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
Q07071 UniProt NPD GO	GCKR_RAT	Glucokinase regulatory protein (Glucokinase regulator)	0.28	-	mit	0					626
Q7YS37 UniProt NPD GO	G6PD_BOSIN	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.28	-	cyt	0					514
Q9SW97 UniProt NPD GO	GLR35_ARATH	Glutamate receptor 3.5 precursor (Ligand-gated ion channel 3.5) (Ionotropic glutamate receptor GLR6) ...	0.28	-	end	3 *	Membrane; multi-pass membrane protein				953
P50123 UniProt NPD GO	AMPE_RAT	Glutamyl aminopeptidase (EC 3.4.11.7) (EAP) (Aminopeptidase A) (APA)	0.28	-	mit	1 *	Membrane; single-pass type II membrane protein				945
P16406 UniProt NPD GO	AMPE_MOUSE	Glutamyl aminopeptidase (EC 3.4.11.7) (EAP) (Aminopeptidase A) (APA) (BP-1/6C3 antigen)	0.28	-	mit	1 *	Membrane; single-pass type II membrane protein	plasma membrane [TAS]			945
P46431 UniProt NPD GO	GSTT2_MUSDO	Glutathione S-transferase 2 (EC 2.5.1.18) (GST class-theta)	0.28	-	cyt	0					210
P83325 UniProt NPD GO	GSTP2_BUFBU	Glutathione S-transferase P 2 (EC 2.5.1.18) (BBGSTP2-2) (GST class-pi)	0.28	-	cyt	0					210
P32190 UniProt NPD GO	GLPK_YEAST	Glycerol kinase (EC 2.7.1.30) (ATP:glycerol 3-phosphotransferase) (Glycerokinase) (GK)	0.28	-	mit	0		cytoplasm [IDA]			709
O80437 UniProt NPD GO	GPAT6_ARATH	Glycerol-3-phosphate acyltransferase 6 (EC 2.3.1.15) (AtGPAT6)	0.28	+	end	3 *	Membrane; multi-pass membrane protein (Potential)				501
O49852 UniProt NPD GO	GCSP_FLATR	Glycine dehydrogenase [decarboxylating], mitochondrial precursor (EC 1.4.4.2) (Glycine decarboxylase ...	0.28	-	mit	0	Mitochondrion				1034
P18266 UniProt NPD GO	GSK3B_RAT	Glycogen synthase kinase-3 beta (EC 2.7.11.26) (GSK-3 beta) (Factor A) (FA)	0.28	-	nuc	0		cytoplasm [TAS]			420
Q6CMK4 UniProt NPD GO	NMT_KLULA	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.28	-	nuc	0	Cytoplasm (By similarity)				447
P13265 UniProt NPD GO	GPC3_RAT	Glypican-3 precursor (Intestinal protein OCI-5)	0.28	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				597
Q5R435 UniProt NPD GO	GRPE2_PONPY	GrpE protein homolog 2, mitochondrial precursor (Mt-GrpE#2)	0.28	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				225
Q28024 UniProt NPD GO	GBG12_BOVIN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-12 subunit precursor (Gamma-S1)	0.28	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				71
P62871 UniProt NPD GO	GBB1_BOVIN	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 1 (Transducin beta chain 1)	0.28	-	cyt	0				2TRC	339
P62872 UniProt NPD GO	GBB1_CANFA	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 1 (Transducin beta chain 1)	0.28	-	cyt	0					339
P62873 UniProt NPD GO	GBB1_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 1 (Transducin beta chain 1)	0.28	-	cyt	0			139380		339
P62874 UniProt NPD GO	GBB1_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 1 (Transducin beta chain 1)	0.28	-	cyt	0		heterotrimeric G-protein complex [IPI]			339
P54311 UniProt NPD GO	GBB1_RAT	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 1 (Transducin beta chain 1)	0.28	-	cyt	0		heterotrimeric G-protein complex [TAS]			339
P30682 UniProt NPD GO	GNAI_LYMST	Guanine nucleotide-binding protein G(i) subunit alpha (Adenylate cyclase-inhibiting G alpha protein) ...	0.28	-	cyt	0					353
P63097 UniProt NPD GO	GNAI1_BOVIN	Guanine nucleotide-binding protein G(i), alpha-1 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.28	-	cyt	0					353
P63096 UniProt NPD GO	GNAI1_HUMAN	Guanine nucleotide-binding protein G(i), alpha-1 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.28	-	cyt	0			139310	1Y3A	353
Q5RAD4 UniProt NPD GO	GNAI1_PONPY	Guanine nucleotide-binding protein G(i), alpha-1 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.28	-	cyt	0					353
P29348 UniProt NPD GO	GNAT3_RAT	Guanine nucleotide-binding protein G(t), alpha-3 subunit (Gustducin alpha-3 chain)	0.28	-	gol	0					353
