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
O79997 UniProt NPD GO	CYB_SOREX	Cytochrome b (Fragment)	0.00	-	end	8 *					336
O79461 UniProt NPD GO	CYB_SORPC	Cytochrome b (Fragment)	0.00	-	end	8 *					336
Q35942 UniProt NPD GO	CYB_STUTI	Cytochrome b (Fragment)	0.00	-	end	3 *					134
O47414 UniProt NPD GO	CYB_SYLTR	Cytochrome b (Fragment)	0.00	-	end	9 *					372
P00170 UniProt NPD GO	CYB5_HORSE	Cytochrome b5	0.00	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				133
P00167 UniProt NPD GO	CYB5_HUMAN	Cytochrome b5	0.00	-	cyt	1	Isoform 1: Microsome; microsomal membrane; peripheral membrane protein. Bound to the cytoplasmic sid ...		250790		133
P56395 UniProt NPD GO	CYB5_MOUSE	Cytochrome b5	0.00	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...	microsome [TAS] mitochondrion [IDA]			133
P00173 UniProt NPD GO	CYB5_RAT	Cytochrome b5	0.00	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...			2AXX	133
P40312 UniProt NPD GO	CYB5_YEAST	Cytochrome b5	0.00	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...	endoplasmic reticulum membrane [IDA] microsome [IDA]			120
P00168 UniProt NPD GO	CYB5_ALOSE	Cytochrome b5 (Fragment)	0.00	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				87
P49099 UniProt NPD GO	CYB5S_TOBAC	Cytochrome b5, seed isoform	0.00	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				135
Q85FK5 UniProt NPD GO	PSBE_ADICA	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P48268 UniProt NPD GO	PSBE_CHLRE	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q9MUQ1 UniProt NPD GO	PSBF_MESVI	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				41
Q32RX6 UniProt NPD GO	PSBF_STAPU	Cytochrome b559 subunit beta (PSII reaction center subunit VI)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q6YLT4 UniProt NPD GO	PSBF_WELMI	Cytochrome b559 subunit beta (PSII reaction center subunit VI)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				39
Q85FJ3 UniProt NPD GO	CYB6_ADICA	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q70XX8 UniProt NPD GO	CYB6_AMBTC	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q8WHC6 UniProt NPD GO	CYB6_AMPOP	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				219
Q85A24 UniProt NPD GO	CYB6_ANTFO	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P56773 UniProt NPD GO	CYB6_ARATH	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q8S8W0 UniProt NPD GO	CYB6_ATRBE	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q7YJU8 UniProt NPD GO	CYB6_CALFE	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q8M9Z4 UniProt NPD GO	CYB6_CHAGL	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P13347 UniProt NPD GO	CYB6_CHLPR	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q00471 UniProt NPD GO	CYB6_CHLRE	Cytochrome b6	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein			1Q90	215
P56321 UniProt NPD GO	CYB6_CHLVU	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q71KQ6 UniProt NPD GO	CYB6_COLOB	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q9TLZ7 UniProt NPD GO	CYB6_CYACA	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q85G16 UniProt NPD GO	CYB6_CYAME	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P48121 UniProt NPD GO	CYB6_CYAPA	Cytochrome b6	0.00	-	end	4 *	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein (By similarity)				215
P31480 UniProt NPD GO	CYB6_EUGGR	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)	cytochrome b6f complex [IDA]			214
Q6B903 UniProt NPD GO	CYB6_GRATL	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
O78416 UniProt NPD GO	CYB6_GUITH	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P60161 UniProt NPD GO	CYB6_HORVU	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q5SD23 UniProt NPD GO	CYB6_HUPLU	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q71KN3 UniProt NPD GO	CYB6_KLEBI	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q9BBQ6 UniProt NPD GO	CYB6_LOTJA	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P05642 UniProt NPD GO	CYB6_MAIZE	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P06248 UniProt NPD GO	CYB6_MARPO	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q9MUV3 UniProt NPD GO	CYB6_MESVI	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q9TL31 UniProt NPD GO	CYB6_NEPOL	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q6EW22 UniProt NPD GO	CYB6_NYMAL	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P49488 UniProt NPD GO	CYB6_ODOSI	Cytochrome b6	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q9MTJ5 UniProt NPD GO	CYB6_OENHO	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q6ENE4 UniProt NPD GO	CYB6_ORYNI	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
P12123 UniProt NPD GO	CYB6_ORYSA	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q68RX7 UniProt NPD GO	CYB6_PANGI	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q9XQR2 UniProt NPD GO	CYB6_PEA	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215
Q6YXN2 UniProt NPD GO	CYB6_PHYPA	Cytochrome b6	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				215

You are viewing entries 93851 to 93900 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.