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
Q5ZK01 UniProt NPD GO	PELO_CHICK	Protein pelota homolog	0.40	-	cyt	0	Nucleus (Potential)				385
P79126 UniProt NPD GO	PP2CG_BOVIN	Protein phosphatase 2C isoform gamma (EC 3.1.3.16) (PP2C-gamma) (Protein phosphatase magnesium-depen ...	0.40	-	nuc	0	Cytoplasm (Potential)				543
Q58DN4 UniProt NPD GO	PPME1_BOVIN	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.40	-	mit	0					379
Q5U1Z8 UniProt NPD GO	PREY_RAT	Protein preY, mitochondrial precursor	0.40	-	mit	0	Mitochondrion (Potential)	endoplasmic reticulum membrane [ISS] glycosylphosphatidylinositol-N-acetylglucos... [ISS]			112
P54681 UniProt NPD GO	RTOA_DICDI	Protein rtoA (Ratio-A)	0.40	-	nuc	1 *					400
Q8AV58 UniProt NPD GO	SDK1_CHICK	Protein sidekick-1 precursor	0.40	-	nuc	2 *	Membrane; single-pass type I membrane protein (Potential)				2169
Q7Z5N4 UniProt NPD GO	SDK1_HUMAN	Protein sidekick-1 precursor	0.40	-	cyt	1	Membrane; single-pass membrane protein (Potential)		607216		2213
Q15437 UniProt NPD GO	SC23B_HUMAN	Protein transport protein Sec23B (SEC23-related protein B)	0.40	-	cyt	0		membrane [TAS]			767
Q9NYQ8 UniProt NPD GO	FAT2_HUMAN	Protocadherin Fat 2 precursor (hFat2) (Multiple epidermal growth factor-like domains 1)	0.40	-	end	1	Membrane; single-pass type I membrane protein (Potential)		604269		4349
Q9Y5H4 UniProt NPD GO	PCDG1_HUMAN	Protocadherin gamma A1 precursor (PCDH-gamma-A1)	0.40	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606288		931
P21592 UniProt NPD GO	COX10_YEAST	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.40	-	end	4	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrial inner membrane [TAS]			462
Q9SK55 UniProt NPD GO	NAC42_ARATH	Putative NAC domain-containing protein 42 (ANAC042)	0.40	-	nuc	0	Nucleus (Potential)				275
Q9CWH5 UniProt NPD GO	CF075_MOUSE	Putative RNA methylase C6orf75 homolog (EC 2.1.1.-)	0.40	-	cyt	0					460
Q21565 UniProt NPD GO	AMT3_CAEEL	Putative ammonium transporter 3	0.40	-	end	11 *	Membrane; multi-pass membrane protein (Probable)				687
Q5G8B5 UniProt NPD GO	AP4_TITCO	Putative antimicrobial peptide clone 4 precursor	0.40	-	end	1 *	Secreted protein				73
Q9C7I9 UniProt NPD GO	ARFT_ARATH	Putative auxin response factor 20	0.40	-	nuc	0	Nucleus				606
Q9C8N7 UniProt NPD GO	ARFV_ARATH	Putative auxin response factor 22	0.40	-	cyt	0	Nucleus				598
Q04533 UniProt NPD GO	METX_YEAST	Putative cystathionine gamma-synthase YML082W (EC 2.5.1.48) (O-succinylhomoserine (thiol)-lyase)	0.40	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			649
O82484 UniProt NPD GO	DRL23_ARATH	Putative disease resistance protein At4g10780	0.40	-	cyt	0					892
Q9VB30 UniProt NPD GO	GR98A_DROME	Putative gustatory receptor 98a	0.40	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			391
O62640 UniProt NPD GO	PIAP_PIG	Putative inhibitor of apoptosis	0.40	-	mit	0					358
Q9VT20 UniProt NPD GO	OR67B_DROME	Putative odorant receptor 67b	0.40	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			421
Q9VDM1 UniProt NPD GO	OR92A_DROME	Putative odorant receptor 92a	0.40	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			408
Q9LI83 UniProt NPD GO	ALA10_ARATH	Putative phospholipid-transporting ATPase 10 (EC 3.6.3.1) (Aminophospholipid flippase 10)	0.40	-	end	8	Cell membrane; multi-pass membrane protein (Probable)				1202
O45947 UniProt NPD GO	GLT10_CAEEL	Putative polypeptide N-acetylgalactosaminyltransferase 10 (EC 2.4.1.41) (Protein-UDP acetylgalactosa ...	0.40	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				622
Q00706 UniProt NPD GO	STCK_EMENI	Putative sterigmatocystin biosynthesis fatty acid synthase subunit beta	0.40	-	cyt	0					1914
