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
Q02641 UniProt NPD GO	CACB1_HUMAN	Voltage-dependent L-type calcium channel subunit beta-1 (CAB1) (Calcium channel voltage-dependent su ...	0.67	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side	voltage-gated calcium channel complex [TAS]	114207		598
Q8R3Z5 UniProt NPD GO	CACB1_MOUSE	Voltage-dependent L-type calcium channel subunit beta-1 (CAB1) (Calcium channel voltage-dependent su ...	0.67	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side (By similarity)	voltage-gated calcium channel complex [TAS]			597
P54283 UniProt NPD GO	CACB1_RAT	Voltage-dependent L-type calcium channel subunit beta-1 (CAB1) (Calcium channel voltage-dependent su ...	0.67	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side				597
Q05152 UniProt NPD GO	CAC1B_RABIT	Voltage-dependent N-type calcium channel subunit alpha-1B (Voltage-gated calcium channel subunit alp ...	0.67	-	end	21	Membrane; multi-pass membrane protein				2339
Q9Z0Y8 UniProt NPD GO	CAC1I_RAT	Voltage-dependent T-type calcium channel subunit alpha-1I (Voltage-gated calcium channel subunit alp ...	0.67	+	end	17	Membrane; multi-pass membrane protein				2201
P38164 UniProt NPD GO	YBK4_YEAST	WD repeat protein YBL104C	0.67	+	nuc	0	Cytoplasm	cytoplasm [IDA]			1038
P49953 UniProt NPD GO	WT1_SMIMA	Wilms' tumor protein (Fragment)	0.67	+	nuc	0	Nucleus				239
Q3TUF7 UniProt NPD GO	YETS2_MOUSE	YEATS domain-containing protein 2	0.67	-	nuc	0	Nucleus (Probable)				1407
Q80U44 UniProt NPD GO	ZFY16_MOUSE	Zinc finger FYVE domain-containing protein 16 (Endofin) (Endosomal-associated FYVE domain protein)	0.67	-	nuc	0	Cytoplasm (By similarity). Endosome; early endosome (By similarity). Localized to early endosomes. M ...				1528
Q9H091 UniProt NPD GO	ZMY15_HUMAN	Zinc finger MYND domain-containing protein 15	0.67	+	nuc	0					703
Q80TC6 UniProt NPD GO	ZSWM5_MOUSE	Zinc finger SWIM domain-containing protein 5	0.67	-	nuc	0					1188
Q8CII0 UniProt NPD GO	ZBTB8_MOUSE	Zinc finger and BTB domain-containing protein 8	0.67	-	nuc	0	Nucleus (Potential)				484
Q9NZV7 UniProt NPD GO	ZIM2_HUMAN	Zinc finger imprinted 2	0.67	-	nuc	0	Nucleus (Probable)				527
Q9HCX3 UniProt NPD GO	ZN304_HUMAN	Zinc finger protein 304	0.67	-	nuc	0	Nucleus (Probable)				659
Q96JL9 UniProt NPD GO	ZN333_HUMAN	Zinc finger protein 333	0.67	-	nuc	0	Nucleus (Probable)				665
Q6P1L6 UniProt NPD GO	ZN343_HUMAN	Zinc finger protein 343	0.67	-	nuc	0	Nucleus (Potential)				599
Q9NX65 UniProt NPD GO	ZN434_HUMAN	Zinc finger protein 434	0.67	-	nuc	0	Nucleus (Potential)				485
Q96MN9 UniProt NPD GO	ZN488_HUMAN	Zinc finger protein 488	0.67	-	nuc	0	Nucleus (By similarity)				340
Q6ZSB9 UniProt NPD GO	ZN509_HUMAN	Zinc finger protein 509	0.67	-	nuc	0	Nucleus (Potential)				765
Q9DB42 UniProt NPD GO	ZN593_MOUSE	Zinc finger protein 593 (Zinc finger protein T86)	0.67	-	nuc	0	Nucleus; nucleolus (By similarity)				116
O95159 UniProt NPD GO	ZFPL1_HUMAN	Zinc finger protein-like 1 (Zinc finger protein MCG4)	0.67	-	nuc	1		nucleus [NAS]			310
Q8HY87 UniProt NPD GO	RNZ2_MACFA	Zinc phosphodiesterase ELAC protein 2 (EC 3.1.26.11) (Ribonuclease Z 2) (RNase Z 2) (tRNase Z 2) (tR ...	0.67	-	mit	0	Nucleus (Probable)				826
P38772 UniProt NPD GO	YHK0_YEAST	Zinc-finger protein YHR040W	0.67	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			366
P40376 UniProt NPD GO	KAPB_SCHPO	cAMP-dependent protein kinase catalytic subunit (EC 2.7.11.11)	0.67	-	nuc	0		cAMP-dependent protein kinase complex [TAS]			512
Q8CG03 UniProt NPD GO	PDE5A_MOUSE	cGMP-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) (CGB-PDE) (cGMP-binding cGMP-specific pho ...	0.67	-	nuc	0					865
Q4IR09 UniProt NPD GO	RNA14_GIBZE	mRNA 3'-end processing protein RNA14	0.67	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				997
