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
P06028 UniProt NPD GO	GLPB_HUMAN	Glycophorin B precursor (PAS-3) (Sialoglycoprotein delta) (SS-active sialoglycoprotein) (CD235b anti ...	0.00	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	111740		91
P15421 UniProt NPD GO	GLPE_HUMAN	Glycophorin E precursor	0.00	-	exc	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	138590		78
Q86YW7 UniProt NPD GO	GPHB5_HUMAN	Glycoprotein hormone beta-5 precursor (Thyrostimulin subunit beta)	0.00	-	mit	1 *	Secreted protein		609652		130
Q812B2 UniProt NPD GO	GPHB5_MOUSE	Glycoprotein hormone beta-5 precursor (Thyrostimulin subunit beta)	0.00	-	mit	0	Secreted protein (By similarity)				130
Q9YGP3 UniProt NPD GO	GLHA_ICTPU	Glycoprotein hormones alpha chain precursor (Gonadotropin alpha chain) (GTH-alpha)	0.00	-	mit	0	Secreted protein				116
P41943 UniProt NPD GO	GPR1_YARLI	Glyoxylate pathway regulator	0.00	-	end	6	Membrane; multi-pass membrane protein				270
Q9U5V6 UniProt NPD GO	GDLO_DROME	Gonadal protein gdl-ORF39	0.00	-	exc	0					39
P37205 UniProt NPD GO	GTHB1_THUOB	Gonadotropin beta-1 subunit (Gonadotropin beta-I chain) (GTH-I-beta)	0.00	-	nuc	0	Secreted protein				102
P30971 UniProt NPD GO	GTHB1_FUNHE	Gonadotropin beta-1 subunit precursor (Gonadotropin beta-I chain) (GTH-I-beta)	0.00	-	mit	0	Secreted protein				114
Q9PW99 UniProt NPD GO	GTHB1_TRITC	Gonadotropin beta-1 subunit precursor (Gonadotropin beta-I chain) (GTH-I-beta)	0.00	-	cyt	0	Secreted protein				118
Q8SPZ1 UniProt NPD GO	GNRHR_MACMU	Gonadotropin-releasing hormone receptor (GnRH receptor) (GnRH-R) (Fragment)	0.00	-	cyt	2 *	Membrane; multi-pass membrane protein				59
P69841 UniProt NPD GO	GRAE_GRASX	Grammistin Gs E	0.00	-		0	Secreted protein				13
P69843 UniProt NPD GO	GRA2A_POGPU	Grammistin Pp 2a	0.00	-		0	Secreted protein				13
P69844 UniProt NPD GO	GRA2B_POGPU	Grammistin Pp 2b	0.00	-		0	Secreted protein				13
P69847 UniProt NPD GO	GRA3_POGPU	Grammistin Pp 3	0.00	-	end	1 *	Secreted protein				25
O35478 UniProt NPD GO	OPSG_SCICA	Green-sensitive opsin (Green cone photoreceptor pigment) (Medium wavelength-sensitive cone opsin)	0.00	-	end	7	Membrane; multi-pass membrane protein				364
P22330 UniProt NPD GO	OPSG1_ASTFA	Green-sensitive opsin-1 (Green cone photoreceptor pigment 1)	0.00	-	end	7	Membrane; multi-pass membrane protein				355
P51474 UniProt NPD GO	OPSG3_ASTFA	Green-sensitive opsin-3 (Green cone photoreceptor pigment 3)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
Q9BZM2 UniProt NPD GO	PA2GF_HUMAN	Group IIF secretory phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase GII ...	0.00	-	exc	0	Secreted protein	extracellular region [NAS]			168
Q9QZT4 UniProt NPD GO	PA2GF_MOUSE	Group IIF secretory phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase GII ...	0.00	-	cyt	0	Secreted protein				168
Q61017 UniProt NPD GO	GBGT2_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-T2 subunit precursor (G gamma-C) (G-gamma-8) ...	0.00	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				69
P25387 UniProt NPD GO	GBLP_CHLRE	Guanine nucleotide-binding protein subunit beta-like protein	0.00	-	cyt	0					318
P09646 UniProt NPD GO	RNN1_NEUCR	Guanyl-specific ribonuclease N1 precursor (EC 3.1.27.3) (RNase N1)	0.00	-	exc	0					153
P07446 UniProt NPD GO	RNPB_PENBR	Guanyl-specific ribonuclease Pb1 (EC 3.1.27.3) (RNase Pb1)	0.00	-	vac	0					102
P09647 UniProt NPD GO	RNPC_PENCH	Guanyl-specific ribonuclease Pc (EC 3.1.27.3) (RNase Pc)	0.00	-	cyt	0					102
P26875 UniProt NPD GO	RNT1_TRIHA	Guanyl-specific ribonuclease Th1 (EC 3.1.27.3) (RNase Th1)	0.00	-	cyt	0					106
P79880 UniProt NPD GO	GUC1A_CHICK	Guanylyl cyclase-activating protein 1 (GCAP 1) (Guanylate cyclase activator 1A)	0.00	-	cyt	0					198
