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
Q9BE27 UniProt NPD GO	ZFP30_MACFA	Zinc finger protein 30 homolog (Zfp-30)	0.66	-	nuc	0	Nucleus (Potential)				519
Q8TD17 UniProt NPD GO	ZN398_HUMAN	Zinc finger protein 398 (Zinc finger DNA-binding protein p52/p71)	0.66	-	nuc	0	Nucleus (Probable)	nucleus [NAS]			642
Q8N7K0 UniProt NPD GO	ZN433_HUMAN	Zinc finger protein 433	0.66	-	nuc	0	Nucleus (Potential)				673
O60304 UniProt NPD GO	ZN500_HUMAN	Zinc finger protein 500	0.66	-	nuc	0	Nucleus (Potential)				480
Q96K75 UniProt NPD GO	ZN514_HUMAN	Zinc finger protein 514	0.66	-	nuc	0	Nucleus (Potential)				400
Q6NX49 UniProt NPD GO	ZN544_HUMAN	Zinc finger protein 544	0.66	-	nuc	0	Nucleus (Potential)				715
Q3TXZ1 UniProt NPD GO	ZN575_MOUSE	Zinc finger protein 575	0.66	-	nuc	0	Nucleus (Potential)				239
Q86T29 UniProt NPD GO	ZN605_HUMAN	Zinc finger protein 605	0.66	-	nuc	0	Nucleus (Probable)				641
Q2M218 UniProt NPD GO	ZN630_HUMAN	Zinc finger protein 630	0.66	+	nuc	0	Nucleus (Probable)				657
Q499Z4 UniProt NPD GO	ZN672_HUMAN	Zinc finger protein 672	0.66	-	nuc	0	Nucleus (Probable)				452
Q4R6J4 UniProt NPD GO	ZN684_MACFA	Zinc finger protein 684	0.66	+	nuc	0	Nucleus (Probable)				378
P30373 UniProt NPD GO	CKR1_CHICK	Zinc finger protein CKR1	0.66	-	nuc	0	Nucleus (Probable)				509
P49605 UniProt NPD GO	KAPR_USTMA	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.66	-	nuc	0					522
Q75BK1 UniProt NPD GO	DCP2_ASHGO	mRNA decapping enzyme 2 (EC 3.-.-.-)	0.66	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				880
P40989 UniProt NPD GO	GLS2_YEAST	1,3-beta-glucan synthase component GLS2 (EC 2.4.1.34) (1,3-beta-D-glucan-UDP glucosyltransferase)	0.65	+	end	14	Membrane; multi-pass membrane protein	1,3-beta-glucan synthase complex [TAS] actin cap [IDA] prospore membrane [IDA]			1895
P13217 UniProt NPD GO	PIPA_DROME	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase (EC 3.1.4.11) (Phosphoinositide phospholip ...	0.65	-	nuc	0		inaD signaling complex [IPI] membrane fraction [IDA]		1IHJ	1095
P49259 UniProt NPD GO	PLA2R_BOVIN	180 kDa secretory phospholipase A2 receptor precursor (PLA2-R)	0.65	-	end	1	Membrane; single-pass type I membrane protein				1463
O00232 UniProt NPD GO	PSD12_HUMAN	26S proteasome non-ATPase regulatory subunit 12 (26S proteasome regulatory subunit p55)	0.65	-	cyt	0		proteasome regulatory particle (sensu Eukar... [TAS]	604450		455
P14685 UniProt NPD GO	PSD3_MOUSE	26S proteasome non-ATPase regulatory subunit 3 (26S proteasome regulatory subunit S3) (Proteasome su ...	0.65	-	nuc	0					530
P32782 UniProt NPD GO	PDE1_CANAL	3',5'-cyclic-nucleotide phosphodiesterase (EC 3.1.4.17) (PDEase) (3':5'-CNP)	0.65	-	nuc	0					426
Q8MS27 UniProt NPD GO	RM35_DROME	39S ribosomal protein L35, mitochondrial precursor (L35mt)	0.65	+	mit	0	Mitochondrion (By similarity)	mitochondrion [NAS]			178
P41798 UniProt NPD GO	RS6_KLUMA	40S ribosomal protein S6 (Ribosomal protein S10)	0.65	-	mit	0					235
Q6CJ65 UniProt NPD GO	RT09_KLULA	40S ribosomal protein S9, mitochondrial precursor	0.65	-	nuc	0	Mitochondrion (Potential)				297
P91374 UniProt NPD GO	RL15_CAEEL	60S ribosomal protein L15	0.65	-	nuc	0					204
O82528 UniProt NPD GO	RL15_PETHY	60S ribosomal protein L15	0.65	-	nuc	0					204
