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
Q9FHJ2 UniProt NPD GO	DRL34_ARATH	Probable disease resistance protein At5g45440	0.11	-	cyt	0					346
Q9M1S8 UniProt NPD GO	GCP2_ARATH	Probable glutamate carboxypeptidase 2 (EC 3.4.17.21) (Probable glutamate carboxypeptidase II)	0.11	-	mit	1 *	Membrane; single-pass type II membrane protein	integral to membrane [NAS]			705
Q21944 UniProt NPD GO	GLPK_CAEEL	Probable glycerol kinase (EC 2.7.1.30) (ATP:glycerol 3-phosphotransferase) (Glycerokinase) (GK)	0.11	-	cyt	0					502
P46548 UniProt NPD GO	NMT_CAEEL	Probable glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (My ...	0.11	-	cyt	0	Cytoplasm (Potential)				450
Q07729 UniProt NPD GO	GUAD_YEAST	Probable guanine deaminase (EC 3.5.4.3) (Guanase) (Guanine aminase) (Guanine aminohydrolase) (GAH)	0.11	-	nuc	0		cytoplasm [IDA]			489
O14059 UniProt NPD GO	HIS9_SCHPO	Probable histidinol-phosphatase (EC 3.1.3.15) (HolPase)	0.11	-	cyt	0					306
Q9C944 UniProt NPD GO	H2AV3_ARATH	Probable histone H2A variant 3 (H2A.F/Z 3) (HTA9)	0.11	-	nuc	0	Nucleus (By similarity)				134
O60100 UniProt NPD GO	IMB4_SCHPO	Probable importin beta-4 subunit (Karyopherin beta-4 subunit) (Importin 123)	0.11	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1067
P50094 UniProt NPD GO	IMDH4_YEAST	Probable inosine-5'-monophosphate dehydrogenase IMD4 (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMP ...	0.11	-	cyt	0		cytoplasm [IDA]			524
Q09582 UniProt NPD GO	METH_CAEEL	Probable methionine synthase (EC 2.1.1.13) (5-methyltetrahydrofolate--homocysteine methyltransferase ...	0.11	-	cyt	0					1249
Q9SVN5 UniProt NPD GO	SYM_ARATH	Probable methionyl-tRNA synthetase (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.11	-	cyt	0	Cytoplasm (Probable)				797
Q23381 UniProt NPD GO	MUTA_CAEEL	Probable methylmalonyl-CoA mutase, mitochondrial precursor (EC 5.4.99.2) (MCM)	0.11	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				744
Q9U4L6 UniProt NPD GO	TOM40_DROME	Probable mitochondrial import receptor subunit TOM40 homolog (Translocase of outer membrane 40 kDa s ...	0.11	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				344
O94745 UniProt NPD GO	MPPA_SCHPO	Probable mitochondrial-processing peptidase alpha subunit, mitochondrial precursor (EC 3.4.24.64) (A ...	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				494
Q9ESG8 UniProt NPD GO	ZDH16_MOUSE	Probable palmitoyltransferase ZDHHC16 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 16) ( ...	0.11	-	mit	4	Membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum				361
Q8N0Y7 UniProt NPD GO	PGAM4_HUMAN	Probable phosphoglycerate mutase 4 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13)	0.11	-	cyt	0					254
Q8MKE8 UniProt NPD GO	PGAM4_PANTR	Probable phosphoglycerate mutase 4 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13)	0.11	-	cyt	0					254
O18054 UniProt NPD GO	PFD3_CAEEL	Probable prefoldin subunit 3	0.11	-	cyt	0					185
Q9P6U7 UniProt NPD GO	PSB2_NEUCR	Probable proteasome subunit beta type 2 (EC 3.4.25.1)	0.11	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				203
Q9VNA5 UniProt NPD GO	PSB4_DROME	Probable proteasome subunit beta type 4 (EC 3.4.25.1)	0.11	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				268
Q9VYY2 UniProt NPD GO	SPCS2_DROME	Probable signal peptidase complex subunit 2 (EC 3.4.-.-) (Microsomal signal peptidase 25 kDa subunit ...	0.11	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				199
O94415 UniProt NPD GO	SUCB_SCHPO	Probable succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.4) (Succiny ...	0.11	-	nuc	0	Mitochondrion (By similarity)				433
