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
P48459 UniProt NPD GO	YSD1_CAEEL	Putative serine/threonine-protein phosphatase C23G10.1 in chromosome II (EC 3.1.3.16)	0.00	-	cyt	0					354
Q09496 UniProt NPD GO	PPH6_CAEEL	Putative serine/threonine-protein phosphatase pph-6 (EC 3.1.3.16)	0.00	-	cyt	0					331
Q99PE5 UniProt NPD GO	NID67_MOUSE	Putative small membrane protein NID67 (NGF-induced differentiation clone 67 protein)	0.00	-	nuc	1 *					60
Q99PE6 UniProt NPD GO	NID67_RAT	Putative small membrane protein NID67 (NGF-induced differentiation clone 67 protein)	0.00	-	nuc	1 *					60
Q9SK39 UniProt NPD GO	SBP3_ARATH	Putative steroid-binding protein 3 (AtMP3)	0.00	-	cyt	0	Nucleus (Probable)			1T0G	100
O62215 UniProt NPD GO	DHSD_CAEEL	Putative succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (C ...	0.00	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				145
Q08742 UniProt NPD GO	FMP31_YEAST	Putative thiosulfate sulfurtransferase FMP31, mitochondrial precursor (EC 2.8.1.1) (Found in mitocho ...	0.00	-	mit	0	Mitochondrion	mitochondrion [IDA]			149
Q9ASX2 UniProt NPD GO	TRNH1_ARATH	Putative tropinone reductase homolog At1g07440 (EC 1.1.1.-)	0.00	-	cyt	0				1XQ1	266
Q5VVB8 UniProt NPD GO	CF191_HUMAN	Putative uncharacterized protein C6orf191	0.00	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				128
P39565 UniProt NPD GO	YAN9_YEAST	Putative uncharacterized protein YAR069C/YHR214C-D	0.00	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)				97
P38171 UniProt NPD GO	YBJ6_YEAST	Putative uncharacterized protein YBL096C precursor	0.00	-	exc	0					102
P40436 UniProt NPD GO	YIR5_YEAST	Putative uncharacterized protein YIL175W/YJL222W-B	0.00	-	nuc	0					45
Q04521 UniProt NPD GO	YMI4_YEAST	Putative uncharacterized protein YML084W precursor	0.00	-	end	2 *					102
Q08110 UniProt NPD GO	YO014_YEAST	Putative uncharacterized protein YOL014W	0.00	-	nuc	0					124
P87368 UniProt NPD GO	OPSV_ORYLA	Putative violet-sensitive opsin (Violet cone photoreceptor pigment) (KFH-V)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				334
Q9SEH7 UniProt NPD GO	PMT2_TOBAC	Putrescine N-methyltransferase 2 (EC 2.1.1.53) (PMT 2)	0.00	-	cyt	0					353
Q9D9M5 UniProt NPD GO	PHOP2_MOUSE	Pyridoxal phosphate phosphatase PHOSPHO2 (EC 3.1.3.74)	0.00	-	cyt	0					241
Q03148 UniProt NPD GO	SNZ1_YEAST	Pyridoxin biosynthesis protein SNZ1 (PDX1 homolog 1) (p35)	0.00	-	cyt	0					297
P84362 UniProt NPD GO	PPK6_CELBM	Pyrokinin-6 (FXPRL-amide)	0.00	-		0	Secreted protein				14
P84364 UniProt NPD GO	PPK6_DEREJ	Pyrokinin-6 (FXPRL-amide)	0.00	-		0	Secreted protein				14
P84363 UniProt NPD GO	PPK6_DERER	Pyrokinin-6 (FXPRL-amide)	0.00	-		0	Secreted protein				14
P84365 UniProt NPD GO	PPK6_DERKE	Pyrokinin-6 (FXPRL-amide)	0.00	-		0	Secreted protein				14
P84361 UniProt NPD GO	PPK6_NEORO	Pyrokinin-6 (FXPRL-amide)	0.00	-		0	Secreted protein				14
P84360 UniProt NPD GO	PPK6_PERFU	Pyrokinin-6 (FXPRL-amide)	0.00	-		0	Secreted protein				14
P84367 UniProt NPD GO	PPK6_PSEBJ	Pyrokinin-6 (FXPRL-amide)	0.00	-		0	Secreted protein				14
P84366 UniProt NPD GO	PPK6_PSEFV	Pyrokinin-6 (FXPRL-amide)	0.00	-		0	Secreted protein				14
P84359 UniProt NPD GO	PPK6_PERBR	Pyrokinin-6 (Peb-PK-6) (FXPRL-amide)	0.00	-		0	Secreted protein				14
