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
Q8LX30 UniProt NPD GO	COX1_LEMCA	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 (By similarity)				513
Q36421 UniProt NPD GO	COX1_LOCMI	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
Q9TA27 UniProt NPD GO	COX1_LOXAF	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
Q34941 UniProt NPD GO	COX1_LUMTE	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
P92661 UniProt NPD GO	COX1_MACRO	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
P08742 UniProt NPD GO	COX1_MAIZE	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				528
Q38PS0 UniProt NPD GO	COX1_MAMPR	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
P00397 UniProt NPD GO	COX1_MOUSE	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
P48170 UniProt NPD GO	COX1_ONCMY	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
Q36452 UniProt NPD GO	COX1_ORNAN	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
Q6EGI3 UniProt NPD GO	COX1_ORTHI	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
P14578 UniProt NPD GO	COX1_ORYSA	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
Q6EGI0 UniProt NPD GO	COX1_PAPBU	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
P12700 UniProt NPD GO	COX1_PARLI	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				517
Q00527 UniProt NPD GO	COX1_PHOVI	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
O79876 UniProt NPD GO	COX1_PIG	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
Q95911 UniProt NPD GO	COX1_POLOR	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				518
O79429 UniProt NPD GO	COX1_RABIT	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
P60621 UniProt NPD GO	COX1_RAPSA	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				527
P05503 UniProt NPD GO	COX1_RAT	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
Q96062 UniProt NPD GO	COX1_RHIUN	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
Q9ZZM6 UniProt NPD GO	COX1_SALSA	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
O79403 UniProt NPD GO	COX1_SCYCA	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				517
O78749 UniProt NPD GO	COX1_SHEEP	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
P05502 UniProt NPD GO	COX1_SORBI	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				530
P15544 UniProt NPD GO	COX1_STRPU	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				517
Q4JQI5 UniProt NPD GO	COX1_TETNG	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
P00398 UniProt NPD GO	COX1_XENLA	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				519
Q9B6E7 UniProt NPD GO	COX1_YARLI	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				535
Q6EGH7 UniProt NPD GO	COX1_ZYGTR	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
Q09333 UniProt NPD GO	COX1_ALBTU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.02	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				195
Q34345 UniProt NPD GO	COX1_DROMA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				499
Q34391 UniProt NPD GO	COX1_DROSE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				499
Q34388 UniProt NPD GO	COX1_DROSI	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragments)	0.02	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				511
P34840 UniProt NPD GO	COX2_ANOGA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
Q37411 UniProt NPD GO	COX2_ASTPE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P24986 UniProt NPD GO	COX2_BALPH	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47428 UniProt NPD GO	COX2_BRAFL	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
O79417 UniProt NPD GO	COX2_BRALA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				239
P43370 UniProt NPD GO	COX2_BRECS	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				247
O78682 UniProt NPD GO	COX2_CARAU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
P24987 UniProt NPD GO	COX2_CYPCA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
P29859 UniProt NPD GO	COX2_DROBF	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P13588 UniProt NPD GO	COX2_EMENI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				252
Q37741 UniProt NPD GO	COX2_GADMO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
P00411 UniProt NPD GO	COX2_NEUCR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				250
P48171 UniProt NPD GO	COX2_ONCMY	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
P12701 UniProt NPD GO	COX2_PARLI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P29877 UniProt NPD GO	COX2_PERAM	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
Q02212 UniProt NPD GO	COX2_PHYME	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.02	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				266

You are viewing entries 83201 to 83250 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.