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
P78831 UniProt NPD GO	GHT5_SCHPO	High-affinity glucose transporter ght5 (Hexose transporter 5)	0.06	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			546
P48813 UniProt NPD GO	GNP1_YEAST	High-affinity glutamine permease	0.06	-	end	10	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrion [IDA]			663
P53322 UniProt NPD GO	TNA1_YEAST	High-affinity nicotinic acid transporter (Nicotinic acid permease)	0.06	-	end	12	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			534
P28504 UniProt NPD GO	ITHD_HIRME	Hirudin II	0.06	-	nuc	0	Secreted protein				65
P28503 UniProt NPD GO	ITHC_HIRME	Hirudin IIA	0.06	-	nuc	0	Secreted protein				65
P70349 UniProt NPD GO	HINT1_MOUSE	Histidine triad nucleotide-binding protein 1 (Adenosine 5'-monophosphoramidase) (Protein kinase C in ...	0.06	-	cyt	0	Cytoplasm. Nucleus	nucleus [IDA]			125
P08283 UniProt NPD GO	H1_PEA	Histone H1 (PsH1b) (PsH1b-40)	0.06	-	nuc	0	Nucleus				265
P50567 UniProt NPD GO	H2A_CHLRE	Histone H2A	0.06	-	nuc	0	Nucleus				129
Q75CC6 UniProt NPD GO	H2AZ_ASHGO	Histone H2A.Z	0.06	-	nuc	0	Nucleus (By similarity)				132
Q5AEE1 UniProt NPD GO	H2AZ_CANAL	Histone H2A.Z	0.06	-	nuc	0	Nucleus (By similarity)				132
Q6C341 UniProt NPD GO	H2AZ_YARLI	Histone H2A.Z	0.06	-	nuc	0	Nucleus (By similarity)				140
P08991 UniProt NPD GO	H2AV_STRPU	Histone H2AV (H2A.F/Z) (Fragment)	0.06	-	nuc	0	Nucleus				125
Q7M3Z5 UniProt NPD GO	H4_SEPOF	Histone H4 (Fragment)	0.06	-		0	Nucleus (By similarity)				17
Q8AVH1 UniProt NPD GO	RBBP7_XENLA	Histone-binding protein RBBP7 (Retinoblastoma-binding protein 7) (RBBP-7)	0.06	-	cyt	0	Nucleus (By similarity)				425
Q25054 UniProt NPD GO	HOL2_HOLDI	Holotricin-2 precursor	0.06	-	exc	1 *	Secreted protein				127
Q64204 UniProt NPD GO	DLX2_RAT	Homeobox protein DLX-2 (DLX-5) (Fragment)	0.06	-	nuc	0	Nucleus (Probable)				83
Q58FL6 UniProt NPD GO	LYS4_ASPNG	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.06	-	mit	0	Mitochondrion (By similarity)				769
Q870W1 UniProt NPD GO	LYS4_NEUCR	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.06	-	mit	0	Mitochondrion (By similarity)				784
Q12525 UniProt NPD GO	MHT1_YEAST	Homocysteine S-methyltransferase 1 (EC 2.1.1.10) (S-methylmethionine:homocysteine methyltransferase ...	0.06	-	cyt	0	Cytoplasm	cytoplasm [IDA]			324
Q08985 UniProt NPD GO	SAM4_YEAST	Homocysteine S-methyltransferase 2 (EC 2.1.1.10) (S-methylmethionine:homocysteine methyltransferase ...	0.06	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			325
P40495 UniProt NPD GO	LYS12_YEAST	Homoisocitrate dehydrogenase, mitochondrial precursor (EC 1.1.1.87)	0.06	-	mit	0	Mitochondrion	mitochondrion [IDA]			371
P17423 UniProt NPD GO	KHSE_YEAST	Homoserine kinase (EC 2.7.1.39) (HSK) (HK)	0.06	-	cyt	0					356
Q9D968 UniProt NPD GO	HCFC2_MOUSE	Host cell factor 2 (HCF-2) (C2 factor)	0.06	-	nuc	0				1WFT	241
P83303 UniProt NPD GO	TXH4_ORNHU	Huwentoxin-4 precursor (Huwentoxin-IV) (HwTx-IV)	0.06	-	exc	1 *	Secreted protein			1MB6	89
Q86UW8 UniProt NPD GO	HPLN4_HUMAN	Hyaluronan and proteoglycan link protein 4 precursor (Brain link protein 2)	0.06	-	end	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				402
P52748 UniProt NPD GO	HYP1_PISTI	Hydrophobin-1 precursor	0.06	-	exc	0	Secreted protein (By similarity)				140
P35914 UniProt NPD GO	HMGCL_HUMAN	Hydroxymethylglutaryl-CoA lyase, mitochondrial precursor (EC 4.1.3.4) (HMG-CoA lyase) (HL) (3-hydrox ...	0.06	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS]	246450	2CW6	325
