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
Q00888 UniProt NPD GO	PSG4_HUMAN	Pregnancy-specific beta-1-glycoprotein 4 precursor (PSBG-4) (PSBG-9)	0.36	-	nuc	0	Secreted protein (Potential)	extracellular region [NAS]	176393		419
O78441 UniProt NPD GO	SECA_GUITH	Preprotein translocase secA subunit	0.36	-	nuc	0	Plastid; chloroplast				877
Q36795 UniProt NPD GO	SECA_SPIOL	Preprotein translocase secA subunit, chloroplast precursor	0.36	-	nuc	0	Plastid; chloroplast; chloroplast stroma. Minor fraction: Plastid; chloroplast; chloroplast thylakoi ...				1036
P36147 UniProt NPD GO	PAM17_YEAST	Presequence translocated-associated motor subunit PAM17, mitochondrial precursor	0.36	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			197
Q9P7S2 UniProt NPD GO	RPN6_SCHPO	Probable 26S proteasome regulatory subunit rpn6	0.36	-	nuc	0					421
P55843 UniProt NPD GO	RL14_TRYCO	Probable 60S ribosomal protein L14 (23 kDa cell surface protein homolog)	0.36	-	nuc	0					184
Q96AK3 UniProt NPD GO	ABC3D_HUMAN	Probable DNA dC->dU-editing enzyme APOBEC-3D (EC 3.5.4.-)	0.36	+	cyt	0			609900		386
P22374 UniProt NPD GO	DPOM_ASCIM	Probable DNA polymerase (EC 2.7.7.7)	0.36	-	cyt	0					1202
P33537 UniProt NPD GO	DPOM_NEUCR	Probable DNA polymerase (EC 2.7.7.7)	0.36	-	cyt	0					1021
P33541 UniProt NPD GO	RPOP_NEUIN	Probable DNA-directed RNA polymerase (EC 2.7.7.6)	0.36	-	mit	0					811
Q5T601 UniProt NPD GO	GP110_HUMAN	Probable G-protein coupled receptor 110 precursor (G-protein coupled receptor PGR19) (G-protein coup ...	0.36	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]			911
Q9Y7J0 UniProt NPD GO	NPY1_SCHPO	Probable NADH pyrophosphatase (EC 3.6.1.22)	0.36	-	cyt	0					376
Q94360 UniProt NPD GO	NUKM_CAEEL	Probable NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6 ...	0.36	-	mit	0					199
Q6CVG8 UniProt NPD GO	TAH18_KLULA	Probable NADPH reductase TAH18 (EC 1.-.-.-)	0.36	-	cyt	0					624
P53830 UniProt NPD GO	YN26_YEAST	Probable RNA-binding protein YNL286W	0.36	-	nuc	0		snRNP U2 [IDA]			285
Q9FGR0 UniProt NPD GO	CPSF1_ARATH	Probable cleavage and polyadenylation specificity factor 160 kDa subunit (CPSF 160 kDa subunit)	0.36	-	cyt	0	Nucleus (By similarity)				1448
O74314 UniProt NPD GO	MET7_SCHPO	Probable cystathionine gamma-synthase (EC 2.5.1.48) (O-succinylhomoserine (thiol)-lyase)	0.36	-	cyt	0	Cytoplasm. Nucleus				610
Q6CBH3 UniProt NPD GO	COQ1_YARLI	Probable hexaprenyl pyrophosphate synthetase, mitochondrial precursor (EC 2.5.1.-) (HPS)	0.36	-	mit	0	Mitochondrion (By similarity)				452
Q9D1P2 UniProt NPD GO	MYST1_MOUSE	Probable histone acetyltransferase MYST1 (EC 2.3.1.48) (MYST protein 1) (MOZ, YBF2/SAS3, SAS2 and TI ...	0.36	-	cyt	0	Nucleus (By similarity)	kinetochore [IDA]		1WGS	458
P26725 UniProt NPD GO	YUR1_YEAST	Probable mannosyltransferase YUR1 (EC 2.4.1.131)	0.36	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi apparatus [IDA]			428
Q9P6Q3 UniProt NPD GO	BCS1_SCHPO	Probable mitochondrial chaperone BCS1 (BCS1-like protein)	0.36	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				449
Q2THX0 UniProt NPD GO	ZDHC8_PANTR	Probable palmitoyltransferase ZDHHC8 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 8) (DH ...	0.36	-	mit	4 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (Potential)				765
Q944R1 UniProt NPD GO	PEL15_ARATH	Probable pectate lyase 15 precursor (EC 4.2.2.2) (Pectate lyase A11)	0.36	-	exc	1 *					470
P54679 UniProt NPD GO	PMA1_DICDI	Probable plasma membrane ATPase (EC 3.6.3.6) (Proton pump) (PAT2)	0.36	-	end	9	Cell membrane; multi-pass membrane protein				1058
Q7PC88 UniProt NPD GO	PDR3_ARATH	Probable pleiotropic drug resistance protein 3	0.36	-	end	11	Membrane; multi-pass membrane protein (By similarity)				1426