P52206 UniProt NPD GO	GNA11_CANFA	Guanine nucleotide-binding protein alpha-11 subunit (Fragment)	0.28	-	cyt	0					198
Q09435 UniProt NPD GO	GCY1_CAEEL	Guanylate cyclase receptor-type gcy-1 precursor (EC 4.6.1.2)	0.28	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1137
Q74Z52 UniProt NPD GO	NOP10_ASHGO	H/ACA ribonucleoprotein complex subunit 3 (Nucleolar protein family A member 3) (snoRNP protein NOP1 ...	0.28	-	nuc	0	Nucleus; nucleolus (By similarity)				57
Q9HDC0 UniProt NPD GO	ENK15_HUMAN	HERV-K_3q21.2 provirus ancestral Env polyprotein (Envelope polyprotein) (HERV-K(I) envelope protein) ...	0.28	-	nuc	0					124
P61550 UniProt NPD GO	ENT1_HUMAN	HERV-T_19q13.11 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (HERV-T Env prot ...	0.28	-	end	1 *					626
Q9SSG3 UniProt NPD GO	HIPL1_ARATH	HIPL1 protein precursor	0.28	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor				695
P01892 UniProt NPD GO	1A02_HUMAN	HLA class I histocompatibility antigen, A-2 alpha chain precursor (MHC class I antigen A*2)	0.28	-	end	1	Membrane; single-pass type I membrane protein		142800	3HLA	365
P01891 UniProt NPD GO	1A68_HUMAN	HLA class I histocompatibility antigen, A-68 alpha chain precursor (MHC class I antigen A*68) (Aw-68 ...	0.28	-	end	1	Membrane; single-pass type I membrane protein		142800	2HLA	365
P18465 UniProt NPD GO	1B57_HUMAN	HLA class I histocompatibility antigen, B-57 alpha chain precursor (MHC class I antigen B*57) (Bw-57 ...	0.28	-	end	1 *	Membrane; single-pass type I membrane protein		142830	2BVQ	362
P17804 UniProt NPD GO	HSP70_LEIDO	Heat shock 70 kDa protein	0.28	-	cyt	0					653
Q91291 UniProt NPD GO	HSP70_PLEWA	Heat shock 70 kDa protein (HSP70)	0.28	-	cyt	0					645
P06582 UniProt NPD GO	HSP12_CAEEL	Heat shock protein Hsp-16.2	0.28	-	nuc	0					145
P10591 UniProt NPD GO	HSP71_YEAST	Heat shock protein SSA1 (Heat shock protein YG100)	0.28	-	cyt	0	Cytoplasm. Cell wall	cell wall (sensu Fungi) [IDA] chaperonin-containing T-complex [IPI] cytoplasm [IDA] nucleus [IDA] vacuolar membrane (sensu Fungi) [IDA]			641
P34555 UniProt NPD GO	HLH4_CAEEL	Helix-loop-helix protein 4	0.28	-	mit	0	Nucleus (Potential)				205
P14901 UniProt NPD GO	HMOX1_MOUSE	Heme oxygenase 1 (EC 1.14.99.3) (HO-1) (P32 protein)	0.28	-	nuc	1	Microsome				289
Q06186 UniProt NPD GO	HBEGF_MOUSE	Heparin-binding EGF-like growth factor precursor (HB-EGF) (HBEGF)	0.28	+	end	1	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...				208
Q5QNS5 UniProt NPD GO	TIMD1_MOUSE	Hepatitis A virus cellular receptor 1 homolog precursor (HAVcr-1) (T cell immunoglobulin and mucin d ...	0.28	-	nuc	1	Membrane; single-pass type I membrane protein (Probable)				305
P09867 UniProt NPD GO	ROA1_BOVIN	Heterogeneous nuclear ribonucleoprotein A1 (Helix-destabilizing protein) (Single-strand RNA-binding ...	0.28	-	cyt	0	Nucleus. Cytoplasm. Shuttles continuously between the nucleus and the cytoplasm along with mRNA. Com ...				195
P27595 UniProt NPD GO	HXK1_BOVIN	Hexokinase-1 (EC 2.7.1.1) (Hexokinase type I) (HK I) (Brain form hexokinase)	0.28	-	cyt	0	Mitochondrion; mitochondrial outer membrane. Its hydrophobic N-terminal sequence may be involved in ...				918
P27926 UniProt NPD GO	HXK3_RAT	Hexokinase-3 (EC 2.7.1.1) (Hexokinase type III) (HK III)	0.28	-	cyt	0					924
Q8LQ68 UniProt NPD GO	HXK6_ORYSA	Hexokinase-6 (EC 2.7.1.1) (Hexokinase-2)	0.28	+	nuc	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein (By similarity)				506
P40266 UniProt NPD GO	H11_GLYSA	Histone H1-I	0.28	-	nuc	0	Nucleus				233
P16401 UniProt NPD GO	H15_HUMAN	Histone H1.5 (Histone H1a)	0.28	+	nuc	0	Nucleus	nucleosome [NAS]	142711		225
P62790 UniProt NPD GO	H4_OXYNO	Histone H4	0.28	-	cyt	0	Nucleus (By similarity)				103
P62791 UniProt NPD GO	H4_STYLE	Histone H4	0.28	-	cyt	0	Nucleus (By similarity)				103

You are viewing entries 42301 to 42350 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.