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
Q12080 UniProt NPD GO	YP146_YEAST	Uncharacterized protein YPL146C	0.79	-	nuc	0		nucleolus [IDA] nucleus [IDA]			455
Q9H321 UniProt NPD GO	VCXC_HUMAN	VCX-C protein (Variably charged protein X-C)	0.79	-	nuc	0		nucleolus [ISS] nucleus [ISS]			216
Q8WY21 UniProt NPD GO	SORC1_HUMAN	VPS10 domain-containing receptor SorCS1 precursor (hSorCS)	0.79	-	end	1	Membrane; single-pass type I membrane protein	membrane [IDA]	606283		1168
Q862Z6 UniProt NPD GO	VATG1_PANTR	Vacuolar ATP synthase subunit G 1 (EC 3.6.3.14) (V-ATPase G subunit 1) (Vacuolar proton pump G subun ...	0.79	-	nuc	0					117
P79251 UniProt NPD GO	VATG1_BOVIN	Vacuolar ATP synthase subunit G 1 (EC 3.6.3.14) (V-ATPase G subunit 1) (Vacuolar proton pump G subun ...	0.79	-	nuc	0					117
O75348 UniProt NPD GO	VATG1_HUMAN	Vacuolar ATP synthase subunit G 1 (EC 3.6.3.14) (V-ATPase G subunit 1) (Vacuolar proton pump G subun ...	0.79	-	nuc	0			607296		117
Q1XHY9 UniProt NPD GO	VATG2_PANTR	Vacuolar ATP synthase subunit G 2 (EC 3.6.3.14) (V-ATPase G subunit 2) (Vacuolar proton pump G subun ...	0.79	-	nuc	0					118
Q9TSV6 UniProt NPD GO	VATG2_PIG	Vacuolar ATP synthase subunit G 2 (EC 3.6.3.14) (V-ATPase G subunit 2) (Vacuolar proton pump G subun ...	0.79	-	nuc	0					118
Q9H320 UniProt NPD GO	VCX1_HUMAN	Variable charge X-linked protein 1 (VCX-B1 protein) (Variably charged protein X-B1) (Variable charge ...	0.79	-	nuc	0		nucleolus [IEP] nucleus [IDA]			206
P20946 UniProt NPD GO	VSWA_TRYBR	Variant surface glycoprotein WRATAT A precursor (VSG)	0.79	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				471
Q43358 UniProt NPD GO	VCL_THECC	Vicilin precursor	0.79	-	exc	1 *					525
Q9IAL2 UniProt NPD GO	VSX1_CHICK	Visual system homeobox 1 (Transcription factor VSX1) (Homeobox protein Chx10-1)	0.79	+	nuc	0	Nucleus (By similarity)				350
Q9MYY3 UniProt NPD GO	VKGC_DELLE	Vitamin K-dependent gamma-carboxylase (EC 6.4.-.-) (Gamma-glutamyl carboxylase) (Vitamin K gamma glu ...	0.79	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				758
Q01815 UniProt NPD GO	CAC1C_MOUSE	Voltage-dependent L-type calcium channel subunit alpha-1C (Voltage-gated calcium channel subunit alp ...	0.79	+	end	19	Membrane; multi-pass membrane protein	T-tubule [TAS] voltage-gated calcium channel complex [TAS]			2139
Q02343 UniProt NPD GO	CAC1E_RABIT	Voltage-dependent R-type calcium channel subunit alpha-1E (Voltage-gated calcium channel subunit alp ...	0.79	+	end	19	Membrane; multi-pass membrane protein				2259
Q95JP0 UniProt NPD GO	WDR63_MACFA	WD repeat protein 63	0.79	-	nuc	0					891
Q5F457 UniProt NPD GO	WBP4_CHICK	WW domain-binding protein 4 (WBP-4)	0.79	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				398
P05531 UniProt NPD GO	XLR_MOUSE	X-linked lymphocyte-regulated protein PM1	0.79	-	nuc	0					208
Q7XJ98 UniProt NPD GO	KATAM_ARATH	Xyloglucan galactosyltransferase KATAMARI1 (EC 2.4.1.-) (Protein MURUS3)	0.79	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein				619
Q9JJ48 UniProt NPD GO	ZC3H8_MOUSE	Zinc finger CCCH domain-containing protein 8 (Fetal liver zinc finger protein 1)	0.79	-	nuc	0	Nucleus	nucleus [IDA]			305
Q9CZA5 UniProt NPD GO	ZCH12_MOUSE	Zinc finger CCHC domain-containing protein 12 (Smad-interacting zinc finger protein)	0.79	+	mit	0					402
Q9C0B9 UniProt NPD GO	ZCHC2_HUMAN	Zinc finger CCHC domain-containing protein 2 (Fragment)	0.79	-	nuc	0					899
O95218 UniProt NPD GO	ZRAB2_HUMAN	Zinc finger Ran-binding domain-containing protein 2 Zinc finger protein 265 (Zinc finger, splicing)	0.79	+	nuc	0	Nucleus (Potential)	nucleus [TAS]	604347	1N0Z	337
