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
Q2YEG0 UniProt NPD GO	CXCR1_MACMU	High affinity interleukin-8 receptor A (IL-8R A) (IL-8 receptor type 1) (CXCR-1) (CD181 antigen)	0.04	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				351
Q2YEF9 UniProt NPD GO	CXCR1_PONPY	High affinity interleukin-8 receptor A (IL-8R A) (IL-8 receptor type 1) (CXCR-1) (CD181 antigen)	0.04	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				351
P35343 UniProt NPD GO	CXCR2_MOUSE	High affinity interleukin-8 receptor B (IL-8R B) (CXCR-2) (GRO/MGSA receptor) (CD182 antigen)	0.04	-	end	6 *	Membrane; multi-pass membrane protein				359
P49374 UniProt NPD GO	HGT1_KLULA	High-affinity glucose transporter	0.04	-	end	12 *	Membrane; multi-pass membrane protein				551
P28505 UniProt NPD GO	ITHE_HIRME	Hirudin II'	0.04	-	nuc	0	Secreted protein			1HAG	65
P28510 UniProt NPD GO	ITHJ_HIRME	Hirudin IIIB	0.04	-	nuc	0	Secreted protein			1AIX	65
P97292 UniProt NPD GO	HRH2_MOUSE	Histamine H2 receptor (H2R) (Gastric receptor I)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				358
P42357 UniProt NPD GO	HUTH_HUMAN	Histidine ammonia-lyase (EC 4.3.1.3) (Histidase)	0.04	-	cyt	0			609457		657
P62958 UniProt NPD GO	HINT1_BOVIN	Histidine triad nucleotide-binding protein 1 (Adenosine 5'-monophosphoramidase) (Protein kinase C in ...	0.04	-	cyt	0	Cytoplasm				125
P62959 UniProt NPD GO	HINT1_RAT	Histidine triad nucleotide-binding protein 1 (Adenosine 5'-monophosphoramidase) (Protein kinase C in ...	0.04	-	cyt	0	Cytoplasm (By similarity)				125
P15871 UniProt NPD GO	H11_WHEAT	Histone H1.1 (Fragment)	0.04	-	cyt	0	Nucleus				25
P83865 UniProt NPD GO	H4_PENVA	Histone H4 (Fragments)	0.04	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			51
Q06592 UniProt NPD GO	HPA2_YEAST	Histone acetyltransferase HPA2 (EC 2.3.1.48)	0.04	-	cyt	0		cytoplasm [IDA]		1QSO	156
Q4I7L0 UniProt NPD GO	HAT2_GIBZE	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				423
Q04344 UniProt NPD GO	HNT1_YEAST	Hit family protein 1 (Adenosine 5'-monophosphoramidase)	0.04	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			158
Q2HZ33 UniProt NPD GO	LYS4_CANPA	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.04	-	mit	0	Mitochondrion (By similarity)				688
Q2GN26 UniProt NPD GO	LYS4_CHAGB	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.04	-	mit	0	Mitochondrion (By similarity)				797
Q5K9V9 UniProt NPD GO	LYS4_CRYNE	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.04	-	mit	0	Mitochondrion (By similarity)				728
Q4HVQ9 UniProt NPD GO	LYS4_GIBZE	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.04	-	mit	0	Mitochondrion (By similarity)				776
Q9FUM7 UniProt NPD GO	HMT4_MAIZE	Homocysteine S-methyltransferase 4 (EC 2.1.1.10) (S-methylmethionine:homocysteine methyltransferase ...	0.04	-	cyt	0					342
Q9Y041 UniProt NPD GO	HGD_CAEEL	Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (Homogentisicase) (Homogentisate oxygenase) (Homogentis ...	0.04	-	cyt	0					437
P59851 UniProt NPD GO	KAX2Z_CENLM	Hongotoxin-5 (HgTX5) (Fragment)	0.04	-		0	Secreted protein				20
P53834 UniProt NPD GO	HCH1_YEAST	Hsp90 co-chaperone HCH1 (High-copy Hsp90 suppressor protein 1)	0.04	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			153
O96530 UniProt NPD GO	HYAL_LYTVA	Hyalin (Fragment)	0.04	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				530
