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
Q3V517 UniProt NPD GO	PETL_ACOCL	Cytochrome b6-f complex subunit 6 (Cytochrome b6-f complex subunit VI) (Cytochrome b6-f complex subu ...	0.03	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q5QA80 UniProt NPD GO	PETL_ACOGR	Cytochrome b6-f complex subunit 6 (Cytochrome b6-f complex subunit VI) (Cytochrome b6-f complex subu ...	0.03	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q6IQM2 UniProt NPD GO	CYC_BRARE	Cytochrome c	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				103
P00053 UniProt NPD GO	CYC_CANSA	Cytochrome c	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix				111
P15451 UniProt NPD GO	CYC_CHLRE	Cytochrome c	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix				111
P00069 UniProt NPD GO	CYC_GUIAB	Cytochrome c	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix				111
P00071 UniProt NPD GO	CYC_PASSA	Cytochrome c	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix				111
P00037 UniProt NPD GO	CYC_SAMCY	Cytochrome c	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix				107
P12831 UniProt NPD GO	CYC_SARPE	Cytochrome c	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix				107
O19901 UniProt NPD GO	CCSA_CYACA	Cytochrome c biogenesis protein ccsA	0.03	-	end	8 *	Plastid; chloroplast				293
P12214 UniProt NPD GO	CCSA_MARPO	Cytochrome c biogenesis protein ccsA	0.03	-	end	8 *	Plastid; chloroplast				320
P41650 UniProt NPD GO	CCSA_PINTH	Cytochrome c biogenesis protein ccsA	0.03	-	end	6 *	Plastid; chloroplast				320
P00026 UniProt NPD GO	CYC_CYPCA	Cytochrome c iso-1/iso-2	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix				103
Q12287 UniProt NPD GO	COX17_YEAST	Cytochrome c oxidase copper chaperone	0.03	-	nuc	0	Mitochondrion; mitochondrial intermembrane space	cytosol [IDA] mitochondrial intermembrane space [IDA]		1Z2G	68
Q9P4W1 UniProt NPD GO	COX8_SCHPO	Cytochrome c oxidase polypeptide VIII, mitochondrial precursor (EC 1.9.3.1)	0.03	-	mit	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				66
Q7YRK5 UniProt NPD GO	COX7C_TARSY	Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor (EC 1.9.3.1)	0.03	-	mit	1 *					63
P10817 UniProt NPD GO	CX6A2_RAT	Cytochrome c oxidase polypeptide VIa-heart, mitochondrial precursor (EC 1.9.3.1) (COXVIAH) (Fragment ...	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane				94
P43024 UniProt NPD GO	CX6A1_MOUSE	Cytochrome c oxidase polypeptide VIa-liver, mitochondrial precursor (EC 1.9.3.1)	0.03	-	mit	1 *	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			111
Q37705 UniProt NPD GO	COX1_ARTSF	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.03	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				512
P24881 UniProt NPD GO	COX1_ASCSU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.03	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				525
Q33820 UniProt NPD GO	COX1_ASTPE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.03	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				517
P08681 UniProt NPD GO	COX1_CHLRE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.03	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				505
P34188 UniProt NPD GO	COX1_CROLA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.03	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
P08743 UniProt NPD GO	COX1_OENBE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.03	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				527
P48868 UniProt NPD GO	COX1_PICCA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.03	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				535
Q9ZZ52 UniProt NPD GO	COX1_SQUAC	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.03	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				518
Q36724 UniProt NPD GO	COX1_BLAGE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.03	-	end	11 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [NAS]			508
Q37706 UniProt NPD GO	COX2_ARTSF	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
Q9MIY7 UniProt NPD GO	COX2_BRARE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
P26455 UniProt NPD GO	COX2_CERAE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98020 UniProt NPD GO	COX2_CERGA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50685 UniProt NPD GO	COX2_CRABU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q37472 UniProt NPD GO	COX2_GORBE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P26456 UniProt NPD GO	COX2_GORGO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q96127 UniProt NPD GO	COX2_HYLLA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P25312 UniProt NPD GO	COX2_HYLSY	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P11948 UniProt NPD GO	COX2_MACFA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98038 UniProt NPD GO	COX2_MACMU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98037 UniProt NPD GO	COX2_MANLE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q00227 UniProt NPD GO	COX2_MYTED	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	nuc	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				242
P26457 UniProt NPD GO	COX2_PANPA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50690 UniProt NPD GO	COX2_PANTR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P08748 UniProt NPD GO	COX2_PARPR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				181
P92693 UniProt NPD GO	COX2_PONPA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P92721 UniProt NPD GO	COX2_PONPP	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O79404 UniProt NPD GO	COX2_SCYCA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
Q9ZZ51 UniProt NPD GO	COX2_SQUAC	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
Q4JQI4 UniProt NPD GO	COX2_TETNG	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
P98044 UniProt NPD GO	COX2_THEGE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P00407 UniProt NPD GO	COX2_XENLA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229

You are viewing entries 79651 to 79700 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.