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
P80478 UniProt NPD GO	C560_PORPU	Succinate dehydrogenase cytochrome b560 subunit (Succinate dehydrogenase, subunit III)	0.06	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				125
P80479 UniProt NPD GO	DHSD_PORPU	Succinate dehydrogenase membrane anchor subunit (Succinate dehydrogenase, subunit IV)	0.06	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				95
Q8BWF0 UniProt NPD GO	SSDH_MOUSE	Succinate semialdehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.24) (NAD(+)-dependent succin ...	0.06	-	mit	0		mitochondrion [IDA]			523
P53590 UniProt NPD GO	SUCB2_PIG	Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA syn ...	0.06	-	cyt	0	Mitochondrion			2FPP	433
Q29551 UniProt NPD GO	SCOT_PIG	Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial precursor (EC 2.8.3.5) (Somatic-type ...	0.06	-	mit	0	Mitochondrion			1OPE	520
P49036 UniProt NPD GO	SUS2_MAIZE	Sucrose synthase 2 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 2)	0.06	-	cyt	0					816
O80605 UniProt NPD GO	SUC3_ARATH	Sucrose transport protein SUC3 (Sucrose permease 3) (Sucrose-proton symporter 3) (Sucrose transporte ...	0.06	-	end	12	Cell membrane; multi-pass membrane protein (Probable)				594
Q9C8X2 UniProt NPD GO	SUC5_ARATH	Sucrose transport protein SUC5 (Sucrose permease 5) (Sucrose-proton symporter 5)	0.06	-	end	12 *	Cell membrane; multi-pass membrane protein (Probable)				512
Q9ZVK6 UniProt NPD GO	SUC8_ARATH	Sucrose transport protein SUC8 (Sucrose permease 8) (Sucrose-proton symporter 8)	0.06	-	end	11 *	Cell membrane; multi-pass membrane protein (Probable)				492
Q10710 UniProt NPD GO	STA_RICCO	Sugar carrier protein A	0.06	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				522
O65413 UniProt NPD GO	STP12_ARATH	Sugar transport protein 12 (Hexose transporter 12)	0.06	-	end	12 *	Membrane; multi-pass membrane protein				508
P23622 UniProt NPD GO	CYS14_NEUCR	Sulfate permease 2 (Sulfate permease II)	0.06	-	end	11	Membrane; multi-pass membrane protein				819
Q9MAX3 UniProt NPD GO	SUT12_ARATH	Sulfate transporter 1.2	0.06	-	end	10	Membrane; multi-pass membrane protein (Potential)				653
Q9FEP7 UniProt NPD GO	SUT13_ARATH	Sulfate transporter 1.3	0.06	-	end	10	Membrane; multi-pass membrane protein (Potential)				656
Q9SV13 UniProt NPD GO	SUT31_ARATH	Sulfate transporter 3.1 (AST12) (AtST1)	0.06	-	end	12	Membrane; multi-pass membrane protein (Potential)				658
Q8R086 UniProt NPD GO	SUOX_MOUSE	Sulfite oxidase, mitochondrial precursor (EC 1.8.3.1)	0.06	-	cyt	0	Mitochondrion; mitochondrial intermembrane space	mitochondrion [IDA]			488
P52847 UniProt NPD GO	ST1B1_RAT	Sulfotransferase family cytosolic 1B member 1 (EC 2.8.2.-) (Sulfotransferase 1B1) (DOPA/tyrosine sul ...	0.06	-	cyt	0	Cytoplasm	cytosol [TAS]			299
P41978 UniProt NPD GO	SODM2_MAIZE	Superoxide dismutase [Mn] 3.2, mitochondrial precursor (EC 1.15.1.1)	0.06	-	mit	0	Mitochondrion; mitochondrial matrix				232
Q8HXP0 UniProt NPD GO	SODM_CALJA	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1)	0.06	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				198
Q8HXP1 UniProt NPD GO	SODM_CEBAP	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1)	0.06	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				198
P04179 UniProt NPD GO	SODM_HUMAN	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.06	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	147460	2GDS	222
P09671 UniProt NPD GO	SODM_MOUSE	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.06	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			222
P11796 UniProt NPD GO	SODM_NICPL	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.06	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			228
P07895 UniProt NPD GO	SODM_RAT	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.06	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [NAS]			222
Q05515 UniProt NPD GO	SVF1_YEAST	Survival factor 1	0.06	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			481
