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
Q9H410 UniProt NPD GO	CT172_HUMAN	Uncharacterized protein C20orf172	0.76	-	nuc	0	Nucleus. Associated with the kinetochore		609175		356
Q9NQG5 UniProt NPD GO	CT077_HUMAN	Uncharacterized protein C20orf77	0.76	-	nuc	0					326
Q9CSU0 UniProt NPD GO	CT077_MOUSE	Uncharacterized protein C20orf77 homolog	0.76	-	nuc	0					326
P34224 UniProt NPD GO	YBF9_YEAST	Uncharacterized protein YBL059W	0.76	+	nuc	2		mitochondrion [IDA]			193
P53976 UniProt NPD GO	YNB8_YEAST	Uncharacterized protein YNL018C	0.76	-	nuc	0					612
Q12453 UniProt NPD GO	YO112_YEAST	Uncharacterized protein YOR112W	0.76	-	nuc	0	Cytoplasm	cytoplasm [IDA]			761
Q02873 UniProt NPD GO	YP107_YEAST	Uncharacterized protein YPL107W, mitochondrial precursor	0.76	-	nuc	0	Mitochondrion	mitochondrion [IDA]			248
Q495M9 UniProt NPD GO	USH1G_HUMAN	Usher syndrome type-1G protein (Scaffold protein containing ankyrin repeats and SAM domain)	0.76	-	nuc	0			607696		461
Q9JLC4 UniProt NPD GO	SORC1_MOUSE	VPS10 domain-containing receptor SorCS1 precursor (mSorCS)	0.76	-	vac	1 *	Membrane; single-pass type I membrane protein				1167
Q61JT8 UniProt NPD GO	VPS54_CAEBR	Vacuolar protein sorting protein 54	0.76	-	nuc	0					1055
P0C149 UniProt NPD GO	SNF7_MAGGR	Vacuolar sorting protein SNF7 (Vacuolar protein sorting-associated protein VPS32)	0.76	+	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				226
Q871Y8 UniProt NPD GO	SNF7_NEUCR	Vacuolar sorting protein snf-7 (Vacuolar protein sorting-associated protein vps-32)	0.76	-	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				228
Q9P7F7 UniProt NPD GO	SNF7_SCHPO	Vacuolar sorting protein snf7 (Vacuolar protein sorting-associated protein vps32)	0.76	-	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				222
Q9NZR4 UniProt NPD GO	VSX1_HUMAN	Visual system homeobox 1 (Transcription factor VSX1) (Retinal inner nuclear layer homeobox protein) ...	0.76	+	nuc	0	Nucleus (By similarity)		605020		365
Q5RF50 UniProt NPD GO	VKGC_PONPY	Vitamin K-dependent gamma-carboxylase (EC 6.4.-.-) (Gamma-glutamyl carboxylase) (Vitamin K gamma glu ...	0.76	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				758
P15381 UniProt NPD GO	CAC1C_RABIT	Voltage-dependent L-type calcium channel subunit alpha-1C (Voltage-gated calcium channel subunit alp ...	0.76	+	end	19	Membrane; multi-pass membrane protein				2171
P19517 UniProt NPD GO	CACB1_RABIT	Voltage-dependent L-type calcium channel subunit beta-1 (CAB1) (Calcium channel voltage-dependent su ...	0.76	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side				524
Q9EQ60 UniProt NPD GO	CAC1H_RAT	Voltage-dependent T-type calcium channel subunit alpha-1H (Voltage-gated calcium channel subunit alp ...	0.76	+	end	15	Membrane; multi-pass membrane protein	plasma membrane [IMP]			2359
Q58DC2 UniProt NPD GO	WD21A_BOVIN	WD repeat protein 21A	0.76	-	nuc	0					494
O15213 UniProt NPD GO	WDR46_HUMAN	WD repeat protein 46 (WD repeat protein BING4)	0.76	+	nuc	0					610
Q7KVA1 UniProt NPD GO	XYLT_DROME	Xylosyltransferase oxt (EC 2.4.2.26) (Peptide O-xylosyltransferase) (Imaginal disk type I)	0.76	-	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...	integral to membrane [NAS]			876
Q5T4F4 UniProt NPD GO	ZFY27_HUMAN	Zinc finger FYVE domain-containing protein 27	0.76	-	mit	3	Membrane; multi-pass membrane protein (Potential)			1X4U	411
Q5R7K2 UniProt NPD GO	ZFY27_PONPY	Zinc finger FYVE domain-containing protein 27	0.76	-	mit	3	Membrane; multi-pass membrane protein (Potential)				411
Q9R020 UniProt NPD GO	ZRAB2_MOUSE	Zinc finger Ran-binding domain-containing protein 2 (Zinc finger protein 265) (Zinc finger, splicing ...	0.76	+	nuc	0	Nucleus (Potential)				326