P51413 UniProt NPD GO	RL172_ARATH	60S ribosomal protein L17-2	0.65	-	nuc	0					175
Q9SRX2 UniProt NPD GO	RL191_ARATH	60S ribosomal protein L19-1	0.65	-	nuc	0					214
P12749 UniProt NPD GO	RL26_RAT	60S ribosomal protein L26	0.65	-	nuc	0					145
P49211 UniProt NPD GO	RL321_ARATH	60S ribosomal protein L32-1	0.65	-	nuc	0					133
Q9LZ57 UniProt NPD GO	RL363_ARATH	60S ribosomal protein L36-3	0.65	-	nuc	0					108
Q92365 UniProt NPD GO	RL36A_SCHPO	60S ribosomal protein L36-A	0.65	-	nuc	0					99
O94658 UniProt NPD GO	RL36B_SCHPO	60S ribosomal protein L36-B	0.65	-	nuc	0					99
Q9C0T1 UniProt NPD GO	RL37_EMENI	60S ribosomal protein L37	0.65	-	mit	0					92
P59289 UniProt NPD GO	RL37A_SCHPO	60S ribosomal protein L37-A (L37-1)	0.65	-	mit	0					88
P48166 UniProt NPD GO	RL44_CAEEL	60S ribosomal protein L44 (L41)	0.65	-	nuc	0					104
P21533 UniProt NPD GO	RL6_RAT	60S ribosomal protein L6 (Neoplasm-related protein C140)	0.65	+	nuc	0					297
P14148 UniProt NPD GO	RL7_MOUSE	60S ribosomal protein L7	0.65	+	nuc	0					270
P05426 UniProt NPD GO	RL7_RAT	60S ribosomal protein L7	0.65	+	nuc	0					260
Q9LHP1 UniProt NPD GO	RL74_ARATH	60S ribosomal protein L7-4	0.65	+	cyt	0		cytosolic ribosome (sensu Eukaryota) [IDA]			244
O60143 UniProt NPD GO	RL7C_SCHPO	60S ribosomal protein L7-C	0.65	-	cyt	0					251
P78536 UniProt NPD GO	ADA17_HUMAN	ADAM 17 precursor (EC 3.4.24.86) (A disintegrin and metalloproteinase domain 17) (TNF-alpha-converti ...	0.65	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	603639	2FV9	824
Q61072 UniProt NPD GO	ADAM9_MOUSE	ADAM 9 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 9) (Metalloprotease/disin ...	0.65	-	exc	1	Membrane; single-pass type I membrane protein (Probable)	cytoplasm [IDA] plasma membrane [IDA]			845
Q9R001 UniProt NPD GO	ATS5_MOUSE	ADAMTS-5 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 5) ...	0.65	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				930
Q751D1 UniProt NPD GO	DBP6_ASHGO	ATP-dependent RNA helicase DBP6 (EC 3.6.1.-)	0.65	-	nuc	0	Nucleus; nucleolus (By similarity)				607
Q8TFL3 UniProt NPD GO	DBP7_CANGA	ATP-dependent RNA helicase DBP7 (EC 3.6.1.-)	0.65	-	nuc	0	Nucleus; nucleolus (By similarity)				715
Q6FQZ0 UniProt NPD GO	DBP8_CANGA	ATP-dependent RNA helicase DBP8 (EC 3.6.1.-)	0.65	-	cyt	0	Nucleus; nucleolus (By similarity)				437
Q4I830 UniProt NPD GO	DRS1_GIBZE	ATP-dependent RNA helicase DRS1 (EC 3.6.1.-)	0.65	+	nuc	0	Nucleus; nucleolus (By similarity)				796
Q09775 UniProt NPD GO	ROK1_SCHPO	ATP-dependent RNA helicase rok1 (EC 3.6.1.-)	0.65	+	nuc	0	Nucleus; nucleolus (By similarity)				481
Q8BMG1 UniProt NPD GO	ATRIP_MOUSE	ATR-interacting protein (ATM and Rad3-related-interacting protein)	0.65	-	nuc	0	Nucleus (By similarity). Redistributes to discrete nuclear foci upon DNA damage (By similarity)				785
Q8IZP0 UniProt NPD GO	ABI1_HUMAN	Abl interactor 1 (Abelson interactor 1) (Abi-1) (Spectrin SH3 domain-binding protein 1) (Eps8 SH3 do ...	0.65	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Localized to protruding lamellipodia and filopod ...	cytosol [TAS] endoplasmic reticulum [TAS] soluble fraction [TAS]	603050		507

You are viewing entries 16151 to 16200 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.