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
Q9NYT0 UniProt NPD GO	PLEK2_HUMAN	Pleckstrin-2	0.38	-	cyt	0			608007	1X1G	353
Q9NP85 UniProt NPD GO	PODO_HUMAN	Podocin	0.38	-	nuc	1	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	604766		383
Q80TC5 UniProt NPD GO	POGK_MOUSE	Pogo transposable element with KRAB domain	0.38	-	cyt	0	Nucleus (Probable)				607
P51006 UniProt NPD GO	PAPO3_XENLA	Poly(A) polymerase type 3 (EC 2.7.7.19) (PAP) (Polynucleotide adenylyltransferase) (Fragment)	0.38	-	mit	0	Nucleus				400
Q28165 UniProt NPD GO	PABP2_BOVIN	Polyadenylate-binding protein 2 (Poly(A)-binding protein 2) (Poly(A)-binding protein II) (PABII) (Po ...	0.38	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shuttles between the nucleus and the cytoplasm b ...				305
Q86U42 UniProt NPD GO	PABP2_HUMAN	Polyadenylate-binding protein 2 (Poly(A)-binding protein 2) (Poly(A)-binding protein II) (PABII) (Po ...	0.38	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Shuttles between the nucleus and the cytoplasm b ...		602279		305
P01832 UniProt NPD GO	PIGR_RABIT	Polymeric-immunoglobulin receptor precursor (Poly-Ig receptor) (PIGR) [Contains: Secretory component ...	0.38	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein				773
Q8IXK2 UniProt NPD GO	GLT12_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 12 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.38	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				581
Q6PB93 UniProt NPD GO	GALT2_MOUSE	Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.38	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Resides pr ...	Golgi lumen [TAS]			570
Q8I136 UniProt NPD GO	GALT4_CAEEL	Polypeptide N-acetylgalactosaminyltransferase 4 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.38	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				589
O95279 UniProt NPD GO	KCNK5_HUMAN	Potassium channel subfamily K member 5 (Acid-sensitive potassium channel protein TASK-2) (TWIK-relat ...	0.38	+	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS]	603493		499
Q01956 UniProt NPD GO	KCNC3_RAT	Potassium voltage-gated channel subfamily C member 3 (Voltage-gated potassium channel subunit Kv3.3) ...	0.38	-	end	4	Membrane; multi-pass membrane protein				889
Q8TDN1 UniProt NPD GO	KCNG4_HUMAN	Potassium voltage-gated channel subfamily G member 4 (Voltage-gated potassium channel subunit Kv6.4) ...	0.38	-	end	3	Cell membrane; multi-pass membrane protein. Membrane; multi-pass membrane protein. Has to be associa ...		607603		519
Q60603 UniProt NPD GO	KCNH1_MOUSE	Potassium voltage-gated channel subfamily H member 1 (Voltage-gated potassium channel subunit Kv10.1 ...	0.38	-	end	4	Membrane; multi-pass membrane protein				989
Q9Z1W8 UniProt NPD GO	AT12A_MOUSE	Potassium-transporting ATPase alpha chain 2 (EC 3.6.3.10) (Proton pump) (Non-gastric H(+)/K(+) ATPas ...	0.38	+	end	8	Membrane; multi-pass membrane protein				1035
P54708 UniProt NPD GO	AT12A_RAT	Potassium-transporting ATPase alpha chain 2 (EC 3.6.3.10) (Proton pump) (Non-gastric H(+)/K(+) ATPas ...	0.38	+	end	8	Membrane; multi-pass membrane protein				1036
P32523 UniProt NPD GO	PRP19_YEAST	Pre-mRNA-splicing factor 19	0.38	-	nuc	0	Nucleus	cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA] spliceosome complex [IDA]		2BAY	503
Q6BU51 UniProt NPD GO	ISY1_DEBHA	Pre-mRNA-splicing factor ISY1	0.38	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				298
Q6FUJ7 UniProt NPD GO	SYF1_CANGA	Pre-mRNA-splicing factor SYF1	0.38	-	nuc	0	Nucleus (By similarity)				835
Q4WUJ6 UniProt NPD GO	ISY1_ASPFU	Pre-mRNA-splicing factor isy1	0.38	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				243
Q5B423 UniProt NPD GO	ISY1_EMENI	Pre-mRNA-splicing factor isy1	0.38	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				256
Q5AX35 UniProt NPD GO	SLT11_EMENI	Pre-mRNA-splicing factor slt11	0.38	-	nuc	0	Nucleus (By similarity)				385
O02194 UniProt NPD GO	PSN_DROME	Presenilin homolog (EC 3.4.23.-) (dPS) (DmPS)	0.38	-	end	7	Membrane; multi-pass membrane protein (Potential)	apical plasma membrane [IDA] cell cortex [IDA] cytoplasm [IDA]			541
Q9UH17 UniProt NPD GO	ABC3B_HUMAN	Probable DNA dC->dU-editing enzyme APOBEC-3B (EC 3.5.4.-) (Phorbolin-1-related protein) (Phorbolin-2 ...	0.38	-	nuc	0			607110		382
