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
P55205 UniProt NPD GO	GUC2G_RAT	Guanylate cyclase 2G precursor (EC 4.6.1.2) (Guanylyl cyclase receptor G) (GC-G) (Kinase-like domain ...	0.18	-	end	0	Isoform 1: Cell membrane; single-pass type I membrane protein (Potential). Isoform 2: Cytoplasm (Pot ...				1100
Q16661 UniProt NPD GO	GUC2B_HUMAN	Guanylate cyclase activator 2B precursor [Contains: Guanylate cyclase C-activating peptide 2 (Guanyl ...	0.18	-	exc	1 *	Secreted protein		601271	1UYB	112
P14427 UniProt NPD GO	HA14_MOUSE	H-2 class I histocompatibility antigen, D-P alpha chain precursor (H-2D(P))	0.18	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]			368
P01911 UniProt NPD GO	HB2G_HUMAN	HLA class II histocompatibility antigen, DW2.2/DR2.2 beta chain (Fragment)	0.18	-	cyt	0	Membrane; single-pass type I membrane protein (By similarity)	membrane [NAS]			198
P22623 UniProt NPD GO	HSP72_PARLI	Heat shock 70 kDa protein II (HSP70 II) (Fragment)	0.18	-	cyt	0					372
P02826 UniProt NPD GO	HSP7A_DROSI	Heat shock 70 kDa protein cognate 1 (Heat shock 70 kDa protein 70C) (Fragments)	0.18	-	cyt	0					214
P02517 UniProt NPD GO	HSP26_DROME	Heat shock protein 26	0.18	-	nuc	0					208
Q01528 UniProt NPD GO	HAAF_LIMPO	Hemagglutinin/amebocyte aggregation factor precursor (18K-LAF)	0.18	-	nuc	0	Secreted protein. Secreted from amebocyte large secretory granules				172
P56826 UniProt NPD GO	HCYG_SEPOF	Hemocyanin, units G and H (Fragments)	0.18	-	cyt	0					560
Q8WVV9 UniProt NPD GO	HNRLL_HUMAN	Heterogeneous nuclear ribonucleoprotein L-like (Stromal RNA-regulating factor) (BLOCK24 protein)	0.18	+	nuc	0					542
O08528 UniProt NPD GO	HXK2_MOUSE	Hexokinase-2 (EC 2.7.1.1) (Hexokinase type II) (HK II)	0.18	-	cyt	0					917
P35739 UniProt NPD GO	NTRK1_RAT	High affinity nerve growth factor receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase rec ...	0.18	-	end	0	Cell membrane; single-pass type I membrane protein. Endocytosed to the endosomes upon treatment of c ...				799
Q92339 UniProt NPD GO	GHT3_SCHPO	High-affinity gluconate transporter ght3 (Hexose transporter 3)	0.18	-	end	12 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			555
P58406 UniProt NPD GO	HRH3_MOUSE	Histamine H3 receptor (HH3R)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				445
Q9SAZ5 UniProt NPD GO	AHP3_ARATH	Histidine-containing phosphotransfer protein 3	0.18	-	cyt	0					155
Q6FJX6 UniProt NPD GO	H1_CANGA	Histone H1	0.18	-	nuc	0	Nucleus (Potential)				229
P02254 UniProt NPD GO	H1_SALTR	Histone H1	0.18	+	nuc	0	Nucleus				194
P35061 UniProt NPD GO	H2A_ACRFO	Histone H2A	0.18	-	nuc	0	Nucleus				124
O74268 UniProt NPD GO	H2A_BOTCI	Histone H2A	0.18	-	nuc	0	Nucleus				136
Q5G578 UniProt NPD GO	H2A_MAGGR	Histone H2A	0.18	-	nuc	0	Nucleus (By similarity)				135
P19177 UniProt NPD GO	H2A_PETCR	Histone H2A	0.18	-	cyt	0	Nucleus				149
P55897 UniProt NPD GO	H2A_BUFBG	Histone H2A [Contains: Buforin-1 (Buforin I); Buforin-2 (Buforin II)] (Fragment)	0.18	-	nuc	0	Nucleus				39
P02262 UniProt NPD GO	H2A1_RAT	Histone H2A type 1	0.18	-	nuc	0	Nucleus				129
P06897 UniProt NPD GO	H2A1_XENLA	Histone H2A type 1	0.18	-	nuc	0	Nucleus			1ZBB	129
P0C0S8 UniProt NPD GO	H2A1_HUMAN	Histone H2A type 1 (H2A.1)	0.18	-	nuc	0	Nucleus		602796		129
P0C0S9 UniProt NPD GO	H2A1_BOVIN	Histone H2A type 1 (H2A.1b)	0.18	-	nuc	0	Nucleus				129