P38060 UniProt NPD GO	HMGCL_MOUSE	Hydroxymethylglutaryl-CoA lyase, mitochondrial precursor (EC 4.1.3.4) (HMG-CoA lyase) (HL) (3-hydrox ...	0.06	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			325
Q5R9E1 UniProt NPD GO	HMGCL_PONPY	Hydroxymethylglutaryl-CoA lyase, mitochondrial precursor (EC 4.1.3.4) (HMG-CoA lyase) (HL) (3-hydrox ...	0.06	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				325
P54874 UniProt NPD GO	HMCS_SCHPO	Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) (HMG-CoA synthase) (3-hydroxy-3-methylglutaryl coen ...	0.06	-	cyt	0					447
P54961 UniProt NPD GO	HMCS1_BLAGE	Hydroxymethylglutaryl-CoA synthase 1 (EC 2.3.3.10) (HMG-CoA synthase 1) (3-hydroxy-3-methylglutaryl ...	0.06	-	cyt	0					453
P51354 UniProt NPD GO	YCXL_PORPU	Hypothetical 11.6 kDa protein in ycf19-ycf17 intergenic region (ORF198)	0.06	-	mit	0	Plastid; chloroplast				198
P38233 UniProt NPD GO	YBQ1_YEAST	Hypothetical 13.4 kDa protein in REG2-YRO2 intergenic region	0.06	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				116
P40490 UniProt NPD GO	YIK0_YEAST	Hypothetical 13.5 kDa protein in MOB1-SGA1 intergenic region	0.06	-	cyt	1 *					117
P53726 UniProt NPD GO	YN8E_YEAST	Hypothetical 13.7 kDa protein in SWP73-SEC12 intergenic region	0.06	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				119
P53194 UniProt NPD GO	YGA7_YEAST	Hypothetical 13.8 kDa protein in PMA1-PMC1 intergenic region	0.06	-	mit	1					125
P47028 UniProt NPD GO	YJI6_YEAST	Hypothetical 14.2 kDa protein in TRL1-EXO70 intergenic region	0.06	-	nuc	1					122
P40539 UniProt NPD GO	YIC8_YEAST	Hypothetical 15.0 kDa protein in SSM4-IRR1 intergenic region	0.06	-	mit	0					132
P40219 UniProt NPD GO	YM25_YEAST	Hypothetical 16.4 kDa protein in TIF34-SWP1 intergenic region	0.06	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				148
P38463 UniProt NPD GO	YMF20_MARPO	Hypothetical 18.6 kDa protein in NAD3-NAD7 intergenic region (ORF 167)	0.06	-	nuc	0					167
P48331 UniProt NPD GO	YCXA_CYAPA	Hypothetical 21.2 kDa protein in psbX-ycf33 intergenic region (ORF188)	0.06	-	end	4 *	Plastid; cyanelle				188
P15618 UniProt NPD GO	YM17_PARTE	Hypothetical 26.3 kDa protein (ORF17)	0.06	-	end	6 *					221
P40207 UniProt NPD GO	YM17_YEAST	Hypothetical 27.9 kDa protein in REC114-PSO2 intergenic region	0.06	-	mit	1 *		cytoplasm [IDA] endoplasmic reticulum [IDA] nuclear envelope [IDA]			237
P36086 UniProt NPD GO	YKH1_YEAST	Hypothetical 28.0 kDa protein in STB6-NUP100 intergenic region	0.06	-	mit	0		cytoplasm [IDA]			256
P51393 UniProt NPD GO	YCXR_PORPU	Hypothetical 28.3 kDa protein in ycf26-chlI intergenic region (ORF263)	0.06	-	end	6 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Probable)				263
Q32620 UniProt NPD GO	YCX2_MARPO	Hypothetical 3.3 kDa protein in psbT-psbN intergenic region (ORF27)	0.06	-	mit	0	Plastid; chloroplast				27
P31606 UniProt NPD GO	YCXC_CYAPA	Hypothetical 32.8 kDa protein in ycf23-apcF intergenic region (ORF299)	0.06	-	end	9 *	Plastid; cyanelle; cyanelle membrane; multi-pass membrane protein (Probable)				299
P36007 UniProt NPD GO	YKV8_YEAST	Hypothetical 34.9 kDa protein in COS9-JEN1 intergenic region	0.06	-	cyt	0					326
P47163 UniProt NPD GO	YJ99_YEAST	Hypothetical 39.0 kDa protein in ZMS1-MNS1 intergenic region	0.06	-	cyt	0		cytoplasm [IDA]			339
O78437 UniProt NPD GO	YCF44_GUITH	Hypothetical 47.8 kDa protein ycf44	0.06	-	end	4 *	Plastid; chloroplast				414

You are viewing entries 72251 to 72300 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.