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
P00402 UniProt NPD GO	COX1_EMENI	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				567
P26856 UniProt NPD GO	COX1_MARPO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				522
Q35101 UniProt NPD GO	COX1_METSE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				530
P12786 UniProt NPD GO	COX1_PEA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				527
Q02211 UniProt NPD GO	COX1_PHYME	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				492
O99252 UniProt NPD GO	COX1_PLABE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				476
O99255 UniProt NPD GO	COX1_PLACH	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				476
Q02766 UniProt NPD GO	COX1_PLAFA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				476
Q05143 UniProt NPD GO	COX1_PROWI	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514
P07657 UniProt NPD GO	COX1_SCHPO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				537
P07506 UniProt NPD GO	COX1_SOYBN	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				527
Q01555 UniProt NPD GO	COX1_TRIRU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				528
P68539 UniProt NPD GO	COX1_WHEAT	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				524
O03515 UniProt NPD GO	COX1_APTAU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				337
O03521 UniProt NPD GO	COX1_CASBE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				337
P50668 UniProt NPD GO	COX1_CHOBI	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				274
P50669 UniProt NPD GO	COX1_CHOFU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				274
P67793 UniProt NPD GO	COX1_CHOOC	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				274
P67794 UniProt NPD GO	COX1_CHOPI	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				274
P50671 UniProt NPD GO	COX1_CHORO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				274
Q9B229 UniProt NPD GO	COX1_CHRKN	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to membrane [NAS] respiratory chain complex IV (sensu Eukaryota) [NAS]			219
O03524 UniProt NPD GO	COX1_DRONO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				337
Q9ZZ08 UniProt NPD GO	COX1_HAPMA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				219
Q9TGE6 UniProt NPD GO	COX1_LOLFO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				213
Q8WEW4 UniProt NPD GO	COX1_LOLPE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				223
O03539 UniProt NPD GO	COX1_NOTPE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				337
Q9G6J1 UniProt NPD GO	COX1_OCTVU	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				209
Q96000 UniProt NPD GO	COX1_PECMA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				477
Q9TGD8 UniProt NPD GO	COX1_PLADA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				207
O03546 UniProt NPD GO	COX1_RHEAM	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				337
Q8WEW3 UniProt NPD GO	COX1_SEPOF	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				223
Q957T2 UniProt NPD GO	COX1_SEPPH	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				219
O03554 UniProt NPD GO	COX1_TINMA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I) (Fragment)	0.01	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				337
P48889 UniProt NPD GO	COX2_ALBCO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				224
Q09334 UniProt NPD GO	COX2_ALBTU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				224
Q9GCE7 UniProt NPD GO	COX2_BRAHY	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				231
P43369 UniProt NPD GO	COX2_BREAN	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				243
P43375 UniProt NPD GO	COX2_EENNA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				247
Q2I3H1 UniProt NPD GO	COX2_ELEMA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q9TA26 UniProt NPD GO	COX2_LOXAF	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
Q37545 UniProt NPD GO	COX2_LUMTE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
P00412 UniProt NPD GO	COX2_MAIZE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				260
Q38PR9 UniProt NPD GO	COX2_MAMPR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47496 UniProt NPD GO	COX2_METSE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				248
P08744 UniProt NPD GO	COX2_PEA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				258
P20682 UniProt NPD GO	COX2_PODAN	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				250
P98021 UniProt NPD GO	COX2_SIMVI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
O21400 UniProt NPD GO	COX2_STRCA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P15545 UniProt NPD GO	COX2_STRPU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
P29880 UniProt NPD GO	COX2_SYMST	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.01	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229

You are viewing entries 87901 to 87950 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.