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
P32022 UniProt NPD GO	GIL1_ENTHI	Galactose-inhibitable lectin 170 kDa subunit	0.35	-	nuc	1					1276
P02527 UniProt NPD GO	CRGA_BOVIN	Gamma crystallin A (Gamma crystallin IVB)	0.35	-	cyt	0					174
P55940 UniProt NPD GO	CRG3_XENLA	Gamma crystallin-3 (Gamma crystallin III) (Gamma-3-CRY)	0.35	-	nuc	0					175
P55941 UniProt NPD GO	CRG4_XENLA	Gamma crystallin-4 (Gamma crystallin IV) (Gamma-4-CRY) (Fragment)	0.35	-	nuc	0					172
P20230 UniProt NPD GO	THG_HORVU	Gamma hordothionin	0.35	-	nuc	0				1GPT	47
P60518 UniProt NPD GO	GBRL1_CAVPO	Gamma-aminobutyric acid receptor-associated protein-like 1 (GABA(A) receptor-associated protein-like ...	0.35	-	nuc	0					117
Q8R3R8 UniProt NPD GO	GBRL1_MOUSE	Gamma-aminobutyric acid receptor-associated protein-like 1 (GABA(A) receptor-associated protein-like ...	0.35	-	nuc	0					117
Q9H0R8 UniProt NPD GO	GBRL1_HUMAN	Gamma-aminobutyric acid receptor-associated protein-like 1 (GABA(A) receptor-associated protein-like ...	0.35	-	nuc	0		autophagic vacuole [IDA] plasma membrane [ISS]	607420		117
P08079 UniProt NPD GO	GDB0_WHEAT	Gamma-gliadin precursor (Fragment)	0.35	-	nuc	0					251
O57474 UniProt NPD GO	CXA1_BRARE	Gap junction alpha-1 protein (Connexin-43) (Cx43) (Short fin protein)	0.35	-	end	4 *	Membrane; multi-pass membrane protein				380
P48757 UniProt NPD GO	GAST_MOUSE	Gastrin precursor [Contains: Gastrin 71 (G71); Big gastrin (Gastrin 34) (G34); Gastrin]	0.35	-	exc	0	Secreted protein				101
P18736 UniProt NPD GO	ZG71_XENLA	Gastrula zinc finger protein XLCGF71.1 (Fragment)	0.35	-	nuc	0	Nucleus (Potential)				140
P38413 UniProt NPD GO	GIAG_GIALA	Giardin subunit gamma	0.35	-	nuc	0	Microribbons of ventral disc				311
P46690 UniProt NPD GO	GASA4_ARATH	Gibberellin-regulated protein 4 precursor	0.35	-	nuc	1 *	Secreted protein				106
P62903 UniProt NPD GO	COW_CONMR	Glacontryphan-M precursor	0.35	-	cyt	0	Secreted protein				63
Q8BMF8 UniProt NPD GO	GLDN_MOUSE	Gliomedin (Cancer-related gene liver 2 protein) (CRG-L2)	0.35	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Localizes to the nodes of Ranvier (By similarit ...				549
Q20117 UniProt NPD GO	GSH1_CAEEL	Glutamate--cysteine ligase (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamma-ECS) (GCS)	0.35	-	nuc	0					654
P04905 UniProt NPD GO	GSTM1_RAT	Glutathione S-transferase Mu 1 (EC 2.5.1.18) (GSTM1-1) (Glutathione S-transferase Yb-1) (GST Yb1) (G ...	0.35	-	cyt	0	Cytoplasm	extracellular region [IDA]		6GSY	217
O49954 UniProt NPD GO	GCSP_SOLTU	Glycine dehydrogenase [decarboxylating], mitochondrial precursor (EC 1.4.4.2) (Glycine decarboxylase ...	0.35	-	mit	0	Mitochondrion				1035
Q5MIB6 UniProt NPD GO	PYGB_SHEEP	Glycogen phosphorylase, brain form (EC 2.4.1.1)	0.35	-	nuc	0					842
P47011 UniProt NPD GO	GLG2_YEAST	Glycogen synthesis initiator protein GLG2	0.35	-	cyt	0		cytoplasm [IDA]			380
Q9R062 UniProt NPD GO	GLYG_MOUSE	Glycogenin-1 (EC 2.4.1.186)	0.35	-	cyt	0					332
O08730 UniProt NPD GO	GLYG_RAT	Glycogenin-1 (EC 2.4.1.186)	0.35	-	cyt	0					332
P41250 UniProt NPD GO	SYG_HUMAN	Glycyl-tRNA synthetase (EC 6.1.1.14) (Glycine--tRNA ligase) (GlyRS)	0.35	-	mit	0		cytoplasm [TAS] soluble fraction [TAS]	601472		739
P30969 UniProt NPD GO	GNRHR_RAT	Gonadotropin-releasing hormone receptor (GnRH receptor) (GnRH-R)	0.35	-	nuc	7 *	Membrane; multi-pass membrane protein				327
O88273 UniProt NPD GO	GREM2_MOUSE	Gremlin-2 precursor (Cysteine knot superfamily 1, BMP antagonist 2) (Protein related to DAN and cerb ...	0.35	-	nuc	0	Secreted protein (Probable)				168
P19756 UniProt NPD GO	GHR_PIG	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.35	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				638
