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
P33191 UniProt NPD GO	TUB8_SOLTU	Induced stolen tip protein TUB8 (Fragment)	0.01	-	end	2 *					211
Q6C1T4 UniProt NPD GO	IPYR_YARLI	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.01	-	cyt	0	Cytoplasm (By similarity)				287
P83851 UniProt NPD GO	IUNH_LEIMA	Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1) (IU-nucleoside hydrolase) (IU-NH) (Puri ...	0.01	-	nuc	0				1EZR	313
P45986 UniProt NPD GO	IMT1_MESCR	Inositol 4-methyltransferase (EC 2.1.1.129)	0.01	-	mit	1 *					365
P29218 UniProt NPD GO	IMPA1_HUMAN	Inositol monophosphatase (EC 3.1.3.25) (IMPase) (IMP) (Inositol-1(or 4)-monophosphatase) (Lithium-se ...	0.01	-	cyt	0	Cytoplasm		602064	2HHM	277
O55023 UniProt NPD GO	IMPA1_MOUSE	Inositol monophosphatase (EC 3.1.3.25) (IMPase) (IMP) (Inositol-1(or 4)-monophosphatase) (Lithium-se ...	0.01	-	cyt	0	Cytoplasm				277
O77591 UniProt NPD GO	IMPA1_PIG	Inositol monophosphatase (EC 3.1.3.25) (IMPase) (IMP) (Inositol-1(or 4)-monophosphatase) (Lithium-se ...	0.01	-	cyt	0	Cytoplasm (By similarity)				277
Q5R4X0 UniProt NPD GO	IMPA1_PONPY	Inositol monophosphatase (EC 3.1.3.25) (IMPase) (IMP) (Inositol-1(or 4)-monophosphatase) (Lithium-se ...	0.01	-	cyt	0	Cytoplasm (By similarity)				277
P38710 UniProt NPD GO	INM1_YEAST	Inositol monophosphatase 1 (EC 3.1.3.25) (IMPase 1) (IMP 1) (Inositol-1(or 4)-monophosphatase 1)	0.01	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			295
Q05533 UniProt NPD GO	INM2_YEAST	Inositol monophosphatase 2 (EC 3.1.3.25) (IMPase 2) (IMP 2) (Inositol-1(or 4)-monophosphatase 2)	0.01	-	cyt	0					292
O82200 UniProt NPD GO	MIOX2_ARATH	Inositol oxygenase 2 (EC 1.13.99.1) (Myo-inositol oxygenase 2) (AtMIOX2)	0.01	-	cyt	0	Cytoplasm (Probable)				317
Q9FJU4 UniProt NPD GO	MIOX5_ARATH	Inositol oxygenase 5 (EC 1.13.99.1) (Myo-inositol oxygenase 5) (AtMIOX5)	0.01	-	cyt	0	Cytoplasm (Probable)				314
Q9NBW2 UniProt NPD GO	SCBT_MESMA	Insect beta-neurotoxin BmK abT precursor (BmK BT)	0.01	-	exc	0	Secreted protein (By similarity)				83
P68721 UniProt NPD GO	SIX1A_LEIQH	Insect neurotoxin 1a precursor (Lqh IT1-a) (LqhIT1-a)	0.01	-	end	0	Secreted protein				88
P68722 UniProt NPD GO	SIX1B_LEIQH	Insect neurotoxin 1b precursor (Lqh IT1-b) (LqhIT1-b)	0.01	-	end	0	Secreted protein				88
P01497 UniProt NPD GO	SIX1_ANDAU	Insect toxin 1 precursor (AaH IT1) (AaHIT1) (AaIT1) (AaH IT) (AaHIT)	0.01	-	mit	0	Secreted protein				88
P15147 UniProt NPD GO	SIX2_ANDAU	Insect toxin 2 precursor (AaH IT2) (AaHIT2) (AaIT2)	0.01	-	cyt	0	Secreted protein				88
P68725 UniProt NPD GO	SX21_LEIQH	Insect toxin 2-13 precursor (LqhIT2-13)	0.01	-	exc	0	Secreted protein				83
P82814 UniProt NPD GO	SIX4_BUTSI	Insect toxin 4 (BsIT4) (Bs-dprIT4)	0.01	-	cyt	0	Secreted protein				62
P81240 UniProt NPD GO	SIX5_LEIQH	Insect toxin 5 (Lqh IT5) (LqhIT5)	0.01	-	cyt	0	Secreted protein				61
P59864 UniProt NPD GO	SIX6_BUTOC	Insect toxin 6 (BotIT6)	0.01	-	cyt	0	Secreted protein				62
P60275 UniProt NPD GO	SCXI_TITBA	Insect toxin TbIT-I	0.01	-	nuc	0	Secreted protein				63
P59367 UniProt NPD GO	TX455_PHONI	Insecticidal neurotoxin Tx4(5-5) precursor (Toxin Pn4A)	0.01	-	exc	0	Secreted protein				81
P49126 UniProt NPD GO	TXI92_DIGCA	Insecticidal toxin DTX9.2 precursor	0.01	-	exc	0	Secreted protein				94
P01324 UniProt NPD GO	INS_ACOCA	Insulin [Contains: Insulin B chain; Insulin A chain]	0.01	-	cyt	0	Secreted protein				51
P18109 UniProt NPD GO	INS_DIDMA	Insulin [Contains: Insulin B chain; Insulin A chain]	0.01	-	cyt	0	Secreted protein				51