P52741 UniProt NPD GO	ZN134_HUMAN	Zinc finger protein 134	0.79	+	nuc	0	Nucleus (Potential)	nucleus [NAS]	604076		348
Q14929 UniProt NPD GO	ZN169_HUMAN	Zinc finger protein 169	0.79	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	603404		590
Q96SZ4 UniProt NPD GO	ZN206_HUMAN	Zinc finger protein 206 (Zinc finger and SCAN domain-containing protein 10)	0.79	-	nuc	0	Nucleus (Potential)				725
Q9UK11 UniProt NPD GO	ZN223_HUMAN	Zinc finger protein 223	0.79	-	nuc	0	Nucleus (Probable)				482
Q6A009 UniProt NPD GO	ZN294_MOUSE	Zinc finger protein 294 (Zfp-294)	0.79	-	cyt	0					1767
Q6P9G9 UniProt NPD GO	ZN449_HUMAN	Zinc finger protein 449 (Zinc finger and SCAN domain-containing protein 19)	0.79	-	nuc	0	Nucleus (Potential)				518
Q8WV14 UniProt NPD GO	ZN688_HUMAN	Zinc finger protein 688	0.79	-	nuc	0	Nucleus (Probable)				782
Q99PJ7 UniProt NPD GO	ZN689_RAT	Zinc finger protein 689 (Transcription factor HIT-39)	0.79	-	nuc	0	Nucleus (Probable)				500
Q8K1M4 UniProt NPD GO	GLIS1_MOUSE	Zinc finger protein GLIS1 (GLI-similar 1) (Gli homologous protein 1) (GliH1)	0.79	-	nuc	0	Nucleus	nucleus [IDA]			789
P08045 UniProt NPD GO	XFIN_XENLA	Zinc finger protein Xfin	0.79	-	nuc	0	Cytoplasm			1ZNF	1350
Q04545 UniProt NPD GO	YMI1_YEAST	Zinc finger protein YML081W	0.79	-	nuc	1	Nucleus (Potential)	nucleus [IDA]			1251
P98060 UniProt NPD GO	NAS35_CAEEL	Zinc metalloproteinase dpy-31 precursor (EC 3.4.24.21) (Nematode astacin 35) (Protein dumpy-31) (Tol ...	0.79	-	exc	0	Secreted protein (Probable)				592
Q20942 UniProt NPD GO	NAS38_CAEEL	Zinc metalloproteinase nas-38 precursor (EC 3.4.24.21) (Nematode astacin 38)	0.79	-	nuc	0	Secreted protein (Potential)				745
O13297 UniProt NPD GO	CET1_YEAST	mRNA capping enzyme subunit beta (EC 3.1.3.33) (Polynucleotide 5'-triphosphatase) (mRNA 5'-triphosph ...	0.79	-	nuc	0	Nucleus	nucleus [IPI]		1D8I	549
Q00203 UniProt NPD GO	PACC_ASPNG	pH-response transcription factor pacC/RIM101	0.79	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				667
Q01864 UniProt NPD GO	PACC_PENCH	pH-response transcription factor pacC/RIM101	0.79	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				643
P78978 UniProt NPD GO	PACC_YARLI	pH-response transcription factor pacC/RIM101	0.79	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				585
Q12211 UniProt NPD GO	PUS1_YEAST	tRNA pseudouridine synthase 1 (EC 5.4.99.-) (tRNA-uridine isomerase 1) (tRNA pseudouridylate synthas ...	0.79	-	nuc	0	Nucleus	nucleus [IPI]			544
P13496 UniProt NPD GO	DYNA_DROME	150 kDa dynein-associated polypeptide (DP-150) (DAP-150) (Protein glued)	0.78	-	nuc	0	Cytoplasm (By similarity)	dynactin complex [TAS]			1265
P62247 UniProt NPD GO	RS8_BRARE	40S ribosomal protein S8	0.78	+	nuc	0					207
O94150 UniProt NPD GO	RT09_CANAL	40S ribosomal protein S9, mitochondrial precursor	0.78	-	mit	0	Mitochondrion (Potential)				336
P41123 UniProt NPD GO	RL13_RAT	60S ribosomal protein L13	0.78	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [NAS]			210
Q9DFQ7 UniProt NPD GO	RL24_GILMI	60S ribosomal protein L24	0.78	-	nuc	0					157
P61122 UniProt NPD GO	RL24_MACFA	60S ribosomal protein L24	0.78	+	nuc	0					157
Q8BP67 UniProt NPD GO	RL24_MOUSE	60S ribosomal protein L24	0.78	+	nuc	0					157
P83732 UniProt NPD GO	RL24_RAT	60S ribosomal protein L24 (L30)	0.78	+	nuc	0					157
Q862I1 UniProt NPD GO	RL24_BOVIN	60S ribosomal protein L24 (Ribosomal protein L30)	0.78	+	nuc	0					157

You are viewing entries 9701 to 9750 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.