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
Q9Z2X2 UniProt NPD GO	PSD10_MOUSE	26S proteasome non-ATPase regulatory subunit 10 (26S proteasome regulatory subunit p28) (Gankyrin)	0.03	-	cyt	0					231
Q8W425 UniProt NPD GO	PSD6_ORYSA	26S proteasome non-ATPase regulatory subunit 6 (26S proteasome regulatory particle non-ATPase subuni ...	0.03	-	cyt	0					389
P29184 UniProt NPD GO	HP29_SARPE	29 kDa hemocyte proteinase (EC 3.4.22.-) (Fragment)	0.03	-		0					16
Q8LL69 UniProt NPD GO	DBNBT_TAXCA	3'-N-debenzoyl-2'-deoxytaxol N-benzoyltransferase (EC 2.3.1.-) (DBTNBT)	0.03	-	cyt	0					441
P54960 UniProt NPD GO	HMDH_BLAGE	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.03	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				856
P29058 UniProt NPD GO	HMDH2_HEVBR	3-hydroxy-3-methylglutaryl-coenzyme A reductase 2 (EC 1.1.1.34) (HMG-CoA reductase 2) (Fragment)	0.03	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Mitochondrion; m ...				210
Q60W34 UniProt NPD GO	3HAO_CAEBR	3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (3-HAO) (3-hydroxyanthranilic acid dioxygenase) ...	0.03	-	cyt	0	Cytoplasm (By similarity)				280
P31937 UniProt NPD GO	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase, mitochondrial precursor (EC 1.1.1.31) (HIBADH)	0.03	-	mit	0	Mitochondrion	mitochondrion [NAS]		2GF2	336
O60027 UniProt NPD GO	LEU3_ASHGO	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.03	-	cyt	0	Cytoplasm				372
P87256 UniProt NPD GO	LEU3A_ASPNG	3-isopropylmalate dehydrogenase A (EC 1.1.1.85) (Beta-IPM dehydrogenase A) (IMDH A) (3-IPM-DH A)	0.03	-	cyt	0	Cytoplasm				363
Q6CJC2 UniProt NPD GO	ERG27_KLULA	3-keto-steroid reductase (EC 1.1.1.270)	0.03	-	cyt	1					346
Q05493 UniProt NPD GO	THIK_YARLI	3-ketoacyl-CoA thiolase, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase) (Acetyl-CoA acyltra ...	0.03	-	nuc	0	Peroxisome				414
Q5BE65 UniProt NPD GO	TSC10_EMENI	3-ketodihydrosphingosine reductase tsc10 (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS reduct ...	0.03	-	nuc	0	Endoplasmic reticulum (By similarity)				357
P31213 UniProt NPD GO	S5A2_HUMAN	3-oxo-5-alpha-steroid 4-dehydrogenase 2 (EC 1.3.99.5) (Steroid 5-alpha-reductase 2) (SR type 2) (5 a ...	0.03	-	end	6 *	Microsome; microsomal membrane; multi-pass membrane protein		607306		254
P51857 UniProt NPD GO	AK1D1_HUMAN	3-oxo-5-beta-steroid 4-dehydrogenase (EC 1.3.1.3) (Delta(4)-3-ketosteroid 5-beta-reductase) (Aldo-ke ...	0.03	-	cyt	0	Cytoplasm	cytosol [IDA]	604741		326
P49245 UniProt NPD GO	FABH2_CUPWR	3-oxoacyl-[acyl-carrier-protein] synthase 3 B, chloroplast precursor (EC 2.3.1.41) (3-oxoacyl-[acyl- ...	0.03	-	mit	0	Plastid; chloroplast				402
Q9D404 UniProt NPD GO	OXSM_MOUSE	3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial precursor (EC 2.3.1.41) (Beta-ketoacyl synt ...	0.03	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			459
P23281 UniProt NPD GO	AROA2_TOBAC	3-phosphoshikimate 1-carboxyvinyltransferase 2 (EC 2.5.1.19) (5-enolpyruvylshikimate-3-phosphate syn ...	0.03	-	cyt	0	Plastid; chloroplast				338
P17688 UniProt NPD GO	AROA_BRANA	3-phosphoshikimate 1-carboxyvinyltransferase, chloroplast precursor (EC 2.5.1.19) (5-enolpyruvylshik ...	0.03	-	mit	0	Plastid; chloroplast				516
P10748 UniProt NPD GO	AROA_LYCES	3-phosphoshikimate 1-carboxyvinyltransferase, chloroplast precursor (EC 2.5.1.19) (5-enolpyruvylshik ...	0.03	-	mit	0	Plastid; chloroplast				520
