	cyt	0					610
Q26677 UniProt NPD GO	FCA4_TRYBB	Flagellar calcium-binding protein TB-1.7G (17 kDa calflagin) (17 kDa calcimedin) (Fragment)	0.00	-	nuc	0	Flagellum				229
P17882 UniProt NPD GO	FCA1_TRYBB	Flagellar calcium-binding protein TB-17 (17 kDa calflagin) (17 kDa calcimedin)	0.00	-	cyt	0	Flagellum				233
P55736 UniProt NPD GO	BLVRB_RANCA	Flavin reductase (EC 1.6.99.1) (NADPH-dependent diaphorase) (NADPH-methemoglobin reductase) (NADPH-d ...	0.00	-	cyt	0	Cytoplasm (Potential)				24
P14070 UniProt NPD GO	FLAV_CHOCR	Flavodoxin	0.00	-	cyt	0				2FCR	173
Q03331 UniProt NPD GO	FHP_CANNO	Flavohemoprotein (Hemoglobin-like protein) (Flavohemoglobin) (Nitric oxide dioxygenase) (EC 1.14.12. ...	0.00	-	mit	0					387
P82064 UniProt NPD GO	FLET_LIMFT	Fletcherin	0.00	-		0	Secreted protein				13
P45589 UniProt NPD GO	CU12_HYACE	Flexible cuticle protein 12 precursor	0.00	-	exc	0					105
Q8H6Q0 UniProt NPD GO	DEF2_PETHY	Floral defensin-like protein 2 precursor (PhD2)	0.00	-	exc	1 *	Vacuole (By similarity)				101
P33677 UniProt NPD GO	FDH_PICAN	Formate dehydrogenase (EC 1.2.1.2) (NAD-dependent formate dehydrogenase) (FDH)	0.00	-	nuc	0					361
Q67U69 UniProt NPD GO	FDH2_ORYSA	Formate dehydrogenase 2, mitochondrial precursor (EC 1.2.1.2) (NAD-dependent formate dehydrogenase 2 ...	0.00	-	cyt	0	Mitochondrion (By similarity)				378
Q07511 UniProt NPD GO	FDH_SOLTU	Formate dehydrogenase, mitochondrial precursor (EC 1.2.1.2) (NAD-dependent formate dehydrogenase) (F ...	0.00	-	mit	0	Mitochondrion				381
P82021 UniProt NPD GO	FRE1_LITIN	Frenatin-1	0.00	-		0	Secreted protein				12
P82023 UniProt NPD GO	FRE4_LITIN	Frenatin-4	0.00	-	cyt	0	Secreted protein				24
Q9PTW3 UniProt NPD GO	FZD3_CHICK	Frizzled-3 (Fz-3) (cFz-3) (Fragment)	0.00	-	end	2 *	Membrane; multi-pass membrane protein				76
Q9IA03 UniProt NPD GO	FZD8_CHICK	Frizzled-8 (Fz-8) (cFz-8) (Fragment)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				217
Q9IA02 UniProt NPD GO	FZD9_CHICK	Frizzled-9 (Fz-9) (cFz-9) (Fragment)	0.00	-	end	6 *	Membrane; multi-pass membrane protein				392
P37829 UniProt NPD GO	SCRK_SOLTU	Fructokinase (EC 2.7.1.4)	0.00	-	cyt	0					319
Q944F4 UniProt NPD GO	SCRK1_ORYSA	Fructokinase-1 (EC 2.7.1.4) (Fructokinase I) (OsFKI)	0.00	-	cyt	0					323
Q6XZ79 UniProt NPD GO	SCRK1_MAIZE	Fructokinase-1 (EC 2.7.1.4) (ZmFRK1)	0.00	-	cyt	0					323
Q9URB4 UniProt NPD GO	ALF_CANAL	Fructose-bisphosphate aldolase (EC 4.1.2.13) (37 kDa major allergen) (IgE-binding allergen) (Fragmen ...	0.00	-	cyt	0	Cytoplasm				40
Q968A5 UniProt NPD GO	FUCT1_CAEEL	GDP-fucose transporter	0.00	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein				363
Q9U6Y4 UniProt NPD GO	GFPL2_ZOASP	GFP-like fluorescent chromoprotein FP538 (zFP538) [Contains: GFP-like fluorescent chromoprotein FP53 ...	0.00	-	cyt	0				1XAE	231
P82264 UniProt NPD GO	DHE3_CHAAC	GLutamate dehydrogenase (EC 1.4.1.3) (GDH)	0.00	-	cyt	0	Mitochondrion; mitochondrial matrix				504
Q5KR61 UniProt NPD GO	PIGV_RAT	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Phosphatidylinosito ...	0.00	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				492
Q9V7W1 UniProt NPD GO	PIGV_DROME	GPI mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Protein vegetable)	0.00	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				449
Q8BTP0 UniProt NPD GO	PIGZ_MOUSE	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV) (Phosphatidylinosito ...	0.00	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [ISS]			560
P51598 UniProt NPD GO	GCH1_MUCHA	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I) (Fragment)	0.00	-	cyt	0					80
P78976 UniProt NPD GO	SAR1_TRIRE	GTP-binding protein SAR1	0.00	-	cyt	0					189
P20606 UniProt NPD GO	SAR1_YEAST	GTP-binding protein SAR1	0.00	-	cyt	0	Cytoplasm. Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	COPII vesicle coat [TAS]		1M2O	190
O04834 UniProt NPD GO	SAR1A_ARATH	GTP-binding protein SAR1A	0.00	-	cyt	0					193
O04266 UniProt NPD GO	SAR1A_BRACM	GTP-binding protein SAR1A	0.00	-	mit	0					193
Q01474 UniProt NPD GO	SAR1B_ARATH	GTP-binding protein SAR1B	0.00	-	mit	0					193
O04267 UniProt NPD GO	SAR1B_BRACM	GTP-binding protein SAR1B	0.00	-	mit	0					195
Q9NR31 UniProt NPD GO	SAR1A_HUMAN	GTP-binding protein SAR1a (COPII-associated small GTPase)	0.00	-	cyt	0		cytoplasm [NAS]	607691	2GAO	198
Q3T0T7 UniProt NPD GO	SAR1B_BOVIN	GTP-binding protein SAR1b	0.00	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity). ...				198
Q9CQC9 UniProt NPD GO	SAR1B_MOUSE	GTP-binding protein SAR1b	0.00	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Golgi apparatus; ...				198

You are viewing entries 94601 to 94650 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.