Q4PCV8 UniProt NPD GO	RNA14_USTMA	mRNA 3'-end-processing protein RNA14	0.67	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				945
Q04839 UniProt NPD GO	GFD1_YEAST	mRNA transport factor GFD1 (Good for DBP5 protein 1)	0.67	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side	cytoplasm [IDA] nuclear pore [IDA]			188
P50136 UniProt NPD GO	ODBA_MOUSE	2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial precursor (EC 1.2.4.4) (Branched-chain a ...	0.66	-	mit	0	Mitochondrion; mitochondrial matrix	alpha-ketoglutarate dehydrogenase complex (... [ISS] mitochondrion [ISS]			442
Q2KJ25 UniProt NPD GO	PSD12_BOVIN	26S proteasome non-ATPase regulatory subunit 12	0.66	-	cyt	0					455
Q5RBI3 UniProt NPD GO	PSD12_PONPY	26S proteasome non-ATPase regulatory subunit 12 (26S proteasome regulatory subunit p55)	0.66	-	cyt	0					455
P16237 UniProt NPD GO	HMDH_SCHMA	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.66	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Peroxisome; pero ...				948
Q2HJI0 UniProt NPD GO	RM19_BOVIN	39S ribosomal protein L19, mitochondrial precursor (L19mt) (MRP-L19)	0.66	-	mit	0	Mitochondrion (By similarity)			2FTC	292
Q9SWI6 UniProt NPD GO	RK29_MAIZE	50S ribosomal protein L29, chloroplast precursor	0.66	-	nuc	0	Plastid; chloroplast				161
P91128 UniProt NPD GO	RL13_CAEEL	60S ribosomal protein L13	0.66	-	nuc	0					207
P54780 UniProt NPD GO	RL15B_YEAST	60S ribosomal protein L15-B (YL10) (L13) (RP15R) (YP18)	0.66	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			203
Q6CBS7 UniProt NPD GO	RL17_YARLI	60S ribosomal protein L17	0.66	-	mit	0					184
P50885 UniProt NPD GO	RL18_TRYBB	60S ribosomal protein L18	0.66	-	nuc	0					193
Q94460 UniProt NPD GO	RL32_DROAC	60S ribosomal protein L32 (Ribosomal protein 49)	0.66	-	nuc	0					134
P49622 UniProt NPD GO	RL37_CAEEL	60S ribosomal protein L37	0.66	-	nuc	0					91
P36517 UniProt NPD GO	RM04_YEAST	60S ribosomal protein L4, mitochondrial precursor (YmL4) (MRP-L4)	0.66	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			319
P47911 UniProt NPD GO	RL6_MOUSE	60S ribosomal protein L6 (TAX-responsive enhancer element-binding protein 107) (TAXREB107)	0.66	+	nuc	0					295
P18124 UniProt NPD GO	RL7_HUMAN	60S ribosomal protein L7	0.66	+	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	604166		248
P36028 UniProt NPD GO	NFT1_YEAST	ABC transporter NFT1 (New full-length MRP-type transporter 1)	0.66	-	end	15 *	Membrane; multi-pass membrane protein (Potential)				1558
Q8BNJ2 UniProt NPD GO	ATS4_MOUSE	ADAMTS-4 precursor (EC 3.4.24.82) (A disintegrin and metalloproteinase with thrombospondin motifs 4) ...	0.66	+	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				833
Q9UKP5 UniProt NPD GO	ATS6_HUMAN	ADAMTS-6 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 6) ...	0.66	-	cyt	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		605008		860
P15274 UniProt NPD GO	AMPD_YEAST	AMP deaminase (EC 3.5.4.6) (Myoadenylate deaminase)	0.66	-	nuc	0		cytoplasm [IDA]			810
Q7YRF1 UniProt NPD GO	AP3B1_CANFA	AP-3 complex subunit beta-1 (Adapter-related protein complex 3 beta-1 subunit) (Beta3A-adaptin) (Ada ...	0.66	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				1091
P42380 UniProt NPD GO	CLPP_CHLRE	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.66	+	nuc	0	Plastid; chloroplast				524
O94762 UniProt NPD GO	RECQ5_HUMAN	ATP-dependent DNA helicase Q5 (EC 3.6.1.-) (RecQ protein-like 5) (RecQ5)	0.66	+	nuc	0	Isoform Beta: Nucleus; nucleoplasm. Isoform Alpha, isoform Gamma: Cytoplasm	cytoplasm [NAS] nucleoplasm [NAS]	603781		991

You are viewing entries 15601 to 15650 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.