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
Q9IA22 UniProt NPD GO	HXA4_HETFR	Homeobox protein Hox-A4	0.80	+	nuc	0	Nucleus (By similarity)				247
P17483 UniProt NPD GO	HXB4_HUMAN	Homeobox protein Hox-B4 (Hox-2F) (Hox-2.6)	0.80	+	nuc	0	Nucleus	nucleus [NAS]	142965		251
Q8AWZ0 UniProt NPD GO	HXB8A_BRARE	Homeobox protein Hox-B8a (Hox-B8)	0.80	+	nuc	0	Nucleus (By similarity)				245
P31275 UniProt NPD GO	HXC12_HUMAN	Homeobox protein Hox-C12 (Hox-3F)	0.80	+	nuc	0	Nucleus		142975		282
Q9PVS4 UniProt NPD GO	HXC4_ORYLA	Homeobox protein Hox-C4	0.80	+	nuc	0	Nucleus (By similarity)				261
Q08624 UniProt NPD GO	HXC4_MOUSE	Homeobox protein Hox-C4 (Hox-3.5)	0.80	+	nuc	0	Nucleus				264
Q9PWM3 UniProt NPD GO	HXC4A_BRARE	Homeobox protein Hox-C4a (Hox-C4)	0.80	+	nuc	0	Nucleus (By similarity)				268
P09074 UniProt NPD GO	HXC5A_BRARE	Homeobox protein Hox-C5a (Hox-C5) (Hox-3.4) (Zf-25)	0.80	+	nuc	0	Nucleus				232
Q9IA14 UniProt NPD GO	HXD10_HETFR	Homeobox protein Hox-D10	0.80	+	nuc	0	Nucleus (By similarity)				336
Q5EU40 UniProt NPD GO	HXD12_CARPS	Homeobox protein Hox-D12	0.80	+	nuc	0	Nucleus				270
P35452 UniProt NPD GO	HXD12_HUMAN	Homeobox protein Hox-D12 (Hox-4H)	0.80	+	nuc	0	Nucleus	nuclear chromosome [NAS]	142988		275
P78426 UniProt NPD GO	NKX61_HUMAN	Homeobox protein Nkx-6.1	0.80	+	nuc	0	Nucleus (Probable)		602563		367
P46608 UniProt NPD GO	HSBH1_SOYBN	Homeobox protein SBH1	0.80	+	nuc	0	Nucleus (Probable)				379
P56407 UniProt NPD GO	HM09_CAEEL	Homeobox protein ceh-9	0.80	+	nuc	0	Nucleus (Potential)				147
Q04896 UniProt NPD GO	HME1A_BRARE	Homeobox protein engrailed-1a (Eng1)	0.80	+	nuc	0	Nucleus				231
P05527 UniProt NPD GO	HMIN_DROME	Homeobox protein invected	0.80	+	nuc	0	Nucleus				576
P92953 UniProt NPD GO	ATHB4_ARATH	Homeobox-leucine zipper protein ATHB-4 (HD-ZIP protein ATHB-4)	0.80	+	nuc	0	Nucleus (Probable)				318
P02833 UniProt NPD GO	ANTP_DROME	Homeotic protein antennapedia	0.80	+	nuc	0	Nucleus (Probable)	nucleus [IDA]		9ANT	378
P97779 UniProt NPD GO	HMMR_RAT	Hyaluronan-mediated motility receptor (Intracellular hyaluronic acid-binding protein) (Receptor for ...	0.80	-	nuc	0	Cell surface. Cytoplasm (By similarity)				498
Q03496 UniProt NPD GO	YM8B_YEAST	Hypothetical 163.6 kDa protein in PET111-TIF11 intergenic region	0.80	-	cyt	0		cytoplasm [IDA]			1420
P53227 UniProt NPD GO	YG1T_YEAST	Hypothetical 31.0 kDa protein in BUD9-RME1 intergenic region	0.80	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			271
P39943 UniProt NPD GO	YEL8_YEAST	Hypothetical 43.1 kDa protein in GAL83-YPT8 intergenic region	0.80	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			394
Q10209 UniProt NPD GO	YAY1_SCHPO	Hypothetical J domain-containing protein C4H3.01	0.80	+	nuc	0					392
Q9VUB4 UniProt NPD GO	U171_DROME	Hypothetical UPF0171 protein CG8783	0.80	-	nuc	0					610
Q10162 UniProt NPD GO	YAU6_SCHPO	Hypothetical methyltransferase C26A3.06 in chromosome I	0.80	+	nuc	0					268
P16128 UniProt NPD GO	Y4849_ARATH	Hypothetical protein At4g18490	0.80	-	nuc	0					594
O13776 UniProt NPD GO	YE9G_SCHPO	Hypothetical protein C17A5.16 in chromosome I	0.80	-	nuc	0					925
Q9UUD9 UniProt NPD GO	YNZD_SCHPO	Hypothetical protein C17G9.13c in chromosome II	0.80	-	nuc	0					317
