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
Q23400 UniProt NPD GO	RCL1_CAEEL	Probable RNA 3'-terminal phosphate cyclase-like protein	0.05	-	cyt	0	Nucleus; nucleolus (By similarity)				379
Q7LL14 UniProt NPD GO	RU2B_SCHPO	Probable U2 small nuclear ribonucleoprotein B''	0.05	-	cyt	2 *	Nucleus (By similarity)				111
Q23500 UniProt NPD GO	ACOC_CAEEL	Probable aconitate hydratase, cytoplasmic (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.05	-	cyt	0	Cytoplasm	cytosol [IDA]			887
Q9VYH3 UniProt NPD GO	PEPE_DROME	Probable alpha-aspartyl dipeptidase (EC 3.4.13.21) (Asp-specific dipeptidase) (Dipeptidase E)	0.05	-	mit	0	Cytoplasm (By similarity)				240
O94582 UniProt NPD GO	TRPE_SCHPO	Probable anthranilate synthase component 1 (EC 4.1.3.27) (Anthranilate synthase component I)	0.05	-	nuc	0					489
Q651D5 UniProt NPD GO	PIP27_ORYSA	Probable aquaporin PIP2.7 (Plasma membrane intrinsic protein 2.7) (OsPIP2.7)	0.05	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				290
Q67UL3 UniProt NPD GO	PIN1C_ORYSA	Probable auxin efflux carrier component 1c (OsPIN1c)	0.05	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				592
Q9SRP7 UniProt NPD GO	POLC1_ARATH	Probable calcium-binding protein At3g03430	0.05	-	cyt	0					83
O49482 UniProt NPD GO	CADH2_ARATH	Probable cinnamyl-alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.05	-	cyt	0					357
O74891 UniProt NPD GO	COPZ_SCHPO	Probable coatomer subunit zeta (Zeta-coat protein) (Zeta-COP)	0.05	-	mit	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				190
Q9T0G2 UniProt NPD GO	CYC3_ARATH	Probable cytochrome c At4g10040	0.05	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)				112
Q9UTI0 UniProt NPD GO	PYRC_SCHPO	Probable dihydroorotase (EC 3.5.2.3) (DHOase)	0.05	-	nuc	0					337
P52887 UniProt NPD GO	ALG8_CAEEL	Probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl ...	0.05	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				758
Q6P8H8 UniProt NPD GO	ALG8_MOUSE	Probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl ...	0.05	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				526
Q11190 UniProt NPD GO	ETFD_CAEEL	Probable electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (EC 1.5.5 ...	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				597
O96827 UniProt NPD GO	EF1B_DROME	Probable elongation factor 1-beta (EF-1-beta)	0.05	-	cyt	0		cytosol [NAS]			221
Q9FVT2 UniProt NPD GO	EF1G2_ARATH	Probable elongation factor 1-gamma 2 (EF-1-gamma 2) (eEF-1B gamma 2)	0.05	-	cyt	0					413
O65032 UniProt NPD GO	GSTU1_ORYSA	Probable glutathione S-transferase GSTU1 (EC 2.5.1.18)	0.05	-	nuc	0				1OYJ	231
Q9ZVQ4 UniProt NPD GO	GSTZ2_ARATH	Probable glutathione S-transferase zeta-class 2 (EC 2.5.1.18)	0.05	-	mit	0	Cytoplasm (By similarity)				223
O00086 UniProt NPD GO	IMDH3_CANAL	Probable inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMPD)	0.05	-	cyt	0					521
O14254 UniProt NPD GO	IDHP_SCHPO	Probable isocitrate dehydrogenase [NADP], mitochondrial precursor (EC 1.1.1.42) (Oxalosuccinate deca ...	0.05	-	cyt	0	Mitochondrion (By similarity)				418
Q18938 UniProt NPD GO	MAAI_CAEEL	Probable maleylacetoacetate isomerase (EC 5.2.1.2) (MAAI)	0.05	-	mit	0	Cytoplasm (By similarity)				214
Q9ZRF1 UniProt NPD GO	MTDH_FRAAN	Probable mannitol dehydrogenase (EC 1.1.1.255) (NAD-dependent mannitol dehydrogenase)	0.05	-	cyt	0					359
P25346 UniProt NPD GO	GIT1_YEAST	Probable metabolite transport protein GIT1	0.05	-	end	11 *	Membrane; multi-pass membrane protein (Probable)	plasma membrane [IMP]			518
P43562 UniProt NPD GO	YFE0_YEAST	Probable metabolite transport protein YFL040W	0.05	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				540
Q9VNA0 UniProt NPD GO	TI17A_DROME	Probable mitochondrial import inner membrane translocase subunit Tim17 1	0.05	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				179
