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
Q9CQX3 UniProt NPD GO	PLUCL_MOUSE	Palate lung and nasal carcinoma-like protein precursor (Tongue plunc-like protein) (TPL)	0.01	-	end	0	Secreted protein (Potential)				270
Q6C7D1 UniProt NPD GO	PFA5_YARLI	Palmitoyltransferase PFA5 (EC 2.3.1.-) (Protein fatty acyltransferase 5)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				334
Q5A861 UniProt NPD GO	SWF1_CANAL	Palmitoyltransferase SWF1 (EC 2.3.1.-)	0.01	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				353
Q6BP23 UniProt NPD GO	SWF1_DEBHA	Palmitoyltransferase SWF1 (EC 2.3.1.-)	0.01	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				377
Q6CJC5 UniProt NPD GO	SWF1_KLULA	Palmitoyltransferase SWF1 (EC 2.3.1.-)	0.01	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				324
P84274 UniProt NPD GO	PA1A_RANPA	Palustrin-1a	0.01	-	cyt	0	Secreted protein	extracellular region [IDA]			28
P84275 UniProt NPD GO	PA1B_RANPA	Palustrin-1b	0.01	-	cyt	0	Secreted protein	extracellular region [IDA]			28
P84277 UniProt NPD GO	PA1D_RANPA	Palustrin-1d	0.01	-	nuc	0	Secreted protein	extracellular region [IDA]			27
P84278 UniProt NPD GO	PA2A_RANPA	Palustrin-2a	0.01	-	cyt	0	Secreted protein	extracellular region [IDA]			31
O42266 UniProt NPD GO	OPSP_ICTPU	Parapinopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				346
P81862 UniProt NPD GO	PAP5_PARMA	Pardaxin P-5 (P5)	0.01	-	mit	0	Secreted protein				33
P81864 UniProt NPD GO	PAP2_PARMA	Pardaxin-2 (Pardaxin II) (PXII) (Fragment)	0.01	-		0	Secreted protein				5
P02627 UniProt NPD GO	PRVA_RANES	Parvalbumin alpha	0.01	-	cyt	0					109
P84535 UniProt NPD GO	PRVA_RANTE	Parvalbumin alpha (Fragment)	0.01	-	cyt	0	Cytoplasm. In muscle and nervous system. Secreted protein. In cutaneous mucus				23
P02615 UniProt NPD GO	PRVB_BOACO	Parvalbumin beta	0.01	-	cyt	0					109
P02623 UniProt NPD GO	PRVB_LATCH	Parvalbumin beta	0.01	-	mit	0					108
P19753 UniProt NPD GO	PRVT_CHICK	Parvalbumin, thymic (Avian thymic hormone) (ATH) (Thymus-specific antigen T1)	0.01	-	cyt	0					108
P09042 UniProt NPD GO	PR1C_TOBAC	Pathogenesis-related protein 1C precursor (PR-1C)	0.01	-	cyt	1 *	Vacuole. Accumulates in within the vacuoles of specialized cells known as crystal idioblasts				168
Q00008 UniProt NPD GO	PRMS_MAIZE	Pathogenesis-related protein PRMS precursor	0.01	-	exc	1 *					167
Q01172 UniProt NPD GO	PLYA_ASPNG	Pectin lyase A precursor (EC 4.2.2.10) (PLA) (Pectin lyase II) (PLII)	0.01	-	cyt	0				1IDK	379
P22864 UniProt NPD GO	PLYD_ASPNG	Pectin lyase D precursor (EC 4.2.2.10) (PLD) (Pectin lyase I) (PLI)	0.01	-	cyt	0					373
P84818 UniProt NPD GO	PVAT_TRISI	Pelovaterin	0.01	-	nuc	1 *					42
P27823 UniProt NPD GO	PEPAF_RABIT	Pepsin F precursor (EC 3.4.23.1)	0.01	-	vac	0	Secreted protein				388
P15230 UniProt NPD GO	SCX2_BUTSI	Peptide 2 (Peptide II)	0.01	-	nuc	0	Secreted protein				28
P82697 UniProt NPD GO	PH4_PERAM	Peptide hormone 4 (Pea-YLS-amide)	0.01	-		0					17
P54149 UniProt NPD GO	MSRA_BOVIN	Peptide methionine sulfoxide reductase (EC 1.8.4.6) (Protein-methionine-S-oxide reductase) (Peptide ...	0.01	-	mit	0				1FVG	233
P69928 UniProt NPD GO	TXAM3_ANTMC	Peptide toxin Am III precursor	0.01	-	exc	0	Secreted protein (By similarity). Found in nematocyst (By similarity)				74
Q8INK6 UniProt NPD GO	PGPLB_DROME	Peptidoglycan-recognition protein-LB precursor (EC 3.5.1.28)	0.01	-	cyt	0	Isoform 1: Secreted protein (Potential)	extracellular region [IDA]		1OHT	232
