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
P79337 UniProt NPD GO	TNFA_MACFA	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.08	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
O77510 UniProt NPD GO	TNFA_PAPHU	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.08	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
P33620 UniProt NPD GO	TNFA_PAPSP	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.08	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
P04924 UniProt NPD GO	TNFA_RABIT	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.08	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				235
Q9BEA1 UniProt NPD GO	TNFA_TURTR	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.08	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
Q14642 UniProt NPD GO	I5P1_HUMAN	Type I inositol-1,4,5-trisphosphate 5-phosphatase (EC 3.1.3.56) (5PTase)	0.08	-	cyt	0	Membrane; lipid-anchor	membrane [NAS]	600106		412
Q6QN12 UniProt NPD GO	IOD2_PIG	Type II iodothyronine deiodinase (EC 1.97.1.10) (Type-II 5'deiodinase) (DIOII) (Type 2 DI) (5DII)	0.08	-	end	0					265
P49896 UniProt NPD GO	IOD2_RANCA	Type II iodothyronine deiodinase (EC 1.97.1.10) (Type-II 5'deiodinase) (DIOII) (Type 2 DI) (5DII)	0.08	-	end	0					264
P30555 UniProt NPD GO	AGTR1_PIG	Type-1 angiotensin II receptor (AT1)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				359
P05140 UniProt NPD GO	ISP2_HEMAM	Type-2 ice-structuring protein precursor (Type II antifreeze protein) (AFP)	0.08	-	vac	0	Secreted protein			2AFP	163
P04694 UniProt NPD GO	ATTY_RAT	Tyrosine aminotransferase (EC 2.6.1.5) (L-tyrosine:2-oxoglutarate aminotransferase) (TAT)	0.08	-	cyt	0					454
P16277 UniProt NPD GO	BLK_MOUSE	Tyrosine-protein kinase BLK (EC 2.7.10.2) (B lymphocyte kinase) (p55-BLK)	0.08	-	mit	0				1BLK	498
P09324 UniProt NPD GO	YES_CHICK	Tyrosine-protein kinase Yes (EC 2.7.10.2) (p61-Yes)	0.08	-	nuc	0					540
P28193 UniProt NPD GO	PTP1_STYPL	Tyrosine-protein phosphatase 1 (EC 3.1.3.48) (Fragment)	0.08	-	cyt	0					107
P28206 UniProt NPD GO	PTP14_STYPL	Tyrosine-protein phosphatase 14 (EC 3.1.3.48) (Fragment)	0.08	-	cyt	0					116
Q91WQ3 UniProt NPD GO	SYYC_MOUSE	Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS)	0.08	-	cyt	0	Cytoplasm (By similarity)				527
O14055 UniProt NPD GO	SYYC_SCHPO	Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS)	0.08	-	cyt	0	Cytoplasm				401
Q750Y9 UniProt NPD GO	ALG14_ASHGO	UDP-N-acetylglucosamine transferase subunit ALG14 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.08	+	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				224
O14199 UniProt NPD GO	ALG14_SCHPO	UDP-N-acetylglucosamine transferase subunit alg14 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.08	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				210
P70691 UniProt NPD GO	UD12_MOUSE	UDP-glucuronosyltransferase 1-2 precursor (EC 2.4.1.17) (UDPGT) (UGT1*0) (UGT1-02) (UGT1.2) (UGT1A2) ...	0.08	-	end	1	Microsome (By similarity)				533
P36513 UniProt NPD GO	UDB14_RABIT	UDP-glucuronosyltransferase 2B14 precursor (EC 2.4.1.17) (UDPGT) (EGT12)	0.08	-	end	1	Microsome				530
P59773 UniProt NPD GO	U258_HUMAN	UPF0258 protein	0.08	-	nuc	1					107
P00127 UniProt NPD GO	UCRH_YEAST	Ubiquinol-cytochrome c reductase complex 17 kDa protein (Mitochondrial hinge protein) (Complex III s ...	0.08	-	cyt	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA] respiratory chain complex III (sensu Eukary... [IDA]		1P84	147
P51134 UniProt NPD GO	UCRI4_TOBAC	Ubiquinol-cytochrome c reductase iron-sulfur subunit 4, mitochondrial precursor (EC 1.10.2.2) (Riesk ...	0.08	-	mit	1	Mitochondrion; mitochondrial inner membrane				236
