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
Q6IWY1 UniProt NPD GO	LPAT2_BRAOL	1-acyl-sn-glycerol-3-phosphate acyltransferase 2 (EC 2.3.1.51) (Lysophosphatidyl acyltransferase 2)	0.05	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				391
P31237 UniProt NPD GO	ACCO_ACTCH	1-aminocyclopropane-1-carboxylate oxidase (EC 1.14.17.4) (ACC oxidase) (Ethylene-forming enzyme) (EF ...	0.05	-	nuc	0					319
Q9ZQZ1 UniProt NPD GO	ACCO_DENCR	1-aminocyclopropane-1-carboxylate oxidase (EC 1.14.17.4) (ACC oxidase) (Ethylene-forming enzyme) (EF ...	0.05	-	cyt	0					318
P19464 UniProt NPD GO	ACCO_PERAE	1-aminocyclopropane-1-carboxylate oxidase (EC 1.14.17.4) (ACC oxidase) (Ethylene-forming enzyme) (EF ...	0.05	-	cyt	0					320
Q40634 UniProt NPD GO	ACCO1_ORYSA	1-aminocyclopropane-1-carboxylate oxidase 1 (EC 1.14.17.4) (ACC oxidase 1) (Ethylene-forming enzyme) ...	0.05	-	cyt	0					322
O48882 UniProt NPD GO	ACCO2_MALDO	1-aminocyclopropane-1-carboxylate oxidase 2 (EC 1.14.17.4) (ACC oxidase 2) (Ethylene-forming enzyme) ...	0.05	-	cyt	0					330
P07920 UniProt NPD GO	ACCO2_LYCES	1-aminocyclopropane-1-carboxylate oxidase 2 (EC 1.14.17.4) (ACC oxidase 2) (Ethylene-forming enzyme) ...	0.05	-	cyt	0					316
Q8W250 UniProt NPD GO	DXR_ORYSA	1-deoxy-D-xylulose 5-phosphate reductoisomerase, chloroplast precursor (EC 1.1.1.267) (DXP reductois ...	0.05	-	cyt	0	Plastid; chloroplast (Potential)				473
P34893 UniProt NPD GO	CH10_ARATH	10 kDa chaperonin (Protein CPN10) (Protein groES)	0.05	-	nuc	0	Cytoplasm (Potential)				98
Q5RFM9 UniProt NPD GO	FTHFD_PONPY	10-formyltetrahydrofolate dehydrogenase (EC 1.5.1.6) (10-FTHFDH) (Aldehyde dehydrogenase 1 family me ...	0.05	-	cyt	0	Cytoplasm (By similarity)				902
Q27979 UniProt NPD GO	RDH1_BOVIN	11-cis retinol dehydrogenase (EC 1.1.1.105) (11-cis RDH) (P32)	0.05	-	end	0	Membrane; peripheral membrane protein				318
P39990 UniProt NPD GO	SNU13_YEAST	13 kDa ribonucleoprotein-associated protein	0.05	-	cyt	0	Nucleus; nucleolus	nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI] U4/U6 x U5 tri-snRNP complex [IDA]		1ZWZ	126
Q84J50 UniProt NPD GO	HSP22_ORYSA	17.4 kDa class I heat shock protein 2	0.05	-	mit	0	Cytoplasm				159
Q84Q72 UniProt NPD GO	HSP24_ORYSA	17.4 kDa class I heat shock protein 4	0.05	-	mit	0	Cytoplasm				161
P24632 UniProt NPD GO	HSP22_MAIZE	17.8 kDa class II heat shock protein	0.05	-	cyt	0	Cytoplasm				164
Q8T8B9 UniProt NPD GO	ACMSD_CAEEL	2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (EC 4.1.1.45)	0.05	-	nuc	0					401
P80810 UniProt NPD GO	CWP14_LYCES	23 kDa cell wall protein (Fragment)	0.05	-		0	Cell wall				10
P23951 UniProt NPD GO	CHI2_HORVU	26 kDa endochitinase 2 precursor (EC 3.2.1.14) (CHI-26)	0.05	-	vac	1 *				2BAA	266
P60897 UniProt NPD GO	DSS1_MOUSE	26 proteasome complex subunit DSS1 (Deleted in split hand/split foot protein 1) (Split hand/foot del ...	0.05	-	cyt	0		proteasome complex (sensu Eukaryota) [ISS]			70
P60896 UniProt NPD GO	DSS1_HUMAN	26 proteasome complex subunit DSS1 (Deleted in split hand/split foot protein 1) (Split hand/foot del ...	0.05	-	cyt	0		proteasome complex (sensu Eukaryota) [IDA]	601285	1MJE	70
Q13200 UniProt NPD GO	PSD2_HUMAN	26S proteasome non-ATPase regulatory subunit 2 (26S proteasome regulatory subunit RPN1) (26S proteas ...	0.05	-	ves	0		proteasome regulatory particle (sensu Eukar... [TAS]	606223		908
Q7S8R8 UniProt NPD GO	RPN1_NEUCR	26S proteasome regulatory subunit rpn-1	0.05	-	nuc	0					883
Q05439 UniProt NPD GO	OS28_PLAGA	28 kDa ookinete surface antigen precursor (Pgs28)	0.05	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				222
P82435 UniProt NPD GO	CWP27_TOBAC	29 kDa cell wall protein (Fragment)	0.05	-		0	Cell wall				14
P24815 UniProt NPD GO	3BHS1_MOUSE	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type I (3Beta-HSD I) [Includes: 3-beta-hyd ...	0.05	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
P26149 UniProt NPD GO	3BHS2_MOUSE	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type II (3Beta-HSD II) [Includes: 3-beta-h ...	0.05	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
