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
P05304 UniProt NPD GO	TBB_GIALA	Tubulin beta chain (Beta tubulin)	0.19	-	cyt	0					446
Q4P235 UniProt NPD GO	TBB_USTMA	Tubulin beta chain (Beta tubulin)	0.19	-	cyt	0					448
P12411 UniProt NPD GO	TBB1_ARATH	Tubulin beta-1 chain (Beta-1 tubulin)	0.19	-	cyt	0					447
Q9ZRB2 UniProt NPD GO	TBB1_WHEAT	Tubulin beta-1 chain (Beta-1 tubulin)	0.19	-	cyt	0					445
Q9ZPN8 UniProt NPD GO	TBB3_ELEIN	Tubulin beta-3 chain (Beta-3 tubulin)	0.19	-	cyt	0					446
Q27957 UniProt NPD GO	P25A_BOVIN	Tubulin polymerization-promoting protein (TPPP) (25 kDa brain-specific protein) (p25-alpha)	0.19	-	nuc	0					218
O04350 UniProt NPD GO	TBCA_ARATH	Tubulin-specific chaperone A (Tubulin-folding cofactor A) (CFA) (TCP1-chaperonin cofactor A homolog) ...	0.19	-	nuc	0					113
Q75N23 UniProt NPD GO	TNFA_CAMBA	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.19	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
P59694 UniProt NPD GO	TNFA_LAMGL	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.19	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
O14798 UniProt NPD GO	TR10C_HUMAN	Tumor necrosis factor receptor superfamily member 10C precursor (Decoy receptor 1) (DcR1) (Decoy TRA ...	0.19	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor	integral to plasma membrane [TAS]	603613		259
P07174 UniProt NPD GO	TNR16_RAT	Tumor necrosis factor receptor superfamily member 16 precursor (Low-affinity nerve growth factor rec ...	0.19	-	exc	1	Membrane; single-pass type I membrane protein			1SG1	425
Q9ZWS6 UniProt NPD GO	ARR6_ARATH	Two-component response regulator ARR6	0.19	-	cyt	0	Nucleus				186
P07948 UniProt NPD GO	LYN_HUMAN	Tyrosine-protein kinase Lyn (EC 2.7.10.2)	0.19	-	cyt	0		cytoplasm [ISS] nucleus [ISS]	165120	1WA7	511
P42686 UniProt NPD GO	SRK1_SPOLA	Tyrosine-protein kinase isoform SRK1 (EC 2.7.10.2)	0.19	-	cyt	0	Cytoplasm (Probable)				505
Q8QZX5 UniProt NPD GO	LSM10_MOUSE	U7 snRNA-associated Sm-like protein LSm10	0.19	-	cyt	0	Nucleus (By similarity)				122
Q5KMF9 UniProt NPD GO	ALG14_CRYNE	UDP-N-acetylglucosamine transferase subunit ALG14 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.19	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				229
Q6FSF8 UniProt NPD GO	HUT1_CANGA	UDP-galactose transporter homolog 1	0.19	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				362
O70199 UniProt NPD GO	UGDH_RAT	UDP-glucose 6-dehydrogenase (EC 1.1.1.22) (UDP-Glc dehydrogenase) (UDP-GlcDH) (UDPGDH)	0.19	-	mit	0		cytosol [IDA]			493
Q64435 UniProt NPD GO	UD16_MOUSE	UDP-glucuronosyltransferase 1-6 precursor (EC 2.4.1.17) (UDPGT) (UGT1*6) (UGT1-06) (UGT1.6) (UGT1A6) ...	0.19	-	end	1 *	Microsome	mitochondrial inner membrane [IDA]			531
O01374 UniProt NPD GO	UCR6_SCHMA	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2)	0.19	-	cyt	0	Mitochondrion; mitochondrial inner membrane				130
Q9CZ13 UniProt NPD GO	UQCR1_MOUSE	Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor (EC 1.10.2.2)	0.19	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			480
P14792 UniProt NPD GO	UBIQ_CAEEL	Ubiquitin	0.19	-	cyt	0	Cytoplasm. Nucleus				76
P19848 UniProt NPD GO	UBIQ_COPCO	Ubiquitin	0.19	-	cyt	0	Cytoplasm. Nucleus				76
P59669 UniProt NPD GO	UBIQ_GEOCY	Ubiquitin	0.19	-	cyt	0	Cytoplasm. Nucleus				76
P49635 UniProt NPD GO	UBIQ_LEITA	Ubiquitin	0.19	-	nuc	0	Cytoplasm. Nucleus				76
