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
P97576 UniProt NPD GO	GRPE1_RAT	GrpE protein homolog 1, mitochondrial precursor (Mt-GrpE#1)	0.08	-	mit	0	Mitochondrion; mitochondrial matrix				217
P30671 UniProt NPD GO	GBG7_BOVIN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-7 subunit precursor (Gamma-II)	0.08	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				68
P38407 UniProt NPD GO	GNAT_XENLA	Guanine nucleotide-binding protein G(t) subunit alpha (Transducin alpha chain)	0.08	-	gol	0					349
Q40507 UniProt NPD GO	GBB3_TOBAC	Guanine nucleotide-binding protein subunit beta	0.08	-	cyt	0					375
P93397 UniProt NPD GO	GBB1_TOBAC	Guanine nucleotide-binding protein subunit beta 1	0.08	-	cyt	0					377
P93398 UniProt NPD GO	GBB2_TOBAC	Guanine nucleotide-binding protein subunit beta 2	0.08	-	cyt	0					377
P62883 UniProt NPD GO	GBLP_LEICH	Guanine nucleotide-binding protein subunit beta-like protein (Antigen LACK)	0.08	-	cyt	0					312
P62884 UniProt NPD GO	GBLP_LEIIN	Guanine nucleotide-binding protein subunit beta-like protein (Antigen LACK) (LiP36) (p36Li)	0.08	-	cyt	0					312
P43080 UniProt NPD GO	GUC1A_HUMAN	Guanylyl cyclase-activating protein 1 (GCAP 1) (Guanylate cyclase activator 1A)	0.08	-	cyt	0	Membrane; lipid-anchor		602093		200
P63125 UniProt NPD GO	VPK17_HUMAN	HERV-K_11q22.1 provirus ancestral Pro protein (EC 3.4.23.-) (Protease) (Proteinase) (PR)	0.08	-	cyt	0					156
P63119 UniProt NPD GO	VPK1_HUMAN	HERV-K_12q14.1 provirus ancestral Pro protein (EC 3.4.23.-) (Protease) (Proteinase) (PR)	0.08	-	cyt	0					156
Q99JY6 UniProt NPD GO	HIG1B_MOUSE	HIG1 domain family member 1B	0.08	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				98
P05537 UniProt NPD GO	HB23_HUMAN	HLA class II histocompatibility antigen, DQ(W3) beta chain precursor	0.08	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				261
Q30631 UniProt NPD GO	2DRA_MACMU	HLA class II histocompatibility antigen, DR alpha chain precursor (MHC class II antigen DRA)	0.08	-	end	1	Membrane; single-pass type I membrane protein				254
Q96KN8 UniProt NPD GO	HRSL5_HUMAN	HRAS-like suppressor 5 (H-rev107-like protein 5)	0.08	-	nuc	0					279
P19208 UniProt NPD GO	HSP7C_CAEBR	Heat shock 70 kDa protein C precursor	0.08	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen				661
P27420 UniProt NPD GO	HSP7C_CAEEL	Heat shock 70 kDa protein C precursor	0.08	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				661
P12077 UniProt NPD GO	HSP74_LEIMA	Heat shock 70-related protein 4 (Fragment)	0.08	-	cyt	0					228
P20030 UniProt NPD GO	HSP7C_TRYBB	Heat shock cognate HSP70 protein	0.08	-	cyt	0					676
Q875V0 UniProt NPD GO	HSP7F_SACCA	Heat shock protein homolog SSE1	0.08	-	cyt	0	Cytoplasm (By similarity)				685
Q00649 UniProt NPD GO	HSPB1_CHICK	Heat-shock protein beta-1 (HspB1) (Heat shock 27 kDa protein) (HSP 27) (Actin polymerization inhibit ...	0.08	-	nuc	0	Cytoplasmic granule	cell surface [ISS] contractile fiber [ISS] cytoplasm [IDA] cytoskeleton [ISS] insoluble fraction [ISS] mitochondrion [NAS] nucleus [TAS] plasma membrane [ISS] soluble fraction [ISS] Z disc [ISS]			193
Q9QZ58 UniProt NPD GO	HSPB3_RAT	Heat-shock protein beta-3 (HspB3)	0.08	-	nuc	0					152
P80888 UniProt NPD GO	HCY_PALVU	Hemocyanin	0.08	-	cyt	0	Secreted protein; extracellular space				657
