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
Q10940 UniProt NPD GO	YWS4_CAEEL	Hypothetical protein B0310.4	0.18	-	nuc	0					112
Q9BIB3 UniProt NPD GO	YKD9_CAEEL	Hypothetical protein B0464.9	0.18	-	cyt	0					364
Q5CZ51 UniProt NPD GO	YKT2_CAEEL	Hypothetical protein C07A9.12	0.18	+	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				235
Q09464 UniProt NPD GO	YQ58_CAEEL	Hypothetical protein C16C10.8	0.18	+	cyt	0	Nucleus (Potential)				253
O74751 UniProt NPD GO	YHFA_SCHPO	Hypothetical protein C1734.10c in chromosome II	0.18	-	cyt	0					332
Q9P7R6 UniProt NPD GO	YHV5_SCHPO	Hypothetical protein C211.05 in chromosome II	0.18	-	nuc	0					85
Q09862 UniProt NPD GO	YAF9_SCHPO	Hypothetical protein C29E6.09 in chromosome I	0.18	-	nuc	0					339
Q18416 UniProt NPD GO	YY42_CAEEL	Hypothetical protein C33H5.2	0.18	-	mit	1 *					507
Q09282 UniProt NPD GO	YQIB_CAEEL	Hypothetical protein C45G9.11	0.18	-	end	4					354
O94322 UniProt NPD GO	YGK3_SCHPO	Hypothetical protein C725.03 in chromosome II	0.18	-	nuc	0					257
O14304 UniProt NPD GO	YE88_SCHPO	Hypothetical protein C9G1.08c in chromosome I	0.18	-	nuc	0					241
Q8SVY8 UniProt NPD GO	Y3G2_ENCCU	Hypothetical protein ECU03_1620	0.18	-	end	7 *					261
Q8ST65 UniProt NPD GO	Y5G9_ENCCU	Hypothetical protein ECU05_1690/ECU11_0040	0.18	-	end	7 *					266
Q09304 UniProt NPD GO	YQP5_CAEEL	Hypothetical protein F07F6.5	0.18	-	nuc	0					124
P91851 UniProt NPD GO	YUG4_CAEEL	Hypothetical protein F26H9.4 in chromosome I	0.18	-	mit	0					223
Q09952 UniProt NPD GO	YSR4_CAEEL	Hypothetical protein F59B10.4	0.18	-	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				267
P38358 UniProt NPD GO	YB8G_YEAST	Hypothetical transport protein YBR293W	0.18	-	end	12 *	Membrane; multi-pass membrane protein (Probable)	vacuolar membrane (sensu Fungi) [IDA]			474
P69496 UniProt NPD GO	CXI2_CONIM	I-superfamily conotoxin-2 precursor	0.18	-	mit	1 *	Secreted protein (By similarity)				64
P22560 UniProt NPD GO	RBF1_MOUSE	IFN-response-binding factor 1 (IREBF-1)	0.18	-	mit	0	Nucleus				311
P22304 UniProt NPD GO	IDS_HUMAN	Iduronate 2-sulfatase precursor (EC 3.1.6.13) (Alpha-L-iduronate sulfate sulfatase) (Idursulfase) [C ...	0.18	-	exc	0	Lysosome		309900		550
P01879 UniProt NPD GO	IGHA_RABIT	Ig alpha chain C region (Fragment)	0.18	-	nuc	0					299
P22436 UniProt NPD GO	GC3_MOUSE	Ig gamma-3 chain C region, secreted form	0.18	-	nuc	0					329
P01630 UniProt NPD GO	KV2F_MOUSE	Ig kappa chain V-II region 7S34.1	0.18	-	nuc	0					113
P01662 UniProt NPD GO	KV3J_MOUSE	Ig kappa chain V-III region ABPC 22/PC 9245	0.18	-	nuc	0					111
P01673 UniProt NPD GO	KV3U_MOUSE	Ig kappa chain V-III region PC 2485/PC 4039	0.18	-	nuc	0					111
P01653 UniProt NPD GO	KV5T_MOUSE	Ig kappa chain V-V region W3082	0.18	-	nuc	0					108
Q43072 UniProt NPD GO	HIS7_PEA	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.18	-	mit	0					281
Q4HZ95 UniProt NPD GO	TIM21_GIBZE	Import inner membrane translocase subunit TIM21, mitochondrial precursor	0.18	+	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				229
O77460 UniProt NPD GO	IPYR_DROME	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase) (Nucleosome remodel ...	0.18	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA] NURF complex [IDA]			338
Q9SBA5 UniProt NPD GO	ITPK1_ARATH	Inositol-tetrakisphosphate 1-kinase 1 (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase 1) (EC 2.7.1. ...	0.18	-	cyt	0					319
