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
P14441 UniProt NPD GO	FIBA_BISBO	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				19
P14445 UniProt NPD GO	FIBA_CAVPO	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				13
P68111 UniProt NPD GO	FIBA_CERAE	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P68112 UniProt NPD GO	FIBA_ERYPA	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P14450 UniProt NPD GO	FIBA_FELCA	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P14452 UniProt NPD GO	FIBA_HORSE	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				14
P68109 UniProt NPD GO	FIBA_MACFA	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P68108 UniProt NPD GO	FIBA_MACFU	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P68110 UniProt NPD GO	FIBA_MACMU	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P14456 UniProt NPD GO	FIBA_MELME	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P14458 UniProt NPD GO	FIBA_MUSVI	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P68113 UniProt NPD GO	FIBA_PAPAN	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P68114 UniProt NPD GO	FIBA_PAPHA	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P14461 UniProt NPD GO	FIBA_RABIT	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P14536 UniProt NPD GO	FIBA_TAPTE	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P68115 UniProt NPD GO	FIBA_THEGE	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P68212 UniProt NPD GO	FIBA_VULVU	Fibrinogen alpha chain [Contains: Fibrinopeptide A] (Fragment)	0.01	-		0	Secreted protein				16
P14466 UniProt NPD GO	FIBB_BISBO	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.01	-	cyt	0	Secreted protein				21
P14469 UniProt NPD GO	FIBB_FELCA	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.01	-		0	Secreted protein				20
P14474 UniProt NPD GO	FIBB_MANLE	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.01	-		0	Secreted protein				14
P14478 UniProt NPD GO	FIBB_RABIT	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.01	-		0	Secreted protein				13
P14482 UniProt NPD GO	FIBB_VULVU	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.01	-		0	Secreted protein				19
P81882 UniProt NPD GO	TLB1_BOTJA	Fibrinogen-clotting enzyme TL-BJ isoform 1 (EC 3.4.21.-) (TL-BJ 1) (Fragment)	0.01	-		0					19
P81883 UniProt NPD GO	TLB2_BOTJA	Fibrinogen-clotting enzyme TL-BJ isoform 2 (EC 3.4.21.-) (TL-BJ 2) (Fragment)	0.01	-		0					19
P81884 UniProt NPD GO	TLB3_BOTJA	Fibrinogen-clotting enzyme TL-BJ isoform 3 (EC 3.4.21.-) (TL-BJ 3) (Fragment)	0.01	-		0					19
P08620 UniProt NPD GO	FGF4_HUMAN	Fibroblast growth factor 4 precursor (FGF-4) (Heparin secretory-transforming protein) (HST-1) (HST) ...	0.01	-	end	1 *		extracellular region [TAS]	164980	1IJT	206
O62682 UniProt NPD GO	FGF8_CANFA	Fibroblast growth factor 8 (FGF-8) (HBGF-8) (Androgen-induced growth factor) (AIGF) (Fragment)	0.01	-	cyt	0	Secreted protein				82
Q61075 UniProt NPD GO	FIN15_MOUSE	Fibroblast growth factor-inducible protein 15 (FIN15)	0.01	-	cyt	0					87
Q15485 UniProt NPD GO	FCN2_HUMAN	Ficolin-2 precursor (Collagen/fibrinogen domain-containing protein 2) (Ficolin-B) (Ficolin B) (Serum ...	0.01	-	mit	1 *	Secreted protein		601624		313