Q8BG39 UniProt NPD GO	SV2B_MOUSE	Synaptic vesicle glycoprotein 2B (Synaptic vesicle protein 2B)	0.06	-	end	12	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Associated with synaptic-l ...	synaptic vesicle [IDA]			683
Q496J9 UniProt NPD GO	SV2C_HUMAN	Synaptic vesicle glycoprotein 2C	0.06	-	end	12	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Enriched in small synaptic ...				727
Q69ZS6 UniProt NPD GO	SV2C_MOUSE	Synaptic vesicle glycoprotein 2C (Synaptic vesicle protein 2C)	0.06	-	end	12	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Enriched in small synaptic ...	synaptic vesicle [IDA]			727
Q9Z2I6 UniProt NPD GO	SV2C_RAT	Synaptic vesicle glycoprotein 2C (Synaptic vesicle protein 2C)	0.06	-	end	12	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Enriched in small synaptic ...	synaptic vesicle [IDA]			727
Q5VXT5 UniProt NPD GO	SYPL2_HUMAN	Synaptophysin-like protein 2	0.06	-	end	4 *	Integral membrane protein. Triad junction; the junctional complex between the transverse tubule and ...				272
P55820 UniProt NPD GO	SNP25_RABIT	Synaptosomal-associated protein 25 (SNAP-25) (Synaptosomal-associated 25 kDa protein) (Fragments)	0.06	-	cyt	0					54
P34901 UniProt NPD GO	SDC4_RAT	Syndecan-4 precursor (SYND4) (Ryudocan core protein)	0.06	-	end	1	Membrane; single-pass type I membrane protein				202
Q95KC8 UniProt NPD GO	TIP_MACFA	T-cell immunomodulatory protein (Protein TIP) (Integrin alpha FG-GAP repeat-containing protein 1) (F ...	0.06	-	nuc	1	Secreted protein (By similarity). Cell membrane; single-pass type I membrane protein (Potential)				311
P04437 UniProt NPD GO	TVA2_HUMAN	T-cell receptor alpha chain V region CTL-L17 precursor	0.06	-	cyt	0		plasma membrane [NAS]			139
P06321 UniProt NPD GO	TVB8_MOUSE	T-cell receptor beta chain V region A20.2.25 precursor	0.06	-	mit	0					130
P01852 UniProt NPD GO	TCB1_MOUSE	T-cell receptor beta-1 chain C region	0.06	-	cyt	1				1SBB	173
P06325 UniProt NPD GO	TVC4_MOUSE	T-cell receptor gamma chain V region 5/10-13 precursor	0.06	-	cyt	0					135
P28480 UniProt NPD GO	TCPA_RAT	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.06	-	cyt	0	Cytoplasm	heterochromatin [IDA]			556
P18279 UniProt NPD GO	TCPA_CRIGR	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha) (65 kDa antigen)	0.06	-	cyt	0	Cytoplasm				556
P47208 UniProt NPD GO	TCPD_CAEEL	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.06	-	cyt	0	Cytoplasm				540
P50999 UniProt NPD GO	TCPD_SCHPO	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.06	-	cyt	0	Cytoplasm (Potential)				527
P93348 UniProt NPD GO	TBP_TOBAC	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.06	-	mit	0	Nucleus				200
P32086 UniProt NPD GO	TBP_PLAFA	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.06	-	nuc	0	Nucleus				228
P28148 UniProt NPD GO	TBP2_ARATH	TATA-box-binding protein 2 (TATA-box factor 2) (TATA-binding factor 2) (TATA sequence-binding protei ...	0.06	-	mit	0	Nucleus				200
P38551 UniProt NPD GO	TGFR2_PIG	TGF-beta receptor type-2 precursor (EC 2.7.11.30) (TGF-beta receptor type II) (TGFR-2) (TGF-beta typ ...	0.06	-	nuc	1	Membrane; single-pass type I membrane protein				297
O73895 UniProt NPD GO	TPSN_CHICK	Tapasin precursor (TPSN) (TPN) (TAP-binding protein) (TAP-associated protein)	0.06	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (Probable ...				430
Q05772 UniProt NPD GO	A9_BRANA	Tapetum-specific protein A9 precursor	0.06	-	mit	0					96
P09889 UniProt NPD GO	PPA5_PIG	Tartrate-resistant acid phosphatase type 5 precursor (EC 3.1.3.2) (TR-AP) (Tartrate-resistant acid A ...	0.06	-	nuc	0	Secreted protein			1UTE	340
Q7RTX1 UniProt NPD GO	TS1R1_HUMAN	Taste receptor type 1 member 1 precursor (G-protein coupled receptor 70) (Gm148)	0.06	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [IC]	606225		841
Q646G9 UniProt NPD GO	TA2R1_PANPA	Taste receptor type 2 member 1 (T2R1)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				299

You are viewing entries 73251 to 73300 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.