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
P00036 UniProt NPD GO	CYC_LUCCU	Cytochrome c	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix				107
P00039 UniProt NPD GO	CYC_MANSE	Cytochrome c	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix				107
P00040 UniProt NPD GO	CYC_SCHGR	Cytochrome c	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix				107
P00046 UniProt NPD GO	CYC_SCHPO	Cytochrome c	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix				108
P00054 UniProt NPD GO	CYC_SESIN	Cytochrome c	0.04	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P81459 UniProt NPD GO	CYC_THUAA	Cytochrome c	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix			5CYT	103
P48269 UniProt NPD GO	CCSA_CHLRE	Cytochrome c biogenesis protein ccsA	0.04	-	end	8 *	Plastid; chloroplast				353
P48257 UniProt NPD GO	CCSA_CYAPA	Cytochrome c biogenesis protein ccsA	0.04	-	end	8 *	Plastid; cyanelle				322
P31564 UniProt NPD GO	CCSA_GALSU	Cytochrome c biogenesis protein ccsA	0.04	-	end	8 *	Plastid; chloroplast				306
Q756K8 UniProt NPD GO	CTM1_ASHGO	Cytochrome c lysine N-methyltransferase 1 (EC 2.1.1.59)	0.04	-	cyt	0	Cytoplasm; cytosol (By similarity)				478
Q7TNN2 UniProt NPD GO	COX83_RAT	Cytochrome c oxidase polypeptide 8 isoform 3, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxi ...	0.04	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				72
P06809 UniProt NPD GO	COX4_NEUCR	Cytochrome c oxidase polypeptide IV, mitochondrial precursor (EC 1.9.3.1)	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane				186
Q863G5 UniProt NPD GO	COX82_SAISC	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.04	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				69
Q863G7 UniProt NPD GO	COX82_TRACR	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.04	-	nuc	0	Mitochondrion; mitochondrial inner membrane				69
P17665 UniProt NPD GO	COX7C_MOUSE	Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor (EC 1.9.3.1)	0.04	-	mit	1 *		mitochondrial inner membrane [IDA] mitochondrion [IDA]			63
P41774 UniProt NPD GO	COX1_MYTED	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.04	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				551
O21079 UniProt NPD GO	COX1_MYXGL	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.04	-	end	11 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				517
P03945 UniProt NPD GO	COX1_NEUCR	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.04	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				557
Q6EGI5 UniProt NPD GO	COX1_ORTCH	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.04	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				515
Q6EGI4 UniProt NPD GO	COX1_ORTUN	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.04	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				515
P20681 UniProt NPD GO	COX1_PODAN	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.04	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				541
O99818 UniProt NPD GO	COX1_RHISA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.04	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				512
P98024 UniProt NPD GO	COX2_ALOPA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				231
P33505 UniProt NPD GO	COX2_ANOQU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
O47671 UniProt NPD GO	COX2_CANME	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P34189 UniProt NPD GO	COX2_CROLA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
P50693 UniProt NPD GO	COX2_CULQU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
O79549 UniProt NPD GO	COX2_DINSE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				228
O47672 UniProt NPD GO	COX2_DUSTH	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50688 UniProt NPD GO	COX2_GALSE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q9ZZY8 UniProt NPD GO	COX2_HIPAM	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P00403 UniProt NPD GO	COX2_HUMAN	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein		516040		227
P98036 UniProt NPD GO	COX2_LAGLA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				231
O03848 UniProt NPD GO	COX2_LATCH	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				231
P98035 UniProt NPD GO	COX2_LEMCA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P68297 UniProt NPD GO	COX2_PAPAN	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P68298 UniProt NPD GO	COX2_PAPHA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q37604 UniProt NPD GO	COX2_PETMA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				229
Q96183 UniProt NPD GO	COX2_POLOR	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				230
Q37605 UniProt NPD GO	COX2_PONPY	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47676 UniProt NPD GO	COX2_PSECP	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47677 UniProt NPD GO	COX2_PSEGY	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47678 UniProt NPD GO	COX2_PSESU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q7J6G2 UniProt NPD GO	COX2_PSEVE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P05491 UniProt NPD GO	COX2_SOYBN	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				260
Q37684 UniProt NPD GO	COX2_TUPGL	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q539C6 UniProt NPD GO	COX2_VULCO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47680 UniProt NPD GO	COX2_VULMA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47681 UniProt NPD GO	COX2_VULVU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.04	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P14546 UniProt NPD GO	COX3_LEITA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.04	-	end	9 *					284

You are viewing entries 76751 to 76800 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.