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
Q6M981 UniProt NPD GO	FKB1B_NEUCR	FK506-binding protein 1B (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyc ...	0.00	-	cyt	0	Cytoplasm (By similarity)				110
Q6CUZ8 UniProt NPD GO	FKBP2_KLULA	FK506-binding protein 2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.00	-	exc	0	Endoplasmic reticulum (By similarity)				140
Q9QVC8 UniProt NPD GO	FKBP4_RAT	FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (p59 ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				24
P59724 UniProt NPD GO	FKBP3_VICFA	FKBP-type peptidyl-prolyl cis-trans isomerase, chloroplast (EC 5.2.1.8) (VfFKBP13) (PPIase) (Rotamas ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				45
P79177 UniProt NPD GO	FPRL1_GORGO	FMLP-related receptor I (FMLP-R-I) (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P79190 UniProt NPD GO	FPRL1_MACMU	FMLP-related receptor I (FMLP-R-I) (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P79242 UniProt NPD GO	FPRL1_PANTR	FMLP-related receptor I (FMLP-R-I) (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P79236 UniProt NPD GO	FPRL1_PONPY	FMLP-related receptor I (FMLP-R-I) (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
O08790 UniProt NPD GO	FPRL1_MOUSE	FMLP-related receptor I (FMLP-R-I) (Lipoxin A4 receptor) (LXA4 receptor)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				351
P25090 UniProt NPD GO	FPRL1_HUMAN	FMLP-related receptor I (FMLP-R-I) (Lipoxin A4 receptor) (LXA4 receptor) (Formyl peptide receptor-li ...	0.00	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [TAS]	136538		351
P79178 UniProt NPD GO	FPRL2_GORGO	FMLP-related receptor II (FMLP-R-II) (Formylpeptide receptor-like 2) (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				349
P79243 UniProt NPD GO	FPRL2_PANTR	FMLP-related receptor II (FMLP-R-II) (Formylpeptide receptor-like 2) (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				349
P79237 UniProt NPD GO	FPRL2_PONPY	FMLP-related receptor II (FMLP-R-II) (Formylpeptide receptor-like 2) (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				349
P43173 UniProt NPD GO	FARB_ASCSU	FMRFamide-like neuropeptide AF11	0.00	-		0	Secreted protein				13
P43170 UniProt NPD GO	FAR5_ASCSU	FMRFamide-like neuropeptide AF5	0.00	-		0	Secreted protein				9
P83276 UniProt NPD GO	FAR3_MACRS	FMRFamide-like neuropeptide FLP3 (NYDKNFLRF-amide)	0.00	-		0	Secreted protein				9
P41873 UniProt NPD GO	FAR2_PANRE	FMRFamide-like neuropeptide PF2 (SADPNFLRF-amide)	0.00	-		0	Secreted protein				9
Q14802 UniProt NPD GO	FXYD3_HUMAN	FXYD domain-containing ion transport regulator 3 precursor (Chloride conductance inducer protein Mat ...	0.00	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	604996		87
Q05015 UniProt NPD GO	FSH2_YEAST	Family of serine hydrolases 2 (EC 3.1.-.-)	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA]			223
O64905 UniProt NPD GO	FPPS_HELAN	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes ...	0.00	-	cyt	0	Cytoplasm				341
P49351 UniProt NPD GO	FPPS1_LUPAL	Farnesyl pyrophosphate synthetase 1 (FPP synthetase 1) (FPS 1) (Farnesyl diphosphate synthetase 1) [ ...	0.00	-	cyt	0	Cytoplasm (By similarity)				342
O24241 UniProt NPD GO	FPPS1_PARAR	Farnesyl pyrophosphate synthetase 1 (FPP synthetase 1) (FPS 1) (Farnesyl diphosphate synthetase 1) [ ...	0.00	-	cyt	0	Cytoplasm. Rubber particles				342
P49352 UniProt NPD GO	FPPS2_LUPAL	Farnesyl pyrophosphate synthetase 2 (FPP synthetase 2) (FPS 2) (Farnesyl diphosphate synthetase 2) [ ...	0.00	-	cyt	0	Cytoplasm (By similarity)				342
