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
Q99928 UniProt NPD GO	GBRG3_HUMAN	Gamma-aminobutyric-acid receptor gamma-3 subunit precursor (GABA(A) receptor)	0.45	-	end	4	Membrane; multi-pass membrane protein	integral to membrane [NAS]	600233		467
P04729 UniProt NPD GO	GDB1_WHEAT	Gamma-gliadin B-I precursor	0.45	-	exc	0					304
P18730 UniProt NPD GO	ZG58_XENLA	Gastrula zinc finger protein XLCGF58.1 (Fragment)	0.45	-	nuc	0	Nucleus (Potential)				420
Q21770 UniProt NPD GO	GCC7_CAEEL	Germ cell expressed protein R06C7.1	0.45	-	cyt	0					945
Q91754 UniProt NPD GO	GCKR_XENLA	Glucokinase regulatory protein (Glucokinase regulator)	0.45	-	mit	0					619
P32477 UniProt NPD GO	GSH1_YEAST	Glutamate--cysteine ligase (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamma-ECS) (GCS)	0.45	-	nuc	0		intracellular [TAS]			678
Q9CYK2 UniProt NPD GO	QPCT_MOUSE	Glutaminyl-peptide cyclotransferase precursor (EC 2.3.2.5) (QC) (Glutaminyl-tRNA cyclotransferase) ( ...	0.45	-	mit	0					362
P30116 UniProt NPD GO	GSTMU_MESAU	Glutathione S-transferase (EC 2.5.1.18) (GST class-mu)	0.45	-	cyt	0	Cytoplasm				217
P10386 UniProt NPD GO	GLTB_WHEAT	Glutenin, low molecular weight subunit 1D1 precursor	0.45	-	exc	0					307
P32784 UniProt NPD GO	GPT1_YEAST	Glycerol-3-phosphate O-acyltransferase 1 (EC 2.3.1.15) (G-3-P acyltransferase 1) (Dihydroxyacetone p ...	0.45	-	end	4	Membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum [IDA]			759
P36143 UniProt NPD GO	GLG1_YEAST	Glycogen synthesis initiator protein GLG1	0.45	-	nuc	0					480
O15488 UniProt NPD GO	GLYG2_HUMAN	Glycogenin-2 (EC 2.4.1.186) (GN-2) (GN2)	0.45	-	nuc	0		soluble fraction [TAS]	300198		501
Q66PG3 UniProt NPD GO	LARGE_CHICK	Glycosyltransferase-like protein LARGE1 (EC 2.4.-.-) (Acetylglucosaminyltransferase-like 1A)	0.45	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				756
O95461 UniProt NPD GO	LARGE_HUMAN	Glycosyltransferase-like protein LARGE1 (EC 2.4.-.-) (Acetylglucosaminyltransferase-like 1A)	0.45	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	integral to Golgi membrane [TAS]	608840		756
Q32NJ7 UniProt NPD GO	LRG2B_XENLA	Glycosyltransferase-like protein LARGE2-B (EC 2.4.-.-) (Glycosyltransferase-like 1B-B)	0.45	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				723
P40056 UniProt NPD GO	GET2_YEAST	Golgi to ER traffic protein 2 (Meiotic nuclear division protein 7) (Hydroxyurea resistance protein 2 ...	0.45	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [IDA] GET complex [IMP]			285
Q8UWD8 UniProt NPD GO	GDF8_COLLI	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.45	+	nuc	0	Secreted protein (By similarity)				375
P24799 UniProt NPD GO	GNAS_XENLA	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.45	-	mit	0					379
P34045 UniProt NPD GO	GPA7_DICDI	Guanine nucleotide-binding protein alpha-7 subunit (G alpha-7)	0.45	-	mit	0					390
P62690 UniProt NPD GO	GAK18_HUMAN	HERV-K_22q11.23 provirus ancestral Gag polyprotein (Gag polyprotein) [Contains: Matrix protein; Caps ...	0.45	-	nuc	0	Cell membrane. Cytoplasmic membrane (in a transfection system) (By similarity)				622
P04120 UniProt NPD GO	HS30A_XENLA	Heat shock protein 30A	0.45	-	nuc	0					89
O61998 UniProt NPD GO	HSP90_BRUPA	Heat shock protein 90	0.45	-	cyt	0					717
Q64314 UniProt NPD GO	CD34_MOUSE	Hematopoietic progenitor cell antigen CD34 precursor	0.45	-	nuc	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			382