P11043 UniProt NPD GO	AROA_PETHY	3-phosphoshikimate 1-carboxyvinyltransferase, chloroplast precursor (EC 2.5.1.19) (5-enolpyruvylshik ...	0.03	-	cyt	0	Plastid; chloroplast				516
P80845 UniProt NPD GO	CWP24_ARATH	36 kDa cell wall protein (Fragment)	0.03	-		0	Cell wall				13
Q9CQF0 UniProt NPD GO	RM11_MOUSE	39S ribosomal protein L11, mitochondrial precursor (L11mt) (MRP-L11)	0.03	-	cyt	0	Mitochondrion	mitochondrial large ribosomal subunit [IDA]			192
P41636 UniProt NPD GO	4CL_PINTA	4-coumarate--CoA ligase (EC 6.2.1.12) (4CL) (4-coumaroyl-CoA synthase)	0.03	-	end	0					537
Q9S725 UniProt NPD GO	4CL2_ARATH	4-coumarate--CoA ligase 2 (EC 6.2.1.12) (4CL 2) (At4Cl2) (4-coumaroyl-CoA synthase 2)	0.03	-	end	0					556
P19881 UniProt NPD GO	PNPP_YEAST	4-nitrophenylphosphatase (EC 3.1.3.41) (PNPPase)	0.03	-	mit	0		cytoplasm [IDA] nucleus [IDA]			312
P80812 UniProt NPD GO	CWP16_LYCES	40 kDa cell wall protein (Fragment)	0.03	-		0	Cell wall				15
Q9CR16 UniProt NPD GO	PPID_MOUSE	40 kDa peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-40) (CYP-40 ...	0.03	-	nuc	0	Cytoplasm (By similarity)				369
Q9SMI3 UniProt NPD GO	RS12_CYAPA	40S ribosomal protein S12	0.03	-	cyt	0					136
P80455 UniProt NPD GO	RS12_DROME	40S ribosomal protein S12	0.03	-	cyt	0					139
O13019 UniProt NPD GO	RS12_ORENI	40S ribosomal protein S12	0.03	-	cyt	0					131
O15631 UniProt NPD GO	RS19_ENTHI	40S ribosomal protein S19	0.03	-	cyt	0					148
Q9DFR5 UniProt NPD GO	RS19_GILMI	40S ribosomal protein S19	0.03	-	cyt	0					147
Q9Y0H3 UniProt NPD GO	RS19_MYXGL	40S ribosomal protein S19	0.03	-	cyt	0					145
P49154 UniProt NPD GO	RS2_URECA	40S ribosomal protein S2	0.03	+	cyt	0					278
Q6F477 UniProt NPD GO	RS21_PLUXY	40S ribosomal protein S21	0.03	-	cyt	0					83
P79057 UniProt NPD GO	RS23_SCHPO	40S ribosomal protein S23	0.03	-	nuc	0					143
P47837 UniProt NPD GO	RS4_CANAL	40S ribosomal protein S4 (S7)	0.03	-	mit	0					262
Q861U8 UniProt NPD GO	RS4Y1_GORGO	40S ribosomal protein S4, Y isoform 1	0.03	-	mit	0					262
P22090 UniProt NPD GO	RS4Y1_HUMAN	40S ribosomal protein S4, Y isoform 1	0.03	-	mit	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]	470000		262
P79183 UniProt NPD GO	RS4Y1_MACFU	40S ribosomal protein S4, Y isoform 1	0.03	-	mit	0					262
Q861V0 UniProt NPD GO	RS4Y1_PANPA	40S ribosomal protein S4, Y isoform 1	0.03	-	mit	0					262
Q861U9 UniProt NPD GO	RS4Y1_PANTR	40S ribosomal protein S4, Y isoform 1	0.03	-	mit	0					262
Q861U7 UniProt NPD GO	RS4Y1_PONPY	40S ribosomal protein S4, Y isoform 1	0.03	-	mit	0					262
Q8TD47 UniProt NPD GO	RS4Y2_HUMAN	40S ribosomal protein S4, Y isoform 2	0.03	-	mit	0			400030		262
Q6GVM7 UniProt NPD GO	RS4Y2_PANTR	40S ribosomal protein S4, Y isoform 2	0.03	-	mit	0					262
Q9P3X9 UniProt NPD GO	PPID_NEUCR	41 kDa peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-41) (CYP-41 ...	0.03	-	cyt	0	Cytoplasm (By similarity)				375
P82429 UniProt NPD GO	CWP21_TOBAC	44 kDa cell wall protein (Fragment)	0.03	-		0	Cell wall				9
P29043 UniProt NPD GO	HSP47_HUMAN	47 kDa heat shock protein precursor (Collagen-binding protein 1) (Colligin 1)	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS]	600943		417
P29457 UniProt NPD GO	HSP47_RAT	47 kDa heat shock protein precursor (Collagen-binding protein 1) (GP46)	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				417

You are viewing entries 78851 to 78900 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.