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
P0C0S5 UniProt NPD GO	H2AZ_HUMAN	Histone H2A.Z (H2A/z)	0.09	-	mit	0	Nucleus		142763	1F66	127
P0C0S6 UniProt NPD GO	H2AZ_MOUSE	Histone H2A.Z (H2A/z)	0.09	-	mit	0	Nucleus. Enriched in constitutive heterochromatin. Absent from facultative heterochromatin of the in ...	nucleus [IDA]			127
P22647 UniProt NPD GO	H2AZ_ONCMY	Histone H2A.Z (H2A/z)	0.09	-	mit	0	Nucleus				127
Q5RC42 UniProt NPD GO	H2AZ_PONPY	Histone H2A.Z (H2A/z)	0.09	-	mit	0	Nucleus				127
P0C0S7 UniProt NPD GO	H2AZ_RAT	Histone H2A.Z (H2A/z)	0.09	-	mit	0	Nucleus				127
Q6YNC8 UniProt NPD GO	H2AZ_SHEEP	Histone H2A.Z (H2A/z)	0.09	-	mit	0	Nucleus				127
P08985 UniProt NPD GO	H2AV_DROME	Histone H2Av (H2A.F/Z) (H2A.Z)	0.09	-	nuc	0	Nucleus. Widely distributed in the genome, irrespective of the transcriptional status or coding capa ...	nucleus [IDA] polytene chromosome [IDA]			140
P27807 UniProt NPD GO	H2B1_WHEAT	Histone H2B.1	0.09	+	nuc	0	Nucleus				151
P05621 UniProt NPD GO	H2B2_WHEAT	Histone H2B.2	0.09	-	nuc	0	Nucleus				149
Q43261 UniProt NPD GO	H2B3_MAIZE	Histone H2B.3	0.09	+	nuc	0	Nucleus				152
Q59RH5 UniProt NPD GO	HAT2_CANAL	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				382
Q9BY41 UniProt NPD GO	HDAC8_HUMAN	Histone deacetylase 8 (HD8)	0.09	-	cyt	0	Nucleus. Excluded from the nucleoli	cytoplasm [TAS] histone deacetylase complex [TAS] nuclear chromosome [TAS] nucleus [TAS]	300269	1W22	377
P32561 UniProt NPD GO	RPD3_YEAST	Histone deacetylase RPD3 (Transcriptional regulatory protein RPD3)	0.09	-	cyt	0	Cytoplasm. Nucleus	histone deacetylase complex [IDA]			433
Q04751 UniProt NPD GO	NAT4_YEAST	Histone-specific N-acetyltransferase NAT4 (EC 2.3.1.-)	0.09	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			285
Q92412 UniProt NPD GO	LYS4_EMENI	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.09	-	mit	0	Mitochondrion (By similarity)				775
Q8LAX0 UniProt NPD GO	HMT3_ARATH	Homocysteine S-methyltransferase 3 (EC 2.1.1.10) (S-methylmethionine:homocysteine methyltransferase ...	0.09	-	cyt	0					347
Q9ZRA2 UniProt NPD GO	HGD_ARATH	Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (Homogentisicase) (Homogentisate oxygenase) (Homogentis ...	0.09	-	cyt	0					461
Q96S86 UniProt NPD GO	HPLN3_HUMAN	Hyaluronan and proteoglycan link protein 3 precursor	0.09	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
O35632 UniProt NPD GO	HYAL2_MOUSE	Hyaluronidase-2 precursor (EC 3.2.1.35) (Hyal-2) (Hyaluronoglucosaminidase-2) (LUCA-2)	0.09	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				473
Q52SK7 UniProt NPD GO	HLYS_HYDAT	Hydralysin	0.09	-	cyt	0	Secreted protein (By similarity)				243
P52749 UniProt NPD GO	HYP2_PISTI	Hydrophobin-2 precursor (Fragment)	0.09	-	nuc	1 *	Secreted protein (By similarity)				117
P17961 UniProt NPD GO	YALA_TRYBB	Hypothetical 1.9 kDa protein in aldolase locus (ORFA)	0.09	-		0					17
P49837 UniProt NPD GO	YCF66_ODOSI	Hypothetical 11.3 kDa protein ycf66 (ORF99)	0.09	-	end	3 *	Plastid; chloroplast				99
P40440 UniProt NPD GO	YIR1_YEAST	Hypothetical 11.6 kDa protein in SDL1 5'region	0.09	-	nuc	1	Membrane; multi-pass membrane protein (Probable)				109
P25630 UniProt NPD GO	YCU0_YEAST	Hypothetical 11.7 kDa protein in ARE1-THR4 intergenic region	0.09	-	cyt	0					102
