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
O62846 UniProt NPD GO	KAPCG_MACMU	cAMP-dependent protein kinase, gamma-catalytic subunit (EC 2.7.11.11) (PKA C-gamma) (Fragment)	0.18	-	cyt	0					208
Q12517 UniProt NPD GO	DCP1_YEAST	mRNA decapping enzyme 1	0.18	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...	cytoplasmic mRNA processing body [IDA]		1Q67	231
Q758G4 UniProt NPD GO	PALH_ASHGO	pH-response regulator protein palH/RIM21	0.18	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				502
O74863 UniProt NPD GO	TRM82_SCHPO	tRNA (guanine-N(7)-)-methyltransferase-associated WD repeat protein trm82	0.18	-	mit	0					421
Q96Q11 UniProt NPD GO	TRNT1_HUMAN	tRNA-nucleotidyltransferase 1, mitochondrial precursor (EC 2.7.7.25) (Mitochondrial tRNA nucleotidyl ...	0.18	-	mit	0	Mitochondrion	mitochondrion [IDA]		1OU5	434
Q8L5K3 UniProt NPD GO	RLC1_CITLI	(R)-limonene synthase 1 (EC 4.2.3.20) ((+)-limonene synthase 1)	0.17	-	mit	0					606
Q8NKE1 UniProt NPD GO	GLGB_GLOIN	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme)	0.17	-	cyt	0					683
Q04446 UniProt NPD GO	GLGB_HUMAN	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme) (Brancher enzyme)	0.17	-	cyt	0			607839		702
Q01401 UniProt NPD GO	GLGB_ORYSA	1,4-alpha-glucan branching enzyme, chloroplast precursor (EC 2.4.1.18) (Starch branching enzyme) (Q- ...	0.17	-	cyt	0	Plastid; chloroplast. Plastid; amyloplast				820
Q9D517 UniProt NPD GO	PLCC_MOUSE	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (EC 2.3.1.51) (1-AGP acyltransferase 3) (1-AGPA ...	0.17	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				376
P18485 UniProt NPD GO	1A12_LYCES	1-aminocyclopropane-1-carboxylate synthase 2 (EC 4.4.1.14) (ACC synthase 2) (S-adenosyl-L-methionine ...	0.17	-	cyt	0				1IAY	485
O70456 UniProt NPD GO	1433S_MOUSE	14-3-3 protein sigma (Stratifin)	0.17	-	nuc	0	Or: Cytoplasm (By similarity). Or: Secreted protein (By similarity). May be secreted by a non-classi ...	cytoplasm [IDA]			248
P52908 UniProt NPD GO	1433_CHLRE	14-3-3-like protein	0.17	-	cyt	0					259
P29305 UniProt NPD GO	1433A_HORVU	14-3-3-like protein A (14-3-3A)	0.17	-	cyt	0					262
Q06967 UniProt NPD GO	14336_ORYSA	14-3-3-like protein GF14-F (G-box factor 14-3-3 homolog F) (OsGF14a) (14-3-3-like protein S94) (Stre ...	0.17	-	cyt	0	Cytoplasm. Nucleus				260
Q802F3 UniProt NPD GO	SEP15_BRARE	15 kDa selenoprotein precursor	0.17	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum lumen [ISS]			153
P06623 UniProt NPD GO	CN37_BOVIN	2',3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) (CNP) (CNPase)	0.17	-	cyt	0	Membrane. Firmly bound to membrane structures of brain white matter				400
P82439 UniProt NPD GO	CWP31_TOBAC	200 kDa cell wall protein (Fragment)	0.17	-		0	Cell wall				15
Q4UEQ6 UniProt NPD GO	P23_THEAN	23 kDa piroplasm membrane protein precursor (p23)	0.17	-	end	1 *	Membrane; single-pass membrane protein (Potential)				229
P46073 UniProt NPD GO	MEP20_ASPFL	24 kDa metalloproteinase precursor (EC 3.4.24.39) (Deuterolysin)	0.17	-	mit	0					381
O42587 UniProt NPD GO	PR6AA_XENLA	26S protease regulatory subunit 6A-A (TAT-binding protein 6) (TBP-6)	0.17	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				405
Q3TXS7 UniProt NPD GO	PSD1_MOUSE	26S proteasome non-ATPase regulatory subunit 1 (26S proteasome regulatory subunit RPN2) (26S proteas ...	0.17	-	cyt	0					953
P55034 UniProt NPD GO	PSD4_ARATH	26S proteasome non-ATPase regulatory subunit 4 (26S proteasome regulatory subunit S5A) (Multiubiquit ...	0.17	-	nuc	0					386
