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
O19907 UniProt NPD GO	RPOZ_CYACA	Putative DNA-directed RNA polymerase omega chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase ...	0.11	-	nuc	0	Plastid; chloroplast				72
O15529 UniProt NPD GO	GPR42_HUMAN	Putative G-protein coupled receptor 42	0.11	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603822		346
Q9NTK5 UniProt NPD GO	PTD4_HUMAN	Putative GTP-binding protein PTD004	0.11	-	cyt	0					396
Q9CZ30 UniProt NPD GO	PTD4_MOUSE	Putative GTP-binding protein PTD004 homolog	0.11	-	cyt	0					396
Q9LR09 UniProt NPD GO	HA22G_ARATH	Putative HVA22-like protein g (AtHVA22g)	0.11	-	cyt	0					166
Q09301 UniProt NPD GO	YQOC_CAEEL	Putative RNA-binding protein EEED8.12	0.11	-	nuc	0					197
Q09451 UniProt NPD GO	PPAW_CAEEL	Putative acid phosphatase C05C10.4 (EC 3.1.3.2)	0.11	-	end	0					413
P50245 UniProt NPD GO	SAHH2_DROME	Putative adenosylhomocysteinase 2 (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase 2) (AdoHcyase 2) ...	0.11	+	cyt	0					492
P30632 UniProt NPD GO	ARSA_CAEEL	Putative arsenical pump-driving ATPase (EC 3.6.3.16) (Arsenite-translocating ATPase) (Arsenical resi ...	0.11	-	cyt	0					342
P43547 UniProt NPD GO	AAD6_YEAST	Putative aryl-alcohol dehydrogenase AAD6 (EC 1.1.1.-)	0.11	-	mit	0					212
O36014 UniProt NPD GO	DNPEP_SCHPO	Putative aspartyl aminopeptidase (EC 3.4.11.21)	0.11	-	nuc	0	Cytoplasm (By similarity)				467
O49290 UniProt NPD GO	CPPM_ARATH	Putative carboxyvinyl-carboxyphosphonate phosphorylmutase (EC 2.7.8.23) (Carboxyphosphonoenolpyruvat ...	0.11	-	mit	0					335
Q12198 UniProt NPD GO	METW_YEAST	Putative cystathionine gamma-synthase YLL058W (EC 2.5.1.48) (O-succinylhomoserine (thiol)-lyase)	0.11	-	cyt	0					575
Q9SZ54 UniProt NPD GO	GPX7_ARATH	Putative glutathione peroxidase 7, chloroplast precursor (EC 1.11.1.9)	0.11	-	mit	0	Plastid; chloroplast (Potential)				230
Q09852 UniProt NPD GO	YAEC_SCHPO	Putative inorganic phosphate transporter C23D3.12	0.11	-	end	11 *	Membrane; multi-pass membrane protein (Probable)				559
Q2QSB9 UniProt NPD GO	AMPL1_ORYSA	Putative leucine aminopeptidase 1 (EC 3.4.11.1) (LAP 1) (Leucyl aminopeptidase 1) (Proline aminopept ...	0.11	-	cyt	0	Cytoplasm				542
Q5B0L1 UniProt NPD GO	ATG15_EMENI	Putative lipase atg15 (EC 3.1.1.3) (Autophagy-related protein 15)	0.11	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				590
Q9Y7N6 UniProt NPD GO	PLB5_SCHPO	Putative lysophospholipase C1450.09c precursor (EC 3.1.1.5) (Phospholipase B)	0.11	-	exc	0	Secreted protein (Probable)				633
Q9SYI2 UniProt NPD GO	MDR3_ARATH	Putative multidrug resistance protein 3 (P-glycoprotein 3)	0.11	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				1229
Q9VNB3 UniProt NPD GO	OR83A_DROME	Putative odorant receptor 83a	0.11	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	cell soma [IDA] dendrite [IDA]			453
P38286 UniProt NPD GO	YB09_YEAST	Putative oxidoreductase YBR159W (EC 1.-.-.-)	0.11	-	mit	1 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			347
Q8N966 UniProt NPD GO	ZDH22_HUMAN	Putative palmitoyltransferase ZDHHC22 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 22) ( ...	0.11	-	exc	2 *	Membrane; multi-pass membrane protein (Potential)				160
P78710 UniProt NPD GO	ASD1_NEUCR	Putative rhamnogalacturonase precursor (EC 4.2.2.-) (Rhamnogalacturonan lyase) (RGase) (Ascus develo ...	0.11	-	exc	1 *					540
P52717 UniProt NPD GO	YUW5_CAEEL	Putative serine carboxypeptidase F41C3.5 precursor (EC 3.4.16.-)	0.11	-	exc	0					469
Q00730 UniProt NPD GO	STCW_EMENI	Putative sterigmatocystin biosynthesis monooxygenase stcW (EC 1.14.13.-)	0.11	-	nuc	1					488
