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
P80978 UniProt NPD GO	CX6C2_THUOB	Cytochrome c oxidase polypeptide VIc-2 (EC 1.9.3.1) (Fragments)	0.00	-		0	Mitochondrion; mitochondrial inner membrane				15
P99501 UniProt NPD GO	COX5A_CANFA	Cytochrome c oxidase polypeptide Va (EC 1.9.3.1) (Fragment)	0.00	-		0	Mitochondrion; mitochondrial inner membrane				11
P80328 UniProt NPD GO	COX5A_ONCMY	Cytochrome c oxidase polypeptide Va, mitochondrial (EC 1.9.3.1) (Fragment)	0.00	-		0	Mitochondrion; mitochondrial inner membrane				10
P83012 UniProt NPD GO	COX5A_SCYCA	Cytochrome c oxidase polypeptide Va, mitochondrial (EC 1.9.3.1) (Fragment)	0.00	-		0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			15
P80499 UniProt NPD GO	COX5B_SOLTU	Cytochrome c oxidase polypeptide Vb (EC 1.9.3.1) (Fragment)	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane				28
P80330 UniProt NPD GO	CX5B2_ONCMY	Cytochrome c oxidase polypeptide Vb-liver (EC 1.9.3.1) (Fragment)	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane				33
P80500 UniProt NPD GO	COX5C_SOLTU	Cytochrome c oxidase polypeptide Vc (EC 1.9.3.1) (Cytochrome c oxidase subunit 5c) (Fragment)	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane				30
Q85QA3 UniProt NPD GO	COX1_CANGA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.00	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				534
P20386 UniProt NPD GO	COX1_KLULA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.00	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				534
P98001 UniProt NPD GO	COX1_SACDO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.00	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				534
Q4UJ69 UniProt NPD GO	COX1_THEAN	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.00	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				480
Q36097 UniProt NPD GO	COX1_THEPA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.00	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				481
P00401 UniProt NPD GO	COX1_YEAST	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.00	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	respiratory chain complex IV (sensu Eukaryota) [IPI]			534
P29643 UniProt NPD GO	COX1_AMICA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				188
P50656 UniProt NPD GO	COX1_ANAPL	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				102
Q33375 UniProt NPD GO	COX1_CANSI	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				196
Q36347 UniProt NPD GO	COX1_CAPHI	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				58
Q33439 UniProt NPD GO	COX1_EPHEQ	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				172
P29645 UniProt NPD GO	COX1_GEOSD	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				152
P29646 UniProt NPD GO	COX1_GOMVA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				155
P29647 UniProt NPD GO	COX1_LEPOC	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				163
P29644 UniProt NPD GO	COX1_LEPSP	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				157
P29648 UniProt NPD GO	COX1_MEGAT	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				160
P29649 UniProt NPD GO	COX1_PANBU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				184
P29650 UniProt NPD GO	COX1_POLSP	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				158
P29651 UniProt NPD GO	COX1_POLSX	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				184
P29652 UniProt NPD GO	COX1_POMNI	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				161
P29653 UniProt NPD GO	COX1_SALTR	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				109
P29654 UniProt NPD GO	COX1_SCAPL	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.00	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				157
P98019 UniProt NPD GO	COX2_ANAPL	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
P93285 UniProt NPD GO	COX2_ARATH	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				260
P43372 UniProt NPD GO	COX2_BRENA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				248
P50666 UniProt NPD GO	COX2_CAIMO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
P43373 UniProt NPD GO	COX2_CANGA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				251
P18944 UniProt NPD GO	COX2_CHICK	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P48869 UniProt NPD GO	COX2_CHOCR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				254
P48870 UniProt NPD GO	COX2_CYACA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				255
P43374 UniProt NPD GO	COX2_DEKBR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				245
Q85TA0 UniProt NPD GO	COX2_DROAI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P84201 UniProt NPD GO	COX2_DROAL	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P29856 UniProt NPD GO	COX2_DROAM	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P84202 UniProt NPD GO	COX2_DROAT	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P84287 UniProt NPD GO	COX2_DROAZ	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P29860 UniProt NPD GO	COX2_DROLO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P00408 UniProt NPD GO	COX2_DROME	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
P67797 UniProt NPD GO	COX2_DROMI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P67795 UniProt NPD GO	COX2_DRONR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P67798 UniProt NPD GO	COX2_DROPE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P67799 UniProt NPD GO	COX2_DROPS	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P50253 UniProt NPD GO	COX2_DROSI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.00	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228

You are viewing entries 94051 to 94100 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.