Q9MZD2 UniProt NPD GO	FLNB_RABIT	Filamin-B (FLN-B) (Beta-filamin) (Actin-binding-like protein) (ABP-280-like protein) (C254) (Fragmen ...	0.01	-	cyt	0	Cytoplasm; cell cortex (By similarity)				294
P68512 UniProt NPD GO	FEL_CYPCA	Fish-egg lectin (FEL)	0.01	-	cyt	0	Secreted protein				238
Q27052 UniProt NPD GO	FCA1_TRYRA	Flagellar calcium-binding protein	0.01	-	cyt	0	Flagellum				204
Q923D2 UniProt NPD GO	BLVRB_MOUSE	Flavin reductase (EC 1.5.1.30) (FR) (NADPH-dependent diaphorase) (NADPH-flavin reductase) (FLR) (Bil ...	0.01	-	exc	0	Cytoplasm (Potential)				205
P52556 UniProt NPD GO	BLVRB_BOVIN	Flavin reductase (EC 1.5.1.30) (FR) (NADPH-dependent diaphorase) (NADPH-flavin reductase) (FLR) (Bil ...	0.01	-	vac	0	Cytoplasm (Potential)				205
P30043 UniProt NPD GO	BLVRB_HUMAN	Flavin reductase (EC 1.5.1.30) (FR) (NADPH-dependent diaphorase) (NADPH-flavin reductase) (FLR) (Bil ...	0.01	-	vac	0	Cytoplasm (Potential)		600941	1HE5	205
P05620 UniProt NPD GO	VSP1_TRIFL	Flavoxobin precursor (EC 3.4.21.-)	0.01	-	exc	0					260
Q8H6Q1 UniProt NPD GO	DEF1_PETHY	Floral defensin-like protein 1 precursor (PhD1)	0.01	-	exc	1 *	Vacuole (By similarity)			1N4N	103
O45166 UniProt NPD GO	FOLT3_CAEEL	Folate-like transporter 3	0.01	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				424
P01226 UniProt NPD GO	FSHB_HORSE	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.01	-	end	0	Secreted protein				129
Q6IY73 UniProt NPD GO	FSHB_RABIT	Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) (FSH-beta) (FSH-B)	0.01	-	exc	0	Secreted protein				129
Q9SXP2 UniProt NPD GO	FDH1_ORYSA	Formate dehydrogenase 1, mitochondrial precursor (EC 1.2.1.2) (NAD-dependent formate dehydrogenase 1 ...	0.01	-	mit	0	Mitochondrion (By similarity)				376
Q9S7E4 UniProt NPD GO	FDH_ARATH	Formate dehydrogenase, mitochondrial precursor (EC 1.2.1.2) (NAD-dependent formate dehydrogenase) (F ...	0.01	-	mit	0	Mitochondrion				384
Q9ZRI8 UniProt NPD GO	FDH_HORVU	Formate dehydrogenase, mitochondrial precursor (EC 1.2.1.2) (NAD-dependent formate dehydrogenase) (F ...	0.01	-	mit	0	Mitochondrion (By similarity)				377
Q9WUH4 UniProt NPD GO	FHL1_RAT	Four and a half LIM domains protein 1 (FHL-1)	0.01	-	nuc	0	Cytoplasm (By similarity)				280
P97447 UniProt NPD GO	FHL1_MOUSE	Four and a half LIM domains protein 1 (FHL-1) (Skeletal muscle LIM-protein 1) (SLIM 1) (SLIM) (KyoT) ...	0.01	-	nuc	0	Isoform 1: Cytoplasm. Isoform 2: Nucleus				280
P82022 UniProt NPD GO	FRE2_LITIN	Frenatin-2	0.01	-		0	Secreted protein				15
P56249 UniProt NPD GO	FRE3_LITIN	Frenatin-3	0.01	-		0	Secreted protein				20
Q9IA06 UniProt NPD GO	FZD2_CHICK	Frizzled-2 (Fz-2) (cFz-2) (Fragment)	0.01	-	end	6	Membrane; multi-pass membrane protein				523
O57329 UniProt NPD GO	FZD7_CHICK	Frizzled-7 precursor (Fz-7) (cFz-7)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				567
Q944F5 UniProt NPD GO	SCRK2_ORYSA	Fructokinase-2 (EC 2.7.1.4) (Fructokinase II) (OsFKII)	0.01	-	cyt	0					336

You are viewing entries 88301 to 88350 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.