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
Q6TGS6 UniProt NPD GO	SYYC_BRARE	Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS)	0.25	-	cyt	0	Cytoplasm (By similarity)				529
P09661 UniProt NPD GO	RU2A_HUMAN	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.25	-	nuc	0	Nucleus	snRNP U2 [TAS] spliceosome complex [IDA]	603521	1A9N	255
Q4R8Y8 UniProt NPD GO	RU2A_MACFA	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.25	-	nuc	0	Nucleus (By similarity)				255
Q6C417 UniProt NPD GO	RU2A_YARLI	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.25	-	cyt	0	Nucleus (By similarity)				230
P68543 UniProt NPD GO	UBXD4_HUMAN	UBX domain-containing protein 4	0.25	-	nuc	0					259
Q9N598 UniProt NPD GO	USE1_CAEEL	USE1-like protein	0.25	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				254
P07256 UniProt NPD GO	UQCR1_YEAST	Ubiquinol-cytochrome-c reductase complex core protein 1, mitochondrial precursor (Complex III subuni ...	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane	respiratory chain complex III (sensu Eukary... [IDA]		1P84	457
Q5HYK3 UniProt NPD GO	COQ5_HUMAN	Ubiquinone biosynthesis methyltransferase COQ5, mitochondrial precursor (EC 2.1.1.-)	0.25	-	cyt	0	Mitochondrion (By similarity)				327
Q9Y3A0 UniProt NPD GO	COQ4_HUMAN	Ubiquinone biosynthesis protein COQ4 homolog (Coenzyme Q biosynthesis protein 4 homolog)	0.25	-	mit	0					265
Q75CR6 UniProt NPD GO	COQ9_ASHGO	Ubiquinone biosynthesis protein COQ9, mitochondrial precursor	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side (By similarity ...				246
P22589 UniProt NPD GO	UBIQ_PHYIN	Ubiquitin	0.25	-	nuc	0	Cytoplasm. Nucleus				76
P70362 UniProt NPD GO	UFD1_MOUSE	Ubiquitin fusion degradation protein 1 homolog (UB fusion protein 1)	0.25	-	mit	0					307
P31255 UniProt NPD GO	UBE1Y_MACRU	Ubiquitin-activating enzyme E1 Y (Fragment)	0.25	-	nuc	0					152
Q925F3 UniProt NPD GO	UB7I4_MOUSE	Ubiquitin-conjugating enzyme 7-interacting protein 4 (UbcM4-interacting protein 4) (RING finger prot ...	0.25	-	cyt	1	Nucleus (By similarity)				292
P35129 UniProt NPD GO	UBC2_CAEEL	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase 2) (Ubiquitin carrier prot ...	0.25	-	nuc	0				1Z2U	147
Q9QZU9 UniProt NPD GO	UB2L6_MOUSE	Ubiquitin-conjugating enzyme E2 L6 (EC 6.3.2.19) (Ubiquitin-protein ligase L6) (Ubiquitin carrier pr ...	0.25	-	cyt	0					152
Q04772 UniProt NPD GO	YMW3_YEAST	Uncharacterized heme-binding protein YMR073C	0.25	-	nuc	0		cytoplasm [IDA]			201
P60007 UniProt NPD GO	CK051_MOUSE	Uncharacterized protein C11orf51 homolog	0.25	-	exc	0					132
P38324 UniProt NPD GO	YB78_YEAST	Uncharacterized protein YBR228W	0.25	-	mit	0		nucleus [IC]			304
Q12301 UniProt NPD GO	YD180_YEAST	Uncharacterized protein YDL180W	0.25	-	end	7 *	Vacuole; vacuolar membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			547
P40057 UniProt NPD GO	YER4_YEAST	Uncharacterized protein YER084W	0.25	-	nuc	0					128
P32643 UniProt NPD GO	YE05_YEAST	Uncharacterized protein YER175C	0.25	-	cyt	0		cytosol [IDA]			299
P53133 UniProt NPD GO	YGL7_YEAST	Uncharacterized protein YGL117W	0.25	-	cyt	0					265
P38828 UniProt NPD GO	YHS1_YEAST	Uncharacterized protein YHR121W	0.25	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			187
P40543 UniProt NPD GO	YIC4_YEAST	Uncharacterized protein YIL024C	0.25	-	nuc	0					189
P40159 UniProt NPD GO	YNU8_YEAST	Uncharacterized protein YNL208W	0.25	-	nuc	0	Mitochondrion	mitochondrion [IDA]			199
Q02872 UniProt NPD GO	YP108_YEAST	Uncharacterized protein YPL108W	0.25	-	cyt	0	Cytoplasm	cytoplasm [IDA]			168
Q06104 UniProt NPD GO	YPR09_YEAST	Uncharacterized protein YPR109W	0.25	-	mit	2	Membrane; multi-pass membrane protein (Potential)				294
Q91WW1 UniProt NPD GO	UCN2_RAT	Urocortin-2 precursor (Urocortin II) (Ucn II)	0.25	-	exc	0	Secreted protein	extracellular region [ISS]			109