P53085 UniProt NPD GO	YGW7_YEAST	Hypothetical 12.1 kDa protein in NIF3-CLG1 intergenic region	0.09	-	nuc	0					113
P36127 UniProt NPD GO	YK12_YEAST	Hypothetical 12.4 kDa protein in SPO14-DAL80 intergenic region	0.09	-	nuc	1					104
P51204 UniProt NPD GO	YCF54_PORPU	Hypothetical 12.7 kDa protein ycf54 (ORF108)	0.09	-	cyt	0	Plastid; chloroplast				108
P40584 UniProt NPD GO	YIW0_YEAST	Hypothetical 13.0 kDa protein in HYR1 3'region	0.09	-	cyt	0					110
P49536 UniProt NPD GO	YCF41_ODOSI	Hypothetical 13.2 kDa protein ycf41 (ORF113)	0.09	-	cyt	0	Plastid; chloroplast				113
P53307 UniProt NPD GO	YG4O_YEAST	Hypothetical 13.3 kDa protein CRM1-MRPL9 intergenic region	0.09	-	cyt	0					113
O20120 UniProt NPD GO	YCX2_CHLVU	Hypothetical 14.6 kDa protein in psaC-atpA intergenic region (ORF133)	0.09	-	nuc	0	Plastid; chloroplast				133
P53737 UniProt NPD GO	YN8P_YEAST	Hypothetical 15.3 kDa protein in COQ2-ERG19 intergenic region	0.09	-	nuc	0					142
P36073 UniProt NPD GO	YKL5_YEAST	Hypothetical 15.3 kDa protein in VMA12-APN1 intergenic region	0.09	-	nuc	1					130
P40082 UniProt NPD GO	YEW5_YEAST	Hypothetical 15.4 kDa protein in GLC7-GDI1 intergenic region	0.09	-	nuc	1 *					130
P40532 UniProt NPD GO	YIE0_YEAST	Hypothetical 16.5 kDa protein in CBR5-NOT3 intergenic region	0.09	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA] nuclear envelope [IDA]			138
P40502 UniProt NPD GO	YII7_YEAST	Hypothetical 16.9 kDa protein in SGA1-KTR7 intergenic region	0.09	-	nuc	0		mitochondrion [IDA]			157
P40857 UniProt NPD GO	YJJ7_YEAST	Hypothetical 24.5 kDa protein in SAP185-BCK1 intergenic region	0.09	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA] nuclear envelope-endoplasmic reticulum network [IDA] vacuolar membrane (sensu Fungi) [IDA]			217
P49832 UniProt NPD GO	YCX6_ODOSI	Hypothetical 3.3 kDa protein in psbJ-trnE intergenic region (ORF26A)	0.09	-	mit	0	Plastid; chloroplast				26
P48558 UniProt NPD GO	YN45_YEAST	Hypothetical 33.6 kDa protein in MCK1-RPS19B intergenic region	0.09	-	end	7	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			297
O19883 UniProt NPD GO	YCF39_CYACA	Hypothetical 35.4 kDa protein ycf39	0.09	-	nuc	0	Plastid; chloroplast				312
Q9MUP3 UniProt NPD GO	YCF81_MESVI	Hypothetical 44.0 kDa protein ycf81 (RF81)	0.09	-	end	4 *	Plastid; chloroplast				382
P49833 UniProt NPD GO	YCF90_ODOSI	Hypothetical 44.4 kDa protein ycf90 (ORF380)	0.09	-	end	2	Plastid; chloroplast				380
Q9MTN9 UniProt NPD GO	YCX3_OENHO	Hypothetical 5.4 kDa protein in ycf3 intronic region (ORF51)	0.09	-	nuc	0	Plastid; chloroplast				51
P51223 UniProt NPD GO	YCX9_PORPU	Hypothetical 6.6 kDa protein in psaL-rpl28 intergenic region (ORF58)	0.09	-	nuc	0	Plastid; chloroplast				58
P51366 UniProt NPD GO	YCF18_PORPU	Hypothetical 6.9 kDa protein ycf18 (ORF58)	0.09	-	cyt	0	Plastid; chloroplast				58
Q21268 UniProt NPD GO	YMSO_CAEEL	Hypothetical UPF0046 protein K07C11.7 in chromosome V	0.09	-	cyt	0					290
P34419 UniProt NPD GO	YLZ6_CAEEL	Hypothetical UPF0152 protein F42H10.6 in chromosome III	0.09	-	cyt	0					169
P0C0V2 UniProt NPD GO	YE18A_YEAST	Hypothetical UPF0320 protein YER188C-A	0.09	-	nuc	0					99
P53758 UniProt NPD GO	YN9D_YEAST	Hypothetical UPF0320 protein YNR077C	0.09	-	nuc	0					84

You are viewing entries 66301 to 66350 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.