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
P34976 UniProt NPD GO	AGTR1_RABIT	Type-1 angiotensin II receptor (AT1)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				359
P50052 UniProt NPD GO	AGTR2_HUMAN	Type-2 angiotensin II receptor (AT2)	0.04	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	300034		363
Q06085 UniProt NPD GO	TYDC1_PETCR	Tyrosine decarboxylase 1 (EC 4.1.1.25) (ELI5) (Fragment)	0.04	-	cyt	0					432
P54771 UniProt NPD GO	TYDC5_PAPSO	Tyrosine/DOPA decarboxylase 5 [Includes: DOPA decarboxylase (EC 4.1.1.28) (DDC); Tyrosine decarboxyl ...	0.04	-	cyt	0					523
P57743 UniProt NPD GO	LSM3_YEAST	U6 snRNA-associated Sm-like protein LSm3 (SmX4 protein)	0.04	-	cyt	0	Nucleus. Cytoplasm	nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI] snRNP U6 [IDA] U4/U6 x U5 tri-snRNP complex [IDA]			89
Q6BST1 UniProt NPD GO	ALG13_DEBHA	UDP-N-acetylglucosamine transferase subunit ALG13 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.04	-	cyt	0	Endoplasmic reticulum (By similarity)				212
P38242 UniProt NPD GO	ALG14_YEAST	UDP-N-acetylglucosamine transferase subunit ALG14 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.04	-	end	1 *	Nucleus; nuclear membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic reticulum ...	integral to endoplasmic reticulum membrane [IDA] membrane fraction [IDA] nuclear envelope-endoplasmic reticulum network [IDA] UDP-N-acetylglucosamine transferase complex [IPI]			237
P42881 UniProt NPD GO	GPT_SCHPO	UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.15) (GPT ...	0.04	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [IGI]			446
P87041 UniProt NPD GO	GMS1_SCHPO	UDP-galactose transporter (Golgi UDP-Gal transporter)	0.04	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi membrane [IDA]			353
Q43070 UniProt NPD GO	GALE1_PEA	UDP-glucose 4-epimerase (EC 5.1.3.2) (Galactowaldenase) (UDP-galactose 4-epimerase)	0.04	-	cyt	0					350
Q96558 UniProt NPD GO	UGDH_SOYBN	UDP-glucose 6-dehydrogenase (EC 1.1.1.22) (UDP-Glc dehydrogenase) (UDP-GlcDH) (UDPGDH)	0.04	-	cyt	0					480
P20720 UniProt NPD GO	UD12_RAT	UDP-glucuronosyltransferase 1-2 precursor (EC 2.4.1.17) (UDPGT) (UGT1*0) (UGT1-02) (UGT1.2) (UGT1A2) ...	0.04	-	end	1	Microsome				533
P35503 UniProt NPD GO	UD13_HUMAN	UDP-glucuronosyltransferase 1-3 precursor (EC 2.4.1.17) (UDP-glucuronosyltransferase 1A3) (UDPGT) (U ...	0.04	-	end	1	Microsome		606428		534
P22310 UniProt NPD GO	UD14_HUMAN	UDP-glucuronosyltransferase 1-4 precursor (EC 2.4.1.17) (UDP-glucuronosyltransferase 1A4) (UDPGT) (U ...	0.04	-	end	1	Microsome	endoplasmic reticulum [TAS]	606429		534
Q64638 UniProt NPD GO	UD15_RAT	UDP-glucuronosyltransferase 1-5 precursor (EC 2.4.1.17) (UDPGT) (UGT1*5) (UGT1-05) (UGT1.5) (UGT1A5) ...	0.04	-	end	1	Microsome				531
P36537 UniProt NPD GO	UDB10_HUMAN	UDP-glucuronosyltransferase 2B10 precursor (EC 2.4.1.17) (UDPGT)	0.04	-	cyt	1 *	Microsome		600070		528
O75310 UniProt NPD GO	UDB11_HUMAN	UDP-glucuronosyltransferase 2B11 precursor (EC 2.4.1.17) (UDPGT)	0.04	-	end	1 *	Microsome		603064		529
Q8WN97 UniProt NPD GO	UDB30_MACFA	UDP-glucuronosyltransferase 2B30 precursor (EC 2.4.1.17) (UDPGT)	0.04	-	end	1	Microsome				528
Q9GLD9 UniProt NPD GO	UDB33_MACMU	UDP-glucuronosyltransferase 2B33 precursor (EC 2.4.1.17) (UDPGT)	0.04	-	cyt	1 *	Microsome				529
P06133 UniProt NPD GO	UDB4_HUMAN	UDP-glucuronosyltransferase 2B4 precursor (EC 2.4.1.17) (UDPGT) (Hyodeoxycholic acid) (HLUG25) (UDPG ...	0.04	-	end	1	Microsome	microsome [NAS]	600067		528
P17717 UniProt NPD GO	UDB5_MOUSE	UDP-glucuronosyltransferase 2B5 precursor (EC 2.4.1.17) (UDPGT) (M-1)	0.04	-	end	1	Microsome	mitochondrial inner membrane [IDA]			530
