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
Q8IWZ4 UniProt NPD GO	TRI48_HUMAN	Tripartite motif-containing protein 48 (RING finger protein 101)	0.41	-	cyt	0					375
Q96A61 UniProt NPD GO	TRI52_HUMAN	Tripartite motif-containing protein 52 (RING finger protein 102)	0.41	-	cyt	0					297
Q80VI1 UniProt NPD GO	TRI56_MOUSE	Tripartite motif-containing protein 56	0.41	-	cyt	0					734
Q9C026 UniProt NPD GO	TRIM9_HUMAN	Tripartite motif-containing protein 9 (RING finger protein 91)	0.41	-	nuc	0			606555	2DB8	710
Q9N6K2 UniProt NPD GO	OSA_DROSI	Trithorax group protein osa (Protein eyelid) (Fragment)	0.41	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			324
Q9JKK7 UniProt NPD GO	TMOD2_MOUSE	Tropomodulin-2 (Neuronal tropomodulin) (N-Tmod)	0.41	-	nuc	0					351
Q25457 UniProt NPD GO	TPM_MYTED	Tropomyosin	0.41	-	nuc	0					284
P91958 UniProt NPD GO	TPM_MYTGA	Tropomyosin	0.41	-	nuc	0					284
O16127 UniProt NPD GO	TPM_ECHGR	Tropomyosin (Fragment)	0.41	-	nuc	0					177
P42639 UniProt NPD GO	TPM1_PIG	Tropomyosin 1 alpha chain (Alpha-tropomyosin)	0.41	-	nuc	0				1C1G	284
P06753 UniProt NPD GO	TPM3_HUMAN	Tropomyosin alpha-3 chain (Tropomyosin-3) (Tropomyosin gamma) (hTM5)	0.41	-	nuc	0		cytoskeleton [NAS] muscle thin filament tropomyosin [TAS]	609284		284
Q07068 UniProt NPD GO	TPM1_CIOIN	Tropomyosin, smooth muscle/fibroblast CTM1	0.41	-	nuc	0					284
Q9R187 UniProt NPD GO	EDAR_MOUSE	Tumor necrosis factor receptor superfamily member EDAR precursor (Anhidrotic ectodysplasin receptor ...	0.41	-	exc	1	Membrane; single-pass type I membrane protein (Probable)	apical part of cell [IDA] plasma membrane [IDA]			448
Q80YE2 UniProt NPD GO	T53I1_RAT	Tumor protein p53-inducible nuclear protein 1 (p53-dependent damage-inducible nuclear protein 1) (p5 ...	0.41	-	nuc	0	Nucleus (By similarity)				239
Q9V422 UniProt NPD GO	RYK2_DROME	Tyrosine-protein kinase Dnt precursor (EC 2.7.10.1) (Protein doughnut)	0.41	-	nuc	1					584
Q06806 UniProt NPD GO	TIE1_MOUSE	Tyrosine-protein kinase receptor Tie-1 precursor (EC 2.7.10.1)	0.41	-	end	1	Membrane; single-pass type I membrane protein				1134
P28669 UniProt NPD GO	SYYM_PODAN	Tyrosyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.1) (Tyrosine--tRNA ligase) (TyrRS)	0.41	-	mit	0	Mitochondrion; mitochondrial matrix				640
P40362 UniProt NPD GO	UTP18_YEAST	U3 small nucleolar RNA-associated protein 18 (U3 snoRNA-associated protein 18)	0.41	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI]			594
Q755T8 UniProt NPD GO	IMP4_ASHGO	U3 small nucleolar ribonucleoprotein protein IMP4 (U3 snoRNP protein IMP4)	0.41	-	mit	0	Nucleus; nucleolus (By similarity)				283
Q6FNN7 UniProt NPD GO	IMP4_CANGA	U3 small nucleolar ribonucleoprotein protein IMP4 (U3 snoRNP protein IMP4)	0.41	-	mit	0	Nucleus; nucleolus (By similarity)				288
Q21534 UniProt NPD GO	YVL7_CAEEL	UPF0028 protein M110.7	0.41	-	mit	0					880
Q6AXQ9 UniProt NPD GO	U360_RAT	UPF0360 protein	0.41	-	nuc	0					301
P56399 UniProt NPD GO	UBP5_MOUSE	Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15) (Ubiquitin thioesterase 5) (Ubiquitin-specific ...	0.41	-	cyt	0					858
Q96FW1 UniProt NPD GO	OTUB1_HUMAN	Ubiquitin thioesterase protein OTUB1 (EC 3.4.-.-) (Otubain 1) (OTU domain-containing ubiquitin aldeh ...	0.41	-	cyt	0			608337		271
P52493 UniProt NPD GO	UBC2_NEUCR	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase ubc2) (Ubiquitin carrier p ...	0.41	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				151