O35226 UniProt NPD GO	PSD4_MOUSE	26S proteasome non-ATPase regulatory subunit 4 (26S proteasome regulatory subunit S5A) (Rpn10) (Mult ...	0.17	-	nuc	0					376
P55036 UniProt NPD GO	PSD4_HUMAN	26S proteasome non-ATPase regulatory subunit 4 (26S proteasome regulatory subunit S5A) (Rpn10) (Mult ...	0.17	-	nuc	0		proteasome complex (sensu Eukaryota) [TAS]	601648	1YX6	377
Q8BJY1 UniProt NPD GO	PSD5_MOUSE	26S proteasome non-ATPase regulatory subunit 5 (26S proteasome subunit S5B) (26S protease subunit S5 ...	0.17	-	cyt	0					503
Q9V3G7 UniProt NPD GO	PSD6_DROME	26S proteasome non-ATPase regulatory subunit 6 (26S proteasome regulatory subunit S10) (Rpn7 protein ...	0.17	-	cyt	0		proteasome regulatory particle (sensu Eukar... [IDA]			389
Q20585 UniProt NPD GO	PSD6_CAEEL	26S proteasome non-ATPase regulatory subunit 6 (26S proteasome regulatory subunit rpn-7)	0.17	-	nuc	0					410
P12683 UniProt NPD GO	HMDH1_YEAST	3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (EC 1.1.1.34) (HMG-CoA reductase 1)	0.17	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA] nuclear envelope [IDA]			1054
Q00464 UniProt NPD GO	LEU2_CANMA	3-isopropylmalate dehydratase (EC 4.2.1.33) (Isopropylmalate isomerase) (Alpha-IPM isomerase) (IPMI) ...	0.17	-	mit	0					770
P49601 UniProt NPD GO	LEU2_USTMA	3-isopropylmalate dehydratase (EC 4.2.1.33) (Isopropylmalate isomerase) (Alpha-IPM isomerase) (IPMI) ...	0.17	-	cyt	0					773
Q6BQK1 UniProt NPD GO	TSC10_DEBHA	3-ketodihydrosphingosine reductase TSC10 (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS reduct ...	0.17	-	cyt	1	Endoplasmic reticulum (By similarity)				328
P47910 UniProt NPD GO	RR31_SPIOL	30S ribosomal protein S31, chloroplast (Fragment)	0.17	-	nuc	0	Plastid; chloroplast				43
Q9CQL5 UniProt NPD GO	RM18_MOUSE	39S ribosomal protein L18, mitochondrial precursor (L18mt) (MRP-L18)	0.17	-	mit	0	Mitochondrion				180
O75012 UniProt NPD GO	MRP10_YEAST	40S ribosomal protein MRP10, mitochondrial precursor (Mitochondrial ribosomal protein 10)	0.17	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			95
Q962R9 UniProt NPD GO	RS10_SPOFR	40S ribosomal protein S10	0.17	-	cyt	0	Cytoplasm (By similarity)				158
O13614 UniProt NPD GO	RS10B_SCHPO	40S ribosomal protein S10-B	0.17	-	cyt	0					147
P17093 UniProt NPD GO	RS11_SOYBN	40S ribosomal protein S11	0.17	-	nuc	0					159
Q8I7D6 UniProt NPD GO	RS13_CIOIN	40S ribosomal protein S13	0.17	-	mit	0					150
Q8SRB3 UniProt NPD GO	RS13_ENCCU	40S ribosomal protein S13	0.17	-	mit	0					148
Q962R6 UniProt NPD GO	RS13_SPOFR	40S ribosomal protein S13	0.17	-	mit	0					150
P48855 UniProt NPD GO	RS14_PROCL	40S ribosomal protein S14	0.17	-	nuc	0					151
Q90YQ6 UniProt NPD GO	RS17_ICTPU	40S ribosomal protein S17	0.17	-	nuc	0					133
P55828 UniProt NPD GO	RS20_DROME	40S ribosomal protein S20	0.17	-	nuc	0		small ribosomal subunit [NAS]			120
Q41852 UniProt NPD GO	RS21_MAIZE	40S ribosomal protein S21	0.17	-	mit	0					81
Q8STD9 UniProt NPD GO	RS25_ENCCU	40S ribosomal protein S25	0.17	+	cyt	0					109
Q7S6W5 UniProt NPD GO	RS28_NEUCR	40S ribosomal protein S28	0.17	-	cyt	0					68
P46300 UniProt NPD GO	RS4_SOLTU	40S ribosomal protein S4	0.17	-	mit	0	Cytoplasm				264
P24050 UniProt NPD GO	RS5_RAT	40S ribosomal protein S5	0.17	-	nuc	0					203
Q8LJU5 UniProt NPD GO	RS7_ORYSA	40S ribosomal protein S7	0.17	-	cyt	0					192

You are viewing entries 53901 to 53950 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.