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
Q91289 UniProt NPD GO	FINC_PLEWA	Fibronectin (FN) (Fragment)	0.47	-	nuc	0					1328
O35188 UniProt NPD GO	X3CL1_MOUSE	Fractalkine precursor (CX3CL1) (Neurotactin) (CX3C membrane-anchored chemokine) (Small inducible cyt ...	0.47	-	exc	1 *	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein. Also exists as ...				395
Q8WWM1 UniProt NPD GO	GAGD5_HUMAN	G antigen family D member 5 (Protein XAGE-5)	0.47	-	mit	0					108
Q50DM5 UniProt NPD GO	GPR56_PONPY	G-protein coupled receptor 56 precursor	0.47	-	end	7 *	Membrane; multi-pass membrane protein				687
Q8VDU0 UniProt NPD GO	GPSM2_MOUSE	G-protein signaling modulator 2 (Pins homolog)	0.47	-	nuc	0	Cytoplasm (By similarity). Cytoplasm; cell cortex (By similarity). Localizes in the cytoplasm in the ...				672
Q90459 UniProt NPD GO	CCND1_BRARE	G1/S-specific cyclin-D1	0.47	-	nuc	0					291
P43570 UniProt NPD GO	GYP8_YEAST	GTPase-activating protein GYP8	0.47	-	cyt	0		intracellular [IDA]			497
Q9D4F8 UniProt NPD GO	GCP4_MOUSE	Gamma-tubulin complex component 4 (GCP-4)	0.47	-	mit	0	Centrosome (By similarity)				667
Q9UGJ1 UniProt NPD GO	GCP4_HUMAN	Gamma-tubulin complex component 4 (GCP-4) (hGCP4) (h76p) (Hgrip76)	0.47	-	mit	0	Centrosome	centrosome [TAS] gamma-tubulin ring complex [NAS]	609610		667
P18715 UniProt NPD GO	ZG26_XENLA	Gastrula zinc finger protein XLCGF26.1 (Fragment)	0.47	-	nuc	0	Nucleus (Potential)				337
P18720 UniProt NPD GO	ZG42_XENLA	Gastrula zinc finger protein XLCGF42.1 (Fragment)	0.47	-	nuc	0	Nucleus (Potential)				168
P03069 UniProt NPD GO	GCN4_YEAST	General control protein GCN4 (Amino acid biosynthesis regulatory protein)	0.47	+	nuc	0	Nucleus	nucleus [IPI]		2ZTA	281
Q7Z6J2 UniProt NPD GO	GRASP_HUMAN	General receptor for phosphoinositides 1-associated scaffold protein (GRP1-associated scaffold prote ...	0.47	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Cell membrane; peripheral membrane protein; cytoplasm ...				395
Q39111 UniProt NPD GO	GAOX2_ARATH	Gibberellin 20 oxidase 2 (EC 1.14.11.-) (Gibberellin C-20 oxidase 2) (GA 20-oxidase 2)	0.47	-	nuc	0					378
P01273 UniProt NPD GO	GLUC_MESAU	Glucagon precursor [Contains: Glicentin; Glicentin-related polypeptide (GRPP); Oxyntomodulin (OXY) ( ...	0.47	-	exc	0	Secreted protein				180
Q12096 UniProt NPD GO	GNT1_YEAST	Glucose N-acetyltransferase 1 (EC 2.4.1.-) (N-acetylglucosaminyltransferase)	0.47	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential). Vacuole; vacuolar ...	Golgi medial cisterna [IDA]			491
P25569 UniProt NPD GO	GID7_YEAST	Glucose-induced degradation protein 7	0.47	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			759
Q62645 UniProt NPD GO	NMDE4_RAT	Glutamate [NMDA] receptor subunit epsilon 4 precursor (N-methyl D-aspartate receptor subtype 2D) (NR ...	0.47	-	end	4	Membrane; multi-pass membrane protein	ionotropic glutamate receptor complex [TAS]			1323
O22494 UniProt NPD GO	GSHB_LYCES	Glutathione synthetase, chloroplast precursor (EC 6.3.2.3) (Glutathione synthase) (GSH synthetase) ( ...	0.47	-	nuc	0	Plastid; chloroplast (Potential)				546
P10349 UniProt NPD GO	PLSB_CUCMO	Glycerol-3-phosphate acyltransferase, chloroplast precursor (EC 2.3.1.15) (GPAT)	0.47	-	cyt	0	Plastid; chloroplast; chloroplast stroma			1K30	396
Q9Z1M7 UniProt NPD GO	LARGE_MOUSE	Glycosyltransferase-like protein LARGE1 (EC 2.4.-.-) (Acetylglucosaminyltransferase-like 1A)	0.47	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to Golgi membrane [ISS]			756
P31717 UniProt NPD GO	NMT1_BOVIN	Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) (Peptide N-myristoyltransferase 1) (Myristo ...	0.47	+	nuc	0	Cytoplasm				497
Q9XSZ1 UniProt NPD GO	GHR_PAPAN	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.47	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				638
P41776 UniProt NPD GO	GNAI_HOMAM	Guanine nucleotide-binding protein G(i) subunit alpha (Adenylate cyclase-inhibiting G alpha protein) ...	0.47	-	gol	0					354
O76584 UniProt NPD GO	GPA11_CAEEL	Guanine nucleotide-binding protein alpha-11 subunit	0.47	-	mit	0					363
