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
Q4X1Y0 UniProt NPD GO	PFS2_ASPFU	Polyadenylation factor subunit 2	0.46	-	nuc	0	Nucleus (By similarity)				510
Q9ULD8 UniProt NPD GO	KCNH3_HUMAN	Potassium voltage-gated channel subfamily H member 3 (Voltage-gated potassium channel subunit Kv12.2 ...	0.46	-	end	4	Membrane; multi-pass membrane protein	integral to membrane [NAS]	604527		1083
O89047 UniProt NPD GO	KCNH3_RAT	Potassium voltage-gated channel subfamily H member 3 (Voltage-gated potassium channel subunit Kv12.2 ...	0.46	-	end	4	Membrane; multi-pass membrane protein				1087
Q6CT50 UniProt NPD GO	CWC2_KLULA	Pre-mRNA-splicing factor CWC2	0.46	-	nuc	0	Nucleus (By similarity)				337
P38302 UniProt NPD GO	NTC20_YEAST	Pre-mRNA-splicing factor NTC20 (PRP19-associated complex protein 20) (Synergistic to PRP19 mutation ...	0.46	-	nuc	0	Nucleus	spliceosome complex [IDA]			140
Q9NQI0 UniProt NPD GO	DDX4_HUMAN	Probable ATP-dependent RNA helicase DDX4 (EC 3.6.1.-) (DEAD box protein 4) (VASA homolog)	0.46	-	nuc	0	Cytoplasm		605281		724
Q6GWX0 UniProt NPD GO	DDX4_PIG	Probable ATP-dependent RNA helicase DDX4 (EC 3.6.1.-) (DEAD box protein 4) (VASA homolog) (VASA-like ...	0.46	-	nuc	0	Cytoplasm (By similarity)				722
Q9GLV6 UniProt NPD GO	DDX58_PIG	Probable ATP-dependent RNA helicase DDX58 (EC 3.6.1.-) (DEAD-box protein 58) (Retinoic acid-inducibl ...	0.46	-	nuc	0	Cytoplasm (By similarity)				940
P33539 UniProt NPD GO	RPOP_AGABT	Probable DNA-directed RNA polymerase (EC 2.7.7.6)	0.46	-	mit	0					1102
Q5U431 UniProt NPD GO	GPR39_MOUSE	Probable G-protein coupled receptor 39	0.46	-	end	7 *	Membrane; multi-pass membrane protein				456
Q19084 UniProt NPD GO	YDBM_CAEEL	Probable G-protein coupled receptor F01E11.5	0.46	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				468
Q27905 UniProt NPD GO	ABP1_RIPCL	Probable antibacterial peptide polyprotein	0.46	-	mit	0	Secreted protein (Potential)				678
Q8WSF3 UniProt NPD GO	FDL_DROME	Probable beta-hexosaminidase fdl precursor (EC 3.2.1.52) (Protein fused lobes)	0.46	+	mit	1 *					660
Q9V776 UniProt NPD GO	CP317_DROME	Probable cytochrome P450 317a1 (EC 1.14.-.-) (CYPCCCXVIIA1)	0.46	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				518
Q9FJK8 UniProt NPD GO	RP8L4_ARATH	Probable disease resistance RPP8-like protein 4	0.46	-	cyt	0					908
Q9LXX6 UniProt NPD GO	EXOC6_ARATH	Probable exocyst complex component 6 (Exocyst complex component Sec15)	0.46	+	cyt	0					789
Q12209 UniProt NPD GO	FRE8_YEAST	Probable ferric reductase transmembrane component 8 (EC 1.16.1.7) (Ferric-chelate reductase 8)	0.46	-	vac	5 *	Membrane; multi-pass membrane protein				686
P33550 UniProt NPD GO	KTR2_YEAST	Probable mannosyltransferase KTR2 (EC 2.4.1.131)	0.46	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi apparatus [IDA]			425
Q9LJ98 UniProt NPD GO	PFD2_ARATH	Probable prefoldin subunit 2	0.46	-	nuc	0					148
Q9AXA6 UniProt NPD GO	ABIL1_ORYSA	Probable protein ABIL1 (Abl interactor-like protein 1)	0.46	-	nuc	0					306
P49519 UniProt NPD GO	DNAB_ODOSI	Probable replicative DNA helicase (EC 3.6.1.-)	0.46	-	nuc	0	Plastid; chloroplast				455
Q9UTH3 UniProt NPD GO	KKE1_SCHPO	Probable serine/threonine-protein kinase C1805.01c (EC 2.7.11.1)	0.46	-	mit	0					775
Q9VRX3 UniProt NPD GO	TBBP_DROME	Probable tubulin beta chain	0.46	-	cyt	0		microtubule [NAS]			462
Q9LFG8 UniProt NPD GO	WBC20_ARATH	Probable white-brown complex homolog protein 20	0.46	-	end	6	Membrane; multi-pass membrane protein (By similarity)				739
P22005 UniProt NPD GO	PENK_MOUSE	Proenkephalin A precursor [Contains: Synenkephalin; Met-enkephalin (Opioid growth factor) (OGF); Met ...	0.46	-	exc	0	Secreted protein				269
