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
Q700D9 UniProt NPD GO	MYBF_ARATH	Putative Myb family transcription factor At1g14600	0.69	-	nuc	0	Nucleus (Probable)				255
Q9N2K7 UniProt NPD GO	TBX30_CAEEL	Putative T-box protein 30	0.69	-	nuc	0	Nucleus (Potential)				308
Q7XA40 UniProt NPD GO	RGA3_SOLBU	Putative disease resistance protein RGA3 (RGA1-blb) (Blight resistance protein B149)	0.69	-	cyt	0					992
Q755R3 UniProt NPD GO	MATT_ASHGO	Putative mating-type transcription factor	0.69	+	mit	0	Nucleus (Potential)				142
Q7K755 UniProt NPD GO	GLT11_CAEEL	Putative polypeptide N-acetylgalactosaminyltransferase 11 (EC 2.4.1.41) (Protein-UDP acetylgalactosa ...	0.69	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				605
O74343 UniProt NPD GO	YH2X_SCHPO	Putative pseudouridine synthase C1A4.09 (EC 5.4.99.-)	0.69	-	nuc	0					680
Q9BRQ0 UniProt NPD GO	PYGO2_HUMAN	Pygopus homolog 2	0.69	+	nuc	0	Nucleus (Probable)		606903		406
Q9BXT8 UniProt NPD GO	RNF17_HUMAN	RING finger protein 17	0.69	-	nuc	0			605793		653
Q99MV7 UniProt NPD GO	RNF17_MOUSE	RING finger protein 17	0.69	-	nuc	0		cytoplasm [IDA]			626
Q9Y252 UniProt NPD GO	RNF6_HUMAN	RING finger protein 6 (RING-H2 protein)	0.69	-	nuc	0			604242		685
Q9XF63 UniProt NPD GO	ATL1P_ARATH	RING-H2 finger protein ATL1P (RING-H2 finger protein ATL3)	0.69	+	nuc	1 *					324
Q5EG55 UniProt NPD GO	RYBP_BRARE	RING1 and YY1-binding protein (Death effector domain-associated factor) (DED-associated factor)	0.69	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Primarily found in the nucleus (By similarity)				257
Q12124 UniProt NPD GO	MED2_YEAST	RNA polymerase II mediator complex subunit 2	0.69	-	nuc	0	Nucleus	mediator complex [IDA]			431
Q8R4C2 UniProt NPD GO	RUFY2_MOUSE	RUN and FYVE domain-containing protein 2 (Leucine zipper FYVE-finger protein) (LZ-FYVE)	0.69	-	nuc	0	Nucleus				606
Q9VKB9 UniProt NPD GO	RBGPR_DROME	Rab3 GTPase-activating protein regulatory subunit	0.69	-	nuc	0	Cytoplasm (Probable)	soluble fraction [ISS] synaptic vesicle [NAS]			1341
Q7YR42 UniProt NPD GO	IEX1_PANTR	Radiation-inducible immediate-early gene IEX-1 (Immediate early protein GLY96) (Immediate early resp ...	0.69	-	nuc	0	Membrane; single-pass type II membrane protein (Potential)				156
Q9PWA0 UniProt NPD GO	RGS17_CHICK	Regulator of G-protein signaling 17 (RGS17)	0.69	-	mit	0	Membrane; lipid-anchor (Potential)				210
Q9QZB0 UniProt NPD GO	RGS17_MOUSE	Regulator of G-protein signaling 17 (RGS17) (Regulator of Gz-selective protein signaling 2)	0.69	-	mit	0	Membrane; lipid-anchor (Potential)				210
O42356 UniProt NPD GO	RX1_BRARE	Retinal homeobox protein Rx1	0.69	+	nuc	0	Nucleus (By similarity)				330
O42357 UniProt NPD GO	RX2_BRARE	Retinal homeobox protein Rx2	0.69	+	nuc	0	Nucleus (By similarity)				327
Q9BE31 UniProt NPD GO	RHG12_MACFA	Rho-GTPase-activating protein 12	0.69	-	nuc	0					847
Q9HCJ3 UniProt NPD GO	RAVR2_HUMAN	Ribonucleoprotein PTB-binding 2 (Protein raver-2)	0.69	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). May shuttle between the nucleus and the cytoplas ...		609953	1WG1	691
Q6BH34 UniProt NPD GO	RLP24_DEBHA	Ribosome biogenesis protein RLP24	0.69	-	nuc	0	Nucleus; nucleolus (By similarity)				203
Q60710 UniProt NPD GO	SAMH1_MOUSE	SAM domain and HD domain-containing protein 1 (Interferon-gamma-inducible protein Mg11)	0.69	-	nuc	0		intracellular [ISS]			627
Q9BYB0 UniProt NPD GO	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains protein 3 (Shank3) (Proline-rich synapse-associated protein ...	0.69	-	nuc	0	Cytoplasm (By similarity). Postsynaptic density of neuronal cells (By similarity)		606232		797
Q91Y80 UniProt NPD GO	3BP5_RAT	SH3 domain-binding protein 5 (Vascular endothelial cell-specific protein 18)	0.69	-	nuc	0	Mitochondrion	mitochondrion [IDA]			425
