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
Q6NVG1 UniProt NPD GO	PLCG_MOUSE	1-acyl-sn-glycerol-3-phosphate acyltransferase eta (EC 2.3.1.51) (1-AGP acyltransferase 7) (1-AGPAT ...	0.23	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				524
P27486 UniProt NPD GO	1A1C_DIACA	1-aminocyclopropane-1-carboxylate synthase (EC 4.4.1.14) (ACC synthase) (S-adenosyl-L-methionine met ...	0.23	-	cyt	0					517
Q07215 UniProt NPD GO	1A11_ORYSA	1-aminocyclopropane-1-carboxylate synthase 1 (EC 4.4.1.14) (ACC synthase 1) (S-adenosyl-L-methionine ...	0.23	+	cyt	0		cytoplasm [IEP]			487
P68510 UniProt NPD GO	1433F_MOUSE	14-3-3 protein eta	0.23	-	nuc	0	Cytoplasm	cytoplasm [IDA]			245
P68511 UniProt NPD GO	1433F_RAT	14-3-3 protein eta	0.23	-	nuc	0	Cytoplasm				245
P68509 UniProt NPD GO	1433F_BOVIN	14-3-3 protein eta (Protein kinase C inhibitor protein 1) (KCIP-1)	0.23	-	nuc	0	Cytoplasm				245
O77642 UniProt NPD GO	1433S_SHEEP	14-3-3 protein sigma (Stratifin)	0.23	-	nuc	0	Cytoplasm (By similarity). Cytoplasmic or may be secreted by a non-classical secretory pathway (By s ...				248
Q6P4Z5 UniProt NPD GO	1433Z_XENTR	14-3-3 protein zeta	0.23	-	nuc	0	Cytoplasm				245
Q41418 UniProt NPD GO	14331_SOLTU	14-3-3-like protein	0.23	-	cyt	0					259
Q43470 UniProt NPD GO	1433B_HORVU	14-3-3-like protein B (14-3-3B)	0.23	-	cyt	0					262
P34827 UniProt NPD GO	EF1B_TRYCR	25 kDa elongation factor 1-beta (EF-1-beta)	0.23	-	cyt	0					222
P12019 UniProt NPD GO	PDSA_DICDI	3',5'-cyclic-nucleotide phosphodiesterase precursor (EC 3.1.4.17) (PDEase) (3':5'-CNP)	0.23	-	mit	0					452
P46953 UniProt NPD GO	3HAO_RAT	3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (3-HAO) (3-hydroxyanthranilic acid dioxygenase) ...	0.23	-	nuc	0	Cytoplasm				286
Q6DIZ0 UniProt NPD GO	3HAO_XENTR	3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (3-HAO) (3-hydroxyanthranilic acid dioxygenase) ...	0.23	-	nuc	0	Cytoplasm (By similarity)				280
P18120 UniProt NPD GO	LEU3_YARLI	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.23	-	cyt	0	Cytoplasm				405
Q9FMT1 UniProt NPD GO	LEU33_ARATH	3-isopropylmalate dehydrogenase 3, chloroplast precursor (EC 1.1.1.85) (Beta-IPM dehydrogenase 3) (I ...	0.23	-	cyt	0	Plastid; chloroplast (By similarity)				409
P29102 UniProt NPD GO	LEU3_BRANA	3-isopropylmalate dehydrogenase, chloroplast precursor (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) ...	0.23	-	mit	0	Plastid; chloroplast				406
O97391 UniProt NPD GO	ES30_TRICO	30 kDa antigenic glycoprotein precursor (ESGP30) (Fragment)	0.23	-	nuc	0	Secreted protein				135
Q14318 UniProt NPD GO	FKBP8_HUMAN	38 kDa FK506-binding protein homolog (FKBPR38) (FK506-binding protein 8)	0.23	-	nuc	1			604840	2F2D	355
Q9VFJ2 UniProt NPD GO	RM11_DROME	39S ribosomal protein L11, mitochondrial precursor (L11mt)	0.23	-	nuc	0	Mitochondrion				196
O48604 UniProt NPD GO	HPPD_HORVU	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.23	-	cyt	0	Cytoplasm (By similarity)				434
P26781 UniProt NPD GO	RS11_YEAST	40S ribosomal protein S11 (S18) (YS12) (RP41)	0.23	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]		1K5X	155
P47772 UniProt NPD GO	RS13_ICTPU	40S ribosomal protein S13	0.23	-	mit	0					150
O77303 UniProt NPD GO	RS13_LUMRU	40S ribosomal protein S13	0.23	-	nuc	0					150
