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
Q9GJW7 UniProt NPD GO	GBRAP_BOVIN	Gamma-aminobutyric acid receptor-associated protein (GABA(A) receptor-associated protein)	0.32	-	nuc	0	Intracytoplasmic membrane (By similarity). Cytoskeleton (By similarity). Largely associated with int ...				117
Q9DCD6 UniProt NPD GO	GBRAP_MOUSE	Gamma-aminobutyric acid receptor-associated protein (GABA(A) receptor-associated protein)	0.32	-	nuc	0	Intracytoplasmic membrane (By similarity). Cytoskeleton (By similarity). Largely associated with int ...	actin cytoskeleton [IDA] Golgi apparatus [IDA] lysosome [IDA] microtubule associated complex [IDA] smooth endoplasmic reticulum [IDA]			117
Q8MK68 UniProt NPD GO	GBRAP_RABIT	Gamma-aminobutyric acid receptor-associated protein (GABA(A) receptor-associated protein)	0.32	-	nuc	0	Intracytoplasmic membrane (By similarity). Cytoskeleton (By similarity). Largely associated with int ...				117
P60517 UniProt NPD GO	GBRAP_RAT	Gamma-aminobutyric acid receptor-associated protein (GABA(A) receptor-associated protein)	0.32	-	nuc	0	Intracytoplasmic membrane. Cytoskeleton. Largely associated with intracellular membrane structures i ...			1KJT	117
O95166 UniProt NPD GO	GBRAP_HUMAN	Gamma-aminobutyric acid receptor-associated protein (GABA(A) receptor-associated protein) (MM46)	0.32	-	nuc	0	Intracytoplasmic membrane (By similarity). Cytoskeleton (By similarity). Largely associated with int ...	plasma membrane [TAS]	605125	1KOT	117
Q9Z0U4 UniProt NPD GO	GABR1_RAT	Gamma-aminobutyric acid type B receptor, subunit 1 precursor (GABA-B receptor 1) (GABA-B-R1) (Gb1)	0.32	-	end	7	Cell membrane; multi-pass membrane protein. Moreover coexpression of GABA-B-R1 and GABA-B-R2 appears ...			1SS2	991
P18506 UniProt NPD GO	GBRD_RAT	Gamma-aminobutyric-acid receptor subunit delta precursor (GABA(A) receptor)	0.32	-	nuc	4	Membrane; multi-pass membrane protein				449
P29415 UniProt NPD GO	CX56_CHICK	Gap junction Cx56 protein (Connexin-56)	0.32	-	end	3 *	Membrane; multi-pass membrane protein				510
Q8JFY4 UniProt NPD GO	GHRL_ANGJA	Ghrelin precursor (Ghrelin-21)	0.32	-	gol	1 *	Secreted protein	extracellular space [IC]			111
Q9LK23 UniProt NPD GO	G6PD5_ARATH	Glucose-6-phosphate 1-dehydrogenase, cytoplasmic isoform 1 (EC 1.1.1.49) (G6PD5) (G6PDH5)	0.32	-	nuc	0	Cytoplasm				516
P26591 UniProt NPD GO	GLRK_LYMST	Glutamate receptor precursor	0.32	-	end	3	Membrane; multi-pass membrane protein				917
Q60934 UniProt NPD GO	GRIK1_MOUSE	Glutamate receptor, ionotropic kainate 1 precursor (Glutamate receptor 5) (GluR-5) (GluR5)	0.32	-	end	3	Membrane; multi-pass membrane protein	ionotropic glutamate receptor complex [IC]			836
Q8X0X0 UniProt NPD GO	GSH1_NEUCR	Glutamate--cysteine ligase (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamma-ECS) (GCS)	0.32	-	nuc	0					728
P38795 UniProt NPD GO	NADE_YEAST	Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) (NAD(+) synthase [glutamine-hydrolyzing])	0.32	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			714
