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
P32415 UniProt NPD GO	HPA1_RANES	Hemolytic protein A1 (Fragment)	0.01	-		0	Secreted protein				13
Q9D1L9 UniProt NPD GO	XIP_MOUSE	Hepatitis B virus X-interacting protein homolog (HBX-interacting protein) (HBV X-interacting protein ...	0.01	-	cyt	0	Cytoplasm (By similarity)				91
P58426 UniProt NPD GO	TXHP2_HETVE	Heteropodatoxin-2 (HpTX2) (Toxin KJ6)	0.01	-	cyt	0	Secreted protein			1EMX	30
Q63159 UniProt NPD GO	COQ3_RAT	Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (EC 2.1.1.114) (Dihydroxyhexa ...	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (Probable)				345
Q26609 UniProt NPD GO	HXK_SCHMA	Hexokinase (EC 2.7.1.1)	0.01	-	cyt	0				1BDG	451
Q969A8 UniProt NPD GO	HXK_TOXGO	Hexokinase (EC 2.7.1.1)	0.01	-	cyt	0					468
Q9NFT9 UniProt NPD GO	HXK1_DROME	Hexokinase type 1 (EC 2.7.1.1)	0.01	-	cyt	0					465
P14201 UniProt NPD GO	BAB4_BABBO	High molecular weight antigen (Fragment)	0.01	-	cyt	0					44
Q9GZV3 UniProt NPD GO	SC5A7_HUMAN	High-affinity choline transporter 1 (Solute carrier family 5 member 7) (Hemicholinium-3-sensitive ch ...	0.01	-	end	12 *	Membrane; multi-pass membrane protein	integral to membrane [IDA] plasma membrane [IDA]	608761		580
Q9JMD7 UniProt NPD GO	SC5A7_RAT	High-affinity choline transporter 1 (Solute carrier family 5 member 7) (Hemicholinium-3-sensitive ch ...	0.01	-	end	12 *	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]			580
Q9JK41 UniProt NPD GO	COPT1_RAT	High-affinity copper uptake protein 1 (rCTR1) (Copper transporter 1) (Solute carrier family 31 membe ...	0.01	-	end	3	Membrane; multi-pass membrane protein (Probable)				187
Q5SR56 UniProt NPD GO	HIAL1_HUMAN	Hippocampus abundant transcript-like protein 1	0.01	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				485
Q5VZR4 UniProt NPD GO	HIAL2_HUMAN	Hippocampus abundant transcript-like protein 2	0.01	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)				134
Q07558 UniProt NPD GO	ITH1_HIRMA	Hirudin HM1 precursor	0.01	-	exc	0	Secreted protein				84
P81492 UniProt NPD GO	ITH2_HIRMA	Hirudin HM2 precursor (Hirudin HV1) (Bufrudin)	0.01	-	exc	0	Secreted protein				84
P28508 UniProt NPD GO	ITHH_HIRME	Hirudin IIIA'	0.01	-	nuc	0	Secreted protein			2CF9	65
P21213 UniProt NPD GO	HUTH_RAT	Histidine ammonia-lyase (EC 4.3.1.3) (Histidase)	0.01	-	cyt	0		cytosol [TAS]			657
P80912 UniProt NPD GO	HINT1_RABIT	Histidine triad nucleotide-binding protein 1 (Adenosine 5'-monophosphoramidase) (P13.7)	0.01	-	cyt	0	Cytoplasm			6RHN	125
Q9P777 UniProt NPD GO	HISX_SCHPO	Histidinol dehydrogenase (EC 1.1.1.23) (HDH)	0.01	-	cyt	0					439
P38649 UniProt NPD GO	BGAT_MOUSE	Histo-blood group ABO system transferase (NAGAT) [Includes: Glycoprotein-fucosylgalactoside alpha-N- ...	0.01	-		0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				14
P82898 UniProt NPD GO	H1A_OLILU	Histone H1A (Fragment)	0.01	-	nuc	0	Nucleus				47
Q5K8Y2 UniProt NPD GO	H2AZ_CRYNE	Histone H2A.Z	0.01	-	nuc	0	Nucleus (By similarity)				138
O65759 UniProt NPD GO	H2AX_CICAR	Histone H2AX	0.01	-	nuc	0	Nucleus				139
P81903 UniProt NPD GO	H2B1_ICTPU	Histone H2B 1 (Antibacterial histone-like protein 1) (HLP-1) (Fragment)	0.01	-		0	Nucleus				20
O88895 UniProt NPD GO	HDAC3_MOUSE	Histone deacetylase 3 (HD3)	0.01	-	cyt	0	Nucleus (By similarity)	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]			424