P01328 UniProt NPD GO	INS_HYSCR	Insulin [Contains: Insulin B chain; Insulin A chain]	0.01	-	cyt	0	Secreted protein				51
P09477 UniProt NPD GO	INS_PLAFE	Insulin [Contains: Insulin B chain; Insulin A chain]	0.01	-	cyt	0	Secreted protein				51
P01310 UniProt NPD GO	INS_HORSE	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.01	-	cyt	0	Secreted protein				86
P81025 UniProt NPD GO	INS_ORENI	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.01	-	end	0	Secreted protein				113
Q9W7R2 UniProt NPD GO	INS_VERMO	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.01	-	exc	0	Secreted protein				115
P12705 UniProt NPD GO	INS_TORMA	Insulin precursor [Contains: Insulin B chain; Insulin A chain] (Fragments)	0.01	-	cyt	0	Secreted protein				70
P80747 UniProt NPD GO	ITB5_BOVIN	Integrin beta-5 (Fragment)	0.01	-		0	Membrane; single-pass type I membrane protein (By similarity)				13
P56652 UniProt NPD GO	ITIH3_BOVIN	Inter-alpha-trypsin inhibitor heavy chain H3 (ITI heavy chain H3) (Inter-alpha-inhibitor heavy chain ...	0.01	-	cyt	0					29
Q01629 UniProt NPD GO	IFM2_HUMAN	Interferon-induced transmembrane protein 2 (Interferon-inducible protein 1-8D)	0.01	-	nuc	2	Membrane; multi-pass membrane protein (Potential)		605578		132
Q01628 UniProt NPD GO	IFM3_HUMAN	Interferon-induced transmembrane protein 3 (Interferon-inducible protein 1-8U)	0.01	-	nuc	2	Membrane; multi-pass membrane protein (Potential)		605579		133
P26376 UniProt NPD GO	INIB_RAT	Interferon-inducible protein	0.01	-	nuc	2	Membrane; multi-pass membrane protein (Potential)				137
P35225 UniProt NPD GO	IL13_HUMAN	Interleukin-13 precursor (IL-13)	0.01	-	exc	0	Secreted protein	soluble fraction [TAS]	147683	3ITS	132
Q864V6 UniProt NPD GO	IL13_MACMU	Interleukin-13 precursor (IL-13)	0.01	-	exc	0	Secreted protein (By similarity)				132
P61126 UniProt NPD GO	IL13_PANTR	Interleukin-13 precursor (IL-13)	0.01	-	exc	0	Secreted protein (By similarity)				132
P97604 UniProt NPD GO	IL15_RAT	Interleukin-15 precursor (IL-15)	0.01	-	vac	1 *	Secreted protein				162
Q6UXL0 UniProt NPD GO	I20RB_HUMAN	Interleukin-20 receptor beta chain precursor (IL-20R-beta) (IL-20R2)	0.01	-	nuc	2 *	Membrane; single-pass type I membrane protein (By similarity)		605621		311
Q9XSX5 UniProt NPD GO	IL8_FELCA	Interleukin-8 precursor (IL-8) (CXCL8)	0.01	-	exc	1 *	Secreted protein				101
P67813 UniProt NPD GO	IL8_MACMU	Interleukin-8 precursor (IL-8) (CXCL8)	0.01	-	vac	0	Secreted protein	extracellular space [ISS]			101
P67814 UniProt NPD GO	IL8_MACNE	Interleukin-8 precursor (IL-8) (CXCL8)	0.01	-	vac	0	Secreted protein	extracellular space [ISS]			101
P10145 UniProt NPD GO	IL8_HUMAN	Interleukin-8 precursor (IL-8) (CXCL8) (Monocyte-derived neutrophil chemotactic factor) (MDNCF) (T-c ...	0.01	-	vac	1 *	Secreted protein	extracellular space [TAS]	146930	3IL8	99
P08317 UniProt NPD GO	IL8_CHICK	Interleukin-8 precursor (IL-8) (Embryo fibroblast protein 1) (EMF-1) (9E3) (CEF-4)	0.01	-	exc	0	Secreted protein (Potential)				103
P84526 UniProt NPD GO	ILEC1_XERSP	Inulin-specific lectin (Fragment)	0.01	-		0					13
P10595 UniProt NPD GO	INV3_YEAST	Invertase 3 precursor (EC 3.2.1.26) (Beta-fructofuranosidase 3) (Saccharase) (Fragment)	0.01	-	vac	0					74
P10597 UniProt NPD GO	INV5_YEAST	Invertase 5 precursor (EC 3.2.1.26) (Beta-fructofuranosidase 5) (Saccharase) (Fragment)	0.01	-	vac	0					74

You are viewing entries 89201 to 89250 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.