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
Q9C8E7 UniProt NPD GO	GLR33_ARATH	Glutamate receptor 3.3 precursor (Ligand-gated ion channel 3.3)	0.31	-	end	3	Membrane; multi-pass membrane protein				933
Q63226 UniProt NPD GO	GRID2_RAT	Glutamate receptor delta-2 subunit precursor (GluR delta-2)	0.31	-	end	3	Membrane; multi-pass membrane protein (By similarity)				1007
Q5ZMA6 UniProt NPD GO	NADE1_CHICK	Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) (NAD(+) synthase [glutamine-hydrolyzing]) (NAD(+) ...	0.31	-	cyt	0					707
Q6IA69 UniProt NPD GO	NADE1_HUMAN	Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) (NAD(+) synthase [glutamine-hydrolyzing]) (NAD(+) ...	0.31	-	cyt	0			608285		706
Q00285 UniProt NPD GO	GSTMU_CRILO	Glutathione S-transferase Y1 (EC 2.5.1.18) (Chain 3) (GST class-mu)	0.31	-	cyt	0	Cytoplasm				217
P48168 UniProt NPD GO	GLRB_MOUSE	Glycine receptor beta chain precursor (Glycine receptor 58 kDa subunit)	0.31	+	end	4	Membrane; multi-pass membrane protein				496
P54840 UniProt NPD GO	GYS2_HUMAN	Glycogen [starch] synthase, liver (EC 2.4.1.11)	0.31	-	cyt	0		cell cortex [ISS] cortical actin cytoskeleton [ISS] cytoplasm [ISS] cytoskeleton [ISS] cytosol [ISS] ectoplasm [ISS] insoluble fraction [ISS] soluble fraction [ISS]	240600		703
P28797 UniProt NPD GO	GRN_CAVPO	Granulins precursor (Proepithelin) (PEPI) [Contains: Acrogranin; Granulin-1; Granulin-2; Granulin-3; ...	0.31	-	nuc	0	Secreted protein				591
P38400 UniProt NPD GO	GNAI2_CANFA	Guanine nucleotide-binding protein G(i), alpha-2 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.31	-	gol	0					354
Q4R592 UniProt NPD GO	GNAI2_MACFA	Guanine nucleotide-binding protein G(i), alpha-2 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.31	-	gol	0					354
Q40687 UniProt NPD GO	GBB_ORYSA	Guanine nucleotide-binding protein subunit beta	0.31	-	nuc	0					380
P51840 UniProt NPD GO	GUC2E_RAT	Guanylyl cyclase GC-E precursor (EC 4.6.1.2) (Guanylate cyclase 2E)	0.31	-	end	2 *	Membrane; single-pass type I membrane protein	integral to membrane [TAS]			1108
P10247 UniProt NPD GO	HG2A_RAT	H-2 class II histocompatibility antigen gamma chain (MHC class II-associated invariant chain) (Ia an ...	0.31	-	nuc	1 *	Membrane; single-pass type II membrane protein (Potential)	integral to membrane [TAS]			280
Q6DRH5 UniProt NPD GO	NOLA3_BRARE	H/ACA ribonucleoprotein complex subunit 3 (Nucleolar protein family A member 3)	0.31	-	nuc	0	Nucleus; nucleolus (By similarity)				64
P30461 UniProt NPD GO	1B13_HUMAN	HLA class I histocompatibility antigen, B-13 alpha chain precursor (MHC class I antigen B*13)	0.31	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
P30462 UniProt NPD GO	1B14_HUMAN	HLA class I histocompatibility antigen, B-14 alpha chain precursor (MHC class I antigen B*14)	0.31	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142830		362
P30475 UniProt NPD GO	1B39_HUMAN	HLA class I histocompatibility antigen, B-39 alpha chain precursor (MHC class I antigen B*39)	0.31	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142830		362
P18464 UniProt NPD GO	1B51_HUMAN	HLA class I histocompatibility antigen, B-51 alpha chain precursor (MHC class I antigen B*51)	0.31	-	end	1 *	Membrane; single-pass type I membrane protein		142830	1E28	362
P10319 UniProt NPD GO	1B58_HUMAN	HLA class I histocompatibility antigen, B-58 alpha chain precursor (MHC class I antigen B*58) (Bw-58 ...	0.31	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
Q29940 UniProt NPD GO	1B59_HUMAN	HLA class I histocompatibility antigen, B-59 alpha chain precursor (MHC class I antigen B*59)	0.31	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
