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
Q8SU95 UniProt NPD GO	YAI2_ENCCU	Hypothetical protein ECU10_1820	0.17	-	end	5 *					225
P34430 UniProt NPD GO	YL39_CAEEL	Hypothetical protein F44B9.9	0.17	-	cyt	0					244
P30646 UniProt NPD GO	YNE7_CAEEL	Hypothetical protein R08D7.7 in chromosome III	0.17	-	cyt	0					537
P82622 UniProt NPD GO	SCRL3_ARATH	Hypothetical protein SCRL3 precursor	0.17	-	nuc	1 *					87
Q10018 UniProt NPD GO	YSW3_CAEEL	Hypothetical protein T25D10.3 precursor	0.17	-	exc	0					394
Q10020 UniProt NPD GO	YSX1_CAEEL	Hypothetical protein T28D9.1	0.17	-	cyt	0					129
Q10026 UniProt NPD GO	YSX9_CAEEL	Hypothetical protein T28D9.9	0.17	-	cyt	0					119
P34748 UniProt NPD GO	YO67_CAEEL	Hypothetical protein ZK1098.7	0.17	-	mit	0					133
Q04991 UniProt NPD GO	YM68_YEAST	Hypothetical transporter YMR221C	0.17	-	end	11 *	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA] vacuole (sensu Fungi) [IDA]			504
P01876 UniProt NPD GO	IGHA1_HUMAN	Ig alpha-1 chain C region	0.17	-	nuc	0			146900	1OW0	353
P20762 UniProt NPD GO	GCC_RAT	Ig gamma-2C chain C region	0.17	-	nuc	0					329
P03987 UniProt NPD GO	GC3M_MOUSE	Ig gamma-3 chain C region, membrane-bound form	0.17	-	cyt	1					398
P01681 UniProt NPD GO	KV01_RAT	Ig kappa chain V region S211	0.17	-	nuc	0					109
P04432 UniProt NPD GO	KV1X_HUMAN	Ig kappa chain V-I region Daudi precursor	0.17	-	exc	0		extracellular region [NAS]			129
P01664 UniProt NPD GO	KV3L_MOUSE	Ig kappa chain V-III region CBPC 101	0.17	-	nuc	0					111
P01667 UniProt NPD GO	KV3O_MOUSE	Ig kappa chain V-III region PC 6308	0.17	-	nuc	0					111
P01665 UniProt NPD GO	KV3M_MOUSE	Ig kappa chain V-III region PC 7043	0.17	-	nuc	0				1QNZ	111
P01873 UniProt NPD GO	MUCM_MOUSE	Ig mu chain C region membrane-bound form	0.17	-	cyt	1		B cell receptor complex [IDA] external side of plasma membrane [IDA] immunoglobulin complex, circulating [IDA] perinuclear region [IDA]			475
P04221 UniProt NPD GO	MUCM_RABIT	Ig mu chain C region membrane-bound form	0.17	-	cyt	1					479
P13524 UniProt NPD GO	MA8I_SCHJA	Immunogenic miracidial antigen 8I	0.17	-	mit	0					139
Q98938 UniProt NPD GO	IHH_CHICK	Indian hedgehog protein precursor (IHH) [Contains: Indian hedgehog protein N-product; Indian hedgeho ...	0.17	-	cyt	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				408
P47125 UniProt NPD GO	I23O_YEAST	Indoleamine 2,3-dioxygenase family protein (EC 1.13.11.-) (Biosynthesis of nicotinic acid protein 2) ...	0.17	-	mit	0		cytoplasm [IDA]			453
P46956 UniProt NPD GO	PHO86_YEAST	Inorganic phosphate transporter PHO86	0.17	-	end	2	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			311
P38264 UniProt NPD GO	PHO88_YEAST	Inorganic phosphate transporter PHO88	0.17	-	cyt	1 *	Membrane; multi-pass membrane protein (Potential)	membrane [IDA] mitochondrion [IDA]			188
Q5R8T6 UniProt NPD GO	IPYR_PONPY	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.17	-	cyt	0	Cytoplasm (By similarity)				289
Q9QXN4 UniProt NPD GO	MIOX_RAT	Inositol oxygenase (EC 1.13.99.1) (Myo-inositol oxygenase) (Aldehyde reductase-like 6) (Renal-specif ...	0.17	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS] inclusion body [ISS]			285
P15220 UniProt NPD GO	SCX1_BUTEU	Insectotoxin-I1	0.17	-	nuc	0	Secreted protein				36
Q6IVA5 UniProt NPD GO	IGF1_AILFU	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.17	-	nuc	0	Secreted protein				153
