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
P25719 UniProt NPD GO	CYPC_YEAST	Peptidyl-prolyl cis-trans isomerase C, mitochondrial precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyc ...	0.01	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			182
Q4IPH4 UniProt NPD GO	PPIH_GIBZE	Peptidyl-prolyl cis-trans isomerase H (EC 5.2.1.8) (PPIase H) (Rotamase H)	0.01	-	cyt	0	Nucleus (By similarity)				182
Q9Y237 UniProt NPD GO	PIN4_HUMAN	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 (EC 5.2.1.8) (Rotamase Pin4) (PPIase Pin4) (P ...	0.01	-	cyt	0		mitochondrial matrix [TAS]	300252	1FJD	131
O74729 UniProt NPD GO	PPIH_SCHPO	Peptidyl-prolyl cis-trans isomerase cyp3 (EC 5.2.1.8) (PPIase cyp3) (Rotamase cyp3)	0.01	-	cyt	0	Nucleus. Spindle pole body	nucleus [IDA]			173
P0C1I7 UniProt NPD GO	CYP5_RHIOR	Peptidyl-prolyl cis-trans isomerase cyp5 (EC 5.2.1.8) (PPIase cyp5) (Rotamase cyp5) (Cyclophilin cyp ...	0.01	-	cyt	0					176
P0C1I8 UniProt NPD GO	CYP6_RHIOR	Peptidyl-prolyl cis-trans isomerase cyp6 (EC 5.2.1.8) (PPIase cyp6) (Rotamase cyp6) (Cyclophilin cyp ...	0.01	-	cyt	0					176
P30405 UniProt NPD GO	PPIF_HUMAN	Peptidyl-prolyl cis-trans isomerase, mitochondrial precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclo ...	0.01	-	mit	0	Mitochondrion; mitochondrial matrix	membrane fraction [TAS]	604486	2BIU	207
P29117 UniProt NPD GO	PPIF_RAT	Peptidyl-prolyl cis-trans isomerase, mitochondrial precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclo ...	0.01	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			206
P10255 UniProt NPD GO	CYPH_NEUCR	Peptidyl-prolyl cis-trans isomerase, mitochondrial precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclo ...	0.01	-	mit	0	Mitochondrion. Cytoplasm				223
P28517 UniProt NPD GO	CYPR_CALVI	Peptidyl-prolyl cis-trans isomerase, rhodopsin-specific isozyme precursor (EC 5.2.1.8) (PPIase) (Rot ...	0.01	-	exc	1 *	Membrane; multi-pass membrane protein				234
Q2U6U0 UniProt NPD GO	PPIL1_ASPOR	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) (PPIase) (Rotamase)	0.01	-	cyt	0					161
Q4PCH8 UniProt NPD GO	PPIL3_USTMA	Peptidyl-prolyl cis-trans isomerase-like 3 (EC 5.2.1.8) (PPIase) (Rotamase)	0.01	-	cyt	0					168
Q3ZBL5 UniProt NPD GO	PTH2_BOVIN	Peptidyl-tRNA hydrolase 2, mitochondrial precursor (EC 3.1.1.29) (PTH 2)	0.01	-	nuc	1 *	Mitochondrion (By similarity)				179
P80484 UniProt NPD GO	PCP1_AMPCA	Peridinin-chlorophyll a-binding protein 1, chloroplast precursor (PCP)	0.01	-	cyt	0	Plastid; chloroplast			1PPR	370
P51873 UniProt NPD GO	PCP2_AMPCA	Peridinin-chlorophyll a-binding protein 2, chloroplast precursor (PCP)	0.01	-	mit	0	Plastid; chloroplast				369
P12347 UniProt NPD GO	PER_ACEME	Period clock protein (p230)	0.01	-	mit	0	Plastid; chloroplast				174
Q6WL85 UniProt NPD GO	PMP22_HORSE	Peripheral myelin protein 22 (PMP-22)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				159
Q01453 UniProt NPD GO	PMP22_HUMAN	Peripheral myelin protein 22 (PMP-22)	0.01	-	end	4 *	Membrane; multi-pass membrane protein		601097		160
P25094 UniProt NPD GO	PMP22_RAT	Peripheral myelin protein 22 (PMP-22) (CD25 protein) (SR13 myelin protein) (Schwann cell membrane gl ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein	compact myelin [IMP] integral to membrane [IDA] tight junction [IDA]			160
P16646 UniProt NPD GO	PMP22_MOUSE	Peripheral myelin protein 22 (PMP-22) (Growth-arrest-specific protein 3) (GAS3)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				161
