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
Q9P032 UniProt NPD GO	CF066_HUMAN	UPF0240 protein C6orf66	0.17	-	nuc	0					175
Q9H7V2 UniProt NPD GO	CT039_HUMAN	UPF0338 protein C20orf39	0.17	-	end	2	Membrane; multi-pass membrane protein (Potential)				258
P99028 UniProt NPD GO	UCRH_MOUSE	Ubiquinol-cytochrome c reductase complex 11 kDa protein, mitochondrial precursor (EC 1.10.2.2) (Mito ...	0.17	-	nuc	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			89
P00128 UniProt NPD GO	UCR7_YEAST	Ubiquinol-cytochrome c reductase complex 14 kDa protein (Complex III subunit 7) (Cytochrome b-c1 com ...	0.17	-	cyt	0	Mitochondrion; mitochondrial inner membrane	respiratory chain complex III (sensu Eukary... [IDA]		1P84	127
P49345 UniProt NPD GO	UCR7_KLULA	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit VII)	0.17	-	mit	0	Mitochondrion; mitochondrial inner membrane (Potential)				127
Q9ZPR0 UniProt NPD GO	COQ4_ARATH	Ubiquinone biosynthesis protein COQ4 homolog	0.17	-	cyt	0					226
Q8L6Y1 UniProt NPD GO	UBP14_ARATH	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.1.2.15) (Ubiquitin thioesterase 14) (Ubiquitin-specif ...	0.17	-	cyt	0				1WIV	797
O02741 UniProt NPD GO	UCRP_BOVIN	Ubiquitin cross-reactive protein (Interferon-stimulated gene product 17) (BoUCRP)	0.17	-	nuc	0	Cytoplasm. UCRP conjugates seem to be noncovalently associated with the intermediate filaments and d ...				153
Q9STN8 UniProt NPD GO	SINA4_ARATH	Ubiquitin ligase SINAT4 (EC 6.3.2.-) (Seven in absentia homolog 4)	0.17	-	nuc	0		mitochondrion [IDA]			327
Q42541 UniProt NPD GO	UBC13_ARATH	Ubiquitin-conjugating enzyme E2 13 (EC 6.3.2.19) (Ubiquitin-protein ligase 13) (Ubiquitin carrier pr ...	0.17	-	nuc	0					166
P46595 UniProt NPD GO	UBC4_SCHPO	Ubiquitin-conjugating enzyme E2 4 (EC 6.3.2.19) (Ubiquitin-protein ligase 4) (Ubiquitin carrier prot ...	0.17	-	nuc	0					147
Q42540 UniProt NPD GO	UBC7_ARATH	Ubiquitin-conjugating enzyme E2 7 (EC 6.3.2.19) (Ubiquitin-protein ligase 7) (Ubiquitin carrier prot ...	0.17	-	nuc	0					166
Q921J4 UniProt NPD GO	UBE2S_MOUSE	Ubiquitin-conjugating enzyme E2 S (EC 6.3.2.19) (Ubiquitin-protein ligase S) (Ubiquitin carrier prot ...	0.17	-	cyt	0					223
P35128 UniProt NPD GO	UBCD3_DROME	Ubiquitin-conjugating enzyme E2-17 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.17	-	mit	0					151
P16577 UniProt NPD GO	UBC4_WHEAT	Ubiquitin-conjugating enzyme E2-23 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.17	-	cyt	0					184
P55852 UniProt NPD GO	SMT3_ARATH	Ubiquitin-like protein SMT3	0.17	-	nuc	0					100
Q96VG1 UniProt NPD GO	YBAI_SCHPO	Uncharacterized protein C119.18	0.17	-	nuc	0					69
O95177 UniProt NPD GO	CP003_HUMAN	Uncharacterized protein C16orf3	0.17	-	nuc	0			605179		125
Q5SYH2 UniProt NPD GO	CQ032_MOUSE	Uncharacterized protein C17orf32 homolog	0.17	-	mit	2	Membrane; multi-pass membrane protein (Potential)				208
Q68CL5 UniProt NPD GO	CR010_HUMAN	Uncharacterized protein C18orf10	0.17	-	nuc	0	Nucleus (Potential)				257
Q9H1L0 UniProt NPD GO	CT166_HUMAN	Uncharacterized protein C20orf166	0.17	-	nuc	0					117
P38740 UniProt NPD GO	YHC6_YEAST	Uncharacterized protein YHL026C	0.17	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				315
Q3E746 UniProt NPD GO	YH086_YEAST	Uncharacterized protein YHR086W-A	0.17	-	mit	0					53
Q3E7Z4 UniProt NPD GO	YI046_YEAST	Uncharacterized protein YIL046W-A	0.17	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				54
Q05778 UniProt NPD GO	YL199_YEAST	Uncharacterized protein YLR199C	0.17	-	nuc	0	Cytoplasm	cytoplasm [IDA]			276
Q03880 UniProt NPD GO	YM10_YEAST	Uncharacterized protein YMR123W	0.17	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			122