O35469 UniProt NPD GO	3BHS6_MOUSE	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type VI (3Beta-HSD VI) [Includes: 3-beta-h ...	0.05	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
Q40639 UniProt NPD GO	DPNP_ORYSA	3'(2'),5'-bisphosphate nucleotidase (EC 3.1.3.7) (3'(2'),5-bisphosphonucleoside 3'(2')-phosphohydrol ...	0.05	-	cyt	0					358
O94505 UniProt NPD GO	DPNP_SCHPO	3'(2'),5'-bisphosphate nucleotidase (EC 3.1.3.7) (3'(2'),5-bisphosphonucleoside 3'(2')-phosphohydrol ...	0.05	-	cyt	0					353
P46594 UniProt NPD GO	HAL21_CANAL	3'(2'),5'-bisphosphate nucleotidase 1 (EC 3.1.3.7) (3'(2'),5-bisphosphonucleoside 3'(2')-phosphohydr ...	0.05	-	nuc	0					364
O59821 UniProt NPD GO	CSL4_SCHPO	3'-5' exoribonuclease CSL4 homolog (EC 3.1.13.-)	0.05	-	cyt	0	Nucleus; nucleolus (By similarity)				181
Q05871 UniProt NPD GO	ECI1_YEAST	3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) (Dodecenoyl-CoA isomerase) (Delta(3),delta(2)-enoyl-CoA i ...	0.05	-	cyt	0	Peroxisome. This location is DCI1 dependent	peroxisome [IDA]		1PJH	280
O64967 UniProt NPD GO	HMDH2_GOSHI	3-hydroxy-3-methylglutaryl-coenzyme A reductase 2 (EC 1.1.1.34) (HMG-CoA reductase 2)	0.05	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Mitochondrion; m ...				628
Q41438 UniProt NPD GO	HMDH3_SOLTU	3-hydroxy-3-methylglutaryl-coenzyme A reductase 3 (EC 1.1.1.34) (HMG-CoA reductase 3) (HMG3.3)	0.05	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				574
Q19341 UniProt NPD GO	3HAO_CAEEL	3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (3-HAO) (3-hydroxyanthranilic acid dioxygenase) ...	0.05	-	cyt	0	Cytoplasm (By similarity)				281
Q99L13 UniProt NPD GO	3HIDH_MOUSE	3-hydroxyisobutyrate dehydrogenase, mitochondrial precursor (EC 1.1.1.31) (HIBADH)	0.05	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			335
P07139 UniProt NPD GO	LEU3_CANMA	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.05	-	cyt	0	Cytoplasm				373
P04173 UniProt NPD GO	LEU3_YEAST	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.05	-	cyt	0	Cytoplasm	cytosol [IDA]			364
Q6CE88 UniProt NPD GO	ERG27_YARLI	3-keto-steroid reductase (EC 1.1.1.270)	0.05	-	cyt	0					343
Q570C8 UniProt NPD GO	THIK5_ARATH	3-ketoacyl-CoA thiolase 5, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase 5) (Acetyl-CoA acy ...	0.05	-	cyt	0	Peroxisome (Probable)				457
Q8BWT1 UniProt NPD GO	THIM_MOUSE	3-ketoacyl-CoA thiolase, mitochondrial (EC 2.3.1.16) (Beta-ketothiolase) (Acetyl-CoA acyltransferase ...	0.05	-	cyt	0	Mitochondrion (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			397
P13437 UniProt NPD GO	THIM_RAT	3-ketoacyl-CoA thiolase, mitochondrial (EC 2.3.1.16) (Beta-ketothiolase) (Acetyl-CoA acyltransferase ...	0.05	-	cyt	0	Mitochondrion	mitochondrial matrix [NAS]			397
Q6CLN0 UniProt NPD GO	TSC10_KLULA	3-ketodihydrosphingosine reductase TSC10 (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS reduct ...	0.05	-	cyt	1	Endoplasmic reticulum (By similarity)				313
P38342 UniProt NPD GO	TSC10_YEAST	3-ketodihydrosphingosine reductase TSC10 (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS reduct ...	0.05	-	cyt	1		cytoplasm [IDA] endoplasmic reticulum [IDA] mitochondrial outer membrane [IDA]			320
P97532 UniProt NPD GO	THTM_RAT	3-mercaptopyruvate sulfurtransferase (EC 2.8.1.2) (MST)	0.05	-	cyt	0	Cytoplasm. Mostly. Mitochondrion				296
Q28891 UniProt NPD GO	S5A1_MACFA	3-oxo-5-alpha-steroid 4-dehydrogenase 1 (EC 1.3.99.5) (Steroid 5-alpha-reductase 1) (SR type 1)	0.05	-	nuc	3 *	Microsome; microsomal membrane; multi-pass membrane protein				263
P18405 UniProt NPD GO	S5A1_HUMAN	3-oxo-5-alpha-steroid 4-dehydrogenase 1 (EC 1.3.99.5) (Steroid 5-alpha-reductase 1) (SR type 1) (S5A ...	0.05	-	nuc	4 *	Microsome; microsomal membrane; multi-pass membrane protein		184753		259
P80792 UniProt NPD GO	CWP15_TOBAC	33 kDa cell wall protein (Fragment)	0.05	-		0	Cell wall				11
P80842 UniProt NPD GO	CWP21_ARATH	36 kDa cell wall protein (Fragment)	0.05	-		0	Cell wall				10
Q7YR75 UniProt NPD GO	RM12_BOVIN	39S ribosomal protein L12, mitochondrial precursor (L12mt) (MRP-L12)	0.05	-	mit	0	Mitochondrion			2FTC	198

You are viewing entries 73551 to 73600 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.