Q613V4 UniProt NPD GO	GPA12_CAEBR	Guanine nucleotide-binding protein alpha-12 subunit	0.47	-	nuc	0					355
Q19572 UniProt NPD GO	GPA12_CAEEL	Guanine nucleotide-binding protein alpha-12 subunit	0.47	-	nuc	0					355
Q93743 UniProt NPD GO	GPA6_CAEEL	Guanine nucleotide-binding protein alpha-6 subunit	0.47	-	cyt	0					364
P61549 UniProt NPD GO	ENH5_HUMAN	HERV-H_19p13.11 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Env protein RGH ...	0.47	-	nuc	0					369
Q9N2J8 UniProt NPD GO	ENH3_HUMAN	HERV-H_2q24.1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Env protein HERV- ...	0.47	-	mit	2 *					555
Q9N2K0 UniProt NPD GO	ENH1_HUMAN	HERV-H_2q24.3 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Env protein HERV- ...	0.47	-	mit	3 *					584
P01893 UniProt NPD GO	HLAH_HUMAN	HLA class I histocompatibility antigen, alpha chain H precursor (HLA-AR) (HLA-12.4)	0.47	-	end	1		integral to plasma membrane [NAS]	142800		362
P55737 UniProt NPD GO	HSP82_ARATH	Heat shock protein 81-2 (HSP81-2)	0.47	+	cyt	0	Cytoplasm (Potential)				699
Q02592 UniProt NPD GO	HMT1_SCHPO	Heavy metal tolerance protein precursor	0.47	-	end	10 *	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuolar membrane [IDA]			830
Q9H910 UniProt NPD GO	HN1L_HUMAN	Hematological and neurological expressed 1-like protein (HN1-like protein)	0.47	-	nuc	0	Cytoplasm. Nucleus				190
Q6VYH9 UniProt NPD GO	HSH2D_MOUSE	Hematopoietic SH2 domain-containing protein (Hematopoietic SH2 protein) (Adaptor in lymphocytes of u ...	0.47	-	nuc	0	Cytoplasm. Mitochondrion				334
P32394 UniProt NPD GO	HMOX1_PIG	Heme oxygenase 1 (EC 1.14.99.3) (HO-1)	0.47	-	nuc	1	Microsome				288
Q7LGA3 UniProt NPD GO	HS2ST_HUMAN	Heparan sulfate 2-O-sulfotransferase 1 (EC 2.8.2.-) (2-O-sulfotransferase) (2OST)	0.47	+	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)		604844		356
Q5R621 UniProt NPD GO	HS2ST_PONPY	Heparan sulfate 2-O-sulfotransferase 1 (EC 2.8.2.-) (2-O-sulfotransferase) (2OST)	0.47	+	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				356
P10103 UniProt NPD GO	HMGB1_BOVIN	High mobility group protein B1 (High mobility group protein 1) (HMG-1)	0.47	-	nuc	0	Nucleus	condensed chromosome [ISS]			214
Q6YKA4 UniProt NPD GO	HMGB1_CANFA	High mobility group protein B1 (High mobility group protein 1) (HMG-1)	0.47	-	nuc	0	Nucleus (By similarity)				214
P09429 UniProt NPD GO	HMGB1_HUMAN	High mobility group protein B1 (High mobility group protein 1) (HMG-1)	0.47	-	nuc	0	Nucleus	condensed chromosome [IDA] nucleus [TAS]	163905		214
Q4R844 UniProt NPD GO	HMGB1_MACFA	High mobility group protein B1 (High mobility group protein 1) (HMG-1)	0.47	-	nuc	0	Nucleus (By similarity)				214
P63158 UniProt NPD GO	HMGB1_MOUSE	High mobility group protein B1 (High mobility group protein 1) (HMG-1)	0.47	-	nuc	0	Nucleus. Cytoplasm. Associated with the plasma membrane of filipodia in process-growing cells, and a ...	extracellular space [IDA] nucleus [TAS]			214
P63159 UniProt NPD GO	HMGB1_RAT	High mobility group protein B1 (High mobility group protein 1) (HMG-1) (Amphoterin) (Heparin-binding ...	0.47	-	nuc	0	Nucleus. Cytoplasm. Associated with the plasma membrane of filipodia in process-growing cells, and a ...			1HMF	214
Q13946 UniProt NPD GO	PDE7A_HUMAN	High-affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A (EC 3.1.4.17) (HCP1) (TM22)	0.47	-	nuc	0	PDE7A1 (57 kDa) is located mostly to soluble cellular fractions. PDE7A2 (50 kDa) is located to parti ...	cell fraction [NAS]	171885	1ZKL	482
P70453 UniProt NPD GO	PDE7A_MOUSE	High-affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A (EC 3.1.4.17) (P2A)	0.47	-	mit	0					456
P31389 UniProt NPD GO	HRH1_CAVPO	Histamine H1 receptor	0.47	-	end	7 *	Membrane; multi-pass membrane protein				488
Q5EA83 UniProt NPD GO	DCHS_BOVIN	Histidine decarboxylase (EC 4.1.1.22) (HDC)	0.47	-	mit	0					658
P19113 UniProt NPD GO	DCHS_HUMAN	Histidine decarboxylase (EC 4.1.1.22) (HDC)	0.47	-	mit	0			142704		662

You are viewing entries 26951 to 27000 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.