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
Q58D62 UniProt NPD GO	FETUB_BOVIN	Fetuin-B precursor	0.56	-	exc	0	Secreted protein (Potential)				387
Q9QXC1 UniProt NPD GO	FETUB_MOUSE	Fetuin-B precursor (IRL685)	0.56	+	exc	0	Secreted protein (Potential)				388
P02671 UniProt NPD GO	FIBA_HUMAN	Fibrinogen alpha chain precursor [Contains: Fibrinopeptide A]	0.56	-	exc	0	Secreted protein	extracellular region [NAS] fibrinogen complex [TAS]	105200	1RF1	866
Q9R1K5 UniProt NPD GO	FZR_MOUSE	Fizzy-related protein homolog (Fzr) (Cdh1/Hct1 homolog)	0.56	-	nuc	0					493
P23915 UniProt NPD GO	FLO_ANTMA	Floricaula protein	0.56	-	cyt	0	Nucleus (Potential)				396
Q6VFT7 UniProt NPD GO	FOXL2_BOVIN	Forkhead box protein L2	0.56	-	nuc	0	Nucleus (Potential)				377
Q8MIP2 UniProt NPD GO	FOXL2_CAPHI	Forkhead box protein L2	0.56	-	nuc	0	Nucleus (Potential)				377
P58012 UniProt NPD GO	FOXL2_HUMAN	Forkhead box protein L2	0.56	-	nuc	0	Nucleus	nucleus [IDA]	608996		376
Q6VFT6 UniProt NPD GO	FOXL2_PIG	Forkhead box protein L2	0.56	-	nuc	0	Nucleus (Potential)				377
Q01543 UniProt NPD GO	FLI1_HUMAN	Friend leukemia integration 1 transcription factor (Fli-1 proto-oncogene) (ERGB transcription factor ...	0.56	-	nuc	0	Nucleus		133450	1X66	452
Q50DM6 UniProt NPD GO	GPR56_GORGO	G-protein coupled receptor 56 precursor	0.56	-	end	7 *	Membrane; multi-pass membrane protein				687
Q5U4C1 UniProt NPD GO	GASP1_MOUSE	G-protein coupled receptor-associated sorting protein 1 (GASP-1)	0.56	-	nuc	0	Cytoplasm (By similarity)				1347
O59825 UniProt NPD GO	TDG_SCHPO	G/U mismatch-specific uracil DNA glycosylase (EC 3.2.2.-) (Uracil mismatch repair protein)	0.56	+	nuc	0	Nucleus (Potential)				325
Q92616 UniProt NPD GO	GCN1L_HUMAN	GCN1-like protein 1 (HsGCN1)	0.56	-	end	0			605614		2670
Q99260 UniProt NPD GO	YPT6_YEAST	GTP-binding protein YPT6	0.56	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	Golgi apparatus [TAS]			215
P61315 UniProt NPD GO	G3ST3_MOUSE	Galactose-3-O-sulfotransferase 3 (EC 2.8.2.-) (Galbeta1-3GalNAc 3'-sulfotransferase) (Beta-galactose ...	0.56	-	nuc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)				431
Q9JJA9 UniProt NPD GO	GRASP_MOUSE	General receptor for phosphoinositides 1-associated scaffold protein (GRP1-associated scaffold prote ...	0.56	-	nuc	0	Cytoplasm. Cell membrane. Primarily localized to the plasma membrane but also distributed diffusely ...	plasma membrane [IDA]			392
P03995 UniProt NPD GO	GFAP_MOUSE	Glial fibrillary acidic protein, astrocyte (GFAP)	0.56	-	nuc	0	Cytoplasm (By similarity). Associated with intermediate filaments (By similarity)	intermediate filament [IDA]			430
P01275 UniProt NPD GO	GLUC_HUMAN	Glucagon precursor [Contains: Glicentin; Glicentin-related polypeptide (GRPP); Oxyntomodulin (OXY) ( ...	0.56	-	exc	0	Secreted protein	soluble fraction [TAS]	138030	1NAU	180
O42144 UniProt NPD GO	GLUC2_XENLA	Glucagon-2 precursor (Glucagon II) [Contains: Glucagon; Glucagon-like peptide 1A (GLP-1A); Glucagon- ...	0.56	-	exc	0	Secreted protein				219
Q39639 UniProt NPD GO	PLSB_CUCSA	Glycerol-3-phosphate acyltransferase, chloroplast precursor (EC 2.3.1.15) (GPAT)	0.56	-	mit	0	Plastid; chloroplast; chloroplast stroma				470
P32072 UniProt NPD GO	GBPH_PLAFB	Glycophorin-binding protein-related antigen	0.56	-	nuc	1 *					427
P33440 UniProt NPD GO	GAC_YEAST	Glyoxalase I activity-enhancing protein GAC	0.56	-	nuc	0					106
Q8SZ63 UniProt NPD GO	GOGA5_DROME	Golgin-84	0.56	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)	Golgi apparatus [ISS]			516
Q8TE85 UniProt NPD GO	GRHL3_HUMAN	Grainyhead-like protein 3 homolog (Sister of mammalian grainyhead) (Transcription factor CP2-like 4) ...	0.56	-	nuc	0	Nucleus		608317		626