P84368 UniProt NPD GO	PPK6_PERAU	Pyrokinin-6 (Perau-PK-6) (FXPRL-amide)	0.00	-		0	Secreted protein				14
P34734 UniProt NPD GO	PDC_HANUV	Pyruvate decarboxylase (EC 4.1.1.1)	0.00	-	cyt	0					564
P83779 UniProt NPD GO	PDC1_CANAL	Pyruvate decarboxylase (EC 4.1.1.1) (Fragments)	0.00	-	cyt	0	Cytoplasm				58
Q05326 UniProt NPD GO	PDC2_MAIZE	Pyruvate decarboxylase isozyme 2 (EC 4.1.1.1) (PDC) (Fragment)	0.00	-	cyt	0					106
P49823 UniProt NPD GO	ODPA_CANFA	Pyruvate dehydrogenase E1 component alpha subunit, somatic form (EC 1.2.4.1) (PDHE1-A type I) (Fragm ...	0.00	-		0	Mitochondrion; mitochondrial matrix				13
P51267 UniProt NPD GO	ODPA_PORPU	Pyruvate dehydrogenase E1 component subunit alpha (EC 1.2.4.1)	0.00	-	cyt	0	Plastid; chloroplast				344
P81419 UniProt NPD GO	ODPB_SOLTU	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial (EC 1.2.4.1) (PDHE1-B) (Fragment)	0.00	-		0	Mitochondrion; mitochondrial matrix				16
O44451 UniProt NPD GO	ODPB_CAEEL	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial precursor (EC 1.2.4.1)	0.00	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				352
P26269 UniProt NPD GO	ODPB_ASCSU	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial precursor (EC 1.2.4.1) (PDHE1-B)	0.00	-	mit	0	Mitochondrion; mitochondrial matrix				361
P49432 UniProt NPD GO	ODPB_RAT	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial precursor (EC 1.2.4.1) (PDHE1-B)	0.00	-	cyt	0	Mitochondrion; mitochondrial matrix				359
Q6FV12 UniProt NPD GO	KPYK2_CANGA	Pyruvate kinase 2 (EC 2.7.1.40) (PK 2)	0.00	-	cyt	0					508
P59049 UniProt NPD GO	OMT1_CHRAE	Quercetin 3-O-methyltransferase 1 (EC 2.1.1.76) (Flavonol 3-O-methyltransferase 1)	0.00	-	mit	0					343
Q6ZD89 UniProt NPD GO	OMT1_ORYSA	Quercetin 3-O-methyltransferase 1 (EC 2.1.1.76) (Flavonol 3-O-methyltransferase 1)	0.00	-	mit	0					368
Q42653 UniProt NPD GO	OMT2_CHRAE	Quercetin 3-O-methyltransferase 2 (EC 2.1.1.76) (Flavonol 3-O-methyltransferase 2)	0.00	-	mit	0					343
P11415 UniProt NPD GO	QOR_CAVPO	Quinone oxidoreductase (EC 1.6.5.5) (NADPH:quinone reductase) (Zeta-crystallin)	0.00	-	cyt	0	Cytoplasm				329
Q08257 UniProt NPD GO	QOR_HUMAN	Quinone oxidoreductase (EC 1.6.5.5) (NADPH:quinone reductase) (Zeta-crystallin)	0.00	-	cyt	0	Cytoplasm		123691	1YB5	329
Q28452 UniProt NPD GO	QOR_LAMGU	Quinone oxidoreductase (EC 1.6.5.5) (NADPH:quinone reductase) (Zeta-crystallin)	0.00	-	cyt	0	Cytoplasm				330
P47199 UniProt NPD GO	QOR_MOUSE	Quinone oxidoreductase (EC 1.6.5.5) (NADPH:quinone reductase) (Zeta-crystallin)	0.00	-	cyt	0	Cytoplasm				331
Q5R4S7 UniProt NPD GO	QOR_PONPY	Quinone oxidoreductase (EC 1.6.5.5) (NADPH:quinone reductase) (Zeta-crystallin)	0.00	-	cyt	0	Cytoplasm (By similarity)				329
Q6AYT0 UniProt NPD GO	QOR_RAT	Quinone oxidoreductase (EC 1.6.5.5) (NADPH:quinone reductase) (Zeta-crystallin)	0.00	-	cyt	0	Cytoplasm (By similarity)				329
P31021 UniProt NPD GO	RHO1_ENTHI	RAS-like GTP-binding protein RHO1	0.00	-	cyt	0					208
O76321 UniProt NPD GO	RECG_ENTHI	RAS-related protein racG	0.00	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				199
Q28481 UniProt NPD GO	RHL_MACFA	RH-like protein (Rhesus-like protein)	0.00	-	end	10 *	Membrane; multi-pass membrane protein				416

You are viewing entries 97501 to 97550 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.