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
P31889 UniProt NPD GO	FAF1_ASCSU	FMRFamide-like neuropeptide AF1	0.01	-		0	Secreted protein				7
P42560 UniProt NPD GO	FARP_MYTED	FMRFamide-like neuropeptide ALAGDHFFRF-amide	0.01	-		0	Secreted protein				10
P83275 UniProt NPD GO	FAR2_MACRS	FMRFamide-like neuropeptide FLP2 (ADKNFLRF-amide)	0.01	-		0	Secreted protein				8
P83317 UniProt NPD GO	FAR2_PENMO	FMRFamide-like neuropeptide FLP2 (AYSNLNYLRF-amide)	0.01	-		0	Secreted protein				10
P41872 UniProt NPD GO	FAR1_PANRE	FMRFamide-like neuropeptide PF1 (SDPNFLRF-amide)	0.01	-		0	Secreted protein				8
P41875 UniProt NPD GO	FAR4_PANRE	FMRFamide-like neuropeptide PF4 (KPNFIRF-amide)	0.01	-		0	Secreted protein				7
P82660 UniProt NPD GO	FAR6_PANRE	FMRFamide-like neuropeptide PF6 (NGAPQPFVRF-amide)	0.01	-		0	Secreted protein				10
P59646 UniProt NPD GO	FXYD4_HUMAN	FXYD domain-containing ion transport regulator 4 precursor	0.01	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				89
Q63113 UniProt NPD GO	FXYD4_RAT	FXYD domain-containing ion transport regulator 4 precursor (Channel-inducing factor) (CHIF) (Cortico ...	0.01	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				87
P58550 UniProt NPD GO	FXYD8_HUMAN	FXYD domain-containing ion transport regulator 8 precursor	0.01	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				94
P49350 UniProt NPD GO	FPPS_ARTAN	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes ...	0.01	-	cyt	0	Cytoplasm (By similarity)				343
O24242 UniProt NPD GO	FPPS2_PARAR	Farnesyl pyrophosphate synthetase 2 (FPP synthetase 2) (FPS 2) (Farnesyl diphosphate synthetase 2) [ ...	0.01	-	cyt	0	Cytoplasm. Rubber particles				342
O76821 UniProt NPD GO	FABP_ACASI	Fatty acid-binding protein (Allergen Aca s 13) (Fragment)	0.01	-	nuc	0	Cytoplasm (Potential)				64
Q9UAS2 UniProt NPD GO	FABP1_FASGI	Fatty acid-binding protein 1	0.01	-	cyt	0					131
Q02970 UniProt NPD GO	FABP1_ECHGR	Fatty acid-binding protein homolog 1 (EgFABP1) (EgDf1)	0.01	-	cyt	0				1O8V	133
Q20223 UniProt NPD GO	FABP1_CAEEL	Fatty acid-binding protein homolog 1 precursor (Lipid-binding protein 1)	0.01	-	exc	0	Secreted protein. From the hypodermis into the perivitelline fluid of the developing embryo prior to ...				159
Q7M4G1 UniProt NPD GO	FABP2_FASHE	Fatty acid-binding protein type 2	0.01	-	cyt	0					131
O13008 UniProt NPD GO	FABPH_ONCMY	Fatty acid-binding protein, heart (H-FABP) (Heart-type fatty acid-binding protein)	0.01	-	cyt	0	Cytoplasm				132
P10790 UniProt NPD GO	FABPH_BOVIN	Fatty acid-binding protein, heart (H-FABP) (Heart-type fatty acid-binding protein) (Mammary-derived ...	0.01	-	cyt	0	Or: Cytoplasm. Or: Mitochondrion; mitochondrial matrix			1BWY	132
P05413 UniProt NPD GO	FABPH_HUMAN	Fatty acid-binding protein, heart (H-FABP) (Heart-type fatty acid-binding protein) (Muscle fatty aci ...	0.01	-	cyt	0	Cytoplasm		134651	2HMB	132
P81175 UniProt NPD GO	FABPI_RHASA	Fatty acid-binding protein, intestinal (I-FABP) (FABPI) (Fragments)	0.01	-	cyt	0	Cytoplasm				33
P80425 UniProt NPD GO	FABPL_BOVIN	Fatty acid-binding protein, liver (L-FABP)	0.01	-	cyt	0	Cytoplasm				127
P07148 UniProt NPD GO	FABPL_HUMAN	Fatty acid-binding protein, liver (L-FABP)	0.01	-	cyt	0	Cytoplasm		134650	2F73	127