Q16769 UniProt NPD GO	QPCT_HUMAN	Glutaminyl-peptide cyclotransferase precursor (EC 2.3.2.5) (QC) (Glutaminyl-tRNA cyclotransferase) ( ...	0.32	-	exc	0			607065	2AFZ	361
P10649 UniProt NPD GO	GSTM1_MOUSE	Glutathione S-transferase Mu 1 (EC 2.5.1.18) (GST class-mu 1) (Glutathione S-transferase GT8.7) (pmG ...	0.32	-	cyt	0	Cytoplasm				217
Q2PQH8 UniProt NPD GO	GDE_CANFA	Glycogen debranching enzyme (Glycogen debrancher) [Includes: 4-alpha-glucanotransferase (EC 2.4.1.25 ...	0.32	-	cyt	0					1533
P20736 UniProt NPD GO	BM86_BOOMI	Glycoprotein antigen BM86 precursor (Protective antigen)	0.32	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (Probable)				650
Q5RBL1 UniProt NPD GO	SYG_PONPY	Glycyl-tRNA synthetase (EC 6.1.1.14) (Glycine--tRNA ligase) (GlyRS)	0.32	-	mit	0					739
P22468 UniProt NPD GO	GDL_DROME	Gonadal protein gdl	0.32	-	cyt	0					194
Q95JF2 UniProt NPD GO	GHR_AILME	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.32	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				638
P10912 UniProt NPD GO	GHR_HUMAN	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.32	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...	integral to plasma membrane [TAS]	262500	3HHR	638
Q8HY52 UniProt NPD GO	GDF8_LEPCA	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.32	+	cyt	0	Secreted protein (By similarity)				375
O88396 UniProt NPD GO	GRPE2_MOUSE	GrpE protein homolog 2, mitochondrial precursor (Mt-GrpE#2)	0.32	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA]			224
O13055 UniProt NPD GO	GNAI2_ORYLA	Guanine nucleotide-binding protein G(i) subunit alpha-2 (Adenylate cyclase-inhibiting G alpha protei ...	0.32	-	cyt	0					354
P08754 UniProt NPD GO	GNAI3_HUMAN	Guanine nucleotide-binding protein G(k) subunit alpha (G(i) alpha-3)	0.32	-	cyt	0			139370		353
P08753 UniProt NPD GO	GNAI3_RAT	Guanine nucleotide-binding protein G(k) subunit alpha (G(i) alpha-3)	0.32	-	cyt	0		Golgi membrane [TAS] zymogen granule [IDA]			353
P49082 UniProt NPD GO	GPA1_LOTJA	Guanine nucleotide-binding protein alpha-1 subunit (GP-alpha-1)	0.32	-	nuc	0					384
O04278 UniProt NPD GO	GPA1_PEA	Guanine nucleotide-binding protein alpha-1 subunit (GP-alpha-1)	0.32	-	mit	0					384
Q01369 UniProt NPD GO	GBLP_NEUCR	Guanine nucleotide-binding protein subunit beta-like protein (Cross-pathway control WD-repeat protei ...	0.32	-	cyt	0					316
P01897 UniProt NPD GO	HA1L_MOUSE	H-2 class I histocompatibility antigen, L-D alpha chain precursor	0.32	-	end	1	Membrane; single-pass type I membrane protein			1LDP	362
P04441 UniProt NPD GO	HG2A_MOUSE	H-2 class II histocompatibility antigen gamma chain (MHC class II-associated invariant chain) (Ia an ...	0.32	-	nuc	1 *	Membrane; single-pass type II membrane protein (Potential)	endoplasmic reticulum [IDA] external side of plasma membrane [IDA] Golgi apparatus [IDA] integral to plasma membrane [TAS] lysosome [IDA] multivesicular body [IDA] plasma membrane [IDA]			279
Q94F08 UniProt NPD GO	HIPL2_ARATH	HIPL2 protein precursor	0.32	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				696