P07455 UniProt NPD GO	IGF1_BOVIN	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.17	-	nuc	0	Secreted protein				154
P51457 UniProt NPD GO	IGF1_CAPHI	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.17	-	nuc	0	Secreted protein				154
P16545 UniProt NPD GO	IGF1_PIG	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.17	-	nuc	0	Secreted protein				153
Q68LC0 UniProt NPD GO	IGF1_PYGRO	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.17	-	nuc	0	Secreted protein				153
P01343 UniProt NPD GO	IGF1A_HUMAN	Insulin-like growth factor IA precursor (IGF-IA) (Somatomedin C) (Mechano growth factor) (MGF)	0.17	-	nuc	0	Secreted protein	extracellular region [NAS]	147440	3GF1	153
P47876 UniProt NPD GO	IBP1_MOUSE	Insulin-like growth factor-binding protein 1 precursor (IGFBP-1) (IBP-1) (IGF-binding protein 1)	0.17	-	nuc	0	Secreted protein				272
P38484 UniProt NPD GO	INGR2_HUMAN	Interferon-gamma receptor beta chain precursor (Interferon-gamma receptor accessory factor 1) (AF-1) ...	0.17	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	209950		337
Q96AZ6 UniProt NPD GO	ISG20_HUMAN	Interferon-stimulated gene 20 kDa protein (EC 3.1.13.1) (Promyelocytic leukemia nuclear body-associa ...	0.17	-	cyt	0	Nucleus	nucleoplasm [TAS] PML body [IDA]	604533		181
P51745 UniProt NPD GO	IL1B_CEREL	Interleukin-1 beta precursor (IL-1 beta)	0.17	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				266
P25085 UniProt NPD GO	IL1RA_MOUSE	Interleukin-1 receptor antagonist protein precursor (IL-1ra) (IRAP) (IL1 inhibitor) (IL-1RN)	0.17	-	mit	0	Isoform 1: Secreted protein. Isoform 2: Cytoplasm				178
Q865Y3 UniProt NPD GO	IL12B_PAPAN	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.17	-	exc	1 *	Secreted protein (By similarity)				328
P29460 UniProt NPD GO	IL12B_HUMAN	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.17	-	exc	1 *	Secreted protein	extracellular space [TAS]	161561	1F45	328
Q865W5 UniProt NPD GO	IL13_CAMBA	Interleukin-13 precursor (IL-13)	0.17	-	nuc	0	Secreted protein				136
Q865X3 UniProt NPD GO	IL13_LAMGL	Interleukin-13 precursor (IL-13)	0.17	-	nuc	0	Secreted protein				136
O77620 UniProt NPD GO	IL2_RABIT	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.17	-	exc	0	Secreted protein				153
Q9GZX6 UniProt NPD GO	IL22_HUMAN	Interleukin-22 precursor (IL-22) (IL-10-related T-cell-derived-inducible factor) (IL-TIF)	0.17	-	exc	1 *	Secreted protein	extracellular region [IC]	605330	1YKB	179
P24001 UniProt NPD GO	IL32_HUMAN	Interleukin-32 precursor (IL-32) (Natural killer cells protein 4)	0.17	-	mit	0	Secreted protein	extracellular space [TAS]	606001		234
P56478 UniProt NPD GO	IL7_RAT	Interleukin-7 precursor (IL-7)	0.17	-	exc	0	Secreted protein	extracellular region [ISS]			154
Q01113 UniProt NPD GO	IL9R_HUMAN	Interleukin-9 receptor precursor (IL-9R) (CD129 antigen)	0.17	-	end	0	Cell membrane; single-pass type I membrane protein. Secreted protein	extracellular space [TAS] integral to plasma membrane [TAS]	300007		522
P80196 UniProt NPD GO	RNLX_LYCES	Intracellular ribonuclease LX precursor (EC 3.1.27.1) (RNase LX)	0.17	-	exc	0	Cytoplasm. Intracellular, but extravacuolar				237
P28298 UniProt NPD GO	ACEA_EMENI	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.17	-	cyt	0	Glyoxysome			1DQU	537
P00994 UniProt NPD GO	ISIK_HELPO	Isoinhibitor K	0.17	-	nuc	0	Secreted protein				58

You are viewing entries 54451 to 54500 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.