Q08218 UniProt NPD GO	YO047_YEAST	Uncharacterized protein YOL047C	0.17	-	end	4	Membrane; multi-pass membrane protein (Potential). Cytoplasm. Punctate structures in cytoplasm	cytoplasm [IDA]			356
Q12010 UniProt NPD GO	YO092_YEAST	Uncharacterized protein YOL092W	0.17	-	end	7 *	Vacuole; vacuolar membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA] vacuolar membrane (sensu Fungi) [IDA]			308
P40475 UniProt NPD GO	YIM0_YEAST	Uncharacterized transporter YIL120W	0.17	-	end	11	Membrane; multi-pass membrane protein (Probable)	plasma membrane [IDA]			563
P39542 UniProt NPD GO	YJT3_YEAST	Uncharacterized transporter YJL193W	0.17	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				402
P07374 UniProt NPD GO	UREA_CANEN	Urease (EC 3.5.1.5) (Urea amidohydrolase)	0.17	-	cyt	0					840
O00084 UniProt NPD GO	UREA_SCHPO	Urease (EC 3.5.1.5) (Urea amidohydrolase)	0.17	-	mit	0					835
P36150 UniProt NPD GO	SUMT_YEAST	Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) (Urogen III methylase) (SUMT) (Uroporphyrinogen ...	0.17	-	mit	0					593
P06174 UniProt NPD GO	HEM4_YEAST	Uroporphyrinogen-III synthase (EC 4.2.1.75) (UROS) (Uroporphyrinogen-III cosynthetase) (Hydroxymethy ...	0.17	-	mit	0					275
Q9ZRD6 UniProt NPD GO	YKT61_ARATH	VAMP-like protein YKT61 (AtYKT61) (Geranylgeranylated protein 1) (AtGP1)	0.17	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				199
O65421 UniProt NPD GO	VP282_ARATH	VPS28 protein homolog 2	0.17	-	nuc	0					209
P48414 UniProt NPD GO	VATA_CYACA	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.17	-	cyt	0					587
P49712 UniProt NPD GO	VATB_CHICK	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit)	0.17	-	cyt	0					453
P11574 UniProt NPD GO	VATB_ARATH	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit) ...	0.17	-	cyt	0					486
P31408 UniProt NPD GO	VATB2_BOVIN	Vacuolar ATP synthase subunit B, brain isoform (EC 3.6.3.14) (V-ATPase B2 subunit) (Vacuolar proton ...	0.17	-	mit	0	Membrane; peripheral membrane protein. Endomembrane				511
P25286 UniProt NPD GO	VPP1_RAT	Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1 (V-ATPase 116 kDa isoform a1) (Clat ...	0.17	-	end	6	Integral membrane protein. Coated vesicle				838
P37288 UniProt NPD GO	V1AR_HUMAN	Vasopressin V1a receptor (V1aR) (Vascular/hepatic-type arginine vasopressin receptor) (Antidiuretic ...	0.17	-	end	7	Membrane; multi-pass membrane protein	endosome [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	600821	1YTV	418
P35783 UniProt NPD GO	VA5_VESFL	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Ves f 5) (Ves f V)	0.17	-	nuc	0	Secreted protein. Venom reservoirs				204
P35760 UniProt NPD GO	VA5_VESMC	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Ves m 5) (Ves m V)	0.17	-	nuc	0	Secreted protein. Venom reservoirs				204
Q9C118 UniProt NPD GO	YFFN_SCHPO	Very hypothetical protein C1687.23c in chromosome I	0.17	-	nuc	0					104
P38178 UniProt NPD GO	YBI3_YEAST	Very hypothetical protein YBL083C	0.17	-	cyt	0					141
Q04762 UniProt NPD GO	YYY5_HUMAN	Very very hypothetical protein CMAR	0.17	-	nuc	0		extracellular matrix (sensu Metazoa) [TAS]			142
P49748 UniProt NPD GO	ACADV_HUMAN	Very-long-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.-) (VLCAD)	0.17	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [TAS]	609575		655
P58200 UniProt NPD GO	VTI1B_RAT	Vesicle transport through interaction with t-SNAREs homolog 1B (Vesicle transport v-SNARE protein Vt ...	0.17	-	nuc	0					33
Q62468 UniProt NPD GO	VILI_MOUSE	Villin-1	0.17	-	cyt	0		brush border [TAS]			826

You are viewing entries 55101 to 55150 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.