Q7TQB8 UniProt NPD GO	T2R44_MOUSE	Putative taste receptor type 2 member 44 (T2R44) (mT2r33)	0.11	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			319
Q6DHV5 UniProt NPD GO	CJ130_HUMAN	Putative uncharacterized protein C10orf130	0.11	-	cyt	0					322
P39725 UniProt NPD GO	YAE5_YEAST	Putative uncharacterized protein YAL045C	0.11	-	cyt	0					102
P15503 UniProt NPD GO	DISA_TRIGA	Putative venom metalloproteinase precursor (EC 3.4.24.-) [Contains: Disintegrin trigramin-alpha (Pla ...	0.11	-	mit	0					480
Q8S5M8 UniProt NPD GO	YIPL_ORYSA	Putative yippee-like protein Os10g22410	0.11	-	cyt	0					119
P59097 UniProt NPD GO	P2OX_TRAHI	Pyranose 2-oxidase precursor (EC 1.1.3.10) (P2Ox) (Pyranose oxidase) (PROD) (POD) (POx) (Pyranose:ox ...	0.11	-	cyt	0	Hyphal periplasmic space (By similarity)				622
P21343 UniProt NPD GO	PFPB_SOLTU	Pyrophosphate--fructose 6-phosphate 1-phosphotransferase subunit beta (EC 2.7.1.90) (PFP) (6-phospho ...	0.11	-	cyt	0					552
P52903 UniProt NPD GO	ODPA_SOLTU	Pyruvate dehydrogenase E1 component alpha subunit, mitochondrial precursor (EC 1.2.4.1) (PDHE1-A)	0.11	-	nuc	0	Mitochondrion; mitochondrial matrix				391
P52900 UniProt NPD GO	ODPA_SMIMA	Pyruvate dehydrogenase E1 component alpha subunit, mitochondrial precursor (EC 1.2.4.1) (PDHE1-A) (F ...	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix				363
P08559 UniProt NPD GO	ODPA_HUMAN	Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor (EC 1.2.4.1 ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	300502	1NI4	390
Q5R490 UniProt NPD GO	ODPA_PONPY	Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor (EC 1.2.4.1 ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				390
P29803 UniProt NPD GO	ODPAT_HUMAN	Pyruvate dehydrogenase E1 component alpha subunit, testis-specific form, mitochondrial precursor (EC ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix		179061		388
O96390 UniProt NPD GO	RACF1_DICDI	RAS-related protein racF1	0.11	-	cyt	0	Membrane; lipid-anchor				193
P09806 UniProt NPD GO	RF4_KLULA	RF4 protein	0.11	-	cyt	0					428
Q96GF1 UniProt NPD GO	RN185_HUMAN	RING finger protein 185	0.11	-	cyt	2	Membrane; multi-pass membrane protein (Potential)				192
Q91YT2 UniProt NPD GO	RN185_MOUSE	RING finger protein 185	0.11	-	cyt	2	Membrane; multi-pass membrane protein (Potential)				192
Q5RFK9 UniProt NPD GO	RN185_PONPY	RING finger protein 185	0.11	-	cyt	2	Membrane; multi-pass membrane protein (Potential)				192
Q09463 UniProt NPD GO	RNF5_CAEEL	RING finger protein 5	0.11	-	nuc	2					235
O80927 UniProt NPD GO	ATL2J_ARATH	RING-H2 finger protein ATL2J	0.11	-	nuc	1					235
Q9M313 UniProt NPD GO	ATL3K_ARATH	RING-H2 finger protein ATL3K	0.11	-	nuc	1 *					212
Q23457 UniProt NPD GO	RBX1_CAEEL	RING-box protein 1 (Rbx1) (Ce-rbx-1)	0.11	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				110
Q6IQ97 UniProt NPD GO	RBM4_BRARE	RNA-binding protein 4 (RNA-binding motif protein 4)	0.11	-	nuc	0					419
P08645 UniProt NPD GO	RAS3_DROME	Ras-like protein 3 precursor (Protein roughened)	0.11	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				184
Q99K70 UniProt NPD GO	RRAGC_MOUSE	Ras-related GTP-binding protein C (Rag C) (GTPase-interacting protein 2) (TIB929)	0.11	-	cyt	0	Cytoplasm. Nucleus. Predominantly cytoplasmic. May shuttle between the cytoplasm and nucleus, depend ...	cytoplasm [ISS] nucleus [ISS]			398
Q52NJ1 UniProt NPD GO	RB11A_PIG	Ras-related protein Rab-11A	0.11	-	cyt	0	Cell membrane; peripheral membrane protein (By similarity). Endosome; recycling endosome; recycling ...				215

You are viewing entries 63401 to 63450 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.