P16310 UniProt NPD GO	GHR_RAT	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.35	-	end	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...	cytoplasm [IDA] nucleus [IDA]			638
P54826 UniProt NPD GO	GAS1_HUMAN	Growth-arrest-specific protein 1 precursor (GAS-1)	0.35	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	anchored to plasma membrane [ISS]	139185		345
Q5USW1 UniProt NPD GO	GDF8_BOSGA	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.35	+	cyt	0	Secreted protein (By similarity)				375
Q5RZV4 UniProt NPD GO	GDF8_BOSIN	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.35	+	cyt	0	Secreted protein (By similarity)				375
O18836 UniProt NPD GO	GDF8_BOVIN	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.35	+	cyt	0	Secreted protein				375
Q6X5V1 UniProt NPD GO	GDF8_BUBBU	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.35	+	cyt	0	Secreted protein (By similarity)				375
P27044 UniProt NPD GO	GNAI1_XENLA	Guanine nucleotide-binding protein G(i), alpha-1 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.35	-	cyt	0					353
P08752 UniProt NPD GO	GNAI2_MOUSE	Guanine nucleotide-binding protein G(i), alpha-2 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.35	-	gol	0					354
P04897 UniProt NPD GO	GNAI2_RAT	Guanine nucleotide-binding protein G(i), alpha-2 subunit (Adenylate cyclase-inhibiting G alpha prote ...	0.35	-	gol	0					354
Q40224 UniProt NPD GO	GPA1_LUPLU	Guanine nucleotide-binding protein alpha-1 subunit (GP-alpha-1)	0.35	-	nuc	0					384
Q01821 UniProt NPD GO	GBG_LOLFO	Guanine nucleotide-binding protein subunit gamma precursor	0.35	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				87
P61566 UniProt NPD GO	ENK11_HUMAN	HERV-K_22q11.21 provirus ancestral Env polyprotein (Envelope polyprotein) (HERV-K101 envelope protei ...	0.35	-	end	2					588
P05534 UniProt NPD GO	1A24_HUMAN	HLA class I histocompatibility antigen, A-24 alpha chain precursor (MHC class I antigen A*24) (Aw-24 ...	0.35	-	end	1	Membrane; single-pass type I membrane protein		142800	2BCK	365
P30466 UniProt NPD GO	1B18_HUMAN	HLA class I histocompatibility antigen, B-18 alpha chain precursor (MHC class I antigen B*18)	0.35	-	end	1	Membrane; single-pass type I membrane protein		142830		362
P18463 UniProt NPD GO	1B37_HUMAN	HLA class I histocompatibility antigen, B-37 alpha chain precursor (MHC class I antigen B*37)	0.35	-	end	1	Membrane; single-pass type I membrane protein		142830		362
Q04826 UniProt NPD GO	1B40_HUMAN	HLA class I histocompatibility antigen, B-40 alpha chain precursor (MHC class I antigen B*40) (Bw-60 ...	0.35	-	end	1	Membrane; single-pass type I membrane protein		142830		362
P30493 UniProt NPD GO	1B55_HUMAN	HLA class I histocompatibility antigen, B-55 alpha chain precursor (MHC class I antigen B*55) (Bw-55 ...	0.35	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
P30499 UniProt NPD GO	1C01_HUMAN	HLA class I histocompatibility antigen, Cw-1 alpha chain precursor (MHC class I antigen Cw*1)	0.35	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142840		366
P11144 UniProt NPD GO	HSP70_PLAFA	Heat shock 70 kDa protein (HSP70) (Cytoplasmic antigen) (74.3 kDa protein)	0.35	-	cyt	0					681
Q28222 UniProt NPD GO	HSP71_CERAE	Heat shock 70 kDa protein 1	0.35	-	cyt	0					638
Q04967 UniProt NPD GO	HSP76_PIG	Heat shock 70 kDa protein 6 (Heat shock 70 kDa protein B')	0.35	-	cyt	0					643
P29843 UniProt NPD GO	HSP7A_DROME	Heat shock 70 kDa protein cognate 1 (Heat shock 70 kDa protein 70C)	0.35	-	cyt	0					641
P34696 UniProt NPD GO	HSP11_CAEEL	Heat shock protein Hsp16-1	0.35	-	nuc	0					145

You are viewing entries 35851 to 35900 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.