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
Q8TF08 UniProt NPD GO	CX7B2_HUMAN	Cytochrome c oxidase polypeptide VIIb2, mitochondrial precursor (EC 1.9.3.1)	0.02	-	mit	0			609811		80
P80334 UniProt NPD GO	COX7C_ONCMY	Cytochrome c oxidase polypeptide VIIc (EC 1.9.3.1) (Fragment)	0.02	-	nuc	0	Mitochondrion; mitochondrial inner membrane				25
P80982 UniProt NPD GO	COX7C_THUOB	Cytochrome c oxidase polypeptide VIIc (EC 1.9.3.1) (Fragment)	0.02	-		0	Mitochondrion; mitochondrial inner membrane				10
P61638 UniProt NPD GO	COX7C_GORGO	Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor (EC 1.9.3.1)	0.02	-	mit	0					63
P15954 UniProt NPD GO	COX7C_HUMAN	Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor (EC 1.9.3.1)	0.02	-	mit	0			603774		63
Q8SPI1 UniProt NPD GO	COX7C_MACFA	Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor (EC 1.9.3.1)	0.02	-	mit	1 *					63
P61639 UniProt NPD GO	COX7C_PANPA	Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor (EC 1.9.3.1)	0.02	-	mit	0					63
P60025 UniProt NPD GO	COX7C_PANTR	Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor (EC 1.9.3.1)	0.02	-	mit	0					63
Q8SQ80 UniProt NPD GO	COX7C_PAPHA	Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor (EC 1.9.3.1)	0.02	-	mit	1 *					63
Q8SQ81 UniProt NPD GO	COX7C_PONPY	Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor (EC 1.9.3.1)	0.02	-	mit	0					63
P61900 UniProt NPD GO	CX6A2_CANFA	Cytochrome c oxidase polypeptide VIa-heart (EC 1.9.3.1) (Fragment)	0.02	-		0	Mitochondrion; mitochondrial inner membrane				20
P61901 UniProt NPD GO	CX6A2_SHEEP	Cytochrome c oxidase polypeptide VIa-heart (EC 1.9.3.1) (Fragment)	0.02	-		0	Mitochondrion; mitochondrial inner membrane				19
P61902 UniProt NPD GO	CX6A1_CANFA	Cytochrome c oxidase polypeptide VIa-liver (EC 1.9.3.1) (Fragment)	0.02	-		0	Mitochondrion; mitochondrial inner membrane				20
P61903 UniProt NPD GO	CX6A1_SHEEP	Cytochrome c oxidase polypeptide VIa-liver (EC 1.9.3.1) (Fragment)	0.02	-		0	Mitochondrion; mitochondrial inner membrane				20
P13182 UniProt NPD GO	CX6A1_BOVIN	Cytochrome c oxidase polypeptide VIa-liver (EC 1.9.3.1) (SSG)	0.02	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane				85
Q9TTT7 UniProt NPD GO	CX6A1_RABIT	Cytochrome c oxidase polypeptide VIa-liver, mitochondrial precursor (EC 1.9.3.1)	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane				109
P10818 UniProt NPD GO	CX6A1_RAT	Cytochrome c oxidase polypeptide VIa-liver, mitochondrial precursor (EC 1.9.3.1)	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane				111
P00426 UniProt NPD GO	COX5A_BOVIN	Cytochrome c oxidase polypeptide Va, mitochondrial precursor (EC 1.9.3.1)	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane			2OCC	152
P80972 UniProt NPD GO	COX5A_THUOB	Cytochrome c oxidase polypeptide Va-1 (EC 1.9.3.1) (Fragment)	0.02	-		0	Mitochondrion; mitochondrial inner membrane				20
P48887 UniProt NPD GO	COX1_ALBCO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				509
P80440 UniProt NPD GO	COX1_ALLMA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				536
P34838 UniProt NPD GO	COX1_ANOGA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	11 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514
P33504 UniProt NPD GO	COX1_ANOQU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	11 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514
P60620 UniProt NPD GO	COX1_ARATH	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				527
P41293 UniProt NPD GO	COX1_BALMU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
P24983 UniProt NPD GO	COX1_BALPH	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
P24794 UniProt NPD GO	COX1_BETVU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				524
P00396 UniProt NPD GO	COX1_BOVIN	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein			2OCC	514
Q9MIY8 UniProt NPD GO	COX1_BRARE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
Q9ZZ64 UniProt NPD GO	COX1_CANFA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514
O78681 UniProt NPD GO	COX1_CARAU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
O03198 UniProt NPD GO	COX1_CERSI	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514
P48866 UniProt NPD GO	COX1_CHOCR	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				532
P48867 UniProt NPD GO	COX1_CYACA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				526
P24985 UniProt NPD GO	COX1_CYPCA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
O21327 UniProt NPD GO	COX1_DASNO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				513
P41310 UniProt NPD GO	COX1_DIDMA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				513
P00399 UniProt NPD GO	COX1_DROME	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				512
P00400 UniProt NPD GO	COX1_DROYA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				512
Q8W9N4 UniProt NPD GO	COX1_DUGDU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				513
Q2I3H2 UniProt NPD GO	COX1_ELEMA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				515
P92477 UniProt NPD GO	COX1_EQUAS	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514
P48888 UniProt NPD GO	COX1_FELCA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514
Q36775 UniProt NPD GO	COX1_GADMO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
Q6EGH9 UniProt NPD GO	COX1_GEOBE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
Q6EGH8 UniProt NPD GO	COX1_GEOTE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
P38595 UniProt NPD GO	COX1_HALGR	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514
Q9ZZY9 UniProt NPD GO	COX1_HIPAM	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				515
P48659 UniProt NPD GO	COX1_HORSE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514
O03167 UniProt NPD GO	COX1_LATCH	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				515

You are viewing entries 83151 to 83200 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.