P25810 UniProt NPD GO	GUR_GYMSY	Gurmarin (Sweet taste-suppressing peptide)	0.00	-	cyt	0				1GUR	35
P84200 UniProt NPD GO	GYMN_GYMCH	Gymnin (Fragment)	0.00	-		0					10
P23150 UniProt NPD GO	HA2J_MOUSE	H-2 class II histocompatibility antigen, I-E alpha chain precursor (Fragment)	0.00	-	end	1	Membrane; single-pass type I membrane protein (Potential)	external side of plasma membrane [IDA] lysosome [IDA] MHC class II protein complex [IDA] plasma membrane [IDA]			254
Q6XIP0 UniProt NPD GO	NOLA2_DROYA	H/ACA ribonucleoprotein complex subunit 2-like protein	0.00	+	cyt	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			160
Q6PBV6 UniProt NPD GO	NOLA2_BRARE	H/ACA ribonucleoprotein complex subunit 2-like protein (Nucleolar protein family A member 2-like pro ...	0.00	-	nuc	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			150
Q9V3U2 UniProt NPD GO	NOLA2_DROME	H/ACA ribonucleoprotein complex subunit 2-like protein (Nucleolar protein family A member 2-like pro ...	0.00	+	cyt	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			160
Q9JLR9 UniProt NPD GO	HIG1A_MOUSE	HIG1 domain family member 1A (Hypoxia-inducible gene 1 protein)	0.00	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				95
P01906 UniProt NPD GO	HA26_HUMAN	HLA class II histocompatibility antigen, DQ(6) alpha chain precursor (DX alpha chain) (HLA-DQA1)	0.00	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [NAS]			255
Q9SYX7 UniProt NPD GO	HA22B_ARATH	HVA22-like protein b (AtHVA22b)	0.00	-	mit	0	Membrane; multi-pass membrane protein (Potential)				167
P83591 UniProt NPD GO	TXHA1_SELHA	Hainantoxin-1 (Hainantoxin-I) (HnTx-I)	0.00	-	nuc	0	Secreted protein	extracellular region [NAS]		1X5V	33
P19006 UniProt NPD GO	HPT_CANFA	Haptoglobin [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.00	-	nuc	0	Secreted protein; extracellular space				329
P00738 UniProt NPD GO	HPT_HUMAN	Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.00	-	exc	0	Secreted protein	extracellular region [NAS]	140100		406
O35086 UniProt NPD GO	HPT_MESAU	Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.00	-	vac	0	Secreted protein (By similarity)				346
Q61646 UniProt NPD GO	HPT_MOUSE	Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.00	-	end	0	Secreted protein (By similarity)				347
Q5VAN1 UniProt NPD GO	HPT_PAPHA	Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.00	-	cyt	0	Secreted protein (By similarity)				347
Q8SPS7 UniProt NPD GO	HPT_PIG	Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.00	-	exc	0	Secreted protein (By similarity)				347
Q5R5F6 UniProt NPD GO	HPT_PONPY	Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.00	-	exc	0	Secreted protein (By similarity)				347
P06866 UniProt NPD GO	HPT_RAT	Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.00	-	end	0	Secreted protein				347
P00739 UniProt NPD GO	HPTR_HUMAN	Haptoglobin-related protein precursor	0.00	-	mit	0	Secreted protein (Potential)		140210		348
Q28801 UniProt NPD GO	HPTR_PANTR	Haptoglobin-related protein precursor (Fragment)	0.00	-	mit	0	Secreted protein (Potential)				346
Q05945 UniProt NPD GO	HSP70_HYDOL	Heat shock 70 kDa protein (Fragment)	0.00	-	nuc	0					111
P83581 UniProt NPD GO	HS74L_RAT	Heat shock 70 kDa protein 4L (Osmotic stress protein 94) (Heat shock 70-related protein APG-1) (Frag ...	0.00	-	cyt	0	Cytoplasm. Nucleus. May translocate to the nucleus of germ cells after heat shock	cytoplasm [IDA] nucleus [IDA]			24
P22979 UniProt NPD GO	HSP6C_DROME	Heat shock protein 67B3 (Heat shock 18 kDa protein)	0.00	-	cyt	0					169

You are viewing entries 94901 to 94950 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.