Q9CR73 UniProt NPD GO	PNRC2_MOUSE	Proline-rich nuclear receptor coactivator 2	0.46	-	nuc	0	Nucleus (Potential)				140
Q32P28 UniProt NPD GO	P3H1_HUMAN	Prolyl 3-hydroxylase 1 precursor (EC 1.14.11.7) (Leucine proline-enriched proteoglycan 1) (Leprecan- ...	0.46	-	end	0	Endoplasmic reticulum (By similarity). Secreted protein; extracellular space; extracellular matrix ( ...				736
Q9R224 UniProt NPD GO	BEX1_MOUSE	Protein BEX1 (Brain-expressed X-linked protein 1 homolog) (Reduced expression protein 3) (REX-3)	0.46	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the cytoplasm and the nucleus	cytoplasm [IDA] nucleus [IDA]			128
Q9BXY8 UniProt NPD GO	BEX2_HUMAN	Protein BEX2 (Brain-expressed X-linked protein 2) (hBex2)	0.46	-	nuc	0	Cytoplasm (By similarity). Nucleus				128
P59036 UniProt NPD GO	CU082_HUMAN	Protein C21orf82	0.46	-	mit	0					64
Q8N5N4 UniProt NPD GO	CC022_HUMAN	Protein C3orf22	0.46	-	nuc	0					141
Q95JU3 UniProt NPD GO	CF165_MACFA	Protein C6orf165 homolog	0.46	-	mit	0					622
Q5BJZ6 UniProt NPD GO	CI041_RAT	Protein C9orf41 homolog	0.46	-	mit	0					400
Q6DFA6 UniProt NPD GO	CQ10A_XENLA	Protein COQ10 A, mitochondrial precursor	0.46	-	mit	0	Mitochondrion (Potential)				247
Q9H1H1 UniProt NPD GO	F112A_HUMAN	Protein FAM112A	0.46	-	nuc	0					148
Q567Z7 UniProt NPD GO	G10_BRARE	Protein G10 homolog	0.46	-	nuc	0	Nucleus (Potential)				144
Q08969 UniProt NPD GO	GRE1_YEAST	Protein GRE1 (Genes de respuesta a estres protein 1) (Hydrophilin)	0.46	-	nuc	0	Cytoplasm	cytoplasm [IDA]			168
P40990 UniProt NPD GO	MSS2_YEAST	Protein MSS2, mitochondrial precursor	0.46	-	nuc	0	Mitochondrion; mitochondrial inner membrane (Probable)	mitochondrial inner membrane [IDA]			351
P10849 UniProt NPD GO	NAM1_YEAST	Protein NAM1, mitochondrial precursor (Mitochondrial transcription factor 2)	0.46	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			440
P39008 UniProt NPD GO	POP2_YEAST	Protein POP2 (EC 3.1.13.4) (CCR4-associated factor 1)	0.46	-	nuc	0	Cytoplasm. Nucleus	CCR4-NOT core complex [IPI] cytoplasm [IDA]		1UOC	433
P40486 UniProt NPD GO	SHQ1_YEAST	Protein SHQ1	0.46	-	cyt	0	Nucleus	nucleoplasm [IDA]			507
Q43715 UniProt NPD GO	TOC75_PEA	Protein TOC75, chloroplast precursor (75 kDa translocon at the outer-envelope-membrane of chloroplas ...	0.46	+	mit	0	Plastid; chloroplast; chloroplast outer membrane; multi-pass membrane protein				809
P18491 UniProt NPD GO	EMC_DROME	Protein extra-macrochaetae	0.46	-	nuc	0	Nucleus				199
Q9BY11 UniProt NPD GO	PACN1_HUMAN	Protein kinase C and casein kinase substrate in neurons protein 1	0.46	-	nuc	0	Cytoplasm (By similarity). Colocalizes with dynamin I at vesicular structures in the cell body and n ...	cytoplasm [NAS]	606512		444
Q6P566 UniProt NPD GO	LIX1_MOUSE	Protein limb expression 1 homolog	0.46	-	nuc	0					282
O15355 UniProt NPD GO	PP2CG_HUMAN	Protein phosphatase 2C isoform gamma (EC 3.1.3.16) (PP2C-gamma) (Protein phosphatase magnesium-depen ...	0.46	-	nuc	0	Cytoplasm (Potential)	nucleus [TAS]	605119		546
Q8AV57 UniProt NPD GO	SDK2_CHICK	Protein sidekick-2 precursor	0.46	-	end	1	Membrane; single-pass type I membrane protein (Potential)				2177
O14311 UniProt NPD GO	SPT3_SCHPO	Protein spt3	0.46	-	mit	0	Nucleus				307
Q9HGL3 UniProt NPD GO	SUM2_SCHPO	Protein sum2	0.46	+	nuc	0					426
P33891 UniProt NPD GO	TIP20_YEAST	Protein transport protein TIP20	0.46	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [IDA]			701

You are viewing entries 27851 to 27900 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.