O13969 UniProt NPD GO	SYTM_SCHPO	Probable threonyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.3) (Threonine--tRNA ligase) (Th ...	0.36	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				473
P48359 UniProt NPD GO	YCF29_CYAPA	Probable transcriptional regulator ycf29	0.36	-	cyt	0	Plastid; cyanelle				210
P01211 UniProt NPD GO	PENK_BOVIN	Proenkephalin A precursor [Contains: Synenkephalin; Met-enkephalin (Opioid growth factor) (OGF); Met ...	0.36	-	exc	0	Secreted protein				263
Q9DGC9 UniProt NPD GO	GON2_ORYLA	Progonadoliberin-2 precursor (Progonadoliberin II) (Chicken-type II gonadotropin-releasing hormone) ...	0.36	-	end	0	Secreted protein	extracellular region [ISS]			80
Q2HJ97 UniProt NPD GO	PHB2_BOVIN	Prohibitin-2	0.36	-	mit	0	Mitochondrion; mitochondrial inner membrane. Cytoplasm. Nucleus. Also cytoplasmic and nuclear (By si ...				299
P87495 UniProt NPD GO	PRL_CARAU	Prolactin precursor (PRL)	0.36	-	nuc	1 *	Secreted protein				210
P51904 UniProt NPD GO	PRL_ICTPU	Prolactin precursor (PRL)	0.36	-	mit	0	Secreted protein				212
Q9CQJ5 UniProt NPD GO	PRR13_MOUSE	Proline-rich protein 13	0.36	+	nuc	0					137
P78600 UniProt NPD GO	SYPC_CANAL	Prolyl-tRNA synthetase, cytoplasmic (EC 6.1.1.15) (Proline--tRNA ligase) (ProRS)	0.36	-	nuc	0	Cytoplasm (Potential)				575
O43490 UniProt NPD GO	PROM1_HUMAN	Prominin-1 precursor (Prominin-like protein 1) (Antigen AC133) (CD133 antigen)	0.36	-	end	5	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS]	604365		865
Q9BGL8 UniProt NPD GO	PE2R1_CANFA	Prostaglandin E2 receptor, EP1 subtype (Prostanoid EP1 receptor) (PGE receptor, EP1 subtype)	0.36	-	end	6 *	Membrane; multi-pass membrane protein				403
P35354 UniProt NPD GO	PGH2_HUMAN	Prostaglandin G/H synthase 2 precursor (EC 1.14.99.1) (Cyclooxygenase-2) (COX-2) (Prostaglandin-endo ...	0.36	-	vac	0	Microsome; microsomal membrane; peripheral membrane protein	cytoplasm [IDA] nucleus [ISS]	600262		604
P38293 UniProt NPD GO	UMP1_YEAST	Proteasome maturation factor UMP1	0.36	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			148
Q06541 UniProt NPD GO	ARV1_YEAST	Protein ARV1	0.36	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [IDA] Golgi apparatus [IDA]			321
Q8K3W0 UniProt NPD GO	BRE_MOUSE	Protein BRE (Brain and reproductive organ-expressed protein)	0.36	-	cyt	0	Cytoplasm; cytosol (By similarity). Mainly. Nucleus (By similarity). Also nuclear	cytoplasm [ISS] nuclear ubiquitin ligase complex [ISS] nucleus [ISS]			420
O74414 UniProt NPD GO	YJL1_SCHPO	Protein C14G10.01 in chromosome III	0.36	-	cyt	1	Cytoplasm				236
Q9H7H1 UniProt NPD GO	CU096_HUMAN	Protein C21orf96	0.36	+	nuc	0					129
Q4R616 UniProt NPD GO	CD017_MACFA	Protein C4orf17 homolog	0.36	-	nuc	0					296
Q8C1Y8 UniProt NPD GO	CG028_MOUSE	Protein C7orf28 homolog	0.36	-	cyt	0					480
Q3THF9 UniProt NPD GO	CQ10B_MOUSE	Protein COQ10 B, mitochondrial precursor	0.36	-	mit	0	Mitochondrion (Potential)				240
Q9ES72 UniProt NPD GO	CYR61_RAT	Protein CYR61 precursor (Cysteine-rich, angiogenic inducer, 61) (Insulin-like growth factor-binding ...	0.36	-	mit	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS]			379
Q76EJ0 UniProt NPD GO	YABDL_ORYSA	Protein DROOPING LEAF	0.36	-	nuc	0	Nucleus (Potential)				194
P16151 UniProt NPD GO	ERD1_YEAST	Protein ERD1	0.36	-	end	3 *	Membrane; multi-pass membrane protein	membrane [IDA]			362
Q9NYK6 UniProt NPD GO	EURL_HUMAN	Protein EURL homolog	0.36	-	nuc	0					297
Q9D7G4 UniProt NPD GO	EURL_MOUSE	Protein EURL homolog	0.36	-	nuc	0					290

You are viewing entries 35251 to 35300 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.