Q5DID0 UniProt NPD GO	UROL1_HUMAN	Uromodulin-like 1 precursor (Olfactorin)	0.25	-	end	1	Cell membrane; single-pass type I membrane protein. Isoform 3, isoform 4: Cytoplasm				1318
Q864V4 UniProt NPD GO	UPK3B_BOVIN	Uroplakin-3B precursor (Uroplakin IIIb) (UPIIIb) (p35)	0.25	-	exc	1	Membrane; single-pass type I membrane protein (Potential). Heterodimer formation with Uroplakin Ib i ...				279
Q9U0S4 UniProt NPD GO	VATD_MANSE	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit)	0.25	-	cyt	0					246
O82628 UniProt NPD GO	VATG1_ARATH	Vacuolar ATP synthase subunit G 1 (EC 3.6.3.14) (V-ATPase G subunit 1) (Vacuolar proton pump G subun ...	0.25	-	nuc	0					110
O82702 UniProt NPD GO	VATG1_TOBAC	Vacuolar ATP synthase subunit G 1 (EC 3.6.3.14) (V-ATPase G subunit 1) (Vacuolar proton pump G subun ...	0.25	-	nuc	0					110
P41807 UniProt NPD GO	VATH_YEAST	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump subunit H) ...	0.25	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein	hydrogen-transporting ATPase V1 domain [TAS] vacuolar membrane (sensu Fungi) [TAS]		1HO8	478
P32341 UniProt NPD GO	VPH2_YEAST	Vacuolar ATPase assembly integral membrane protein VPH2 (Protein VMA12)	0.25	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA]			215
Q5BKM4 UniProt NPD GO	VP26B_XENTR	Vacuolar protein sorting 26B (Vesicle protein sorting 26B)	0.25	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Does not localize to endosomes (By similarity)				337
Q6DH23 UniProt NPD GO	V26BB_BRARE	Vacuolar protein sorting 26B-B (Vesicle protein sorting 26B-B)	0.25	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Does not localize to endosomes (By similarity)				329
Q6DFB9 UniProt NPD GO	V26BB_XENLA	Vacuolar protein sorting 26B-B (Vesicle protein sorting 26B-B)	0.25	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Does not localize to endosomes (By similarity)				337
P36116 UniProt NPD GO	VPS51_YEAST	Vacuolar protein sorting protein 51 (Apical bud growth protein 3)	0.25	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. End ...	GARP complex [IPI] Golgi apparatus [IDA]		2C5K	164
P52917 UniProt NPD GO	VPS4_YEAST	Vacuolar protein sorting-associated protein VPS4 (END13 protein) (DOA4-independent degradation prote ...	0.25	-	cyt	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity)	cytoplasm [IDA] endoplasmic reticulum [IDA]			437
Q06263 UniProt NPD GO	VTA1_YEAST	Vacuolar protein sorting-associated protein VTA1 (VPS20-associated protein 1)	0.25	-	nuc	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein	endosome [IDA] multivesicular body [IDA]			330
Q5KL29 UniProt NPD GO	SNF7_CRYNE	Vacuolar sorting protein SNF7 (Vacuolar protein sorting-associated protein VPS32)	0.25	-	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				220
P02896 UniProt NPD GO	VSM4_TRYBB	Variant surface glycoprotein MITAT 1.4A precursor (VSG 117)	0.25	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				526
P39710 UniProt NPD GO	YAG6_YEAST	Very hypothetical protein YAL066W	0.25	-	mit	2 *					102
Q9LFP1 UniProt NPD GO	VA713_ARATH	Vesicle-associated membrane protein 713 (AtVAMP713)	0.25	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				221
P46460 UniProt NPD GO	NSF_MOUSE	Vesicle-fusing ATPase (EC 3.6.4.6) (Vesicular-fusion protein NSF) (N-ethylmaleimide sensitive fusion ...	0.25	-	cyt	0	Cytoplasm				744
Q5J3N1 UniProt NPD GO	VN1B6_RAT	Vomeronasal type-1 receptor B6 (M24 pheromone receptor)	0.25	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				308
Q5RAW8 UniProt NPD GO	WDR48_PONPY	WD repeat protein 48	0.25	-	nuc	0	Lysosome (By similarity)				677
Q8TAF3 UniProt NPD GO	WDR48_HUMAN	WD repeat protein 48 (WD repeat endosomal protein) (p80)	0.25	-	nuc	0	Lysosome				677

You are viewing entries 45851 to 45900 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.