P01918 UniProt NPD GO	HB21_HUMAN	HLA class II histocompatibility antigen, DQ(1) beta chain precursor (DC-3 beta chain)	0.31	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)			1S9V	261
Q8GXE9 UniProt NPD GO	HA22J_ARATH	HVA22-like protein j (AtHVA22j)	0.31	-	mit	0					258
Q96331 UniProt NPD GO	HS23M_ARATH	Heat shock 22 kDa protein, mitochondrial precursor	0.31	-	mit	0	Mitochondrion				210
Q01233 UniProt NPD GO	HSP70_NEUCR	Heat shock 70 kDa protein (HSP70)	0.31	-	cyt	0					646
P11503 UniProt NPD GO	HSP70_ONCVO	Heat shock 70 kDa protein (HSP70) (Fragment)	0.31	-	nuc	0					322
Q61696 UniProt NPD GO	HS70A_MOUSE	Heat shock 70 kDa protein 1A (Heat shock 70 kDa protein 3) (HSP70.3) (Hsp68)	0.31	-	cyt	0					641
P17879 UniProt NPD GO	HS70B_MOUSE	Heat shock 70 kDa protein 1B (HSP70.1)	0.31	-	cyt	0					642
Q9U639 UniProt NPD GO	HSP7D_MANSE	Heat shock 70 kDa protein cognate 4 (Hsc 70-4)	0.31	-	cyt	0	Nucleus (By similarity)				652
P20583 UniProt NPD GO	HSP71_TRYCR	Heat shock 70 kDa protein, mitochondrial precursor	0.31	-	mit	0	Mitochondrion. Associated with kinetoplast DNA in the mitochondrion, in the region where kdna replic ...				656
P09189 UniProt NPD GO	HSP7C_PETHY	Heat shock cognate 70 kDa protein	0.31	-	cyt	0					651
P30220 UniProt NPD GO	HS30E_XENLA	Heat shock protein 30E (Fragment)	0.31	-	nuc	0					91
P04810 UniProt NPD GO	HSP83_DROSI	Heat shock protein 83 (HSP 82) (Fragment)	0.31	-	cyt	0	Cytoplasm	centrosome [ISS]			375
P04811 UniProt NPD GO	HSP83_DROVI	Heat shock protein 83 (HSP 82) (Fragment)	0.31	-	cyt	0	Cytoplasm	centrosome [ISS]			374
P14659 UniProt NPD GO	HSP72_RAT	Heat shock-related 70 kDa protein 2 (Heat shock protein 70.2) (Testis-specific heat shock protein-re ...	0.31	-	cyt	0					633
P83427 UniProt NPD GO	HELN_HELVI	Heliocin	0.31	-	mit	0	Secreted protein				22
Q5E9F2 UniProt NPD GO	HMOX1_BOVIN	Heme oxygenase 1 (EC 1.14.99.3) (HO-1)	0.31	-	cyt	1	Microsome (By similarity)				289
P51859 UniProt NPD GO	HDGF_MOUSE	Hepatoma-derived growth factor (HDGF)	0.31	-	nuc	0	Cytoplasm (By similarity)	extracellular space [IDA] nucleus [IDA]			237
Q9D0E1 UniProt NPD GO	HNRPM_MOUSE	Heterogeneous nuclear ribonucleoprotein M (hnRNP M)	0.31	-	cyt	0	Nucleus (By similarity)				728
P19367 UniProt NPD GO	HXK1_HUMAN	Hexokinase-1 (EC 2.7.1.1) (Hexokinase type I) (HK I) (Brain form hexokinase)	0.31	-	cyt	0	Mitochondrion; mitochondrial outer membrane. Its hydrophobic N-terminal sequence may be involved in ...		142600	1QHA	917
Q5W676 UniProt NPD GO	HXK5_ORYSA	Hexokinase-5 (EC 2.7.1.1) (Hexokinase I)	0.31	+	mit	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein (By similarity)				507
P11873 UniProt NPD GO	HMGC_TETTH	High mobility group protein C (Nonhistone chromosomal protein LG-1)	0.31	-	nuc	0	Nucleus. Macronuclei				100
P14586 UniProt NPD GO	HRP3_PLAFS	Histidine-rich protein	0.31	-	mit	1					82
Q9UV33 UniProt NPD GO	H1_ASCIM	Histone H1	0.31	-	nuc	0	Nucleus (Potential)				213
P40263 UniProt NPD GO	H11_GLYBA	Histone H1-I	0.31	-	nuc	0	Nucleus				233
P07796 UniProt NPD GO	H1G_STRPU	Histone H1-gamma, late	0.31	+	nuc	0	Nucleus				217
Q4WWC5 UniProt NPD GO	H2B_ASPFU	Histone H2B	0.31	-	nuc	0	Nucleus (By similarity)				139
P81196 UniProt NPD GO	H39_STYLE	Histone H3-2 (Fragment)	0.31	-	nuc	0	Nucleus (By similarity)				114
P81201 UniProt NPD GO	H37_STYLE	Histone H3-7 (Fragment)	0.31	-	nuc	0	Nucleus (By similarity)				114
P35059 UniProt NPD GO	H4_ACRFO	Histone H4	0.31	-	cyt	0	Nucleus (By similarity)				102
Q6LAF1 UniProt NPD GO	H4_DENKL	Histone H4	0.31	-	cyt	0	Nucleus (By similarity)				102

You are viewing entries 39451 to 39500 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.