Q28294 UniProt NPD GO	GNAQ_CANFA	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q)	0.56	-	cyt	0					353
P50148 UniProt NPD GO	GNAQ_HUMAN	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q)	0.56	-	cyt	0		cytoplasm [TAS] plasma membrane [TAS]	600998		353
Q2PKF4 UniProt NPD GO	GNAQ_PIG	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q)	0.56	-	cyt	0					353
O95837 UniProt NPD GO	GNA14_HUMAN	Guanine nucleotide-binding protein alpha-14 subunit (G-protein alpha subunit 14)	0.56	-	cyt	0		heterotrimeric G-protein complex [TAS] plasma membrane [TAS]	604397		355
P60508 UniProt NPD GO	EFR1_HUMAN	HERV-FRD_6p24.1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (HERV-FRD) (Sync ...	0.56	-	exc	2				1Y4M	538
Q96L62 UniProt NPD GO	ENH4_HUMAN	HERV-H_1q41 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Env protein HERV-Hc ...	0.56	-	mit	1 *					402
Q09160 UniProt NPD GO	1A80_HUMAN	HLA class I histocompatibility antigen, A-80 alpha chain precursor (MHC class I antigen A*80) (Aw-80 ...	0.56	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142800		365
P41809 UniProt NPD GO	HKR1_YEAST	Hansenula MRAKII killer toxin-resistant protein 1 precursor	0.56	-	end	1	Membrane; single-pass type I membrane protein (Probable)	plasma membrane [IDA]			1802
O57521 UniProt NPD GO	HS90B_BRARE	Heat shock protein HSP 90-beta	0.56	+	nuc	0	Cytoplasm				725
Q2QLC0 UniProt NPD GO	MET_CALMO	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.56	-	end	1	Membrane; single-pass type I membrane protein				1381
O42097 UniProt NPD GO	HNF3B_ORYLA	Hepatocyte nuclear factor 3-beta (HNF-3B) (Me-HNF3B) (Forkhead box protein A2)	0.56	+	nuc	0	Nucleus (By similarity)				415
P79926 UniProt NPD GO	HNF4B_XENLA	Hepatocyte nuclear factor 4-beta (HNF-4-beta)	0.56	-	nuc	0	Nucleus (By similarity)				446
P84586 UniProt NPD GO	HNRPG_RAT	Heterogeneous nuclear ribonucleoprotein G (hnRNP G) (RNA-binding motif protein, X chromosome)	0.56	-	nuc	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)				388
P38159 UniProt NPD GO	HNRPG_HUMAN	Heterogeneous nuclear ribonucleoprotein G (hnRNP G) (RNA-binding motif protein, X chromosome) (Glyco ...	0.56	-	nuc	0	Nucleus. Component of ribonucleosomes	heterogeneous nuclear ribonucleoprotein com... [NAS]	300199		391
P17095 UniProt NPD GO	HMGA1_MOUSE	High mobility group protein HMG-I/HMG-Y (HMG-I(Y)) (High mobility group AT-hook protein 1) (High mob ...	0.56	+	nuc	0	Nucleus				106
P07746 UniProt NPD GO	HMGT_ONCMY	High mobility group-T protein (HMG-T) (HMG-T1) (HMG-1)	0.56	-	nuc	0	Nucleus				204
Q07133 UniProt NPD GO	H1T_MOUSE	Histone H1t (Testicular H1 histone)	0.56	-	nuc	0	Nucleus				207
P78567 UniProt NPD GO	H2B_AGABI	Histone H2B	0.56	+	nuc	0	Nucleus				142
P02281 UniProt NPD GO	H2B11_XENLA	Histone H2B 1.1 (H2B1.1)	0.56	+	nuc	0	Nucleus			2F8N	125
P62808 UniProt NPD GO	H2B1_BOVIN	Histone H2B type 1	0.56	+	nuc	0	Nucleus	nucleosome [ISS]			125
Q5R893 UniProt NPD GO	H2B1_PONPY	Histone H2B type 1	0.56	+	nuc	0	Nucleus				125
Q6ZWY9 UniProt NPD GO	H2B1C_MOUSE	Histone H2B type 1-C/E/G	0.56	+	nuc	0	Nucleus	nucleosome [ISS]			125
Q93079 UniProt NPD GO	H2B1H_HUMAN	Histone H2B type 1-H (H2B.j) (H2B/j)	0.56	+	nuc	0	Nucleus	nucleosome [NAS]	602806		125
P35069 UniProt NPD GO	H2B3_TIGCA	Histone H2B.3	0.56	-	nuc	0	Nucleus				122
Q9C5P0 UniProt NPD GO	SUVH8_ARATH	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH8 (EC 2.1.1.43) (Histone H3-K9 methyltr ...	0.56	-	nuc	0	Nucleus (By similarity). Associates with centromeric constitutive heterochromatin (By similarity)				755

You are viewing entries 21351 to 21400 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.