P05472 UniProt NPD GO	RPOL_KLULA	Probable DNA-directed RNA polymerase (EC 2.7.7.6) (Killer plasmid PGKL2 protein 6)	0.38	-	nuc	0					982
Q86SQ4 UniProt NPD GO	GP126_HUMAN	Probable G-protein coupled receptor 126 precursor	0.38	-	end	8 *	Membrane; multi-pass membrane protein				1221
Q9LFU5 UniProt NPD GO	TRM1_ARATH	Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase (EC 2.1.1.32) (tRNA(guanine-26,N(2)-N(2) ...	0.38	-	nuc	0					586
Q75B78 UniProt NPD GO	TAH18_ASHGO	Probable NADPH reductase TAH18 (EC 1.-.-.-)	0.38	-	nuc	0					620
O62246 UniProt NPD GO	COPE_CAEEL	Probable coatomer subunit epsilon (Epsilon-coat protein) (Epsilon-COP)	0.38	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				292
Q9VW43 UniProt NPD GO	CP305_DROME	Probable cytochrome P450 305a1 (EC 1.14.-.-) (CYPCCCVA1)	0.38	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				504
Q9V771 UniProt NPD GO	C6A23_DROME	Probable cytochrome P450 6a23 (EC 1.14.-.-) (CYPVIA23)	0.38	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				502
Q9V676 UniProt NPD GO	CP6T3_DROME	Probable cytochrome P450 6t3 (EC 1.14.-.-) (CYPVIT3)	0.38	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				501
Q05775 UniProt NPD GO	IF31_YEAST	Probable eukaryotic translation initiation factor 3 30 kDa subunit (eIF-3 30 kDa) (eIF3j)	0.38	-	nuc	0		eukaryotic translation initiation factor 3 ... [IPI]			265
Q27876 UniProt NPD GO	H2B4_CAEEL	Probable histone H2B 4	0.38	-	nuc	0	Nucleus				122
Q6FIT7 UniProt NPD GO	SPC25_CANGA	Probable kinetochore protein SPC25	0.38	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				237
Q5KGI8 UniProt NPD GO	SPC25_CRYNE	Probable kinetochore protein SPC25	0.38	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				272
Q10740 UniProt NPD GO	LKHA4_YEAST	Probable leukotriene A-4 hydrolase (EC 3.3.2.6) (LTA-4 hydrolase) (Leukotriene A(4) hydrolase)	0.38	-	mit	0	Cytoplasm (By similarity)	cytoplasm [IDA] nucleus [IDA]			671
Q42290 UniProt NPD GO	MPPB_ARATH	Probable mitochondrial-processing peptidase subunit beta, mitochondrial precursor (EC 3.4.24.64) (Be ...	0.38	-	mit	0	Mitochondrion				531
Q9NTI2 UniProt NPD GO	AT8A2_HUMAN	Probable phospholipid-transporting ATPase IB (EC 3.6.3.1) (ATPase class I type 8A member 2) (ML-1)	0.38	-	end	8	Membrane; multi-pass membrane protein		605870		1148
O70228 UniProt NPD GO	ATP9A_MOUSE	Probable phospholipid-transporting ATPase IIA (EC 3.6.3.1) (ATPase class II type 9A)	0.38	-	end	11	Membrane; multi-pass membrane protein (By similarity)				1047
O49629 UniProt NPD GO	PAP2_ARATH	Probable plastid-lipid-associated protein 2, chloroplast precursor (AtPap2) (Fibrillin-2)	0.38	-	mit	0	Plastid; chloroplast (Potential)	thylakoid membrane (sensu Viridiplantae) [IDA]			310
Q02595 UniProt NPD GO	KPK2_PLAFK	Probable serine/threonine-protein kinase 2 (EC 2.7.11.1)	0.38	-	nuc	0	Membrane				510
P10091 UniProt NPD GO	CYSA_MARPO	Probable sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATP ...	0.38	-	mit	0	Plastid; chloroplast				370
O24175 UniProt NPD GO	FL_ORYSA	Probable transcription factor FL (RFL)	0.38	-	cyt	0	Nucleus (Probable)				389
Q8SSL0 UniProt NPD GO	TPP_ENCCU	Probable trehalose-phosphatase (EC 3.1.3.12) (Trehalose 6-phosphate phosphatase) (TPP)	0.38	-	cyt	0					718
Q8LDS2 UniProt NPD GO	XTH27_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 27 precursor (EC 2.4.1.207) (At-XTH27) (X ...	0.38	-	vac	1 *	Secreted protein; extracellular space; apoplast (Probable)				333
Q9R1J8 UniProt NPD GO	P3H1_RAT	Prolyl 3-hydroxylase 1 precursor (EC 1.14.11.7) (Leucine proline-enriched proteoglycan 1) (Leprecan- ...	0.38	-	end	0	Endoplasmic reticulum. Secreted protein; extracellular space; extracellular matrix. Secreted into th ...				728
P30557 UniProt NPD GO	PE2R3_MOUSE	Prostaglandin E2 receptor, EP3 subtype (Prostanoid EP3 receptor) (PGE receptor, EP3 subtype)	0.38	+	end	6 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			365
P32194 UniProt NPD GO	PG1_PIG	Protegrin-1 precursor (PG-1) (Neutrophil peptide 1)	0.38	-	mit	1 *	Secreted protein			1PG1	149
Q5T1B1 UniProt NPD GO	CJ091_HUMAN	Protein C10orf91	0.38	-	nuc	0					145

You are viewing entries 33651 to 33700 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.