P98068 UniProt NPD GO	SPAN_STRPU	SPAN protein precursor (EC 3.4.24.-)	0.69	+	exc	0					616
O42467 UniProt NPD GO	SNF5_TETFL	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1	0.69	-	nuc	0	Nucleus (By similarity)				373
P13728 UniProt NPD GO	SGS3_DROYA	Salivary glue protein Sgs-3 precursor	0.69	-	exc	0					263
P13521 UniProt NPD GO	SCG2_HUMAN	Secretogranin-2 precursor (Secretogranin II) (SgII) (Chromogranin C) [Contains: Secretoneurin (SN)]	0.69	-	exc	1 *	Neuroendocrine and endocrine secretory granules	extracellular space [IDA]	118930		617
P30945 UniProt NPD GO	SCG2_RANRI	Secretogranin-2 precursor (Secretogranin II) (SgII) [Contains: Secretoneurin (SN) (Brain peptide)]	0.69	-	exc	1 *					601
P51141 UniProt NPD GO	DVL1_MOUSE	Segment polarity protein dishevelled homolog DVL-1 (Dishevelled-1) (DSH homolog 1)	0.69	+	nuc	0	Cytoplasm (Potential)	cytoplasmic membrane-bound vesicle [IDA]		1MC7	695
Q9WVB9 UniProt NPD GO	DVL1_RAT	Segment polarity protein dishevelled homolog DVL-1 (Dishevelled-1) (DSH homolog 1)	0.69	+	nuc	0	Cytoplasm (Potential)				695
Q9NTN9 UniProt NPD GO	SEM4G_HUMAN	Semaphorin-4G precursor	0.69	-	exc	1	Membrane; single-pass type I membrane protein				838
Q6FP74 UniProt NPD GO	CBK1_CANGA	Serine/threonine-protein kinase CBK1 (EC 2.7.11.1)	0.69	-	nuc	0					773
P31034 UniProt NPD GO	CBK1_KLULA	Serine/threonine-protein kinase CBK1 (EC 2.7.11.1)	0.69	-	nuc	0					718
Q6FRE7 UniProt NPD GO	PTK2_CANGA	Serine/threonine-protein kinase PTK2 (EC 2.7.11.1)	0.69	-	nuc	0					777
Q04002 UniProt NPD GO	SCC2_YEAST	Sister chromatid cohesion protein 2	0.69	-	cyt	0	Nucleus. Associates with chromatin	nuclear cohesin complex [TAS]			1493
Q2TBK8 UniProt NPD GO	SPN1_BOVIN	Snurportin-1 (RNA U transporter 1)	0.69	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleoplasmic shuttling protein. Its nuclear imp ...				362
P15389 UniProt NPD GO	SCN5A_RAT	Sodium channel protein type 5 subunit alpha (Sodium channel protein type V subunit alpha) (Voltage-g ...	0.69	-	end	19	Membrane; multi-pass membrane protein				2019
Q92673 UniProt NPD GO	SORL_HUMAN	Sortilin-related receptor precursor (Sorting protein-related receptor containing LDLR class A repeat ...	0.69	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	602005		2214
Q9UNH6 UniProt NPD GO	SNX7_HUMAN	Sorting nexin-7	0.69	-	cyt	0					387
Q12874 UniProt NPD GO	SF3A3_HUMAN	Splicing factor 3A subunit 3 (Spliceosome-associated protein 61) (SAP 61) (SF3a60)	0.69	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle	spliceosome complex [IDA]	605596		501
Q9D554 UniProt NPD GO	SF3A3_MOUSE	Splicing factor 3A subunit 3 (Spliceosome-associated protein 61) (SAP 61) (SF3a60)	0.69	-	nuc	0	Nucleus (By similarity)				501
O57683 UniProt NPD GO	SF3B1_XENLA	Splicing factor 3B subunit 1 (Spliceosome-associated protein 155) (SAP 155) (SF3b155) (Pre-mRNA-spli ...	0.69	-	end	0	Nucleus				1307
Q94C11 UniProt NPD GO	SF04_ARATH	Splicing factor 4-like protein (SF4-like protein)	0.69	-	nuc	0	Nucleus (Potential)				443
P32572 UniProt NPD GO	SPS18_YEAST	Sporulation protein SPS18 (Sporulation-specific protein SPX18)	0.69	-	nuc	0					300
P45819 UniProt NPD GO	SPO74_YEAST	Sporulation-specific protein 74	0.69	-	nuc	0	Localizes to the meiotic outer plaque of the spindle pole body (SPB), at the end of the meiotic spin ...	spindle pole body [IDA]			413
O55183 UniProt NPD GO	STC1_MOUSE	Stanniocalcin-1 precursor (STC-1)	0.69	-	exc	0	Secreted protein	extracellular space [IDA]			247
Q06321 UniProt NPD GO	ATG26_YEAST	Sterol 3-beta-glucosyltransferase (EC 2.4.1.173) (Autophagy-related protein 26) (UDP-glycosyltransfe ...	0.69	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	cytoplasm [IDA]			1198

You are viewing entries 14451 to 14500 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.