P36885 UniProt NPD GO	LSKP_PERAM	Perisulfakinin (Pea-SK-I)	0.01	-		0					11
P84354 UniProt NPD GO	PVK1_MUSDO	Periviscerokinin-1 (Musdo-PVK-1)	0.01	-		0	Secreted protein				13
P84352 UniProt NPD GO	PVK1_SARBU	Periviscerokinin-1 (Neobu-PVK-1)	0.01	-		0	Secreted protein				13
P84658 UniProt NPD GO	PVK1_PANVI	Periviscerokinin-1 (Panvi-PVK-1)	0.01	-		0	Secreted protein				11
P83926 UniProt NPD GO	PVK2_LEUMA	Periviscerokinin-2 (Lem-PVK-2)	0.01	-		0	Secreted protein				11
P84355 UniProt NPD GO	PVK2_MUSDO	Periviscerokinin-2 (Musdo-PVK-2)	0.01	-		0	Secreted protein				9
P83928 UniProt NPD GO	PVK2_BLACR	Periviscerokinin-2 (PVK-2)	0.01	-		0	Secreted protein				11
P83929 UniProt NPD GO	PVK2_BLADU	Periviscerokinin-2 (PVK-2)	0.01	-		0	Secreted protein				11
P84592 UniProt NPD GO	PVK2_BLAGI	Periviscerokinin-2 (PVK-2)	0.01	-		0	Secreted protein				11
P83930 UniProt NPD GO	PVK2_GROPO	Periviscerokinin-2 (PVK-2)	0.01	-		0	Secreted protein				11
P83927 UniProt NPD GO	PVK2_NAUCI	Periviscerokinin-2 (PVK-2)	0.01	-		0	Secreted protein				11
P81555 UniProt NPD GO	PVK2_PERAM	Periviscerokinin-2 (Pea-PVK-2)	0.01	-		0	Secreted protein				12
P84373 UniProt NPD GO	PVK22_CELBM	Periviscerokinin-2 type 2 (PVK-2 type 2)	0.01	-		0	Secreted protein				11
P84379 UniProt NPD GO	PVK2_DEREJ	Periviscerokinin-2.1 (PVK-2.1) [Contains: Periviscerokinin-2.2 (PVK-2.2)]	0.01	-		0	Secreted protein				12
P84380 UniProt NPD GO	PVK2_DERER	Periviscerokinin-2.1 (PVK-2.1) [Contains: Periviscerokinin-2.2 (PVK-2.2)]	0.01	-		0	Secreted protein				12
P84378 UniProt NPD GO	PVK2_DERKE	Periviscerokinin-2.1 (PVK-2.1) [Contains: Periviscerokinin-2.2 (PVK-2.2)]	0.01	-		0	Secreted protein				12
P84375 UniProt NPD GO	PVK2_EURFL	Periviscerokinin-2.1 (PVK-2.1) [Contains: Periviscerokinin-2.2 (PVK-2.2)]	0.01	-		0	Secreted protein				12
P84376 UniProt NPD GO	PVK2_PSEFO	Periviscerokinin-2.1 (PVK-2.1) [Contains: Periviscerokinin-2.2 (PVK-2.2)]	0.01	-		0	Secreted protein				12
P84377 UniProt NPD GO	PVK2_PSEFV	Periviscerokinin-2.1 (PVK-2.1) [Contains: Periviscerokinin-2.2 (PVK-2.2)]	0.01	-		0	Secreted protein				12
P84438 UniProt NPD GO	PVK21_BLAOR	Periviscerokinin-2.1 (Pea-PVK-2-like peptide)	0.01	-		0	Secreted protein				12
P84440 UniProt NPD GO	PVK21_NEORO	Periviscerokinin-2.1 (Pea-PVK-2-like peptide)	0.01	-		0	Secreted protein				12
P84436 UniProt NPD GO	PVK21_PERAU	Periviscerokinin-2.1 (Pea-PVK-2-like peptide)	0.01	-		0	Secreted protein				12
P84435 UniProt NPD GO	PVK21_PERBR	Periviscerokinin-2.1 (Pea-PVK-2-like peptide)	0.01	-		0	Secreted protein				12
P84437 UniProt NPD GO	PVK21_PERFU	Periviscerokinin-2.1 (Pea-PVK-2-like peptide)	0.01	-		0	Secreted protein				12
P84441 UniProt NPD GO	PVK21_PSEBJ	Periviscerokinin-2.1 (Pea-PVK-2-like peptide)	0.01	-		0	Secreted protein				12
P84439 UniProt NPD GO	PVK21_SHELA	Periviscerokinin-2.1 (Pea-PVK-2-like peptide)	0.01	-		0	Secreted protein				12
P84426 UniProt NPD GO	PVK22_BLAOR	Periviscerokinin-2.2 (Lem-PVK-2-like peptide)	0.01	-		0	Secreted protein				11
P84428 UniProt NPD GO	PVK22_NEORO	Periviscerokinin-2.2 (Lem-PVK-2-like peptide)	0.01	-		0	Secreted protein				11
P84422 UniProt NPD GO	PVK22_PERAM	Periviscerokinin-2.2 (Lem-PVK-2-like peptide)	0.01	-		0	Secreted protein				11
P84424 UniProt NPD GO	PVK22_PERAU	Periviscerokinin-2.2 (Lem-PVK-2-like peptide)	0.01	-		0	Secreted protein				11

You are viewing entries 90201 to 90250 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.