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
Q8IZ69 UniProt NPD GO	HTF9C_HUMAN	HpaII tiny fragments locus 9c protein	0.45	-	cyt	0					625
Q9U6V9 UniProt NPD GO	HUGA_POLAN	Hyalurononglucosaminidase precursor (EC 3.2.1.35) (Hyaluronidase) (Allergen Pol a 2) (Fragment)	0.45	-	cyt	0					367
Q04436 UniProt NPD GO	YMZ3_YEAST	Hypothetical 13.3 kDa protein in SNZ1-YPK2 intergenic region	0.45	-	mit	1 *					120
Q03675 UniProt NPD GO	YMO7_YEAST	Hypothetical 14.5 kDa protein in PLB2-PLB1 intergenic region	0.45	+	mit	0					126
P14723 UniProt NPD GO	YWIS_WHEAT	Hypothetical 16 kDa protein in middle repetitive insertion sequence WIS1	0.45	-	mit	0					151
P48277 UniProt NPD GO	YCF37_CYAPA	Hypothetical 20.5 kDa protein ycf37	0.45	-	mit	1 *	Plastid; cyanelle				172
Q04705 UniProt NPD GO	YME7_YEAST	Hypothetical 41.4 kDa protein in GAL80-PRP39 intergenic region	0.45	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				352
P48012 UniProt NPD GO	YLEU_DEBOC	Hypothetical 43.6 kDa protein	0.45	-	mit	0					379
P41907 UniProt NPD GO	YHH7_SACDO	Hypothetical 44.4 kDa protein in SPO13-ARG4 intergenic region	0.45	-	nuc	0					385
P53870 UniProt NPD GO	YNT3_YEAST	Hypothetical 63.9 kDa protein in WHI3-CHS1 intergenic region	0.45	-	nuc	0					558
Q09406 UniProt NPD GO	YRG5_CAEEL	Hypothetical WD repeat protein K06A1.5	0.45	-	nuc	0					464
O13714 UniProt NPD GO	YDZ7_SCHPO	Hypothetical membrane protein C14C4.07 in chromosome I	0.45	-	end	12	Membrane; multi-pass membrane protein (Potential)				644
Q93196 UniProt NPD GO	YI31_CAEEL	Hypothetical protein C09E9.1 in chromosome I	0.45	-	nuc	0					123
Q09708 UniProt NPD GO	YAGG_SCHPO	Hypothetical protein C12G12.16c	0.45	-	nuc	0					496
Q10275 UniProt NPD GO	YD3B_SCHPO	Hypothetical protein C13G7.11 in chromosome I	0.45	-	mit	0					269
O42925 UniProt NPD GO	YBD1_SCHPO	Hypothetical protein C16C6.01c in chromosome II	0.45	-	nuc	0					473
O60153 UniProt NPD GO	YHY4_SCHPO	Hypothetical protein C19C7.04c in chromosome II	0.45	-	nuc	0					124
Q9UUI5 UniProt NPD GO	YIY8_SCHPO	Hypothetical protein C22F8.08 in chromosome I	0.45	-	nuc	0					926
O14175 UniProt NPD GO	YE5B_SCHPO	Hypothetical protein C4D7.11 in chromosome I	0.45	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				281
Q09886 UniProt NPD GO	YC9C_SCHPO	Hypothetical protein C584.12 in chromosome III	0.45	-	nuc	1					115
Q09313 UniProt NPD GO	YQT1_CAEEL	Hypothetical protein F25B5.1	0.45	-	nuc	0					923
Q09317 UniProt NPD GO	YQX4_CAEEL	Hypothetical protein F34H10.4	0.45	-	nuc	0					452
Q10128 UniProt NPD GO	YSO2_CAEEL	Hypothetical protein F56D1.2 precursor	0.45	-	end	1 *					718
P34553 UniProt NPD GO	YNK2_CAEEL	Hypothetical protein R10E12.2	0.45	-	exc	1					395
P01639 UniProt NPD GO	KV5G_MOUSE	Ig kappa chain V-V region MOPC 41 precursor	0.45	-	exc	0					130
Q61249 UniProt NPD GO	IGBP1_MOUSE	Immunoglobulin-binding protein 1 (CD79a-binding protein 1) (Alpha4 phosphoprotein) (Lymphocyte signa ...	0.45	-	nuc	0	Cytoplasm (Potential)				340
Q3SZB3 UniProt NPD GO	TIM50_BOVIN	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.45	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				355
P52171 UniProt NPD GO	IMA2_XENLA	Importin alpha-2 subunit (Karyopherin alpha-2 subunit)	0.45	-	cyt	0	Cytoplasm				522
Q8K0C1 UniProt NPD GO	IPO13_MOUSE	Importin-13 (Imp13)	0.45	-	end	0	Cytoplasm (By similarity). Nucleus (By similarity)				963
