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
Q9XTN0 UniProt NPD GO	PGRP_BOMMO	Peptidoglycan recognition protein precursor	0.00	-	end	0					196
P24525 UniProt NPD GO	CYPH_BRANA	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.00	-	cyt	0	Cytoplasm				171
O49886 UniProt NPD GO	CYPH_LUPLU	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.00	-	cyt	0	Cytoplasm			1MD5	172
P21569 UniProt NPD GO	CYPH_MAIZE	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.00	-	cyt	0	Cytoplasm				172
P35627 UniProt NPD GO	CYPX_USEUD	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.00	-	cyt	0	Cytoplasm (Probable)				169
P54985 UniProt NPD GO	PPIA_BLAGE	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.00	-	cyt	0	Cytoplasm				164
P18253 UniProt NPD GO	CYPH_SCHPO	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.00	-	cyt	0	Cytoplasm				162
P14832 UniProt NPD GO	CYPH_YEAST	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.00	-	cyt	0	Cytoplasm	histone deacetylase complex [IPI] nucleus [IDA]		1VDN	161
P52017 UniProt NPD GO	CYP10_CAEEL	Peptidyl-prolyl cis-trans isomerase 10 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-10)	0.00	-	cyt	0					161
P52018 UniProt NPD GO	CYP11_CAEEL	Peptidyl-prolyl cis-trans isomerase 11 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-11)	0.00	-	cyt	0					183
P52010 UniProt NPD GO	CYP2_CAEEL	Peptidyl-prolyl cis-trans isomerase 2 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-2)	0.00	-	cyt	0					172
P52013 UniProt NPD GO	CYP5_CAEEL	Peptidyl-prolyl cis-trans isomerase 5 precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-5)	0.00	-	end	0	Cytoplasm			1H0P	204
Q6DTV9 UniProt NPD GO	PPIA_AOTTR	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm (By similarity)				163
P62935 UniProt NPD GO	PPIA_BOVIN	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm				163
P62938 UniProt NPD GO	PPIA_CERAE	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm				164
P14851 UniProt NPD GO	PPIA_CRIGR	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm				163
Q8HXS3 UniProt NPD GO	PPIA_FELCA	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm (By similarity)				163
P62937 UniProt NPD GO	PPIA_HUMAN	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm		123840	5CYH	164
P62940 UniProt NPD GO	PPIA_MACMU	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm				164
P62941 UniProt NPD GO	PPIA_PAPAN	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm				164
P62936 UniProt NPD GO	PPIA_PIG	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm				163
Q5R8S7 UniProt NPD GO	PPIA_PONPY	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm (By similarity)				164
Q9TTC6 UniProt NPD GO	PPIA_RABIT	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm (By similarity)				163
P17742 UniProt NPD GO	PPIA_MOUSE	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm	cytosol [IDA]			163
P10111 UniProt NPD GO	PPIA_RAT	Peptidyl-prolyl cis-trans isomerase A (EC 5.2.1.8) (PPIase A) (Rotamase A) (Cyclophilin A) (Cyclospo ...	0.00	-	cyt	0	Cytoplasm				163
P0C1H8 UniProt NPD GO	PPIA2_RHIOR	Peptidyl-prolyl cis-trans isomerase A2 (EC 5.2.1.8) (PPIase A2) (Rotamase A2) (Cyclophilin A2) (Cycl ...	0.00	-	cyt	0	Cytoplasm (By similarity)				161
Q01490 UniProt NPD GO	PPIB_ORPSP	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin B)	0.00	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				203
P0C1I0 UniProt NPD GO	PPIB2_RHIOR	Peptidyl-prolyl cis-trans isomerase B2 precursor (EC 5.2.1.8) (PPIase B2) (Rotamase B2)	0.00	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				209
Q38900 UniProt NPD GO	CP19A_ARATH	Peptidyl-prolyl cis-trans isomerase CYP19-1 (EC 5.2.1.8) (PPIase CYP19-1) (Rotamase cyclophilin-3) ( ...	0.00	-	cyt	0	Cytoplasm (Probable)				173
Q38867 UniProt NPD GO	CP19C_ARATH	Peptidyl-prolyl cis-trans isomerase CYP19-3 (EC 5.2.1.8) (PPIase CYP19-3) (Rotamase cyclophilin-2) ( ...	0.00	-	cyt	0	Cytoplasm (Probable)				176