Q05877 UniProt NPD GO	HHCM_HUMAN	Hepatocellular carcinoma protein HHCM (HHC(M))	0.45	-	nuc	0					467
Q22037 UniProt NPD GO	ROA1_CAEEL	Heterogeneous nuclear ribonucleoprotein A1	0.45	-	cyt	0	Nucleus. Binds to telomeres				346
P36194 UniProt NPD GO	HMGB1_CHICK	High mobility group protein B1 (High mobility group protein 1) (HMG-1)	0.45	+	nuc	0	Nucleus				200
O08593 UniProt NPD GO	PDE7A_RAT	High-affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A (EC 3.1.4.17) (Rolipram-insensitive ph ...	0.45	-	nuc	0					426
P02287 UniProt NPD GO	H2BE1_PSAMI	Histone H2B.1, embryonic	0.45	-	nuc	0	Nucleus				122
P13283 UniProt NPD GO	H2BS3_ECHES	Histone H2B.3, sperm (Fragment)	0.45	-	mit	0	Nucleus				40
P68430 UniProt NPD GO	H3_ONOVI	Histone H3	0.45	-	nuc	0	Nucleus (By similarity)				135
P68427 UniProt NPD GO	H3_PEA	Histone H3	0.45	-	nuc	0	Nucleus				135
P08437 UniProt NPD GO	H3_VOLCA	Histone H3	0.45	-	nuc	0	Nucleus (By similarity)				134
P68428 UniProt NPD GO	H3_WHEAT	Histone H3	0.45	-	nuc	0	Nucleus				135
P68432 UniProt NPD GO	H31_BOVIN	Histone H3.1	0.45	-	nuc	0	Nucleus				135
P68433 UniProt NPD GO	H31_MOUSE	Histone H3.1	0.45	-	nuc	0	Nucleus			1U35	135
P68431 UniProt NPD GO	H31_HUMAN	Histone H3.1 (H3/a) (H3/b) (H3/c) (H3/d) (H3/f) (H3/h) (H3/i) (H3/j) (H3/k) (H3/l)	0.45	-	nuc	0	Nucleus		142780	2CV5	135
P68429 UniProt NPD GO	H31_MEDSA	Histone H3.1 (Major histone H3)	0.45	-	nuc	0	Nucleus				135
Q5M939 UniProt NPD GO	HAT1_RAT	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.45	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear in S-phase cells and cytoplasmic (By sim ...				419
Q4PBE6 UniProt NPD GO	HAT1_USTMA	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.45	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				448
Q9FJT8 UniProt NPD GO	HATB_ARATH	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48) (HAT B)	0.45	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				467
Q12214 UniProt NPD GO	HOS1_YEAST	Histone deacetylase HOS1	0.45	-	cyt	0		histone deacetylase complex [TAS]			470
Q9FNC7 UniProt NPD GO	SUVR2_ARATH	Histone-lysine N-methyltransferase SUVR2 (EC 2.1.1.43) (Suppressor of variegation 3-9-related protei ...	0.45	-	nuc	0	Nucleus (By similarity). Associates with euchromatic regions (By similarity)				717
Q9DED6 UniProt NPD GO	BAX1B_CHICK	Homeobox protein BarH-like 1b (Bar class homeoprotein Barx1b)	0.45	+	nuc	0	Nucleus (Potential)				247
P17138 UniProt NPD GO	HMA2_HELTR	Homeobox protein HTR-A2 (Fragment)	0.45	+	nuc	0	Nucleus (Potential)				60
Q01822 UniProt NPD GO	HXD1_MOUSE	Homeobox protein Hox-D1 (Hox-4.9)	0.45	+	nuc	0	Nucleus				327
P70217 UniProt NPD GO	HXD13_MOUSE	Homeobox protein Hox-D13 (Hox-4.8)	0.45	+	nuc	0	Nucleus	nucleus [IDA]			339
O42370 UniProt NPD GO	HXD3A_BRARE	Homeobox protein Hox-D3a (Hox-D3) (Fragment)	0.45	+	nuc	0	Nucleus				167
Q2VL77 UniProt NPD GO	MSX1_LEPED	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.45	+	nuc	0	Nucleus (By similarity)				297
Q99JP6 UniProt NPD GO	HOME3_MOUSE	Homer protein homolog 3 (Homer-3)	0.45	-	nuc	0	Cytoplasm (By similarity). Postsynaptic density of neuronal cells (By similarity)				356
Q9JJK5 UniProt NPD GO	HERPU_MOUSE	Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein	0.45	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [IDA] integral to membrane [IDA]			391

You are viewing entries 28301 to 28350 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.