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
Q6A2H1 UniProt NPD GO	SSDH_GORGO	Succinate semialdehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.24) (NAD(+)-dependent succin ...	0.04	-	mit	0					535
Q3MSM3 UniProt NPD GO	SSDH_HYLLA	Succinate semialdehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.24) (NAD(+)-dependent succin ...	0.04	-	mit	0					535
Q3MSM4 UniProt NPD GO	SSDH_PANPA	Succinate semialdehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.24) (NAD(+)-dependent succin ...	0.04	-	mit	0					535
Q6A2H0 UniProt NPD GO	SSDH_PANTR	Succinate semialdehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.24) (NAD(+)-dependent succin ...	0.04	-	mit	0					535
Q6A2H2 UniProt NPD GO	SSDH_PONPY	Succinate semialdehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.24) (NAD(+)-dependent succin ...	0.04	-	mit	0					535
Q3MHX5 UniProt NPD GO	SUCB2_BOVIN	Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA syn ...	0.04	-	cyt	0	Mitochondrion (By similarity)				432
Q96I99 UniProt NPD GO	SUCB2_HUMAN	Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA syn ...	0.04	-	cyt	0	Mitochondrion		603922		432
Q8LAD2 UniProt NPD GO	SUCA2_ARATH	Succinyl-CoA ligase [GDP-forming] subunit alpha-2, mitochondrial precursor (EC 6.2.1.4) (Succinyl-Co ...	0.04	-	mit	0	Mitochondrion				341
P55809 UniProt NPD GO	SCOT_HUMAN	Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial precursor (EC 2.8.3.5) (Somatic-type ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix		245050		520
Q39231 UniProt NPD GO	SUC2_ARATH	Sucrose transport protein SUC2 (Sucrose permease 2) (Sucrose-proton symporter 2) (Sucrose transporte ...	0.04	-	end	12 *	Cell membrane; multi-pass membrane protein (Probable)				512
Q9SFG0 UniProt NPD GO	STP6_ARATH	Sugar transport protein 6 (Hexose transporter 6)	0.04	-	end	12 *	Membrane; multi-pass membrane protein				507
P39932 UniProt NPD GO	STL1_YEAST	Sugar transporter STL1	0.04	-	end	11 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]			569
Q8NBK3 UniProt NPD GO	SUMF1_HUMAN	Sulfatase-modifying factor 1 precursor (C-alpha-formyglycine-generating enzyme 1)	0.04	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen		272200	2AIK	374
P58735 UniProt NPD GO	S26A1_MOUSE	Sulfate anion transporter 1 (SAT-1) (Solute carrier family 26 member 1)	0.04	-	end	9	Membrane; multi-pass membrane protein (By similarity)				704
P45380 UniProt NPD GO	S26A1_RAT	Sulfate anion transporter 1 (SAT-1) (Solute carrier family 26 member 1) (Canalicular sulfate transpo ...	0.04	-	end	9	Membrane; multi-pass membrane protein				703
Q9SAY1 UniProt NPD GO	SUT11_ARATH	Sulfate transporter 1.1 (High-affinity sulfate transporter 1) (Hst1At) (AST101)	0.04	-	end	10	Membrane; multi-pass membrane protein (Potential)				649
P51687 UniProt NPD GO	SUOX_HUMAN	Sulfite oxidase, mitochondrial precursor (EC 1.8.3.1)	0.04	-	cyt	0	Mitochondrion; mitochondrial intermembrane space		272300	1MJ4	488
Q9BR01 UniProt NPD GO	ST4A1_HUMAN	Sulfotransferase 4A1 (EC 2.8.2.-) (Brain sulfotransferase-like protein) (hBR-STL) (hBR-STL-1) (Nervo ...	0.04	-	cyt	0	Cytoplasm (By similarity)	cytosol [NAS]	608359		284
Q6BZU2 UniProt NPD GO	CCS1_YARLI	Superoxide dismutase 1 copper chaperone	0.04	-	cyt	0	Cytoplasm (By similarity)				234
P83684 UniProt NPD GO	SODC_HUMLT	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (HlSOD)	0.04	-	cyt	0	Cytoplasm (By similarity)				152
O15905 UniProt NPD GO	SODF_BABBO	Superoxide dismutase [Fe] (EC 1.15.1.1)	0.04	-	cyt	0					199
P34107 UniProt NPD GO	SODF_ENTHI	Superoxide dismutase [Fe] (EC 1.15.1.1)	0.04	-	cyt	0					190
Q8HXP5 UniProt NPD GO	SODM_HYLLA	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1)	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				198
Q8HXP7 UniProt NPD GO	SODM_PANTR	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1)	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				198
