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
P49312 UniProt NPD GO	ROA1_MOUSE	Heterogeneous nuclear ribonucleoprotein A1 (Helix-destabilizing protein) (Single-strand-binding prot ...	0.44	+	cyt	0	Nucleus. Cytoplasm. Shuttles continuously between the nucleus and the cytoplasm along with mRNA. Com ...	nucleus [IDA] spliceosome complex [ISS]			319
P37218 UniProt NPD GO	H1_LYCES	Histone H1	0.44	-	nuc	0	Nucleus				287
P43278 UniProt NPD GO	H10_RAT	Histone H1.0 (H1(0)) (Histone H1')	0.44	+	nuc	0	Nucleus				193
Q94972 UniProt NPD GO	H13_DROVI	Histone H1.3	0.44	+	nuc	0	Nucleus				250
P40273 UniProt NPD GO	H161_TRYCR	Histone H1.M6.1	0.44	+	nuc	0					80
Q59VP1 UniProt NPD GO	H2B2_CANAL	Histone H2B.2	0.44	+	nuc	0	Nucleus (By similarity)				129
P22843 UniProt NPD GO	H3_ACRFO	Histone H3	0.44	-	nuc	0	Nucleus (By similarity)				135
P15512 UniProt NPD GO	H32_TETPY	Histone H3.2	0.44	-	nuc	0	Nucleus (By similarity)				135
P02302 UniProt NPD GO	H32_XENLA	Histone H3.2	0.44	-	nuc	0	Nucleus			1M1A	135
Q9FVI6 UniProt NPD GO	FWA_ARATH	Homeobox protein FWA	0.44	-	nuc	0	Nucleus (Probable)				686
P31261 UniProt NPD GO	HXA2_NOTVI	Homeobox protein Hox-A2 (NvHbox-2.8) (Fragment)	0.44	+	nuc	0	Nucleus				90
P14651 UniProt NPD GO	HXB3_HUMAN	Homeobox protein Hox-B3 (Hox-2G) (Hox-2.7)	0.44	+	nuc	0	Nucleus		142966		431
O02786 UniProt NPD GO	MSX1_BOVIN	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.44	+	nuc	0	Nucleus				297
Q9R101 UniProt NPD GO	LIPS_SPETR	Hormone-sensitive lipase (EC 3.1.1.79) (HSL)	0.44	-	nuc	0					763
P47107 UniProt NPD GO	YJ09_YEAST	Hypothetical 127.4 kDa protein in HUL4-GEF1 intergenic region	0.44	+	cyt	0		mitochondrion [IDA]			1121
P40448 UniProt NPD GO	YIQ3_YEAST	Hypothetical 14.0 kDa protein in SDL1-SUC2 intergenic region	0.44	-	nuc	0					117
P53080 UniProt NPD GO	YGX2_YEAST	Hypothetical 19.2 kDa protein in GOG5-NIF3 intergenic region	0.44	-	nuc	0		cytoplasm [IDA]			175
P15609 UniProt NPD GO	YM08_PARTE	Hypothetical 28.6 kDa protein (ORF8)	0.44	+	cyt	0					241
P53155 UniProt NPD GO	YGI2_YEAST	Hypothetical 43.3 kDa protein in SCY1-DBP3 intergenic region	0.44	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			381
P53109 UniProt NPD GO	YGR0_YEAST	Hypothetical 65.8 kDa protein in SUT1-RCK1 intergenic region	0.44	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				570
P38738 UniProt NPD GO	YHC9_YEAST	Hypothetical 77.8 kDa protein in GUT1-RIM1 intergenic region	0.44	-	nuc	0		cytoplasm [IDA]			679
P12195 UniProt NPD GO	YCF15_TOBAC	Hypothetical 8.5 kDa protein ycf15 (ORF 70) (ORF 87)	0.44	-	cyt	0	Plastid; chloroplast				70
Q20059 UniProt NPD GO	YPR4_CAEEL	Hypothetical WD repeat protein F35G12.4	0.44	-	nuc	0					683
Q09392 UniProt NPD GO	YR49_CAEEL	Hypothetical WD repeat protein F47D12.9	0.44	-	mit	0					545
P05470 UniProt NPD GO	YKP4_KLULA	Hypothetical killer plasmid pGKL-2 protein 4 (EC 3.6.1.-) (Hypothetical killer plasmid pGKL-2 helica ...	0.44	-	nuc	0					597
P92511 UniProt NPD GO	M690_ARATH	Hypothetical mitochondrial ribosomal S3-like protein AtMg00690 (ORF240a)	0.44	-	nuc	1	Mitochondrion (Potential)				240
Q17529 UniProt NPD GO	YQE4_CAEEL	Hypothetical protein B0564.4 in chromosome IV	0.44	-	end	4 *					523
P34273 UniProt NPD GO	YKH5_CAEEL	Hypothetical protein C02C2.5 in chromosome III	0.44	-	end	1					344