Q6CMG6 UniProt NPD GO	UBC6_KLULA	Ubiquitin-conjugating enzyme E2 6 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC6) (Ubiquitin carrier p ...	0.41	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane (By similarity)				251
P25153 UniProt NPD GO	UBCD6_DROME	Ubiquitin-conjugating enzyme E2-17 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.41	-	nuc	0	Nucleus				151
P40566 UniProt NPD GO	YIS7_YEAST	Uncharacterized glycosyl hydrolase YIR007W (EC 3.2.1.-)	0.41	-	nuc	0		cytoplasm [IDA]			764
Q00058 UniProt NPD GO	MI25_ORYSA	Uncharacterized mitochondrial 22 kDa protein (ORF 25)	0.41	-	nuc	0					197
Q5R562 UniProt NPD GO	CP045_PONPY	Uncharacterized protein C16orf45 homolog	0.41	-	nuc	0					204
Q8IVV7 UniProt NPD GO	CQ039_HUMAN	Uncharacterized protein C17orf39	0.41	-	nuc	0					300
Q8R092 UniProt NPD GO	CA043_MOUSE	Uncharacterized protein C1orf43 homolog	0.41	-	nuc	1 *					253
Q52LD8 UniProt NPD GO	CB011_HUMAN	Uncharacterized protein C2orf11	0.41	-	nuc	0					501
P45967 UniProt NPD GO	YNZ7_CAEEL	Uncharacterized protein T09A5.7	0.41	-	nuc	0					103
P25355 UniProt NPD GO	YCU4_YEAST	Uncharacterized protein YCR054C	0.41	-	cyt	0		cytoplasm [IDA]			563
P33199 UniProt NPD GO	YGB5_YEAST	Uncharacterized protein YGL015C	0.41	-	nuc	0					130
Q01163 UniProt NPD GO	YGM9_YEAST	Uncharacterized protein YGL129C	0.41	-	nuc	0		mitochondrial small ribosomal subunit [IDA]			488
P53281 UniProt NPD GO	YG3D_YEAST	Uncharacterized protein YGR136W	0.41	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			241
P38813 UniProt NPD GO	YHQ1_YEAST	Uncharacterized protein YHR101C precursor	0.41	-	end	1		integral to endoplasmic reticulum membrane [IDA]			335
P38833 UniProt NPD GO	YHS7_YEAST	Uncharacterized protein YHR127W	0.41	-	nuc	0		nucleus [IDA]			243
P47031 UniProt NPD GO	YJI2_YEAST	Uncharacterized protein YJL082W	0.41	-	nuc	0		cytoplasm [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA] nucleus [IDA]			731
Q3E7A7 UniProt NPD GO	YK018_YEAST	Uncharacterized protein YKL018C-A precursor	0.41	-	cyt	0	Cytoplasm	cytoplasm [IDA]			99
Q12015 UniProt NPD GO	YO223_YEAST	Uncharacterized protein YOR223W	0.41	-	end	2	Membrane; multi-pass membrane protein (Potential)				292
P38750 UniProt NPD GO	YHA8_YEAST	Uncharacterized transporter YHL008C	0.41	-	end	6 *	Membrane; multi-pass membrane protein (Probable)	vacuole (sensu Fungi) [IDA]			627
P81615 UniProt NPD GO	UCN1_MOUSE	Urocortin precursor	0.41	-	exc	0	Secreted protein				122
P32648 UniProt NPD GO	VIP_MOUSE	VIP peptides precursor [Contains: Intestinal peptide PHI-42; Intestinal peptide PHI-27 (Peptide hist ...	0.41	-	exc	1 *	Secreted protein				170
P69771 UniProt NPD GO	DID2_YEAST	Vacuolar protein sorting protein 46 (Charged multivesicular body protein 1) (DOA4-independent degrad ...	0.41	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein. Intracellular membrane; peripheral membra ...	cytoplasm [IDA] late endosome [IDA]			204
P49696 UniProt NPD GO	SYV_FUGRU	Valyl-tRNA synthetase (EC 6.1.1.9) (Valine--tRNA ligase) (ValRS)	0.41	-	nuc	0					1217
P07806 UniProt NPD GO	SYV_YEAST	Valyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.9) (Valine--tRNA ligase) (ValRS)	0.41	-	mit	0	Mitochondrion. Cytoplasm	cytoplasm [IMP] mitochondrion [IDA]			1104
Q9NFP1 UniProt NPD GO	VNNL1_DROME	Vanin-like protein 1 precursor	0.41	-	exc	1 *		extrinsic to membrane [NAS]			558

You are viewing entries 31501 to 31550 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.