O81235 UniProt NPD GO	SODM_ARATH	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.04	-	mit	0	Mitochondrion; mitochondrial matrix				231
Q9Y783 UniProt NPD GO	SODM_NEUCR	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				245
P49114 UniProt NPD GO	SODM_CAVPO	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1) (Fragment)	0.04	-	mit	0	Mitochondrion; mitochondrial matrix				211
P82865 UniProt NPD GO	HFN40_MAIZE	Suppressor protein HFN40 (Fragments)	0.04	-	cyt	0					33
Q4WVE5 UniProt NPD GO	SVF1_ASPFU	Survival factor 1	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				396
Q8BRU6 UniProt NPD GO	VMAT2_MOUSE	Synaptic vesicular amine transporter (Monoamine transporter) (Vesicular amine transporter 2) (VAT2) ...	0.04	-	end	11 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (By similarity)				517
P33328 UniProt NPD GO	SNC2_YEAST	Synaptobrevin homolog 2	0.04	-	nuc	1	Intracytoplasmic membrane; single-pass type IV membrane protein. Post-Golgi vesicle membrane (Probab ...	transport vesicle [TAS]			115
Q6FW27 UniProt NPD GO	YKT6_CANGA	Synaptobrevin homolog YKT6	0.04	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				205
O43759 UniProt NPD GO	SNG1_HUMAN	Synaptogyrin-1	0.04	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603925		234
O55100 UniProt NPD GO	SNG1_MOUSE	Synaptogyrin-1	0.04	-	end	4 *	Membrane; multi-pass membrane protein				234
Q62876 UniProt NPD GO	SNG1_RAT	Synaptogyrin-1 (p29)	0.04	-	end	4 *	Membrane; multi-pass membrane protein	synaptic vesicle membrane [IDA]			234
Q8VCK7 UniProt NPD GO	SYCN_MOUSE	Syncollin (Fragment)	0.04	-	mit	1 *	Zymogen granule membrane protein (By similarity)				145
P01411 UniProt NPD GO	TS822_DENAN	Synergistic-type venom protein C8S2, chain 2	0.04	-	nuc	0	Secreted protein				62
Q9H190 UniProt NPD GO	SDCB2_HUMAN	Syntenin-2 (Syndecan-binding protein 2)	0.04	-	cyt	0		cytoplasm [IDA] plasma membrane [IC]			292
P01733 UniProt NPD GO	TVB1_HUMAN	T-cell receptor beta chain V region YT35 precursor	0.04	-	nuc	0		plasma membrane [NAS]			135
P80943 UniProt NPD GO	CD1B3_SHEEP	T-cell surface glycoprotein CD1b-3 (CD1b-3 antigen) (SCD1T10) (Fragment)	0.04	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				232
Q9QZY8 UniProt NPD GO	CD1C1_CAVPO	T-cell surface glycoprotein CD1c1 precursor (CD1-c1 antigen)	0.04	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				332
P22646 UniProt NPD GO	CD3E_MOUSE	T-cell surface glycoprotein CD3 epsilon chain precursor (T-cell surface antigen T3/Leu-4 epsilon cha ...	0.04	-	end	1	Membrane; single-pass type I membrane protein	alpha-beta T cell receptor complex [IDA] external side of plasma membrane [IDA] immunological synapse [IDA]		1XMW	189
P42943 UniProt NPD GO	TCPH_YEAST	T-complex protein 1 subunit eta (TCP-1-eta) (CCT-eta)	0.04	-	cyt	0	Cytoplasm (By similarity)	chaperonin-containing T-complex [IPI] cytoplasm [IDA] cytoskeleton [TAS]			550
Q6YCH1 UniProt NPD GO	TDPZ5_MOUSE	TD and POZ domain-containing protein 5	0.04	-	cyt	0					340
Q64729 UniProt NPD GO	TGFR1_MOUSE	TGF-beta receptor type-1 precursor (EC 2.7.11.30) (TGF-beta receptor type I) (TGFR-1) (TGF-beta type ...	0.04	-	end	2 *	Membrane; single-pass type I membrane protein				503
Q8VE80 UniProt NPD GO	THOC3_MOUSE	THO complex subunit 3 (Tho3)	0.04	-	mit	0	Nucleus (Probable)				351
Q96J01 UniProt NPD GO	THOC3_HUMAN	THO complex subunit 3 (Tho3) (TEX1 homolog)	0.04	-	cyt	0	Nucleus (Probable)		606929		351
Q2KIA2 UniProt NPD GO	TR112_BOVIN	TRM112-like protein	0.04	-	mit	0					125
O45241 UniProt NPD GO	TR112_CAEEL	TRM112-like protein	0.04	-	cyt	0					125
P82470 UniProt NPD GO	TKN1_SCHGR	Tachykinin-1 (Scg-midgut-TK)	0.04	-		0	Secreted protein				14

You are viewing entries 78501 to 78550 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.