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
Q15118 UniProt NPD GO	PDK1_HUMAN	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.39	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	602524		436
Q9P0J1 UniProt NPD GO	PDP1_HUMAN	[Pyruvate dehydrogenase [lipoamide]]-phosphatase 1, mitochondrial precursor (EC 3.1.3.43) (PDP 1) (P ...	0.39	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)		605993		537
O00408 UniProt NPD GO	PDE2A_HUMAN	cGMP-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) (Cyclic GMP-stimulated phosphodiesterase ...	0.39	-	cyt	0	Membrane; peripheral membrane protein (Potential)		602658	1Z1L	941
Q68FJ6 UniProt NPD GO	PK1IP_XENLA	p21-activated protein kinase-interacting protein 1-like (PAK1-interacting protein 1-like)	0.39	+	mit	0	Nucleus; nucleolus (By similarity)				363
Q5KGJ9 UniProt NPD GO	PALC_CRYNE	pH-response regulator protein palC	0.39	-	nuc	0					488
Q6BNJ2 UniProt NPD GO	PALI_DEBHA	pH-response regulator protein palI/RIM9	0.39	-	end	4 *	Cell membrane; multi-pass membrane protein (By similarity)				365
Q43714 UniProt NPD GO	DCS3_GOSAR	(+)-delta-cadinene synthase isozyme A (EC 4.2.3.13) (D-cadinene synthase)	0.38	-	nuc	0					555
O49853 UniProt NPD GO	DCS4_GOSAR	(+)-delta-cadinene synthase isozyme C2 (EC 4.2.3.13) (D-cadinene synthase)	0.38	-	cyt	0					554
Q60HE2 UniProt NPD GO	ODO1_MACFA	2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2) (Alpha-ketoglutarate ...	0.38	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				1023
Q5RCB8 UniProt NPD GO	ODO1_PONPY	2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2) (Alpha-ketoglutarate ...	0.38	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				1023
P54778 UniProt NPD GO	PRS6B_SOLTU	26S protease regulatory subunit 6B homolog	0.38	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				413
Q04062 UniProt NPD GO	RPN9_YEAST	26S proteasome regulatory subunit RPN9 (Proteasome non-ATPase subunit 7)	0.38	-	cyt	0		proteasome regulatory particle, lid subcomp... [IDA]			393
Q9EPJ3 UniProt NPD GO	RT26_RAT	28S ribosomal protein S26, mitochondrial precursor (MRP-S26) (Protein 5'OT-EST)	0.38	-	mit	0	Mitochondrion (By similarity)				200
Q9XHP1 UniProt NPD GO	2SS1_SESIN	2S seed storage protein 1 precursor (beta-globulin) (2S albumin storage protein) [Contains: 2S seed ...	0.38	-	exc	0		protein body [NAS]			148
Q3T0L3 UniProt NPD GO	RM17_BOVIN	39S ribosomal protein L17, mitochondrial precursor (L17mt) (MRP-L17)	0.38	-	nuc	0	Mitochondrion (Potential)				172
Q9BQ48 UniProt NPD GO	RM34_HUMAN	39S ribosomal protein L34, mitochondrial precursor (L34mt) (MRP-L34)	0.38	-	nuc	0	Mitochondrion (Potential)	mitochondrial ribosome [NAS]			92
Q6AXT0 UniProt NPD GO	RM37_RAT	39S ribosomal protein L37, mitochondrial precursor (L37mt) (MRP-L37)	0.38	-	cyt	0	Mitochondrion (By similarity)				423
Q4MYY1 UniProt NPD GO	RS17_THEPA	40S ribosomal protein S17	0.38	-	mit	0					129
Q9LZ17 UniProt NPD GO	RS17D_ARATH	40S ribosomal protein S17-4	0.38	-	nuc	0					140
Q8ISP0 UniProt NPD GO	RS18_BRABE	40S ribosomal protein S18	0.38	-	nuc	0	Cytoplasm				152
P51431 UniProt NPD GO	RS27A_ORYSA	40S ribosomal protein S27a	0.38	+	nuc	0					79
P62084 UniProt NPD GO	RS7_BRARE	40S ribosomal protein S7	0.38	-	nuc	0					194
Q6Q0N3 UniProt NPD GO	NT5D2_RAT	5'-nucleotidase domain-containing protein 2	0.38	-	nuc	0					553
O80361 UniProt NPD GO	RK4_TOBAC	50S ribosomal protein L4, chloroplast precursor (R-protein L4)	0.38	-	mit	0	Plastid; chloroplast				282
P70265 UniProt NPD GO	F262_MOUSE	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (6PF-2-K/Fru-2,6-P2ASE heart-type isozyme) (PF ...	0.38	-	cyt	0					519
O94200 UniProt NPD GO	K6PF2_CANAL	6-phosphofructokinase subunit beta (EC 2.7.1.11) (Phosphofructokinase 2) (Phosphohexokinase) (6PF-1- ...	0.38	-	cyt	0	Cytoplasm (By similarity)				946
