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
P35039 UniProt NPD GO	TRY5_ANOGA	Trypsin-5 precursor (EC 3.4.21.4)	0.06	-	vac	0	Secreted protein				274
P19425 UniProt NPD GO	TMOF_AEDAE	Trypsin-modulating oostatic factor (TMOF) (OOSH)	0.06	-		0					10
Q9BZJ3 UniProt NPD GO	TRYD_HUMAN	Tryptase delta precursor (EC 3.4.21.59) (Delta tryptase) (Mast cell mMCP-7-like) (Tryptase-3) (HmMCP ...	0.06	-	end	0	Released from the secretory granules upon mast cell activation (By similarity)				235
O94128 UniProt NPD GO	TBA_MYCGR	Tubulin alpha chain	0.06	-	cyt	0					450
Q07972 UniProt NPD GO	TBAA_PNECA	Tubulin alpha chain (Fragment)	0.06	-	cyt	0					212
P24634 UniProt NPD GO	TBA2_EMENI	Tubulin alpha-2 chain	0.06	-	cyt	0					451
P08070 UniProt NPD GO	TBA2_CHICK	Tubulin alpha-2 chain (Testis-specific)	0.06	-	cyt	0					446
Q9GSR5 UniProt NPD GO	TBB_ENCIN	Tubulin beta chain (Beta tubulin)	0.06	-	cyt	0					439
Q6QDC9 UniProt NPD GO	TBB_MYCGR	Tubulin beta chain (Beta tubulin)	0.06	-	cyt	0	Cytoplasm				447
P12458 UniProt NPD GO	TBB2_PHYPO	Tubulin beta-2 chain (Tubulin beta-major chain)	0.06	-	cyt	0	Spindle. Mitosis in the slime mold Plasmodium differs from the process in many eukaryotes. The tubul ...				454
P53904 UniProt NPD GO	TBCB_YEAST	Tubulin-specific chaperone B (Tubulin folding cofactor B) (Alpha-tubulin formation protein 1)	0.06	-	cyt	0	Cytoplasm. Microtubule-associated	cytoplasm [IDA] nucleus [IDA]			254
Q9UNG2 UniProt NPD GO	TNF18_HUMAN	Tumor necrosis factor ligand superfamily member 18 (Glucocorticoid-induced TNF-related ligand) (hGIT ...	0.06	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)		603898		177
P30556 UniProt NPD GO	AGTR1_HUMAN	Type-1 angiotensin II receptor (AT1) (AT1AR) (AT1BR)	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	106165		359
O42713 UniProt NPD GO	TYRO_AGABI	Tyrosinase (EC 1.14.18.1) (Monophenol monooxygenase) (Phenolase) (Monophenol oxidase) (Cresolase)	0.06	-	nuc	0					556
P28213 UniProt NPD GO	PTP21_STYPL	Tyrosine-protein phosphatase 21 (EC 3.1.3.48) (Fragment)	0.06	-	cyt	0					115
P28196 UniProt NPD GO	PTP4_STYPL	Tyrosine-protein phosphatase 4 (EC 3.1.3.48) (Fragment)	0.06	-	nuc	0					109
P54768 UniProt NPD GO	TYDC1_PAPSO	Tyrosine/DOPA decarboxylase 1 [Includes: DOPA decarboxylase (EC 4.1.1.28) (DDC); Tyrosine decarboxyl ...	0.06	-	cyt	0					518
O35900 UniProt NPD GO	LSM2_MOUSE	U6 snRNA-associated Sm-like protein LSm2 (snRNP core Sm-like protein Sm-x5) (Protein G7b)	0.06	-	cyt	0	Nucleus (Potential)				95
Q9Y333 UniProt NPD GO	LSM2_HUMAN	U6 snRNA-associated Sm-like protein LSm2 (snRNP core Sm-like protein Sm-x5) (Small nuclear ribonucle ...	0.06	-	cyt	0	Nucleus (Potential)	nucleus [NAS]	607282		95
Q9TLX3 UniProt NPD GO	LPXC_CYACA	UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) (UDP-3-O-acyl-GlcNAc deace ...	0.06	-	cyt	0	Plastid; chloroplast				282
P36509 UniProt NPD GO	UD12_HUMAN	UDP-glucuronosyltransferase 1-2 precursor (EC 2.4.1.17) (UDP-glucuronosyltransferase 1A2) (UDPGT) (U ...	0.06	-	end	1	Microsome	microsome [NAS]	191740		530
Q9HAW9 UniProt NPD GO	UD18_HUMAN	UDP-glucuronosyltransferase 1-8 precursor (EC 2.4.1.17) (UDP-glucuronosyltransferase 1A8) (UDPGT) (U ...	0.06	-	end	1	Microsome		606433		530
O60656 UniProt NPD GO	UD19_HUMAN	UDP-glucuronosyltransferase 1-9 precursor (EC 2.4.1.17) (UDP-glucuronosyltransferase 1A9) (UDPGT) (U ...	0.06	-	end	1	Microsome		606434		530
P36512 UniProt NPD GO	UDB13_RABIT	UDP-glucuronosyltransferase 2B13 precursor (EC 2.4.1.17) (UDPGT) (EGT10)	0.06	-	end	1	Microsome				531
Q62789 UniProt NPD GO	UDB8_RAT	UDP-glucuronosyltransferase 2B8 precursor (EC 2.4.1.17) (UDPGT) (UGT2B-RH4)	0.06	-	end	1	Microsome				530
Q95KB4 UniProt NPD GO	S35B4_MACFA	UDP-xylose and UDP-N-acetylglucosamine transporter (Solute carrier family 35 member B4)	0.06	-	end	9 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				331