P49924 UniProt NPD GO	FABPL_PIG	Fatty acid-binding protein, liver (L-FABP)	0.01	-	cyt	0	Cytoplasm				127
P41509 UniProt NPD GO	FABPM_LOCMI	Fatty acid-binding protein, muscle (M-FABP)	0.01	-	cyt	0	Cytoplasm			2FLJ	133
P41496 UniProt NPD GO	FABPM_SCHGR	Fatty acid-binding protein, muscle (M-FABP)	0.01	-	cyt	0	Cytoplasm			1FTP	133
P80565 UniProt NPD GO	FABPM_CHICK	Fatty acid-binding protein, smooth muscle (SM-FABP) (Fragments)	0.01	-	cyt	0					71
P34382 UniProt NPD GO	FAR1_CAEEL	Fatty-acid and retinol-binding protein 1 precursor	0.01	-	exc	0	Secreted protein (By similarity)				182
Q38856 UniProt NPD GO	IRT1_ARATH	Fe(II) transport protein 1 precursor (Iron-regulated transporter 1)	0.01	-	end	8 *	Cell membrane; multi-pass membrane protein				339
Q8LE59 UniProt NPD GO	IRT3_ARATH	Fe(II) transport protein 3, chloroplast precursor (Iron-regulated transporter 3)	0.01	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Potential)				389
P15697 UniProt NPD GO	FP_CRIMI	Female protein precursor (FP) (Serum amyloid P-component)	0.01	-	exc	0	Secreted protein				231
P00223 UniProt NPD GO	FER_ARCLA	Ferredoxin	0.01	-	cyt	0	Plastid; chloroplast				97
P13106 UniProt NPD GO	FER_BUMFI	Ferredoxin	0.01	-	cyt	0	Plastid; chloroplast				98
P11425 UniProt NPD GO	FER_ENTHI	Ferredoxin	0.01	-	cyt	0					59
P00233 UniProt NPD GO	FER_GLEJA	Ferredoxin	0.01	-	cyt	0	Plastid; chloroplast				95
P83522 UniProt NPD GO	FER_HORVU	Ferredoxin	0.01	-	cyt	0	Plastid; chloroplast (By similarity)				97
P00225 UniProt NPD GO	FER_LEUGL	Ferredoxin	0.01	-	cyt	0	Plastid; chloroplast				96
P49522 UniProt NPD GO	FER_ODOSI	Ferredoxin	0.01	-	cyt	0	Plastid; chloroplast				98
P51320 UniProt NPD GO	FER_PORPU	Ferredoxin	0.01	-	cyt	0	Plastid; chloroplast				98
P00242 UniProt NPD GO	FER_PORUM	Ferredoxin	0.01	-	cyt	0	Plastid; chloroplast				98
Q9ZTS2 UniProt NPD GO	FER_CAPAN	Ferredoxin, chloroplast precursor (PFLP)	0.01	-	cyt	0	Plastid; chloroplast				144
P84210 UniProt NPD GO	FENR_IMPCY	Ferredoxin--NADP reductase, chloroplast (EC 1.18.1.2) (FNR) (Fragments)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...				37
Q43517 UniProt NPD GO	FER1_LYCES	Ferredoxin-1, chloroplast precursor (Ferredoxin I)	0.01	-	cyt	0	Plastid; chloroplast				144
O04683 UniProt NPD GO	FER1_MESCR	Ferredoxin-1, chloroplast precursor (Ferredoxin I)	0.01	-	mit	0	Plastid; chloroplast				148
P00224 UniProt NPD GO	FER2_SPIOL	Ferredoxin-2 (Ferredoxin II)	0.01	-	exc	0	Plastid; chloroplast				97
P25699 UniProt NPD GO	FRI_PHAVU	Ferritin, chloroplast precursor (EC 1.16.3.1)	0.01	-	nuc	0	Plastid; chloroplast. Plastid				254
P19975 UniProt NPD GO	FRI1_PEA	Ferritin-1, chloroplast precursor (EC 1.16.3.1)	0.01	-	nuc	0	Plastid; chloroplast. Plastid				253
P83445 UniProt NPD GO	FRI2_PEA	Ferritin-2, chloroplast (EC 1.16.3.1) (Fragment)	0.01	-		0	Plastid; chloroplast; chloroplast inner membrane. And other plastids				13
Q41709 UniProt NPD GO	FRI2_VIGUN	Ferritin-2, chloroplast precursor (EC 1.16.3.1)	0.01	-	nuc	0	Plastid; chloroplast				250
Q948P6 UniProt NPD GO	FRI3_SOYBN	Ferritin-3, chloroplast precursor (EC 1.16.3.1) (SFerH-3)	0.01	-	nuc	0	Plastid; chloroplast (By similarity)				256

You are viewing entries 88251 to 88300 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.