O94829 UniProt NPD GO	IPO13_HUMAN	Importin-13 (Imp13) (Ran-binding protein 13) (RanBP13) (Karyopherin 13) (Kap13)	0.45	-	end	0	Cytoplasm. Nucleus				963
P25360 UniProt NPD GO	PHO87_YEAST	Inorganic phosphate transporter PHO87	0.45	-	end	12	Membrane; multi-pass membrane protein (Potential)				923
P98154 UniProt NPD GO	IDD_MOUSE	Integral membrane protein DGCR2/IDD precursor (Seizure-related membrane-bound adhesion protein)	0.45	-	exc	1	Membrane; single-pass type I membrane protein				548
Q3V0T4 UniProt NPD GO	ITAD_MOUSE	Integrin alpha-D precursor (CD11d antigen)	0.45	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				1168
Q13349 UniProt NPD GO	ITAD_HUMAN	Integrin alpha-D precursor (Leukointegrin alpha D) (ADB2) (CD11d antigen)	0.45	-	cyt	1	Membrane; single-pass type I membrane protein	integrin complex [TAS]	602453		1162
Q9W1M8 UniProt NPD GO	ITA5_DROME	Integrin alpha-PS5 precursor (Position-specific antigen 5 alpha chain)	0.45	-	nuc	1	Membrane; single-pass type I membrane protein	integrin complex [NAS]			1000
P79263 UniProt NPD GO	ITIH4_PIG	Inter-alpha-trypsin inhibitor heavy chain H4 precursor (ITI heavy chain H4) (Inter-alpha-inhibitor h ...	0.45	-	vac	0					921
Q14624 UniProt NPD GO	ITIH4_HUMAN	Inter-alpha-trypsin inhibitor heavy chain H4 precursor (ITI heavy chain H4) (Inter-alpha-inhibitor h ...	0.45	-	mit	0		extracellular region [NAS]	600564		930
P32881 UniProt NPD GO	IFNA8_HUMAN	Interferon alpha-8 precursor (Interferon alpha-B2) (Interferon alpha-B) (LeIF B)	0.45	-	mit	0	Secreted protein		147568		189
P01576 UniProt NPD GO	IFNB2_BOVIN	Interferon beta-2 precursor	0.45	-	mit	0	Secreted protein				186
P01577 UniProt NPD GO	IFNB3_BOVIN	Interferon beta-3 precursor	0.45	-	mit	0	Secreted protein				186
Q62574 UniProt NPD GO	IFNG_MERUN	Interferon gamma precursor (IFN-gamma)	0.45	-	exc	0	Secreted protein (By similarity)				173
P28172 UniProt NPD GO	IFNT_OVIMO	Interferon tau precursor (IFN-tau) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin) ( ...	0.45	-	exc	0	Secreted protein. Secreted into the uterine lumen				195
P01583 UniProt NPD GO	IL1A_HUMAN	Interleukin-1 alpha precursor (IL-1 alpha) (Hematopoietin-1)	0.45	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...	extracellular space [TAS]	147760	2ILA	271
Q865X8 UniProt NPD GO	IL1B_LAMGL	Interleukin-1 beta precursor (IL-1 beta)	0.45	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				267
Q9Y616 UniProt NPD GO	IRAK3_HUMAN	Interleukin-1 receptor-associated kinase 3 (EC 2.7.11.1) (IRAK-3) (IL-1 receptor-associated kinase M ...	0.45	-	exc	0			604459		596
Q61728 UniProt NPD GO	IL12A_MARMO	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.45	-	exc	0	Secreted protein				223
P29459 UniProt NPD GO	IL12A_HUMAN	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.45	-	exc	0	Secreted protein	interleukin-12 complex [NAS]	161560	1F45	219
Q76LU6 UniProt NPD GO	IL21_PIG	Interleukin-21 precursor (IL-21)	0.45	-	nuc	0	Secreted protein				146
Q28809 UniProt NPD GO	IL3_PANTR	Interleukin-3 precursor (IL-3) (Multipotential colony-stimulating factor) (Hematopoietic growth fact ...	0.45	-	exc	0	Secreted protein	extracellular space [ISS]			152
P78859 UniProt NPD GO	ISA1_SCHPO	Iron sulfur assembly protein 1	0.45	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [TAS]			190

You are viewing entries 28351 to 28400 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.