Q9W5D0 UniProt NPD GO	Y34F_DROME	Hypothetical protein CG12467 in chromosome 1	0.80	-	nuc	0					1561
Q9VFB7 UniProt NPD GO	Y623_DROME	Hypothetical protein CG6623	0.80	-	cyt	0					1145
Q03615 UniProt NPD GO	YN06_CAEEL	Hypothetical protein T23G5.6	0.80	+	nuc	0					305
Q22712 UniProt NPD GO	YW91_CAEEL	Hypothetical protein T24A11.1 in chromosome III	0.80	+	nuc	0					938
Q5R8C7 UniProt NPD GO	ILDR1_PONPY	Immunoglobulin-like domain-containing receptor 1 precursor	0.80	-	exc	2 *	Cell membrane; single-pass type I membrane protein (By similarity)				546
Q22647 UniProt NPD GO	TIM50_CAEEL	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.80	-	nuc	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				452
O35345 UniProt NPD GO	IMA7_MOUSE	Importin alpha-7 subunit (Karyopherin alpha-6 subunit) (Importin alpha S2)	0.80	-	nuc	0	Cytoplasm				533
P53843 UniProt NPD GO	IST1_YEAST	Increased sodium tolerance protein 1	0.80	-	nuc	0		endosome [IDA]			298
Q9NXR8 UniProt NPD GO	ING3_HUMAN	Inhibitor of growth protein 3 (p47ING3 protein)	0.80	-	nuc	0	Nucleus		275355	1X4I	418
P29993 UniProt NPD GO	ITPR_DROME	Inositol 1,4,5-trisphosphate receptor (InsP3 receptor) (InsP3R)	0.80	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				2838
P24593 UniProt NPD GO	IBP5_HUMAN	Insulin-like growth factor-binding protein 5 precursor (IGFBP-5) (IBP-5) (IGF-binding protein 5)	0.80	-	exc	0	Secreted protein	extracellular region [NAS]	146734	1H59	272
P17803 UniProt NPD GO	IFNG_PIG	Interferon gamma precursor (IFN-gamma)	0.80	-	exc	0	Secreted protein				166
Q08619 UniProt NPD GO	IFI5_MOUSE	Interferon-activable protein 205 (IFI-205) (D3 protein)	0.80	-	nuc	0					425
P32455 UniProt NPD GO	GBP1_HUMAN	Interferon-induced guanylate-binding protein 1 (GTP-binding protein 1) (Guanine nucleotide-binding p ...	0.80	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		600411	2D4H	592
Q63663 UniProt NPD GO	GBP2_RAT	Interferon-induced guanylate-binding protein 2 (GTP-binding protein 2) (Guanine nucleotide-binding p ...	0.80	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				589
P23730 UniProt NPD GO	IFEA_ASCSU	Intermediate filament protein A (IF-A) (Fragment)	0.80	-	nuc	0	Cytoplasm				497
Q19289 UniProt NPD GO	IFB1_CAEEL	Intermediate filament protein ifb-1 (Intermediate filament protein B1) (IF-B1) (Cel IF B1)	0.80	-	nuc	0	Cytoplasm (By similarity)				589
Q07821 UniProt NPD GO	ISA1_YEAST	Iron sulfur assembly protein 1	0.80	+	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			250
Q9GQF1 UniProt NPD GO	JIP3_DROME	JNK-interacting protein 3 (Protein sunday driver)	0.80	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS] trans-Golgi network transport vesicle [IDA]			1227
O43087 UniProt NPD GO	KMS2_SCHPO	Karyogamy meiotic segregation protein 2	0.80	-	nuc	1	Nucleus. Cytoplasm. Associates with the spindle pole body (SPB)	cytoplasm [IDA] nucleus [IDA]			457
Q8J1G4 UniProt NPD GO	KIP1_ASHGO	Kinesin-like protein KIP1	0.80	-	nuc	0	Spindle (By similarity). Spindle microtubules that lie between the poles (By similarity)				1129
P28739 UniProt NPD GO	KLPA_EMENI	Kinesin-like protein klpA	0.80	-	nuc	0					770

You are viewing entries 8901 to 8950 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.