P30685 UniProt NPD GO	1B35_HUMAN	HLA class I histocompatibility antigen, B-35 alpha chain precursor (MHC class I antigen B*35)	0.32	-	end	1 *	Membrane; single-pass type I membrane protein		142830	2AXG	362
Q95365 UniProt NPD GO	1B38_HUMAN	HLA class I histocompatibility antigen, B-38 alpha chain precursor (MHC class I antigen B*38) (Bw-4) ...	0.32	-	end	1	Membrane; single-pass type I membrane protein		142830		362
P30490 UniProt NPD GO	1B52_HUMAN	HLA class I histocompatibility antigen, B-52 alpha chain precursor (MHC class I antigen B*52) (Bw-52 ...	0.32	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
P30491 UniProt NPD GO	1B53_HUMAN	HLA class I histocompatibility antigen, B-53 alpha chain precursor (MHC class I antigen B*53) (Bw-53 ...	0.32	-	end	1 *	Membrane; single-pass type I membrane protein		142830	1A1O	362
P30492 UniProt NPD GO	1B54_HUMAN	HLA class I histocompatibility antigen, B-54 alpha chain precursor (MHC class I antigen B*54) (Bw-54 ...	0.32	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
P30498 UniProt NPD GO	1B78_HUMAN	HLA class I histocompatibility antigen, B-78 alpha chain precursor (MHC class I antigen B*78)	0.32	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
Q31610 UniProt NPD GO	1B81_HUMAN	HLA class I histocompatibility antigen, B-81 alpha chain precursor (MHC class I antigen B*81) (B'DT) ...	0.32	-	end	1	Membrane; single-pass type I membrane protein		142830		362
Q95604 UniProt NPD GO	1C17_HUMAN	HLA class I histocompatibility antigen, Cw-17 alpha chain precursor (MHC class I antigen Cw*17)	0.32	-	end	1 *	Membrane; single-pass type I membrane protein		142840		372
P17693 UniProt NPD GO	HLAG_HUMAN	HLA class I histocompatibility antigen, alpha chain G precursor (HLA G antigen)	0.32	-	end	1	Membrane; single-pass type I membrane protein		142871	2D31	338
Q95IT1 UniProt NPD GO	HLAG_PANTR	HLA class I histocompatibility antigen, alpha chain G precursor (HLA G antigen)	0.32	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				338
Q07439 UniProt NPD GO	HSP71_RAT	Heat shock 70 kDa protein 1A/1B (Heat shock 70 kDa protein 1/2) (HSP70.1/2)	0.32	-	cyt	0					641
P55063 UniProt NPD GO	HS70L_RAT	Heat shock 70 kDa protein 1L (Heat shock 70 kDa protein 1-like) (Heat shock 70 kDa protein 3) (HSP70 ...	0.32	-	cyt	0					641
P11147 UniProt NPD GO	HSP7D_DROME	Heat shock 70 kDa protein cognate 4 (Heat shock 70 kDa protein 88E)	0.32	-	cyt	0	Cytoplasm; perinuclear region. Localized to a meshwork of cytoplasmic fibers around the nucleus. Nuc ...				651
P53623 UniProt NPD GO	HSP72_PICAN	Heat shock protein 70 2	0.32	-	cyt	0	Cytoplasm (By similarity)				642
P33125 UniProt NPD GO	HSP82_AJECA	Heat shock protein 82	0.32	-	cyt	0					679
Q61W58 UniProt NPD GO	HSP90_CAEBR	Heat shock protein 90 (Abnormal dauer formation protein 21)	0.32	-	cyt	0	Cytoplasm; perinuclear region. Perinuclear region of somatic cells (By similarity)				706
P54652 UniProt NPD GO	HSP72_HUMAN	Heat shock-related 70 kDa protein 2 (Heat shock 70 kDa protein 2)	0.32	-	cyt	0		cell surface [IEP]	140560		639

You are viewing entries 38501 to 38550 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.