Q7ZTM6 UniProt NPD GO	TOM40_XENLA	Probable mitochondrial import receptor subunit TOM40 homolog (Translocase of outer membrane 40 kDa s ...	0.05	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				336
Q10457 UniProt NPD GO	PUR6_CAEEL	Probable multifunctional protein ADE2 [Includes: Phosphoribosylaminoimidazole-succinocarboxamide syn ...	0.05	-	cyt	0					423
P47137 UniProt NPD GO	YJ66_YEAST	Probable oxidoreductase YJR096W (EC 1.-.-.-)	0.05	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			282
Q9CWU2 UniProt NPD GO	ZDH13_MOUSE	Probable palmitoyltransferase ZDHHC13 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 13) ( ...	0.05	-	end	7	Membrane; multi-pass membrane protein (Potential)				622
O80840 UniProt NPD GO	PMM_ARATH	Probable phosphomannomutase (EC 5.4.2.8) (PMM)	0.05	-	cyt	0	Cytoplasm (By similarity)				246
Q67UC7 UniProt NPD GO	HAK17_ORYSA	Probable potassium transporter 17 (OsHAK17)	0.05	-	end	11 *	Membrane; multi-pass membrane protein (By similarity)				707
O60078 UniProt NPD GO	TYR1_SCHPO	Probable prephenate dehydrogenase [NADP+] (EC 1.3.1.13) (PRDH)	0.05	-	cyt	0					431
Q9XI01 UniProt NPD GO	PDI1_ARATH	Probable protein disulfide-isomerase 1 precursor (EC 5.3.4.1) (PDI 1)	0.05	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				501
Q11067 UniProt NPD GO	PDIA6_CAEEL	Probable protein disulfide-isomerase A6 precursor (EC 5.3.4.1)	0.05	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				440
P49596 UniProt NPD GO	PP2C2_CAEEL	Probable protein phosphatase 2C T23F11.1 (EC 3.1.3.16) (PP2C)	0.05	-	cyt	0					356
O43002 UniProt NPD GO	SC61B_SCHPO	Probable protein transport protein sec61 subunit beta	0.05	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				102
Q92345 UniProt NPD GO	PDC2_SCHPO	Probable pyruvate decarboxylase C1F8.07c (EC 4.1.1.1)	0.05	-	cyt	0					594
P52899 UniProt NPD GO	ODPA_CAEEL	Probable pyruvate dehydrogenase E1 component alpha subunit, mitochondrial precursor (EC 1.2.4.1) (PD ...	0.05	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				397
Q9ZU38 UniProt NPD GO	RPIA_ARATH	Probable ribose-5-phosphate isomerase (EC 5.3.1.6) (Phosphoriboisomerase)	0.05	-	cyt	0					265
Q9H3G5 UniProt NPD GO	CPVL_HUMAN	Probable serine carboxypeptidase CPVL precursor (EC 3.4.16.-) (Carboxypeptidase, vitellogenic-like) ...	0.05	-	end	0			609780		476
P34525 UniProt NPD GO	SPCS3_CAEEL	Probable signal peptidase complex subunit 3 (EC 3.4.-.-) (Microsomal signal peptidase 22 kDa subunit ...	0.05	-	exc	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (Potential)				180
Q9LGB4 UniProt NPD GO	SPCS3_ORYSA	Probable signal peptidase complex subunit 3 (EC 3.4.-.-) (Microsomal signal peptidase 22 kDa subunit ...	0.05	-	cyt	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (Potential)				147
P53588 UniProt NPD GO	SUCB1_CAEEL	Probable succinyl-CoA ligase [ADP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.5) (Succiny ...	0.05	-	mit	0	Mitochondrion (By similarity)				435
P53596 UniProt NPD GO	SUCA_CAEEL	Probable succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial precursor (EC 6.2.1.4) (Succ ...	0.05	-	mit	0	Mitochondrion (By similarity)				322
Q67YF8 UniProt NPD GO	SUC7_ARATH	Probable sucrose transport protein SUC7 (Sucrose permease 7) (Sucrose-proton symporter 7)	0.05	-	end	12 *	Cell membrane; multi-pass membrane protein (Probable)				491
O13940 UniProt NPD GO	GLY1_SCHPO	Probable threonine aldolase (EC 4.1.2.5)	0.05	-	cyt	0					376
P34604 UniProt NPD GO	EI2BA_CAEEL	Probable translation initiation factor eIF-2B subunit alpha (eIF-2B GDP-GTP exchange factor subunit ...	0.05	-	cyt	0					305
P80361 UniProt NPD GO	EI2BG_CAEEL	Probable translation initiation factor eIF-2B subunit gamma (eIF-2B GDP-GTP exchange factor subunit ...	0.05	-	cyt	0					404
O59698 UniProt NPD GO	YN41_SCHPO	Probable transporter C36.01c	0.05	-	end	12	Membrane; multi-pass membrane protein				580

You are viewing entries 75301 to 75350 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.