Q8LDP4 UniProt NPD GO	CP19D_ARATH	Peptidyl-prolyl cis-trans isomerase CYP19-4 precursor (EC 5.2.1.8) (PPIase CYP19-4) (Rotamase CYP19- ...	0.00	-	vac	0	Cytoplasm. Membrane. Endoplasmic reticulum. Mostly cytoplasmic, also membrane-associated. Present in ...				201
P34791 UniProt NPD GO	CP20C_ARATH	Peptidyl-prolyl cis-trans isomerase CYP20-3, chloroplast precursor (EC 5.2.1.8) (PPIase CYP20-3) (Ro ...	0.00	-	mit	0	Plastid; chloroplast; chloroplast stroma. Probably associated to membranes				260
Q9D868 UniProt NPD GO	PPIH_MOUSE	Peptidyl-prolyl cis-trans isomerase H (EC 5.2.1.8) (PPIase H) (Rotamase H)	0.00	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with spliceosomal snRNPs. Cytopla ...				188
Q7SG06 UniProt NPD GO	PPIH_NEUCR	Peptidyl-prolyl cis-trans isomerase H (EC 5.2.1.8) (PPIase H) (Rotamase H)	0.00	-	cyt	0	Nucleus (By similarity)				182
O43447 UniProt NPD GO	PPIH_HUMAN	Peptidyl-prolyl cis-trans isomerase H (EC 5.2.1.8) (PPIase H) (Rotamase H) (U-snRNP-associated cyclo ...	0.00	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle. Colocalizes with spliceosomal snRNPs. Cytoplasm. A small prop ...	spliceosome complex [TAS]	606095	1QOI	177
P82536 UniProt NPD GO	TLP20_SPIOL	Peptidyl-prolyl cis-trans isomerase TLP20, chloroplast (EC 5.2.1.8) (PPIase) (Rotamase) (Thylakoid l ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				45
P84343 UniProt NPD GO	PPIA_NEOCA	Peptidyl-prolyl cis-trans isomerase precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (NcCyP) ...	0.00	-	exc	0					178
Q99KR7 UniProt NPD GO	PPIF_MOUSE	Peptidyl-prolyl cis-trans isomerase, mitochondrial precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclo ...	0.00	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			206
P15425 UniProt NPD GO	CYPR_DROME	Peptidyl-prolyl cis-trans isomerase, rhodopsin-specific isozyme precursor (EC 5.2.1.8) (PPIase) (Rot ...	0.00	-	mit	2 *	Membrane; multi-pass membrane protein	cytoplasmic membrane-bound vesicle [IDA] endoplasmic reticulum cisterna [IDA] integral to membrane [IDA] membrane fraction [IDA]			237
Q4WMB6 UniProt NPD GO	PPIL3_ASPFU	Peptidyl-prolyl cis-trans isomerase-like 3 (EC 5.2.1.8) (PPIase) (Rotamase)	0.00	-	cyt	0					212
P0C1I5 UniProt NPD GO	PPIL3_RHIOR	Peptidyl-prolyl cis-trans isomerase-like 3 (EC 5.2.1.8) (PPIase) (Rotamase)	0.00	-	cyt	0					170
Q5ZLV2 UniProt NPD GO	PPIL3_CHICK	Peptidyl-prolyl cis-trans isomerase-like 3 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-like protei ...	0.00	-	cyt	0					161
Q9D6L8 UniProt NPD GO	PPIL3_MOUSE	Peptidyl-prolyl cis-trans isomerase-like 3 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-like protei ...	0.00	-	cyt	0					161
Q812D3 UniProt NPD GO	PPIL3_RAT	Peptidyl-prolyl cis-trans isomerase-like 3 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-like protei ...	0.00	-	cyt	0					161
Q9H2H8 UniProt NPD GO	PPIL3_HUMAN	Peptidyl-prolyl cis-trans isomerase-like 3 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-like protei ...	0.00	-	cyt	0				1XYH	161
Q8LGG0 UniProt NPD GO	FKB12_ARATH	Peptidyl-prolyl isomerase FKBP12 (EC 5.2.1.8) (12 kDa FK506-binding protein) (12 kDa FKBP) (FKBP-12) ...	0.00	-	nuc	0	Cytoplasm (Potential)				112
P51889 UniProt NPD GO	PCP_ALECO	Peridinin-chlorophyll a-binding protein (PCP) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				49
P51874 UniProt NPD GO	PCP_SYMSP	Peridinin-chlorophyll a-binding protein, chloroplast precursor (PCP)	0.00	-	mit	0	Plastid; chloroplast				365
Q9TQZ3 UniProt NPD GO	PMP22_BOVIN	Peripheral myelin protein 22 (PMP-22) (PAS positive glycoprotein) (PASII) (Fragments)	0.00	-	exc	2 *	Membrane; multi-pass membrane protein (By similarity)				75
P30536 UniProt NPD GO	BZRP_HUMAN	Peripheral-type benzodiazepine receptor (PBR) (PKBS) (Mitochondrial benzodiazepine receptor)	0.00	-	nuc	5 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrial outer membrane [NAS]	109610		169

You are viewing entries 96301 to 96350 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.