P80547 UniProt NPD GO	SCP2_YARLI	Fatty acid-binding protein	0.00	-	nuc	0					129
Q17284 UniProt NPD GO	FABP_BLOTA	Fatty acid-binding protein (Allergen Blo t 13) (Bt6)	0.00	-	cyt	0	Cytoplasm (Potential)				130
Q9U5P1 UniProt NPD GO	FABP_LEPDS	Fatty acid-binding protein (Allergen Lep d 13)	0.00	-	cyt	0	Cytoplasm (Potential)				131
P31416 UniProt NPD GO	FABP1_MANSE	Fatty acid-binding protein 1 (FABP 1)	0.00	-	cyt	0	Cytoplasm				132
P31417 UniProt NPD GO	FABP2_MANSE	Fatty acid-binding protein 2 (FABP 2)	0.00	-	cyt	0	Cytoplasm			1MDC	131
Q7M4G0 UniProt NPD GO	FABP1_FASHE	Fatty acid-binding protein Fh15	0.00	-	cyt	0					131
Q965W1 UniProt NPD GO	FABP9_CAEEL	Fatty acid-binding protein homolog 9	0.00	-	cyt	0					152
Q09139 UniProt NPD GO	FABPB_BOVIN	Fatty acid-binding protein, brain (B-FABP)	0.00	-	cyt	0	Cytoplasm				131
P51880 UniProt NPD GO	FABPB_MOUSE	Fatty acid-binding protein, brain (B-FABP) (Brain lipid-binding protein) (BLBP)	0.00	-	cyt	0	Cytoplasm				131
P55051 UniProt NPD GO	FABPB_RAT	Fatty acid-binding protein, brain (B-FABP) (Brain lipid-binding protein) (BLBP)	0.00	-	cyt	0	Cytoplasm				131
O15540 UniProt NPD GO	FABPB_HUMAN	Fatty acid-binding protein, brain (B-FABP) (Brain lipid-binding protein) (BLBP) (Mammary-derived gro ...	0.00	-	cyt	0	Cytoplasm		602965	1JJX	131
Q865F7 UniProt NPD GO	FABPH_MYOLU	Fatty acid-binding protein, heart (H-FABP) (Heart-type fatty acid-binding protein)	0.00	-	cyt	0	Cytoplasm				132
O02772 UniProt NPD GO	FABPH_PIG	Fatty acid-binding protein, heart (H-FABP) (Heart-type fatty acid-binding protein)	0.00	-	cyt	0	Cytoplasm				132
P07483 UniProt NPD GO	FABPH_RAT	Fatty acid-binding protein, heart (H-FABP) (Heart-type fatty acid-binding protein)	0.00	-	cyt	0	Cytoplasm				132
P12710 UniProt NPD GO	FABPL_MOUSE	Fatty acid-binding protein, liver (L-FABP) (14 kDa selenium-binding protein)	0.00	-	cyt	0	Cytoplasm				127
P82145 UniProt NPD GO	FABPL_CHAVI	Fatty acid-binding protein, liver (L-FABP) (Fragments)	0.00	-	cyt	0	Cytoplasm (By similarity)				95
P02692 UniProt NPD GO	FABPL_RAT	Fatty acid-binding protein, liver (L-FABP) (Z-protein) (Squalene- and sterol-carrier protein) (SCP) ...	0.00	-	cyt	0	Cytoplasm			1LFO	127
Q05423 UniProt NPD GO	FABPR_CHICK	Fatty acid-binding protein, retina (R-FABP)	0.00	-	cyt	0	Cytoplasm				131
P02871 UniProt NPD GO	LEC_VICFA	Favin (Lectin) [Contains: Favin beta chain; Favin alpha chain]	0.00	-	cyt	0				2B7Y	233
O81850 UniProt NPD GO	IRT2_ARATH	Fe(II) transport protein 2 precursor (Iron-regulated transporter 2)	0.00	-	end	9 *	Cell membrane; multi-pass membrane protein (Potential)				350
P02451 UniProt NPD GO	KRFT_LARNO	Feather keratin (F-ker)	0.00	-	nuc	0					98
O77420 UniProt NPD GO	HBP1_RHIAP	Female-specific histamine-binding protein 1 precursor (FS-HBP1)	0.00	-	exc	0	Secreted protein				190
O77421 UniProt NPD GO	HBP2_RHIAP	Female-specific histamine-binding protein 2 precursor (FS-HBP2)	0.00	-	exc	0	Secreted protein			1QFV	190
P84872 UniProt NPD GO	FER_ATRBE	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast				97
P00227 UniProt NPD GO	FER_BRANA	Ferredoxin	0.00	-	nuc	0	Plastid; chloroplast				96
P07838 UniProt NPD GO	FER_BRYMA	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast				98
P83527 UniProt NPD GO	FER_CAPAA	Ferredoxin	0.00	-	cyt	0	Plastid; chloroplast	chloroplast [TAS] cytoplasm [NAS]			97

You are viewing entries 94501 to 94550 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.