P05017 UniProt NPD GO	IGF1_MOUSE	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.18	-	nuc	0	Secreted protein	extracellular space [IDA]			153
O02833 UniProt NPD GO	ALS_PAPHA	Insulin-like growth factor-binding protein complex acid labile chain precursor (ALS)	0.18	-	exc	0	Secreted protein; extracellular space				605
O55222 UniProt NPD GO	ILK_MOUSE	Integrin-linked protein kinase (EC 2.7.11.1)	0.18	-	cyt	0	Cytoplasm (By similarity)	focal adhesion [IDA]			452
Q63416 UniProt NPD GO	ITIH3_RAT	Inter-alpha-trypsin inhibitor heavy chain H3 precursor (ITI heavy chain H3) (Inter-alpha-inhibitor h ...	0.18	-	vac	0		extracellular region [TAS]			887
Q5NKV1 UniProt NPD GO	ICAM2_GORGO	Intercellular adhesion molecule 2 precursor (ICAM-2)	0.18	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				275
Q14653 UniProt NPD GO	IRF3_HUMAN	Interferon regulatory factor 3 (IRF-3)	0.18	-	cyt	0	Cytoplasm. Nucleus. Shuttles between cytoplasmic and nuclear compartments, with export being the pre ...		603734	1ZOQ	427
Q764M8 UniProt NPD GO	INAR1_PIG	Interferon-alpha/beta receptor alpha chain precursor (IFN-alpha-REC)	0.18	-	end	1	Membrane; single-pass type I membrane protein				560
P25086 UniProt NPD GO	IL1RA_RAT	Interleukin-1 receptor antagonist protein precursor (IL-1ra) (IRAP) (IL1 inhibitor) (IL-1RN)	0.18	-	end	0	Secreted protein (By similarity)				178
P48411 UniProt NPD GO	IL10_CANFA	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.18	-	exc	0	Secreted protein	extracellular region [NAS]			181
Q29408 UniProt NPD GO	IL10_SHEEP	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.18	-	exc	0	Secreted protein	extracellular region [NAS]			177
Q25BC1 UniProt NPD GO	IL10_VULVU	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.18	-	exc	0	Secreted protein				179
Q5RF19 UniProt NPD GO	I11RA_PONPY	Interleukin-11 receptor alpha chain precursor (IL-11R-alpha) (IL-11RA)	0.18	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				422
Q924V5 UniProt NPD GO	IL12B_CAVPO	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.18	-	exc	1 *	Secreted protein				332
P48095 UniProt NPD GO	IL12B_MACMU	Interleukin-12 beta chain precursor (IL-12B) (IL-12 p40) (Cytotoxic lymphocyte maturation factor 40 ...	0.18	-	exc	1 *	Secreted protein				328
Q14116 UniProt NPD GO	IL18_HUMAN	Interleukin-18 precursor (IL-18) (Interferon-gamma-inducing factor) (IFN-gamma-inducing factor) (Int ...	0.18	-	nuc	0	Secreted protein	extracellular region [TAS]	600953	1J0S	193
Q5PXD0 UniProt NPD GO	IL2_AILME	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.18	-	exc	0	Secreted protein (By similarity)				155
Q9XT84 UniProt NPD GO	IL2_DELLE	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.18	-	exc	0	Secreted protein (By similarity)				154
Q865X2 UniProt NPD GO	IL2_LAMGL	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.18	-	exc	0	Secreted protein				154
Q9JHX3 UniProt NPD GO	IL21R_MOUSE	Interleukin-21 receptor precursor (IL-21R) (Novel interleukin receptor) (Lymphocyte receptor beta) ( ...	0.18	-	end	0	Membrane; single-pass type I membrane protein				529
Q9JJY9 UniProt NPD GO	IL22_MOUSE	Interleukin-22 precursor (IL-22) (IL-10-related T-cell-derived-inducible factor) (IL-TIF) (IL-TIF al ...	0.18	-	exc	1 *	Secreted protein				179

You are viewing entries 53151 to 53200 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.