Q9V3B7 UniProt NPD GO	PGSC1_DROME	Peptidoglycan-recognition protein-SC1a/b precursor (EC 3.5.1.28)	0.01	-	mit	0	Secreted protein (Potential)	extracellular region [NAS]			185
Q70PU2 UniProt NPD GO	PGSC1_DROSI	Peptidoglycan-recognition protein-SC1a/b precursor (EC 3.5.1.28)	0.01	-	mit	0	Secreted protein (Potential)	extracellular region [ISS]			185
P81054 UniProt NPD GO	PLMP_GRIFR	Peptidyl-Lys metalloendopeptidase precursor (EC 3.4.24.20) (MEP) (GfMEP)	0.01	-	mit	0	Secreted protein (Probable). Binds strongly to beta-1,3-glucan and chitin, major polysaccharides con ...			1GE7	348
Q39613 UniProt NPD GO	CYPH_CATRO	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.01	-	cyt	0	Cytoplasm				172
P21568 UniProt NPD GO	CYPH_LYCES	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.01	-	cyt	0	Cytoplasm				171
P91791 UniProt NPD GO	PPIA_HEMPU	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.01	-	nuc	0	Cytoplasm (By similarity)				164
P22011 UniProt NPD GO	PPIA_CANAL	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.01	-	cyt	0	Cytoplasm				162
O00060 UniProt NPD GO	CYPH_UROFA	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.01	-	cyt	0	Cytoplasm (By similarity)				163
P81531 UniProt NPD GO	CYPH_BETVE	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.01	-	cyt	0	Cytoplasm				42
P84342 UniProt NPD GO	PPIA_NAEFO	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (NF008) (Fragment ...	0.01	-	nuc	0					21
P52009 UniProt NPD GO	CYP1_CAEEL	Peptidyl-prolyl cis-trans isomerase 1 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-1)	0.01	-	mit	0					192
P52011 UniProt NPD GO	CYP3_CAEEL	Peptidyl-prolyl cis-trans isomerase 3 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-3)	0.01	-	cyt	0		cell [IDA]		1E8K	173
P52014 UniProt NPD GO	CYP6_CAEEL	Peptidyl-prolyl cis-trans isomerase 6 precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-6)	0.01	-	exc	0					201
P52015 UniProt NPD GO	CYP7_CAEEL	Peptidyl-prolyl cis-trans isomerase 7 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-7)	0.01	-	cyt	0					171
P0C1H7 UniProt NPD GO	PPIA1_RHIOR	Peptidyl-prolyl cis-trans isomerase A1 (EC 5.2.1.8) (PPIase A1) (Rotamase A1) (Cyclophilin A1) (Cycl ...	0.01	-	cyt	0	Cytoplasm (By similarity)				164
Q2UGK2 UniProt NPD GO	PPIB_ASPOR	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase B) (Rotamase B)	0.01	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				192
Q5KEB7 UniProt NPD GO	PPIB_CRYNE	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase B) (Rotamase B)	0.01	-	vac	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				231
Q5B4R3 UniProt NPD GO	PPIB_EMENI	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase B) (Rotamase B)	0.01	-	vac	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				214
Q4I5R9 UniProt NPD GO	PPIB_GIBZE	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase B) (Rotamase B)	0.01	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				207
Q27774 UniProt NPD GO	PPIB_SCHJA	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase B) (Rotamase B) (Cyclophilin B) ...	0.01	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				213
P23285 UniProt NPD GO	CYPB_YEAST	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin B) (Cy ...	0.01	-	exc	0	Secreted protein				205
Q26551 UniProt NPD GO	PPIB_SCHMA	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin B) (S- ...	0.01	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				213

You are viewing entries 90151 to 90200 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.