P13272 UniProt NPD GO	UCRI_BOVIN	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane			3BCC	274
Q6FSJ3 UniProt NPD GO	UQCR2_CANGA	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2)	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				364
Q9DB77 UniProt NPD GO	UQCR2_MOUSE	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2) (Comp ...	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			453
P32551 UniProt NPD GO	UQCR2_RAT	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2) (Comp ...	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				452
P87230 UniProt NPD GO	COQ5_SCHPO	Ubiquinone biosynthesis methyltransferase coq5, mitochondrial precursor (EC 2.1.1.-)	0.08	-	mit	0	Mitochondrion (By similarity)				305
Q19584 UniProt NPD GO	UFD1_CAEEL	Ubiquitin fusion degradation protein 1 homolog (UB fusion protein 1)	0.08	-	nuc	0					342
Q8LG98 UniProt NPD GO	OTUBL_ARATH	Ubiquitin thioesterase otubain-like protein (EC 3.4.-.-) (Ubiquitin-specific-processing protease otu ...	0.08	-	cyt	0					306
Q9XVR6 UniProt NPD GO	OTUBL_CAEEL	Ubiquitin thioesterase otubain-like protein (EC 3.4.-.-) (Ubiquitin-specific-processing protease otu ...	0.08	-	cyt	0					284
P35131 UniProt NPD GO	UBC8_ARATH	Ubiquitin-conjugating enzyme E2-17 kDa 8 (EC 6.3.2.19) (Ubiquitin-protein ligase 8) (Ubiquitin carri ...	0.08	-	nuc	0					148
O00102 UniProt NPD GO	UBC7_SCHPO	Ubiquitin-conjugating enzyme E2-18 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.08	-	nuc	0					166
Q9R1T2 UniProt NPD GO	ULE1A_MOUSE	Ubiquitin-like 1-activating enzyme E1A (SUMO-1-activating enzyme subunit 1)	0.08	-	cyt	0		nucleus [ISS]			350
P53889 UniProt NPD GO	YNQ8_YEAST	Uncharacterized hydrolase YNL168C (EC 3.-.-.-)	0.08	-	mit	0		mitochondrion [IDA]		1NKQ	259
Q06485 UniProt NPD GO	YL356_YEAST	Uncharacterized mitochondrial membrane protein YLR356W	0.08	-	end	4 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			197
Q8BMD6 UniProt NPD GO	CN101_MOUSE	Uncharacterized protein C14orf101 homolog	0.08	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				703
Q9P1N6 UniProt NPD GO	CN091_HUMAN	Uncharacterized protein C14orf91	0.08	-	cyt	0					82
Q9UJQ1 UniProt NPD GO	CT103_HUMAN	Uncharacterized protein C20orf103 precursor	0.08	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				280
Q6UXV4 UniProt NPD GO	CX033_HUMAN	Uncharacterized protein CXorf33 precursor	0.08	-	nuc	0	Secreted protein (Potential)				268
P38218 UniProt NPD GO	YBN2_YEAST	Uncharacterized protein YBR022W	0.08	-	nuc	0					177
P25349 UniProt NPD GO	YCP4_YEAST	Uncharacterized protein YCR004C	0.08	-	cyt	0	Cytoplasm (Probable)	cytoplasm [IDA] mitochondrion [IDA]			247
Q3E7B5 UniProt NPD GO	YM230_YEAST	Uncharacterized protein YMR230W-A	0.08	-	nuc	0					62
Q3E7Z1 UniProt NPD GO	YN146_YEAST	Uncharacterized protein YNL146C-A	0.08	-	mit	0					64
Q3E7A5 UniProt NPD GO	YO16W_YEAST	Uncharacterized protein YOL164W-A	0.08	-	mit	0					60
Q3E7B9 UniProt NPD GO	YO008_YEAST	Uncharacterized protein YOR008C-A precursor	0.08	-	cyt	1 *	Membrane; single-pass type I membrane protein (Potential)				74
Q3E735 UniProt NPD GO	YO034_YEAST	Uncharacterized protein YOR034C-A	0.08	-	cyt	1 *	Membrane; single-pass membrane protein (Potential)				80
P53283 UniProt NPD GO	YG3F_YEAST	Uncharacterized transporter YGR138C	0.08	-	end	12	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA] vacuolar membrane [IMP]			614
Q5FZI9 UniProt NPD GO	URIC_CANFA	Uricase (EC 1.7.3.3) (Urate oxidase)	0.08	-	pox	0	Peroxisome (By similarity)				303

You are viewing entries 69201 to 69250 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.