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
Q70Y23 UniProt NPD GO	NU1M_TOLMA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.03	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
P50658 UniProt NPD GO	NU1M_ANAPL	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragment)	0.03	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				117
P48902 UniProt NPD GO	NU2M_ALBCO	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.03	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				307
O47495 UniProt NPD GO	NU2M_METSE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.03	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				385
O21554 UniProt NPD GO	NU3M_CALCL	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					115
O78686 UniProt NPD GO	NU3M_CARAU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					116
P41306 UniProt NPD GO	NU3M_DIDMA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					116
P51940 UniProt NPD GO	NU3M_DROSU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					117
P92482 UniProt NPD GO	NU3M_EQUAS	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					115
P48654 UniProt NPD GO	NU3M_HORSE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					115
Q36422 UniProt NPD GO	NU3M_LOCMI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					115
Q38PR5 UniProt NPD GO	NU3M_MAMPR	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					115
Q37108 UniProt NPD GO	NU3M_ONCMA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					116
P20688 UniProt NPD GO	NU3M_ONCNE	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					116
Q9T9V8 UniProt NPD GO	NU3M_PANTR	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					115
O21513 UniProt NPD GO	NU3M_PHOSU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					115
Q95915 UniProt NPD GO	NU3M_POLOR	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					115
P92697 UniProt NPD GO	NU3M_PONPA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					115
O21569 UniProt NPD GO	NU3M_REIAU	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					115
O03252 UniProt NPD GO	NU3M_SALTR	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					116
O79408 UniProt NPD GO	NU3M_SCYCA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					116
O78753 UniProt NPD GO	NU3M_SHEEP	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					115
Q9ZZ47 UniProt NPD GO	NU3M_SQUAC	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					116
Q4JQI0 UniProt NPD GO	NU3M_TETNG	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.03	-	end	3 *					117
P19043 UniProt NPD GO	NU3M_ARTSA	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3) (Fragments)	0.03	-	mit	1 *					70
P33511 UniProt NPD GO	NU4M_ANOQU	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.03	-	end	13 *					448
P34941 UniProt NPD GO	NU4M_ARBLI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.03	-	end	12 *					457
P34194 UniProt NPD GO	NU4M_CROLA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.03	-	end	12 *					460
P55781 UniProt NPD GO	NU4M_GADMO	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.03	-	end	13 *					460
Q9B6D6 UniProt NPD GO	NU4M_YARLI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.03	-	end	12 *					486
P50660 UniProt NPD GO	NU4M_SIMVI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.03	-	mit	2 *					79
P69238 UniProt NPD GO	NU4LM_BRAFL	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.03	-	end	2 *					91
P69239 UniProt NPD GO	NU4LM_BRALA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.03	-	end	2 *					91
Q9MIY2 UniProt NPD GO	NU4LM_BRARE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.03	-	end	3 *					98
Q34049 UniProt NPD GO	NU4LM_CERCA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.03	-	end	3 *					96
P48930 UniProt NPD GO	NU4LM_CHOCR	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.03	-	end	3 *					101
P23633 UniProt NPD GO	NU4LM_GADMO	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.03	-	exc	3 *					98
P55782 UniProt NPD GO	NU5M_GADMO	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.03	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				612
Q34947 UniProt NPD GO	NU5M_LUMTE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.03	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				574
Q00232 UniProt NPD GO	NU5M_MYTED	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.03	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				568
P20679 UniProt NPD GO	NU5M_PODAN	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.03	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				652
P51899 UniProt NPD GO	NU5M_ANOAR	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.03	-	end	11 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				384
P24999 UniProt NPD GO	NU5M_PISOC	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.03	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				30
P24885 UniProt NPD GO	NU6M_CAEEL	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.03	-	end	5 *					144
Q9TA18 UniProt NPD GO	NU6M_LOXAF	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.03	-	end	5 *					175
Q38PR1 UniProt NPD GO	NU6M_MAMPR	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.03	-	end	5 *					175
P15959 UniProt NPD GO	NU6M_PODAN	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.03	-	end	5 *					221
Q36836 UniProt NPD GO	NU6M_TRIRU	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.03	-	end	5 *					203
P22237 UniProt NPD GO	NUGM_DICDI	NADH-ubiquinone oxidoreductase subunit 9 (EC 1.6.5.3) (EC 1.6.99.3)	0.03	-	cyt	0	Mitochondrion; mitochondrial inner membrane				209
P28227 UniProt NPD GO	MAOX_ANAPL	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME)	0.03	-	mit	0	Cytoplasm				557

You are viewing entries 80701 to 80750 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.