P38567 UniProt NPD GO	HYALP_HUMAN	Hyaluronidase PH-20 precursor (EC 3.2.1.35) (Hyal-PH20) (Sperm surface protein PH-20) (Sperm adhesio ...	0.04	-	end	2	Cell membrane; lipid-anchor; GPI-anchor	plasma membrane [TAS]	600930		509
P38568 UniProt NPD GO	HYALP_MACFA	Hyaluronidase PH-20 precursor (EC 3.2.1.35) (Hyal-PH20) (Sperm surface protein PH-20) (Sperm adhesio ...	0.04	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				510
P52751 UniProt NPD GO	MPG1_MAGGR	Hydrophobin-like protein MPG1 precursor	0.04	-	exc	0	Secreted protein				112
P54873 UniProt NPD GO	HMCS_ARATH	Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) (HMG-CoA synthase) (3-hydroxy-3-methylglutaryl coen ...	0.04	-	cyt	0					461
P48560 UniProt NPD GO	YN40_YEAST	Hypothetical 10.2 kDa protein in RPL18B-TRF5 intergenic region	0.04	-	nuc	1		cell wall (sensu Fungi) [IDA]			102
Q9TM45 UniProt NPD GO	YCF19_CYACA	Hypothetical 10.5 kDa protein ycf19	0.04	-	end	2 *	Plastid; chloroplast				91
P38294 UniProt NPD GO	YB24_YEAST	Hypothetical 11.5 kDa protein in SMY2-RPS6B intergenic region	0.04	-	nuc	0					104
P34238 UniProt NPD GO	YKR7_YEAST	Hypothetical 12.3 kDa protein in STE3-GIN10 intergenic region	0.04	-	mit	0					112
P47021 UniProt NPD GO	YJL9_YEAST	Hypothetical 12.4 kDa protein in POS18-PHO86 intergenic region	0.04	-	nuc	0					107
P51217 UniProt NPD GO	YCF83_PORPU	Hypothetical 12.4 kDa protein ycf83 (ORF114)	0.04	-	nuc	0	Plastid; chloroplast				114
P47078 UniProt NPD GO	YJA9_YEAST	Hypothetical 12.7 kDa protein in CCT3-CCT8 intergenic region	0.04	-	nuc	2 *					108
P15603 UniProt NPD GO	YM01_PARTE	Hypothetical 12.8 kDa protein (ORF1)	0.04	-	end	3 *					113
P38220 UniProt NPD GO	YBN7_YEAST	Hypothetical 12.8 kDa protein in MRF1-CDS1 intergenic region	0.04	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				110
P38864 UniProt NPD GO	YHX3_YEAST	Hypothetical 12.9 kDa protein in NMD3-ENO2 intergenic region	0.04	-	mit	0					112
P53229 UniProt NPD GO	YG1V_YEAST	Hypothetical 13.6 kDa protein in RME1-TFC4 intergenic region	0.04	-	nuc	3 *					120
P47118 UniProt NPD GO	YJ37_YEAST	Hypothetical 16.1 kDa protein in TOR1-RFC2 intergenic region	0.04	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			141
P25585 UniProt NPD GO	YCF8_YEAST	Hypothetical 17.1 kDa protein in CHA1-PRD1 intergenic region	0.04	-	end	2 *					152
P25571 UniProt NPD GO	YCE1_YEAST	Hypothetical 19.1 kDa protein in PDI1-GLK1 intergenic region	0.04	-	end	3 *					164
P51191 UniProt NPD GO	YCF37_PORPU	Hypothetical 20.0 kDa protein ycf37 (ORF173)	0.04	-	exc	1 *	Plastid; chloroplast				173
P15614 UniProt NPD GO	YM13_PARTE	Hypothetical 20.2 kDa protein (ORF13)	0.04	-	mit	2					169
P48324 UniProt NPD GO	YCX2_CYAPA	Hypothetical 24.3 kDa protein in psbH-rpl11 intergenic region (ORF182)	0.04	-	end	4 *	Plastid; cyanelle				182
Q04304 UniProt NPD GO	YMY0_YEAST	Hypothetical 24.9 kDa protein in RCA1-NPL6 intergenic region	0.04	-	cyt	0		cytoplasm [IDA]			227
P51364 UniProt NPD GO	YCXN_PORPU	Hypothetical 26.5 kDa protein in ycf44-cpcG intergenic region (ORF240)	0.04	-	end	6 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Probable)				240
P40516 UniProt NPD GO	YIG4_YEAST	Hypothetical 28.7 kDa protein in RNR3-ARC15 intergenic region	0.04	-	cyt	0		cytoplasm [IDA]			257
P40101 UniProt NPD GO	YE16_YEAST	Hypothetical 35.9 kDa protein in ISC10 3'region	0.04	-	cyt	0					306
P35735 UniProt NPD GO	YKF1_YEAST	Hypothetical 40.5 kDa protein in NUP120-CSE4 intergenic region	0.04	-	end	6 *		plasma membrane [IDA]			353

You are viewing entries 77251 to 77300 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.