Q95P08 UniProt NPD GO	HCYA_SCUCO	Hemocyanin subunit A precursor	0.08	-	vac	0	Secreted protein; extracellular space	extracellular region [IDA]			656
Q8IFJ8 UniProt NPD GO	HCYB_SCUCO	Hemocyanin subunit B precursor	0.08	-	exc	0	Secreted protein; extracellular space	extracellular region [IDA]			659
P56824 UniProt NPD GO	HCYC_SEPOF	Hemocyanin, units C and D (Fragments)	0.08	-	cyt	0					250
P02130 UniProt NPD GO	HBB_ALLMI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.08	-	cyt	0					146
P50828 UniProt NPD GO	HEMO_PIG	Hemopexin precursor (Hyaluronidase) (EC 3.2.1.35)	0.08	-	mit	0	Secreted protein				459
Q7SIF8 UniProt NPD GO	FGF1_NOTVI	Heparin-binding growth factor 1 (HBGF-1) (Fibroblast growth factor 1) (FGF-1) (Acidic fibroblast gro ...	0.08	-	nuc	0				1FMM	132
P19596 UniProt NPD GO	FGF1_CHICK	Heparin-binding growth factor 1 precursor (HBGF-1) (Acidic fibroblast growth factor) (aFGF) (Alpha-e ...	0.08	-	cyt	0					155
Q6GLR6 UniProt NPD GO	FGF1_XENLA	Heparin-binding growth factor 1 precursor (HBGF-1) (Fibroblast growth factor 1) (FGF-1) (Acidic fibr ...	0.08	-	nuc	0					155
P23472 UniProt NPD GO	CHLY_HEVBR	Hevamine-A precursor [Includes: Chitinase (EC 3.2.1.14); Lysozyme (EC 3.2.1.17)]	0.08	-	exc	1 *	Vacuole. In the lutoids (vacuoles) from rubber latex			2HVM	311
P53387 UniProt NPD GO	KHT2_KLULA	Hexose transporter 2	0.08	-	end	11	Membrane; multi-pass membrane protein				566
P39924 UniProt NPD GO	HXT13_YEAST	Hexose transporter HXT13	0.08	-	end	12	Membrane; multi-pass membrane protein				564
P53631 UniProt NPD GO	HXT17_YEAST	Hexose transporter HXT17	0.08	-	end	12	Membrane; multi-pass membrane protein				564
Q2YEG2 UniProt NPD GO	CXCR1_BUNHO	High affinity interleukin-8 receptor A (IL-8R A) (IL-8 receptor type 1) (CXCR-1) (CD181 antigen)	0.08	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				351
P06775 UniProt NPD GO	HIP1_YEAST	Histidine permease	0.08	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [IMP]			603
P05228 UniProt NPD GO	HRP2_PLAFA	Histidine-rich protein precursor (Clone PFHRP-III)	0.08	-	nuc	0					241
Q9C5U8 UniProt NPD GO	HISX_ARATH	Histidinol dehydrogenase, chloroplast precursor (EC 1.1.1.23) (HDH)	0.08	-	mit	0	Plastid; chloroplast				466
Q9HGX4 UniProt NPD GO	H2A_AGABI	Histone H2A	0.08	-	nuc	0	Nucleus				138
Q5KMT5 UniProt NPD GO	H2A_CRYNE	Histone H2A	0.08	-	nuc	0	Nucleus (By similarity)				130
O23628 UniProt NPD GO	H2AV1_ARATH	Histone H2A variant 1 (H2A.F/Z 1) (HTA11) (H2AvAt)	0.08	-	nuc	0	Nucleus (By similarity)				136
P16865 UniProt NPD GO	H2A3_VOLCA	Histone H2A-III	0.08	-	nuc	0	Nucleus				129
P16866 UniProt NPD GO	H2A4_VOLCA	Histone H2A-IV	0.08	-	nuc	0	Nucleus				129
Q43208 UniProt NPD GO	H2A4_WHEAT	Histone H2A.4	0.08	-	nuc	0	Nucleus (By similarity)				134
Q9LD28 UniProt NPD GO	H2A6_ARATH	Histone H2A.6 (Protein RESISTANT TO AGROBACTERIUM TRANSFORMATION 5) (HTA1)	0.08	-	nuc	0	Nucleus (By similarity)				130
Q6CUC8 UniProt NPD GO	H2AZ_KLULA	Histone H2A.Z	0.08	-	nuc	0	Nucleus (By similarity)				131
Q6DER6 UniProt NPD GO	H2AZL_XENTR	Histone H2A.Z-like (H2A.Zl)	0.08	-	nuc	0	Nucleus (By similarity)				127
P70094 UniProt NPD GO	H2AZL_XENLA	Histone H2A.Z-like (H2A.Zl) (H2A.Z1) (XH2AZ)	0.08	-	nuc	0	Nucleus (By similarity)				127
Q27511 UniProt NPD GO	H2AV_CAEEL	Histone H2AV (H2A.F/Z)	0.08	-	nuc	0	Nucleus (By similarity)				139

You are viewing entries 68151 to 68200 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.