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
Q96VB9 UniProt NPD GO	HSP7F_CANAL	Heat shock protein homolog SSE1 (Chaperone protein MSI3)	0.12	-	cyt	0	Cytoplasm				702
P32590 UniProt NPD GO	HSP79_YEAST	Heat shock protein homolog SSE2	0.12	-	cyt	0		cytoplasm [IDA]			692
P42929 UniProt NPD GO	HSPB1_CANFA	Heat-shock protein beta-1 (HspB1) (Heat shock 27 kDa protein) (HSP 27)	0.12	-	nuc	0					209
P15991 UniProt NPD GO	HSPB1_CRILO	Heat-shock protein beta-1 (HspB1) (Heat shock 27 kDa protein) (HSP 27)	0.12	-	mit	0					213
O35878 UniProt NPD GO	HSPB2_RAT	Heat-shock protein beta-2 (HspB2)	0.12	-	cyt	0					182
P43242 UniProt NPD GO	HMOX2_RABIT	Heme oxygenase 2 (EC 1.14.99.3) (HO-2)	0.12	-	nuc	1	Microsome				312
P81732 UniProt NPD GO	HC2C_MEGCR	Hemocyanin 2-c chain (KLH2-c)	0.12	-	cyt	0	Secreted protein; extracellular space (By similarity)				420
P47776 UniProt NPD GO	HEP2_RABIT	Heparin cofactor 2 precursor (Heparin cofactor II) (HC-II) (Protease inhibitor leuserpin 2)	0.12	-	end	0					480
P20003 UniProt NPD GO	FGF2_SHEEP	Heparin-binding growth factor 2 precursor (HBGF-2) (Basic fibroblast growth factor) (BFGF) (Prostatr ...	0.12	-	nuc	0					155
Q9Z0Z4 UniProt NPD GO	HEPH_MOUSE	Hephaestin precursor (EC 1.-.-.-)	0.12	+	end	1	Membrane; single-pass type I membrane protein (Potential)				1157
Q920H8 UniProt NPD GO	HEPH_RAT	Hephaestin precursor (EC 1.-.-.-)	0.12	+	end	1	Membrane; single-pass type I membrane protein (Potential)				1157
Q60HC3 UniProt NPD GO	HNRPF_MACFA	Heterogeneous nuclear ribonucleoprotein F (hnRNP F)	0.12	-	cyt	0	Nucleus; nucleoplasm (By similarity)				414
P29589 UniProt NPD GO	AHT1_YEAST	Hexose transport activator protein	0.12	-	mit	0					182
P43581 UniProt NPD GO	HXT10_YEAST	Hexose transporter HXT10	0.12	-	end	11 *	Membrane; multi-pass membrane protein (Probable)	mitochondrion [IDA]			546
P50135 UniProt NPD GO	HNMT_HUMAN	Histamine N-methyltransferase (EC 2.1.1.8) (HMT)	0.12	-	cyt	0	Cytoplasm		605238	2AOX	292
P16442 UniProt NPD GO	BGAT_HUMAN	Histo-blood group ABO system transferase (NAGAT) [Includes: Glycoprotein-fucosylgalactoside alpha-N- ...	0.12	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...	extracellular region [NAS] integral to Golgi membrane [NAS]	110300	2A8W	354
P84408 UniProt NPD GO	H1_SALSA	Histone H1 [Contains: SAMP H1] (Fragment)	0.12	-	nuc	0	Nucleus. SAMP H1 is secreted				54
P10771 UniProt NPD GO	H11_CAEEL	Histone H1.1	0.12	+	nuc	0	Nucleus				207
P40275 UniProt NPD GO	H1A_CHITE	Histone H1A	0.12	+	nuc	0	Nucleus				232
P09588 UniProt NPD GO	H2A_CAEEL	Histone H2A	0.12	-	mit	0	Nucleus				126
P30756 UniProt NPD GO	H2B2_MAIZE	Histone H2B.2	0.12	+	nuc	0	Nucleus				149
Q969S8 UniProt NPD GO	HDA10_HUMAN	Histone deacetylase 10 (HD10)	0.12	-	cyt	0	Cytoplasm. Nucleus. Excluded from the nucleoli	cytoplasm [IDA] histone deacetylase complex [IDA] nucleus [IDA]	608544		669
Q569C4 UniProt NPD GO	HDA10_RAT	Histone deacetylase 10 (HD10)	0.12	-	end	0	Cytoplasm (By similarity). Nucleus (By similarity). Excluded from the nucleoli (By similarity)				588
Q9M4T3 UniProt NPD GO	HD2D_ARATH	Histone deacetylase 2d (HD-tuins protein 4)	0.12	-	cyt	0	Nucleus; nucleolus (Probable)				203
Q9BPY8 UniProt NPD GO	HOP_HUMAN	Homeodomain-only protein (Lung cancer-associated Y protein) (Odd homeobox protein 1) (Not expressed ...	0.12	-	nuc	0	Nucleus (By similarity)		607275		73
P05048 UniProt NPD GO	UBX_DROFU	Homeotic protein ultrabithorax (Fragment)	0.12	-	nuc	0	Nucleus				253