Q96DT7 UniProt NPD GO	ZBT10_HUMAN	Zinc finger and BTB domain-containing protein 10 (Zinc finger protein RIN ZF)	0.76	-	nuc	0	Nucleus (Potential)				847
O15062 UniProt NPD GO	ZBTB5_HUMAN	Zinc finger and BTB domain-containing protein 5	0.76	+	nuc	0	Nucleus (Potential)				677
Q62394 UniProt NPD GO	ZN185_MOUSE	Zinc finger protein 185 (LIM-domain protein Zfp185) (P1-A)	0.76	-	nuc	0	Nucleus (Potential)				352
Q9UIE0 UniProt NPD GO	ZN230_HUMAN	Zinc finger protein 230 (Zinc finger protein FDZF2)	0.76	-	nuc	0	Nucleus (Probable)				474
Q14591 UniProt NPD GO	ZN271_HUMAN	Zinc finger protein 271 (Zinc finger protein HZF7) (Zinc finger protein ZNFphex133) (Epstein-Barr vi ...	0.76	-	nuc	0	Nucleus (Probable)		604754		655
Q9D0B1 UniProt NPD GO	ZN524_MOUSE	Zinc finger protein 524	0.76	+	nuc	0	Nucleus (Probable)				321
Q6P9A3 UniProt NPD GO	ZN549_HUMAN	Zinc finger protein 549	0.76	-	nuc	0	Nucleus (Probable)				640
Q5RBQ3 UniProt NPD GO	ZN549_PONPY	Zinc finger protein 549	0.76	-	nuc	0	Nucleus (Probable)				640
Q3V080 UniProt NPD GO	ZN583_MOUSE	Zinc finger protein 583	0.76	-	nuc	0	Nucleus (Potential)				568
Q9HCG1 UniProt NPD GO	KR18_HUMAN	Zinc finger protein Kr18 (HKr18)	0.76	-	nuc	0	Nucleus (Probable)	nucleus [NAS]			818
O89084 UniProt NPD GO	PDE4A_MOUSE	cAMP-dependent 3',5'-cyclic phosphodiesterase 4A (EC 3.1.4.17)	0.76	-	nuc	0					844
Q9C0H9 UniProt NPD GO	SNIP_HUMAN	p130Cas-associated protein (p140Cap) (SNAP-25-interacting protein) (SNIP)	0.76	-	nuc	0	Localized to the perinuclear region, lamellopodia, cortical actin and actin stress fibers but not to ...	actin cytoskeleton [IDA] focal adhesion [IDA]			1055
Q5XL24 UniProt NPD GO	PACC_ASPGI	pH-response transcription factor pacC/RIM101	0.76	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				678
Q96UW0 UniProt NPD GO	PACC_ASPPA	pH-response transcription factor pacC/RIM101	0.76	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				662
Q80UN9 UniProt NPD GO	MOD5_MOUSE	tRNA isopentenyltransferase, mitochondrial precursor (EC 2.5.1.8) (Isopentenyl-diphosphate:tRNA isop ...	0.76	+	mit	0	Isoform 1: Mitochondrion (Potential). Isoform 2: Cytoplasm (Potential). Nucleus (Potential)				467
O74475 UniProt NPD GO	BGS4_SCHPO	1,3-beta-glucan synthase component bgs4 (EC 2.4.1.34) (1,3-beta-D-glucan-UDP glucosyltransferase)	0.75	+	end	16	Membrane; multi-pass membrane protein (Potential)	cell septum [IDA] cell tip [IDA] contractile ring [IDA]			1955
Q3UHX2 UniProt NPD GO	HAP28_MOUSE	28 kDa heat- and acid-stable phosphoprotein (PDGF-associated protein) (PAP) (PDGFA-associated protei ...	0.75	-	nuc	0					181
Q62785 UniProt NPD GO	HAP28_RAT	28 kDa heat- and acid-stable phosphoprotein (PDGF-associated protein) (PAP) (PDGFA-associated protei ...	0.75	-	nuc	0					181
Q9D7N3 UniProt NPD GO	RT09_MOUSE	28S ribosomal protein S9, mitochondrial precursor (S9mt) (MRP-S9)	0.75	-	mit	0	Mitochondrion (By similarity)				390
P28320 UniProt NPD GO	YKJ5_YEAST	32.3 kDa protein in CWP1-MBR1 intergenic region	0.75	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			278
Q9ZT56 UniProt NPD GO	RS8_GRIJA	40S ribosomal protein S8	0.75	+	nuc	0					204
Q9XYC2 UniProt NPD GO	RL15_ORCLI	60S ribosomal protein L15	0.75	-	nuc	0					203
P38665 UniProt NPD GO	RL24_KLULA	60S ribosomal protein L24 (Ribosomal protein L30)	0.75	+	nuc	0					155
P17702 UniProt NPD GO	RL28_RAT	60S ribosomal protein L28	0.75	+	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [ISS]			136
P36527 UniProt NPD GO	RM28_YEAST	60S ribosomal protein L28, mitochondrial precursor (YmL28)	0.75	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			147
Q769J6 UniProt NPD GO	ATS13_MOUSE	ADAMTS-13 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 13 ...	0.75	-	nuc	1 *	Secreted				1426

You are viewing entries 11151 to 11200 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.