Q09275 UniProt NPD GO	ULP4_CAEEL	Putative thiol protease ulp-4 (EC 3.4.22.-) (Ubiquitin-like protease 4)	0.40	-	cyt	0					342
Q12104 UniProt NPD GO	YO166_YEAST	Putative transcriptional activator YOR166C	0.40	-	nuc	0					458
P38354 UniProt NPD GO	YB8A_YEAST	Putative uncharacterized protein YBR285W	0.40	-	nuc	0					144
Q96D59 UniProt NPD GO	RN183_HUMAN	RING finger protein 183	0.40	-	nuc	1	Membrane; single-pass membrane protein (Potential)				192
Q8BH75 UniProt NPD GO	RNF41_MOUSE	RING finger protein 41	0.40	-	cyt	0					317
Q5FWL3 UniProt NPD GO	RNF41_XENLA	RING finger protein 41	0.40	-	cyt	0					317
Q570X5 UniProt NPD GO	ATL1G_ARATH	RING-H2 finger protein ATL1G	0.40	-	nuc	1 *					261
Q6BIK6 UniProt NPD GO	REXO4_DEBHA	RNA exonuclease 4 (EC 3.1.-.-)	0.40	-	nuc	0	Nucleus (By similarity)				272
P38304 UniProt NPD GO	MED8_YEAST	RNA polymerase II mediator complex subunit 8 (RNA polymerase II transcriptional regulation mediator ...	0.40	-	nuc	0	Nucleus (Probable)	mediator complex [IDA]			222
Q10667 UniProt NPD GO	RNP1_CAEEL	RNA-binding protein rnp-1	0.40	-	nuc	0					305
Q9W704 UniProt NPD GO	RIPA_XENLA	RPA-interacting protein A (RPA-interacting protein alpha) (XRIPalpha)	0.40	-	cyt	0	Nucleus				226
P16391 UniProt NPD GO	HA12_RAT	RT1 class I histocompatibility antigen, AA alpha chain precursor	0.40	-	end	1	Membrane; single-pass type I membrane protein			1KJM	371
Q9Z1C7 UniProt NPD GO	RPGF4_RAT	Rap guanine nucleotide exchange factor 4 (cAMP-regulated guanine nucleotide exchange factor II) (cAM ...	0.40	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein (By similarity)				436
P34443 UniProt NPD GO	RASL_CAEEL	Ras-like protein F54C8.5	0.40	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				207
Q15256 UniProt NPD GO	PTPRR_HUMAN	Receptor-type tyrosine-protein phosphatase R precursor (EC 3.1.3.48) (Protein-tyrosine phosphatase P ...	0.40	-	end	1	Isoform alpha, isoform beta: Cell membrane; single-pass type I membrane protein. Isoform delta, isof ...	cell surface [IEP]	602853	2A8B	657
Q8K0T0 UniProt NPD GO	RTN1_MOUSE	Reticulon-1 (Neuroendocrine-specific protein)	0.40	-	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			780
Q15291 UniProt NPD GO	RBBP5_HUMAN	Retinoblastoma-binding protein 5 (RBBP-5) (Retinoblastoma-binding protein RBQ-3)	0.40	+	cyt	0	Nucleus	nucleus [IDA]	600697		538
Q90415 UniProt NPD GO	RXRAB_BRARE	Retinoic acid receptor RXR-alpha b (Retinoid x receptor alpha b)	0.40	+	nuc	0	Nucleus	nucleus [NAS]			379
Q9BYZ6 UniProt NPD GO	RHBT2_HUMAN	Rho-related BTB domain-containing protein 2 (Deleted in breast cancer 2 gene protein) (p83)	0.40	-	mit	0			607352		727
P61588 UniProt NPD GO	RND3_MOUSE	Rho-related GTP-binding protein RhoE (Rho family GTPase 3) (Rnd3)	0.40	-	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein			1GWN	244
Q6SA80 UniProt NPD GO	RND3_RAT	Rho-related GTP-binding protein RhoE (Rho family GTPase 3) (Rnd3)	0.40	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				244
O77683 UniProt NPD GO	RND3_PIG	Rho-related GTP-binding protein RhoE (Rho family GTPase 3) (Rnd3) (Rho8)	0.40	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				244
P61587 UniProt NPD GO	RND3_HUMAN	Rho-related GTP-binding protein RhoE (Rho family GTPase 3) (Rnd3) (Rho8) (MemB protein)	0.40	-	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein		602924	1M7B	244
Q7YRG9 UniProt NPD GO	RNAS9_SAIBB	Ribonuclease-like protein 9 precursor	0.40	-	exc	0	Secreted protein (Probable)				206

You are viewing entries 32151 to 32200 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.