Q8CIA5 UniProt NPD GO	S35B4_MOUSE	UDP-xylose and UDP-N-acetylglucosamine transporter (Solute carrier family 35 member B4)	0.06	-	end	10 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				331
Q5R8M3 UniProt NPD GO	S35B4_PONPY	UDP-xylose and UDP-N-acetylglucosamine transporter (Solute carrier family 35 member B4)	0.06	-	end	9 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				331
Q969S0 UniProt NPD GO	S35B4_HUMAN	UDP-xylose and UDP-N-acetylglucosamine transporter (Solute carrier family 35 member B4) (YEA4 homolo ...	0.06	-	end	9 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi apparatus [IDA]			331
P39547 UniProt NPD GO	UIP3_YEAST	ULP1-interacting protein 3 (DUP240 protein UIP3)	0.06	-	end	2 *	Nucleus; nuclear membrane; multi-pass membrane protein. Cell membrane; multi-pass membrane protein	nuclear envelope [IDA]			235
P25637 UniProt NPD GO	YCU9_YEAST	UPF0029 protein YCR059C	0.06	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			258
Q10121 UniProt NPD GO	YSD2_CAEEL	UPF0076 protein C23G10.2	0.06	-	cyt	0					171
Q9P7T6 UniProt NPD GO	YIW4_SCHPO	UPF0160 protein C694.04c	0.06	-	cyt	0					324
Q922R1 UniProt NPD GO	CP070_MOUSE	UPF0183 protein C16orf70 homolog	0.06	-	cyt	0					422
Q07130 UniProt NPD GO	UGPA2_BOVIN	UTP--glucose-1-phosphate uridylyltransferase 2 (EC 2.7.7.9) (UDP-glucose pyrophosphorylase 2) (UDPGP ...	0.06	-	cyt	0	Cytoplasm				507
Q16851 UniProt NPD GO	UGPA2_HUMAN	UTP--glucose-1-phosphate uridylyltransferase 2 (EC 2.7.7.9) (UDP-glucose pyrophosphorylase 2) (UDPGP ...	0.06	-	cyt	0	Cytoplasm (By similarity)		191760		507
P46268 UniProt NPD GO	UCR7_PICJA	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit VII)	0.06	-	cyt	0	Mitochondrion; mitochondrial inner membrane (Potential)				126
Q69BJ7 UniProt NPD GO	UCRI_SAISC	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.06	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity)				274
Q6BPY6 UniProt NPD GO	UQCR2_DEBHA	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2)	0.06	-	nuc	0	Mitochondrion; mitochondrial inner membrane (By similarity)				376
O60044 UniProt NPD GO	UQCR2_NEUCR	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2)	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane				454
Q6C2E3 UniProt NPD GO	UQCR2_YARLI	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2)	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				417
P31930 UniProt NPD GO	UQCR1_HUMAN	Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor (EC 1.10.2.2)	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial electron transport chain [TAS]	191328		480
P49017 UniProt NPD GO	COQ5_YEAST	Ubiquinone biosynthesis methyltransferase COQ5, mitochondrial precursor (EC 2.1.1.-)	0.06	-	mit	0	Mitochondrion	mitochondrion [IDA]			307
P35127 UniProt NPD GO	UBL1_YEAST	Ubiquitin carboxyl-terminal hydrolase YUH1 (EC 3.4.19.12) (Ubiquitin thioesterase)	0.06	-	mit	0		cytoplasm [IC]		1CMX	236
Q9CZY3 UniProt NPD GO	UB2V1_MOUSE	Ubiquitin-conjugating enzyme E2 variant 1 (UEV-1) (CROC-1)	0.06	-	mit	0	Nucleus				147
P61085 UniProt NPD GO	UBC1_BOVIN	Ubiquitin-conjugating enzyme E2-25 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.06	-	nuc	0	Cytoplasm			2BF8	199
P61086 UniProt NPD GO	UBC1_HUMAN	Ubiquitin-conjugating enzyme E2-25 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.06	-	nuc	0	Cytoplasm (By similarity)		602846	1YLA	199
P61087 UniProt NPD GO	UBC1_MOUSE	Ubiquitin-conjugating enzyme E2-25 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.06	-	nuc	0	Cytoplasm (By similarity)				199
Q3E842 UniProt NPD GO	YM122_YEAST	Uncharacterized endoplamic reticulum membrane protein YMR122W-A	0.06	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			84
P42938 UniProt NPD GO	YG4F_YEAST	Uncharacterized kinase YGR205W (EC 2.7.-.-)	0.06	-	mit	0		cytoplasm [IDA] nucleus [IDA]		1ODF	290

You are viewing entries 73401 to 73450 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.