O94225 UniProt NPD GO	HOSM_PENCH	Homocitrate synthase, mitochondrial precursor (EC 2.3.3.14)	0.01	-	cyt	0	Mitochondrion				474
Q9Y823 UniProt NPD GO	HOSM_SCHPO	Homocitrate synthase, mitochondrial precursor (EC 2.3.3.14)	0.01	-	cyt	0	Mitochondrion (Potential)				418
Q9FUM8 UniProt NPD GO	HMT3_MAIZE	Homocysteine S-methyltransferase 3 (EC 2.1.1.10) (S-methylmethionine:homocysteine methyltransferase ...	0.01	-	cyt	0					338
P21794 UniProt NPD GO	HIP70_RAT	Hormone-induced protein 70 kDa (HIP-70) (Fragment)	0.01	-		0					19
P82961 UniProt NPD GO	PRPR_MAIZE	Husk leaf blades expansion-promoting protein (Fragment)	0.01	-		0					8
P68424 UniProt NPD GO	TXH10_ORNHU	Huwentoxin-10 (Huwentoxin-X) (HwTx-X)	0.01	-	nuc	0	Secreted protein (By similarity)			1Y29	28
Q86C49 UniProt NPD GO	TXH23_ORNHU	Huwentoxin-2a precursor (Huwentoxin-IIa)	0.01	-	exc	0	Secreted protein (By similarity)				83
P61104 UniProt NPD GO	TXH5_ORNHU	Huwentoxin-5 precursor (Huwentoxin-V) (HwTx-V) [Contains: Mutant of huwentoxin-5 (Mutant of huwentox ...	0.01	-	vac	1 *	Secreted protein				86
P41746 UniProt NPD GO	RODL_ASPFU	Hydrophobin precursor (Rodlet protein)	0.01	-	end	0	Secreted protein				159
P52754 UniProt NPD GO	HYP1_TRIRE	Hydrophobin-1 precursor (Hydrophobin I) (HFBI)	0.01	-	end	0	Cell wall. Secreted protein. Secreted in aqueous environment				97
O74300 UniProt NPD GO	SC6_SCHCO	Hydrophobin-6 precursor	0.01	-	exc	0	Secreted protein (By similarity)				185
O43122 UniProt NPD GO	HYP4_AGABI	Hydrophobin-B precursor	0.01	-	mit	1 *	Secreted protein				119
Q9UJM8 UniProt NPD GO	HAOX1_HUMAN	Hydroxyacid oxidase 1 (EC 1.1.3.15) (HAOX1) (Glycolate oxidase) (GOX)	0.01	-	cyt	0	Peroxisome	peroxisome [TAS]	605023		370
Q16775 UniProt NPD GO	GLO2_HUMAN	Hydroxyacylglutathione hydrolase (EC 3.1.2.6) (Glyoxalase II) (GLX II)	0.01	-	cyt	0			138760	2F50	260
P84002 UniProt NPD GO	HYB1_HYLBI	Hylin-b1 (Hy-b1)	0.01	-		0	Secreted protein	extracellular region [IDA]			19
P84258 UniProt NPD GO	HTF2_BLAOR	Hypertrehalosaemic factor 2 (Hypertrehalosaemic factor II) (Hypertrehalosaemic neuropeptide II)	0.01	-		0	Secreted protein				8
P84257 UniProt NPD GO	HTF2_LEPDE	Hypertrehalosaemic factor 2 (Hypertrehalosaemic factor II) (LeD-CC-II)	0.01	-		0	Secreted protein				8
P84256 UniProt NPD GO	HTF2_PERAM	Hypertrehalosaemic factor 2 (Hypertrehalosaemic factor II) (Neuropeptide M-II) (Periplanetin CC-2) ( ...	0.01	-		0	Secreted protein				8
P50720 UniProt NPD GO	CE3D_HYPCU	Hyphancin-3D precursor (Hyphancin IIID)	0.01	-	end	1 *	Secreted protein				63
P50721 UniProt NPD GO	CE3E_HYPCU	Hyphancin-3E precursor (Hyphancin IIIE)	0.01	-	end	1 *	Secreted protein				63
P50722 UniProt NPD GO	CE3F_HYPCU	Hyphancin-3F precursor (Hyphancin IIIF)	0.01	-	end	1 *	Secreted protein				63
P50723 UniProt NPD GO	CE3G_HYPCU	Hyphancin-3G precursor (Hyphancin IIIG)	0.01	-	end	1 *	Secreted protein				63
P35587 UniProt NPD GO	HYPA_HYPLI	Hypodermin A precursor (EC 3.4.21.-) (HA)	0.01	-	exc	1 *	Secreted protein				256
P01153 UniProt NPD GO	HY7_PIG	Hypothalamic heptapeptide	0.01	-		0					7
P40521 UniProt NPD GO	YIF8_YEAST	Hypothetical 10.3 kDa protein in SNP1-GPP1 intergenic region	0.01	-	nuc	0					94

You are viewing entries 89001 to 89050 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.