P05756 UniProt NPD GO	RS13_YEAST	40S ribosomal protein S13 (S27A) (YS15)	0.23	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]		1K5X	150
Q9XEK6 UniProt NPD GO	RS14_TORRU	40S ribosomal protein S14	0.23	-	cyt	0					134
P19115 UniProt NPD GO	RS14_NEUCR	40S ribosomal protein S14 (CRP2)	0.23	-	nuc	0					150
Q9FY64 UniProt NPD GO	RS15D_ARATH	40S ribosomal protein S15-4	0.23	-	cyt	0	Cytoplasm				152
Q9W6Y0 UniProt NPD GO	RS30_ORYLA	40S ribosomal protein S30	0.23	-	mit	0					59
P49395 UniProt NPD GO	RS3A_APLCA	40S ribosomal protein S3a (Lysine-rich protein KRP-A)	0.23	+	nuc	0					264
P46299 UniProt NPD GO	RS4_GOSHI	40S ribosomal protein S4	0.23	-	mit	0	Cytoplasm				262
O81363 UniProt NPD GO	RS4_PRUAR	40S ribosomal protein S4	0.23	-	mit	0	Cytoplasm				261
Q9LDC0 UniProt NPD GO	FKB42_ARATH	42 kDa peptidyl-prolyl isomerase (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotama ...	0.23	-	cyt	1	Cell membrane; single-pass membrane protein. Vacuole; vacuolar membrane; single-pass membrane protei ...			2F4E	365
P55028 UniProt NPD GO	TYRP1_CARAU	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (EC 1.14.18.-) (DHICA oxidase) (Tyrosinase-r ...	0.23	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein (Potential)				522
Q75DX7 UniProt NPD GO	HEM1_ASHGO	5-aminolevulinate synthase, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic acid synthase) ( ...	0.23	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				556
Q64264 UniProt NPD GO	5HT1A_MOUSE	5-hydroxytryptamine 1A receptor (5-HT-1A) (Serotonin receptor 1A) (5-HT1A)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				421
P60020 UniProt NPD GO	5HT1B_PANTR	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B)	0.23	-	end	7	Membrane; multi-pass membrane protein				390
P56496 UniProt NPD GO	5HT1B_SPAEH	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				386
P28222 UniProt NPD GO	5HT1B_HUMAN	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B) (5-HT-1D-beta) (Serotonin ...	0.23	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182131		390
Q9R1C8 UniProt NPD GO	5HT6R_MOUSE	5-hydroxytryptamine 6 receptor (5-HT-6) (Serotonin receptor 6)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				440
P11994 UniProt NPD GO	SM50_STRPU	50 kDa spicule matrix protein precursor	0.23	-	exc	0					445
Q8SAY0 UniProt NPD GO	RK18_ORYSA	50S ribosomal protein L18, chloroplast precursor	0.23	-	mit	0	Plastid; chloroplast				170
P27684 UniProt NPD GO	RK40_SPIOL	50S ribosomal protein L40, chloroplast precursor (CL40)	0.23	-	mit	0	Plastid; chloroplast				142
O22431 UniProt NPD GO	RL10_PINTA	60S ribosomal protein L10 (Wilms tumor suppressor homolog)	0.23	-	mit	0					228
P53028 UniProt NPD GO	RL10A_TRYBR	60S ribosomal protein L10a	0.23	+	nuc	0					214
P42795 UniProt NPD GO	RL111_ARATH	60S ribosomal protein L11-1 (L16A)	0.23	-	cyt	0	Cytoplasm				182
P36523 UniProt NPD GO	RM15_YEAST	60S ribosomal protein L15, mitochondrial precursor (YmL15) (MRP-L15)	0.23	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			253
Q9GS21 UniProt NPD GO	RL28_DICDI	60S ribosomal protein L28	0.23	-	nuc	0					132
Q9C9C6 UniProt NPD GO	RL62_ARATH	60S ribosomal protein L6-2	0.23	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [IDA]			233
Q9C9C5 UniProt NPD GO	RL63_ARATH	60S ribosomal protein L6-3	0.23	-	nuc	0					233

You are viewing entries 47001 to 47050 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.