Q4WUL6 UniProt NPD GO	LYS4_ASPFU	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.12	-	mit	0	Mitochondrion (By similarity)				777
Q8SQG7 UniProt NPD GO	HYAL2_SHEEP	Hyaluronidase-2 precursor (EC 3.2.1.35) (Hyal-2) (Hyaluronoglucosaminidase-2) (LUCA-2)	0.12	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				476
P17425 UniProt NPD GO	HMCS1_RAT	Hydroxymethylglutaryl-CoA synthase, cytoplasmic (EC 2.3.3.10) (HMG-CoA synthase) (3-hydroxy-3-methyl ...	0.12	-	cyt	0	Cytoplasm	cytosol [TAS]			520
P34249 UniProt NPD GO	YKK2_YEAST	Hypothetical 11.4 kDa protein in APE1/LAP4-CWP1 intergenic region	0.12	-	mit	0					101
P46994 UniProt NPD GO	YJQ9_YEAST	Hypothetical 14.0 kDa protein in CPS1-FPP1 intergenic region	0.12	-	cyt	0					122
P53143 UniProt NPD GO	YGK2_YEAST	Hypothetical 16.2 kDa protein in RPL28-SEH1 intergenic region	0.12	-	mit	0					142
P36154 UniProt NPD GO	YK54_YEAST	Hypothetical 18.4 kDa protein in SIS2-MTD1 intergenic region	0.12	-	cyt	0		cytoplasm [IDA]			155
P40188 UniProt NPD GO	YIF7_YEAST	Hypothetical 19.2 kDa protein in SNP1-GPP1 intergenic region	0.12	-	cyt	0		cytoplasm [IDA]			164
P31919 UniProt NPD GO	YCX8_EUGGR	Hypothetical 33.1 kDa protein in rbcL-atpE intergenic region (ORF281B)	0.12	-	cyt	0	Plastid; chloroplast				281
P47133 UniProt NPD GO	YJ58_YEAST	Hypothetical 33.9 kDa protein in STE18-GRR1 intergenic region	0.12	-	cyt	0		endoplasmic reticulum [IDA]			292
P40896 UniProt NPD GO	YJV3_YEAST	Hypothetical 35.9 kDa protein in HXT8-CRT1 intergenic region	0.12	-	mit	0					331
P10579 UniProt NPD GO	YMS2_MAIZE	Hypothetical 39 kDa protein in mitochondrial S-1 and S-2 DNA (URF 2)	0.12	-	mit	0					339
Q03151 UniProt NPD GO	YMY7_YEAST	Hypothetical 42.1 kDa protein in SNZ1-YPK2 intergenic region	0.12	-	mit	0		mitochondrial inner membrane [IDA]			367
Q03730 UniProt NPD GO	YMB8_YEAST	Hypothetical 43.7 kDa protein in OST6-PSP2 intergenic region	0.12	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	vacuolar membrane (sensu Fungi) [IDA]			393
Q04235 UniProt NPD GO	YMA5_YEAST	Hypothetical 52.7 kDa protein in PDR4-GLO1 intergenic region	0.12	-	cyt	0		cytoplasm [IDA]			462
Q03218 UniProt NPD GO	YM43_YEAST	Hypothetical 56.2 kDa protein in SIP18-SPT21 intergenic region	0.12	-	nuc	1	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			510
O14078 UniProt NPD GO	YEAD_SCHPO	Hypothetical GTP-binding protein UNK4.13c in chromosome I	0.12	-	mit	0					407
P0C043 UniProt NPD GO	Y4791_ARATH	Hypothetical PPR-repeat protein At4g17915	0.12	-	cyt	0					463
Q09251 UniProt NPD GO	YQ55_CAEEL	Hypothetical RING finger protein C16C10.5 in chromosome III	0.12	-	end	5	Membrane; multi-pass membrane protein (Potential)				409
Q7TNS2 UniProt NPD GO	U327_MOUSE	Hypothetical UPF0327 protein	0.12	-	cyt	1 *					76
P93276 UniProt NPD GO	M030_ARATH	Hypothetical mitochondrial protein AtMg00030 (ORF107a)	0.12	-	nuc	0	Mitochondrion (Potential)				107
P93302 UniProt NPD GO	M470_ARATH	Hypothetical mitochondrial protein AtMg00470 (ORF122a)	0.12	-	cyt	0	Mitochondrion (Potential)				122
P93315 UniProt NPD GO	M600_ARATH	Hypothetical mitochondrial protein AtMg00600 (ORF106c)	0.12	-	nuc	0	Mitochondrion (Potential)				106
P92555 UniProt NPD GO	M1250_ARATH	Hypothetical mitochondrial protein AtMg01250 (ORF102)	0.12	-	mit	0	Mitochondrion (Potential)				122

You are viewing entries 61251 to 61300 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.