Q10225 UniProt NPD GO	YAZ4_SCHPO	Hypothetical protein C13D6.04c in chromosome I	0.44	-	cyt	0		ubiquitin ligase complex [IPI]			523
O60071 UniProt NPD GO	YBB9_SCHPO	Hypothetical protein C13G1.09 in chromosome II	0.44	-	nuc	0					449
O42995 UniProt NPD GO	YBC2_SCHPO	Hypothetical protein C27B12.02 in chromosome II	0.44	-	nuc	0					109
Q09806 UniProt NPD GO	YAB4_SCHPO	Hypothetical protein C2G11.04 in chromosome I	0.44	-	nuc	0					301
O14205 UniProt NPD GO	YDQD_SCHPO	Hypothetical protein C5D6.13 in chromosome I	0.44	-	nuc	0					337
Q10307 UniProt NPD GO	YD52_SCHPO	Hypothetical protein C6C3.02c in chromosome I	0.44	-	mit	0					172
Q09305 UniProt NPD GO	YQQ2_CAEEL	Hypothetical protein F10B5.2 in chromosome II	0.44	-	mit	0					357
Q09400 UniProt NPD GO	YRB3_CAEEL	Hypothetical protein F58F12.3	0.44	-	nuc	0					463
P34612 UniProt NPD GO	YOG3_CAEEL	Hypothetical protein ZK112.3	0.44	+	end	1 *					160
Q23679 UniProt NPD GO	YWM3_CAEEL	Hypothetical protein ZK970.3 in chromosome II	0.44	-	nuc	0					157
Q5B8A8 UniProt NPD GO	ISN1_EMENI	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.44	-	mit	0					444
P01883 UniProt NPD GO	IGHD_RAT	Ig delta chain C region (Fragment)	0.44	-	nuc	0					202
O74476 UniProt NPD GO	IMB3_SCHPO	Importin beta-3 subunit	0.44	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			1095
Q9P0U5 UniProt NPD GO	INGX_HUMAN	Inhibitor of growth protein, X-linked (Inhibitor of growth protein 2) (ING1-like tumor suppressor pr ...	0.44	-	nuc	0			300452		42
Q4WCV3 UniProt NPD GO	MRS2_ASPFU	Inner membrane magnesium transporter mrs2, mitochondrial precursor (RNA-splicing protein mrs2)	0.44	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				597
Q6B9Z0 UniProt NPD GO	IGFL_MOUSE	Insulin growth factor-like family member precursor	0.44	-	nuc	0	Secreted protein (Potential)				140
Q9PVZ4 UniProt NPD GO	INSR_XENLA	Insulin receptor precursor (EC 2.7.10.1) (IR) (Xe-InsR) (XTK-1b) [Contains: Insulin receptor subunit ...	0.44	-	end	0	Cell membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [IDA]			1362
Q60751 UniProt NPD GO	IGF1R_MOUSE	Insulin-like growth factor 1 receptor precursor (EC 2.7.10.1) (Insulin-like growth factor I receptor ...	0.44	+	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			1373
P24062 UniProt NPD GO	IGF1R_RAT	Insulin-like growth factor 1 receptor precursor (EC 2.7.10.1) (Insulin-like growth factor I receptor ...	0.44	+	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			1370
O02466 UniProt NPD GO	ILPR_BRALA	Insulin-like peptide receptor precursor (EC 2.7.10.1) (ILP receptor) [Contains: Insulin-like peptide ...	0.44	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				1363
P05555 UniProt NPD GO	ITAM_MOUSE	Integrin alpha-M precursor (Cell surface glycoprotein MAC-1 alpha subunit) (CR-3 alpha chain) (Leuko ...	0.44	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] integral to membrane [IDA] nucleus [IDA]			1153
P11584 UniProt NPD GO	ITBX_DROME	Integrin beta-PS precursor (Position-specific antigen beta chain) (Protein myospheroid) (Protein olf ...	0.44	-	exc	1	Membrane; single-pass type I membrane protein	integrin complex [NAS]			846

You are viewing entries 29001 to 29050 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.