Q6FI13 UniProt NPD GO	H2A2A_HUMAN	Histone H2A type 2-A (H2A.2)	0.18	-	nuc	0	Nucleus		142720		129
Q6GSS7 UniProt NPD GO	H2A2A_MOUSE	Histone H2A type 2-A (H2A.2) (H2a-614) (H2a-615)	0.18	-	nuc	0	Nucleus				129
P69142 UniProt NPD GO	H2AE_PSAMI	Histone H2A, embryonic	0.18	-	nuc	0	Nucleus				123
P69141 UniProt NPD GO	H2A_STRPU	Histone H2A, embryonic	0.18	-	nuc	0	Nucleus				123
Q59SU5 UniProt NPD GO	H2A1_CANAL	Histone H2A.1	0.18	-	nuc	0	Nucleus (By similarity)				131
P25469 UniProt NPD GO	H2A1_LYCES	Histone H2A.1 (LeH2A-1)	0.18	-	nuc	0	Nucleus				146
Q08702 UniProt NPD GO	HNT3_YEAST	Hit family protein 3	0.18	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			217
Q8MJD6 UniProt NPD GO	HOP_PIG	Homeodomain-only protein (Odd homeobox protein 1)	0.18	-	nuc	0	Nucleus (By similarity)				73
P03994 UniProt NPD GO	HPLN1_RAT	Hyaluronan and proteoglycan link protein 1 precursor (Proteoglycan link protein) (Cartilage link pro ...	0.18	-	exc	0					354
Q9ESM2 UniProt NPD GO	HPLN2_RAT	Hyaluronan and proteoglycan link protein 2 precursor (Brain link protein 1)	0.18	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				341
O57428 UniProt NPD GO	HASS_XENLA	Hyaluronan synthase-related protein (xHAS-RS)	0.18	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				583
P38566 UniProt NPD GO	HYALP_RABIT	Hyaluronidase PH-20 precursor (EC 3.2.1.35) (Hyal-PH20) (Sperm surface protein PH-20) (Sperm adhesio ...	0.18	-	mit	1 *	Cell membrane; lipid-anchor; GPI-anchor				545
Q12891 UniProt NPD GO	HYAL2_HUMAN	Hyaluronidase-2 precursor (EC 3.2.1.35) (Hyal-2) (Hyaluronoglucosaminidase-2) (LUCA-2)	0.18	-	end	0	Cell membrane; lipid-anchor; GPI-anchor	lysosome [TAS]	603551		473
P49371 UniProt NPD GO	HUGA_DOLMA	Hyalurononglucosaminidase (EC 3.2.1.35) (Hyaluronidase) (Allergen Dol m 2) (Dol m II)	0.18	-	cyt	0					331
P48336 UniProt NPD GO	YCXF_CYAPA	Hypothetical 11.2 kDa protein in ycf23-apcF intergenic region (ORF91)	0.18	-	mit	0	Plastid; cyanelle				91
P38269 UniProt NPD GO	YBX4_YEAST	Hypothetical 13.2 kDa protein in TFC1-CIF1 intergenic region	0.18	-	end	1					119
P53884 UniProt NPD GO	YNR4_YEAST	Hypothetical 21.0 kDa protein in RPS3-PSD1 intergenic region	0.18	-	nuc	4 *	Membrane; multi-pass membrane protein (Potential)				190
P53106 UniProt NPD GO	YGR5_YEAST	Hypothetical 21.9 kDa protein in ACE1-RAD54 intergenic region	0.18	-	nuc	2 *					192
P40451 UniProt NPD GO	YIP8_YEAST	Hypothetical 22.8 kDa protein in FOX3-UBP7 intergenic region	0.18	-	nuc	1 *		vacuole (sensu Fungi) [IDA]			204
P15604 UniProt NPD GO	YM02_PARTE	Hypothetical 23.3 kDa protein (ORF2)	0.18	-	end	4					196
P47008 UniProt NPD GO	YJO5_YEAST	Hypothetical 34.4 kDa protein in IDS2-MPI2 intergenic region	0.18	-	cyt	0		cytosol [IDA] microsome [IDA]			294
P38799 UniProt NPD GO	YHN8_YEAST	Hypothetical 63.3 kDa protein in NMD2-IRE1 intergenic region	0.18	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				552
P36173 UniProt NPD GO	YK86_YEAST	Hypothetical 69.0 kDa protein in SIR1 3'region	0.18	-	end	12	Membrane; multi-pass membrane protein (Potential)				615
O94336 UniProt NPD GO	YHM3_SCHPO	Hypothetical FCP1 homology domain-containing protein SPBC1271.03c	0.18	-	nuc	0					244

You are viewing entries 53101 to 53150 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.