P20685 UniProt NPD GO	UBIQ_TETPY	Ubiquitin	0.19	-	cyt	0	Cytoplasm. Nucleus				76
Q16763 UniProt NPD GO	UBE2S_HUMAN	Ubiquitin-conjugating enzyme E2 S (EC 6.3.2.19) (Ubiquitin-protein ligase S) (Ubiquitin carrier prot ...	0.19	-	cyt	0				1ZDN	222
P52487 UniProt NPD GO	UBC84_DROME	Ubiquitin-conjugating enzyme E2-18 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.19	-	nuc	0					153
Q29503 UniProt NPD GO	UB2R1_RABIT	Ubiquitin-conjugating enzyme E2-32 kDa complementing (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiqu ...	0.19	-	nuc	0					238
P32622 UniProt NPD GO	YEF1_YEAST	Uncharacterized kinase YEL041W (EC 2.7.1.-)	0.19	-	cyt	0					495
P09004 UniProt NPD GO	MI25_MAIZE	Uncharacterized mitochondrial 22 kDa protein (ORF 25)	0.19	-	mit	0					219
Q4WFV6 UniProt NPD GO	YA880_ASPFU	Uncharacterized protein Afu3g00880 precursor	0.19	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				219
Q96IZ2 UniProt NPD GO	CF105_HUMAN	Uncharacterized protein C6orf105	0.19	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				230
Q8WWP5 UniProt NPD GO	CH006_HUMAN	Uncharacterized protein C8orf6	0.19	-	cyt	0					94
P38222 UniProt NPD GO	YBO0_YEAST	Uncharacterized protein YBR030W	0.19	-	cyt	0		nucleus [IDA]			552
P53062 UniProt NPD GO	YGZ7_YEAST	Uncharacterized protein YGL247W	0.19	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	nuclear envelope [IDA]			197
P53215 UniProt NPD GO	YG1G_YEAST	Uncharacterized protein YGR024C	0.19	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			237
P40499 UniProt NPD GO	YIJ0_YEAST	Uncharacterized protein YIL090W	0.19	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			491
P36101 UniProt NPD GO	YKC7_YEAST	Uncharacterized protein YKL027W	0.19	-	cyt	1 *		mitochondrial outer membrane [IDA] mitochondrion [IDA]			447
Q08045 UniProt NPD GO	YL104_YEAST	Uncharacterized protein YLR104W precursor	0.19	-	exc	1 *					131
P53980 UniProt NPD GO	YNB1_YEAST	Uncharacterized protein YNL011C	0.19	-	mit	0					444
P53895 UniProt NPD GO	YNP9_YEAST	Uncharacterized protein YNL159C	0.19	-	end	2	Membrane; multi-pass membrane protein (Potential)				289
Q12314 UniProt NPD GO	YO021_YEAST	Uncharacterized protein YOR021C	0.19	-	cyt	0	Cytoplasm				213
P11684 UniProt NPD GO	UTER_HUMAN	Uteroglobin precursor (Secretoglobin family 1A member 1) (Clara cell phospholipid-binding protein) ( ...	0.19	-	exc	0	Secreted protein		192020		91
P11593 UniProt NPD GO	VATB_NEUCR	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit) ...	0.19	-	cyt	0					513
P31412 UniProt NPD GO	VATC_YEAST	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit) ...	0.19	-	cyt	0	Vacuole; vacuolar membrane; peripheral membrane protein	hydrogen-transporting ATPase V1 domain [TAS] vacuolar membrane (sensu Fungi) [TAS]		1U7L	391
Q9SP55 UniProt NPD GO	VATG_CITLI	Vacuolar ATP synthase subunit G (EC 3.6.3.14) (V-ATPase G subunit) (Vacuolar proton pump G subunit)	0.19	-	cyt	0					110
O82703 UniProt NPD GO	VATG2_TOBAC	Vacuolar ATP synthase subunit G 2 (EC 3.6.3.14) (V-ATPase G subunit 2) (Vacuolar proton pump G subun ...	0.19	-	nuc	0					111
Q94KJ7 UniProt NPD GO	VPS33_ARATH	Vacuolar protein-sorting protein 33 homolog (AtVPS33)	0.19	-	cyt	0					592
Q39119 UniProt NPD GO	VPEG_ARATH	Vacuolar-processing enzyme gamma-isozyme precursor (EC 3.4.22.-) (Gamma-VPE)	0.19	-	exc	1 *	Vacuole				490

You are viewing entries 52551 to 52600 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.