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
Q5R7U4 UniProt NPD GO	GBG2_PONPY	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-2 subunit precursor	0.09	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				70
P63212 UniProt NPD GO	GBG2_BOVIN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-2 subunit precursor (G gamma-I)	0.09	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)			2BCJ	70
P59768 UniProt NPD GO	GBG2_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-2 subunit precursor (G gamma-I)	0.09	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		606981		70
P63213 UniProt NPD GO	GBG2_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-2 subunit precursor (G gamma-I)	0.09	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				70
P50150 UniProt NPD GO	GBG4_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-4 subunit precursor	0.09	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	plasma membrane [TAS]	604388		75
Q5R639 UniProt NPD GO	GBG4_PONPY	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-4 subunit precursor	0.09	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				75
P63078 UniProt NPD GO	GBG8_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-8 subunit precursor (Gamma-9)	0.09	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				70
P63077 UniProt NPD GO	GBG8_RAT	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-8 subunit precursor (Gamma-9)	0.09	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				70
P93339 UniProt NPD GO	GBB_NICPL	Guanine nucleotide-binding protein subunit beta (NpGPB1)	0.09	-	cyt	0	Cell membrane. Endoplasmic reticulum; endoplasmic reticulum membrane				377
O18640 UniProt NPD GO	GBLP_DROME	Guanine nucleotide-binding protein subunit beta-like protein (Receptor of activated protein kinase C ...	0.09	-	cyt	0					318
P70664 UniProt NPD GO	GUC2A_CAVPO	Guanylin precursor (Guanylate cyclase activator 2A)	0.09	-	mit	0	Secreted protein				107
P46065 UniProt NPD GO	GUC1A_BOVIN	Guanylyl cyclase-activating protein 1 (GCAP 1) (Guanylate cyclase activator 1A)	0.09	-	cyt	0	Membrane; lipid-anchor				204
O73761 UniProt NPD GO	GUC1A_RANPI	Guanylyl cyclase-activating protein 1 (GCAP 1) (Guanylate cyclase activator 1A)	0.09	-	cyt	0					204
P14426 UniProt NPD GO	HA13_MOUSE	H-2 class I histocompatibility antigen, D-K alpha chain precursor (H-2D(K))	0.09	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]			362
P01901 UniProt NPD GO	HA1B_MOUSE	H-2 class I histocompatibility antigen, K-B alpha chain precursor (H-2K(B))	0.09	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]		2VAB	369
P01915 UniProt NPD GO	HB22_MOUSE	H-2 class II histocompatibility antigen, E-D beta chain precursor	0.09	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				264
P63120 UniProt NPD GO	VPK3_HUMAN	HERV-K_19q12 provirus ancestral Pro protein (EC 3.4.23.-) (HERV-K(C19) Pro protein) (Protease) (Prot ...	0.09	-	cyt	0					156
P63129 UniProt NPD GO	VPK11_HUMAN	HERV-K_22q11.21 provirus ancestral Pro protein (EC 3.4.23.-) (HERV-K101 envelope protein) (Protease) ...	0.09	-	cyt	0					156
Q5ZJ74 UniProt NPD GO	HBLD2_CHICK	HESB-like domain-containing protein 2, mitochondrial precursor (Iron sulfur assembly protein IscA)	0.09	-	mit	0	Mitochondrion (By similarity)				129
Q9CQJ1 UniProt NPD GO	HIG2A_MOUSE	HIG1 domain family member 2A	0.09	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)				106
P01914 UniProt NPD GO	HB2C_HUMAN	HLA class II histocompatibility antigen, DR-1 beta chain precursor (Clone P2-beta-4)	0.09	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				266