Q9VWP4 UniProt NPD GO	SUOX_DROME	Probable sulfite oxidase, mitochondrial precursor (EC 1.8.3.1)	0.11	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)	mitochondrial intermembrane space [NAS]			573
Q6BQZ1 UniProt NPD GO	SODM_DEBHA	Probable superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				211
P55966 UniProt NPD GO	SCX8_LEIQH	Probable toxin Lqh 8/6	0.11	-	nuc	0	Secreted protein				38
P36032 UniProt NPD GO	MCH2_YEAST	Probable transporter MCH2	0.11	-	end	11 *	Membrane; multi-pass membrane protein (Probable)				473
O59771 UniProt NPD GO	UMPK_SCHPO	Probable uridylate kinase (EC 2.7.4.-) (UK) (Uridine monophosphate kinase) (UMP kinase)	0.11	-	cyt	0					191
O13742 UniProt NPD GO	VPH1_SCHPO	Probable vacuolar ATP synthase 91 kDa subunit (Vacuolar ATPase 91 kDa subunit)	0.11	-	end	6	Vacuole; vacuolar membrane; multi-pass membrane protein (Potential)				805
O08976 UniProt NPD GO	PBAS_MOUSE	Probasin precursor (PB)	0.11	-	mit	0	Secreted protein (Probable)				174
P32006 UniProt NPD GO	PROF1_STRPU	Profilin (SpCoel1)	0.11	-	nuc	0					141
Q95335 UniProt NPD GO	GON1_TUPGB	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.11	-	end	1 *	Secreted protein				92
P84173 UniProt NPD GO	PHB_CHICK	Prohibitin	0.11	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity)				272
Q8R413 UniProt NPD GO	PROK2_RAT	Prokineticin-2 precursor (PK2)	0.11	-	mit	0	Secreted protein (By similarity)				107
P55752 UniProt NPD GO	PRL2_ALLMI	Prolactin-2 (Prolactin II) (PRL-II)	0.11	-	cyt	0	Secreted protein				199
P60987 UniProt NPD GO	PIP_CAVPO	Prolactin-inducible protein homolog precursor	0.11	-	vac	0	Secreted protein (By similarity)				146
Q99946 UniProt NPD GO	PRRT1_HUMAN	Proline-rich transmembrane protein 1	0.11	-	end	2	Membrane; multi-pass membrane protein (Potential)				306
P05166 UniProt NPD GO	PCCB_HUMAN	Propionyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.3) (PCCase subunit beta) (Pr ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	606054		539
P70263 UniProt NPD GO	PD2R_MOUSE	Prostaglandin D2 receptor (Prostanoid DP receptor) (PGD receptor)	0.11	-	end	7 *	Membrane; multi-pass membrane protein				357
Q29487 UniProt NPD GO	PTGDS_FELCA	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.11	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Detected on rough endoplasmic re ...	extracellular region [ISS] Golgi apparatus [ISS] nuclear envelope [ISS] rough endoplasmic reticulum [ISS]			191
P49721 UniProt NPD GO	PSB2_HUMAN	Proteasome subunit beta type 2 (EC 3.4.25.1) (Proteasome component C7-I) (Macropain subunit C7-I) (M ...	0.11	-	cyt	0	Cytoplasm. Nucleus	proteasome complex (sensu Eukaryota) [TAS]	602175		201
O23717 UniProt NPD GO	PSB5A_ARATH	Proteasome subunit beta type 5-A precursor (EC 3.4.25.1) (20S proteasome beta subunit E-1) (Proteaso ...	0.11	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				274
P97783 UniProt NPD GO	AF1Q_MOUSE	Protein AF1q	0.11	-	nuc	0					90
Q9H2C2 UniProt NPD GO	ARV1_HUMAN	Protein ARV1 (hARV1)	0.11	-	end	3	Membrane; multi-pass membrane protein (Potential)				271
Q6ID70 UniProt NPD GO	Y3377_ARATH	Protein At3g03773	0.11	-	nuc	0				1XO9	150
O49453 UniProt NPD GO	Y4844_ARATH	Protein At4g28440	0.11	-	cyt	0				1WJJ	153
Q5H9J7 UniProt NPD GO	BEX5_HUMAN	Protein BEX5 (Brain-expressed X-linked protein 5) (NGFRAP1-like 1) (Nerve growth factor receptor-ass ...	0.11	-	cyt	0	Cytoplasm				111
P41505 UniProt NPD GO	BP4A_BRANA	Protein BP4A	0.11	-	nuc	1 *					63
Q8BZA9 UniProt NPD GO	CL005_MOUSE	Protein C12orf5 homolog	0.11	-	mit	0					269
Q5BL31 UniProt NPD GO	CF106_BRARE	Protein C6orf106 homolog	0.11	-	cyt	0					283
Q9D9V4 UniProt NPD GO	CF206_MOUSE	Protein C6orf206 homolog	0.11	-	mit	0					276

You are viewing entries 63301 to 63350 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.