Q6MY48 UniProt NPD GO	RL17_ASPFU	60S ribosomal protein L17	0.38	-	mit	0					194
P37380 UniProt NPD GO	RL17_PODCA	60S ribosomal protein L17 (L23)	0.38	-	nuc	0					183
Q90YU9 UniProt NPD GO	RL18A_ICTPU	60S ribosomal protein L18a	0.38	-	mit	0					176
Q943F3 UniProt NPD GO	RL18A_ORYSA	60S ribosomal protein L18a	0.38	-	nuc	0					178
P41165 UniProt NPD GO	RL23A_TRYBB	60S ribosomal protein L23a (L25)	0.38	-	mit	0					164
P49629 UniProt NPD GO	RL26_XENLA	60S ribosomal protein L26 (Fragment)	0.38	-	nuc	0					33
Q90YT5 UniProt NPD GO	RL34_ICTPU	60S ribosomal protein L34	0.38	-	mit	0					116
Q9XF97 UniProt NPD GO	RL4_PRUAR	60S ribosomal protein L4 (L1)	0.38	-	nuc	0					408
P60039 UniProt NPD GO	RL73_ARATH	60S ribosomal protein L7-3	0.38	-	cyt	0					242
Q91348 UniProt NPD GO	F26L_CHICK	6PF-2-K/Fru-2,6-P2ASE liver isozyme [Includes: 6-phosphofructo-2-kinase (EC 2.7.1.105); Fructose-2,6 ...	0.38	-	mit	0					470
Q06010 UniProt NPD GO	STE23_YEAST	A-factor-processing enzyme (EC 3.4.99.-)	0.38	-	mit	0		integral to membrane [TAS]			1027
O35817 UniProt NPD GO	AKA14_RAT	A-kinase anchor protein 14 (Testis-specific A-kinase-anchoring protein TAKAP-80) (TAKAP-1.2)	0.38	+	cyt	0	Cytoplasm (Probable). In fibrous sheath from epididymal sperm				502
Q8BYZ1 UniProt NPD GO	ABI3_MOUSE	ABI gene family member 3 (New molecule including SH3) (Nesh)	0.38	-	nuc	0	Cytoplasm (By similarity)				367
Q9NRP4 UniProt NPD GO	ACN9_HUMAN	ACN9 protein homolog, mitochondrial precursor	0.38	-	mit	0	Mitochondrion (Potential)	mitochondrial intermembrane space [ISS]			125
Q95194 UniProt NPD GO	ADA18_MACFA	ADAM 18 precursor (A disintegrin and metalloproteinase domain 18) (Transmembrane metalloproteinase-l ...	0.38	-	cyt	1	Membrane; single-pass type I membrane protein				746
Q9EPJ9 UniProt NPD GO	ARFG1_MOUSE	ADP-ribosylation factor GTPase-activating protein 1 (ADP-ribosylation factor 1 GTPase-activating pro ...	0.38	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus (By similarity). Associates with the Golgi complex (By si ...				414
Q62848 UniProt NPD GO	ARFG1_RAT	ADP-ribosylation factor GTPase-activating protein 1 (ADP-ribosylation factor 1 GTPase-activating pro ...	0.38	-	nuc	0	Cytoplasm. Golgi apparatus. Associates with the Golgi complex	Golgi membrane [IDA]			415
Q9MUT1 UniProt NPD GO	ATPF_MESVI	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.38	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane				186
P40491 UniProt NPD GO	FMC1_YEAST	ATP synthase assembly factor FMC1, mitochondrial precursor (Formation of mitochondrial complexes pro ...	0.38	-	nuc	0	Mitochondrion	mitochondrion [IDA]			155
P28288 UniProt NPD GO	ABCD3_HUMAN	ATP-binding cassette sub-family D member 3 (70 kDa peroxisomal membrane protein) (PMP70)	0.38	-	mit	3	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to peroxisomal membrane [TAS] peroxisomal membrane [TAS] peroxisome [IDA]	170995		659
O74208 UniProt NPD GO	CGR1_CANGA	ATP-binding cassette transporter CGR1 (Pleiomorphic drug resistance homolog)	0.38	-	end	10	Membrane; multi-pass membrane protein (Potential)				1542
Q24731 UniProt NPD GO	DDX1_DROVI	ATP-dependent RNA helicase Ddx1 (EC 3.6.1.-) (DEAD box protein 1) (Fragment)	0.38	-	cyt	0					400
Q12099 UniProt NPD GO	FAL1_YEAST	ATP-dependent RNA helicase FAL1 (EC 3.6.1.-) (Translation initiation factor four A-like protein 1)	0.38	-	cyt	0	Nucleus; nucleolus	nucleolus [TAS]			399
Q4WIN6 UniProt NPD GO	DBP5_ASPFU	ATP-dependent RNA helicase dbp5 (EC 3.6.1.-)	0.38	-	end	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				511

You are viewing entries 33151 to 33200 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.