Q18779 UniProt NPD GO	SQV7_CAEEL	UDP-sugar transporter sqv-7 (Squashed vulva protein 7)	0.04	-	end	9 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein				329
P53157 UniProt NPD GO	YGI0_YEAST	UPF0041 protein YGL080W	0.04	-	mit	2 *		mitochondrion [IDA]			130
P40093 UniProt NPD GO	YEY6_YEAST	UPF0160 protein YER156C	0.04	-	mit	0		cytoplasm [IDA] nucleus [IDA]			338
Q9VVA8 UniProt NPD GO	U197_DROME	UPF0197 protein CG9669	0.04	-	end	2 *					78
P36142 UniProt NPD GO	YK31_YEAST	UPF0206 protein YKR051W	0.04	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				418
Q69BK0 UniProt NPD GO	UCRI_COLPO	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				274
Q69BJ6 UniProt NPD GO	UCRI_HYLSY	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				274
Q9CR68 UniProt NPD GO	UCRI_MOUSE	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			274
P43266 UniProt NPD GO	UCR9_EUGGR	Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial precursor (EC 1.10.2.2)	0.04	-	mit	1	Mitochondrion; mitochondrial inner membrane				100
Q9Y2Z9 UniProt NPD GO	COQ6_HUMAN	Ubiquinone biosynthesis monooxygenase COQ6 (EC 1.14.13.-)	0.04	-	mit	0					468
Q8R1S0 UniProt NPD GO	COQ6_MOUSE	Ubiquinone biosynthesis monooxygenase COQ6 (EC 1.14.13.-)	0.04	-	nuc	0					469
Q9C7F7 UniProt NPD GO	UGPI5_ARATH	Uncharacterized GPI-anchored protein At1g27950 precursor	0.04	-	end	2 *	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			193
P39729 UniProt NPD GO	YAD6_YEAST	Uncharacterized GTP-binding protein YAL036C	0.04	-	mit	0		cytoplasm [IDA]			369
P47153 UniProt NPD GO	YJ86_YEAST	Uncharacterized TLC domain-containing protein YJR116W	0.04	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				279
Q12082 UniProt NPD GO	YD157_YEAST	Uncharacterized mitochondrial protein YDL157C	0.04	-	cyt	0	Mitochondrion	mitochondrion [IDA]			118
Q566Q8 UniProt NPD GO	CK068_RAT	Uncharacterized protein C11orf68 homolog (Basophilic leukemia expressed protein Bles03)	0.04	-	cyt	0					251
Q96KH6 UniProt NPD GO	CR012_HUMAN	Uncharacterized protein C18orf12 (Protein HEIL1)	0.04	-	cyt	0					178
Q9D387 UniProt NPD GO	CT103_MOUSE	Uncharacterized protein C20orf103 homolog precursor	0.04	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				280
P59266 UniProt NPD GO	CT142_MOUSE	Uncharacterized protein C20orf142 homolog precursor	0.04	-	end	5	Membrane; multi-pass membrane protein (Potential)				262
Q9BUV8 UniProt NPD GO	CT024_HUMAN	Uncharacterized protein C20orf24 (Rab5-interacting protein) (RIP5)	0.04	-	end	2 *					137
Q9CQT9 UniProt NPD GO	CT024_MOUSE	Uncharacterized protein C20orf24 homolog	0.04	-	end	3 *					129
Q9CYY7 UniProt NPD GO	CT045_MOUSE	Uncharacterized protein C20orf45 homolog	0.04	-	cyt	0					195
Q9DAH1 UniProt NPD GO	CT079_MOUSE	Uncharacterized protein C20orf79 homolog	0.04	-	cyt	0					156
Q5NVS6 UniProt NPD GO	CX033_PONPY	Uncharacterized protein CXorf33 homolog precursor	0.04	-	cyt	0	Secreted protein (Potential)				266
P38341 UniProt NPD GO	YB9I_YEAST	Uncharacterized protein YBR262C	0.04	-	cyt	0		mitochondrion [IDA]			106
Q03034 UniProt NPD GO	YD539_YEAST	Uncharacterized protein YDR539W	0.04	-	mit	0		cytoplasm [IDA]			503
Q8TGU0 UniProt NPD GO	YG007_YEAST	Uncharacterized protein YGL007C-A	0.04	-	nuc	0					28
P53219 UniProt NPD GO	YG1L_YEAST	Uncharacterized protein YGR031W	0.04	-	mit	0		mitochondrion [IDA]			342
Q3E815 UniProt NPD GO	YH175_YEAST	Uncharacterized protein YHR175W-A	0.04	-	cyt	1 *	Membrane; single-pass membrane protein (Potential)				49

You are viewing entries 78701 to 78750 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.