Q9TQE0 UniProt NPD GO	2B19_HUMAN	HLA class II histocompatibility antigen, DRB1-9 beta chain precursor (MHC class I antigen DRB1*9) (D ...	0.09	-	end	1 *	Membrane; single-pass type I membrane protein		142857		266
Q9S784 UniProt NPD GO	HA22C_ARATH	HVA22-like protein c (AtHVA22c)	0.09	-	cyt	3 *	Membrane; multi-pass membrane protein (Potential)				184
O15885 UniProt NPD GO	CLP_TRYCR	Heat shock protein 100 (CLP protein) (Fragment)	0.09	-	cyt	0					138
P02516 UniProt NPD GO	HSP23_DROME	Heat shock protein 23	0.09	-	cyt	0					186
Q16082 UniProt NPD GO	HSPB2_HUMAN	Heat-shock protein beta-2 (HspB2) (DMPK-binding protein) (MKBP)	0.09	-	cyt	0		cytosol [TAS]	602179		182
Q2KHU9 UniProt NPD GO	HSPB3_BOVIN	Heat-shock protein beta-3 (HspB3)	0.09	-	nuc	0					149
Q9QZ57 UniProt NPD GO	HSPB3_MOUSE	Heat-shock protein beta-3 (HspB3)	0.09	-	nuc	0					154
Q9QUK5 UniProt NPD GO	HSPB7_RAT	Heat-shock protein beta-7 (HspB7) (Cardiovascular heat shock protein) (cvHsp) (Fragment)	0.09	-	nuc	0					90
P14750 UniProt NPD GO	HCYA_EURCA	Hemocyanin A chain (HcA)	0.09	-	cyt	0	Secreted protein; extracellular space	extracellular space [ISS]			630
P56823 UniProt NPD GO	HCYG_HELPO	Hemocyanin, beta-C chain unit G (Fragment)	0.09	-	cyt	0					404
P02131 UniProt NPD GO	HBB_CAICR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.09	-	cyt	0					146
P02129 UniProt NPD GO	HBB_CRONI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.09	-	cyt	0					146
P06890 UniProt NPD GO	HBAT_PONPY	Hemoglobin subunit theta-1 (Hemoglobin theta-1 chain) (Theta-1-globin)	0.09	-	mit	0					141
Q91X72 UniProt NPD GO	HEMO_MOUSE	Hemopexin precursor	0.09	-	exc	1 *	Secreted protein				460
P20059 UniProt NPD GO	HEMO_RAT	Hemopexin precursor	0.09	-	exc	1 *	Secreted protein				460
P03968 UniProt NPD GO	FGF1_BOVIN	Heparin-binding growth factor 1 precursor (HBGF-1) (Acidic fibroblast growth factor) (aFGF) (Prostat ...	0.09	-	cyt	0				1BAR	155
Q6I6M7 UniProt NPD GO	FGF1_CYNPY	Heparin-binding growth factor 1 precursor (HBGF-1) (Fibroblast growth factor 1) (FGF-1) (Acidic fibr ...	0.09	-	cyt	0					148
Q8TDQ0 UniProt NPD GO	TIMD3_HUMAN	Hepatitis A virus cellular receptor 2 precursor (HAVcr-2) (T cell immunoglobulin and mucin domain-co ...	0.09	-	mit	1	Membrane; single-pass type I membrane protein (Potential)		606652		301
Q9DFD6 UniProt NPD GO	HEPC_ONCMY	Hepcidin precursor (Fragment)	0.09	-	nuc	0	Secreted protein				61
Q9BQS7 UniProt NPD GO	HEPH_HUMAN	Hephaestin precursor (EC 1.-.-.-)	0.09	+	nuc	1	Membrane; single-pass type I membrane protein (Potential)		300167		1158
P43082 UniProt NPD GO	HEVL_ARATH	Hevein-like protein precursor	0.09	-	exc	0					212
Q07423 UniProt NPD GO	HEX6_RICCO	Hexose carrier protein HEX6	0.09	-	end	10 *	Membrane; multi-pass membrane protein				510
Q09055 UniProt NPD GO	HP55_TAMSI	Hibernation-specific plasma protein HP-55 precursor (Hibernator-specific blood complex, 55 kDa subun ...	0.09	-	end	0	Secreted protein				413
O74713 UniProt NPD GO	HGT1_CANAL	High-affinity glucose transporter	0.09	-	end	12 *	Membrane; multi-pass membrane protein				545
Q91VF2 UniProt NPD GO	HNMT_MOUSE	Histamine N-methyltransferase (EC 2.1.1.8) (HMT)	0.09	-	mit	0	Cytoplasm (By similarity)				295
P70076 UniProt NPD GO	SYH_FUGRU	Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.09	-	nuc	0	Cytoplasm				519
P15796 UniProt NPD GO	H12_CAEEL	Histone H1.2 (Histone H1-like protein 2)	0.09	+	nuc	0	Nucleus				190
P0C0S4 UniProt NPD GO	H2AZ_BOVIN	Histone H2A.Z (H2A/z)	0.09	-	mit	0	Nucleus				127
Q5ZMD6 UniProt NPD GO	H2AZ_CHICK	Histone H2A.Z (H2A/z)	0.09	-	mit	0	Nucleus (By similarity)				127

You are viewing entries 66251 to 66300 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.