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
Q9TA21 UniProt NPD GO	NU4LM_LOXAF	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
Q7J3C3 UniProt NPD GO	NU4LM_MACFA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	2 *					98
Q9XK21 UniProt NPD GO	NU4LM_MACHE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	2 *					98
Q9XL48 UniProt NPD GO	NU4LM_MACNR	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	2 *					98
Q38PR4 UniProt NPD GO	NU4LM_MAMPR	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
O47492 UniProt NPD GO	NU4LM_METSE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					99
O21520 UniProt NPD GO	NU4LM_MICPE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	2 *					98
Q00230 UniProt NPD GO	NU4LM_MYTED	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					93
Q36457 UniProt NPD GO	NU4LM_ORNAN	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
O21514 UniProt NPD GO	NU4LM_PHOSU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	2 *					98
Q37598 UniProt NPD GO	NU4LM_PHYIN	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					100
P56632 UniProt NPD GO	NU4LM_PIG	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
Q9B8T5 UniProt NPD GO	NU4LM_PRODD	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
O79435 UniProt NPD GO	NU4LM_RABIT	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
Q96067 UniProt NPD GO	NU4LM_RHIUN	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
O63851 UniProt NPD GO	NU4LM_SARGL	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					97
Q94ZI2 UniProt NPD GO	NU4LM_SCHCO	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					88
P15554 UniProt NPD GO	NU4LM_STRPU	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					97
O21787 UniProt NPD GO	NU4LM_TRALE	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	3 *					98
Q9B6D4 UniProt NPD GO	NU4LM_YARLI	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.00	-	end	2 *					89
Q37131 UniProt NPD GO	NU4LM_ONCMA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L) (Fragment)	0.00	-	exc	3 *					76
Q85T01 UniProt NPD GO	NU5M_CRYNV	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3)	0.00	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				662
O47430 UniProt NPD GO	NU5M_BRAFL	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.00	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				599
O79422 UniProt NPD GO	NU5M_BRALA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.00	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				598
P08739 UniProt NPD GO	NU5M_CHLRE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.00	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				546
Q35099 UniProt NPD GO	NU5M_METSE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.00	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				600
P50367 UniProt NPD GO	NU5M_RHIST	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.00	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				654
P43189 UniProt NPD GO	NU6M_AETCR	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P43191 UniProt NPD GO	NU6M_AETPY	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P48922 UniProt NPD GO	NU6M_ALBCO	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	4 *					155
P43193 UniProt NPD GO	NU6M_ALCTO	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P43192 UniProt NPD GO	NU6M_ALLAL	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P24873 UniProt NPD GO	NU6M_ASCSU	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					144
Q33817 UniProt NPD GO	NU6M_ASTPE	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	4 *					162
P43194 UniProt NPD GO	NU6M_BRABR	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P43195 UniProt NPD GO	NU6M_BRAMA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
Q9MIX9 UniProt NPD GO	NU6M_BRARE	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					172
P43196 UniProt NPD GO	NU6M_CALMA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
Q9ZZ56 UniProt NPD GO	NU6M_CANFA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					175
P48923 UniProt NPD GO	NU6M_CANPA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	4 *					155
O78689 UniProt NPD GO	NU6M_CARAU	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P43197 UniProt NPD GO	NU6M_CEPCO	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P43198 UniProt NPD GO	NU6M_CEPGR	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	6 *					173
P18941 UniProt NPD GO	NU6M_CHICK	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P10329 UniProt NPD GO	NU6M_CHLRE	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	4 *					162
P24981 UniProt NPD GO	NU6M_COTJA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P34196 UniProt NPD GO	NU6M_CROLA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P43199 UniProt NPD GO	NU6M_CYCPS	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P24982 UniProt NPD GO	NU6M_CYPCA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					172
O79557 UniProt NPD GO	NU6M_DINSE	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					166

You are viewing entries 95901 to 95950 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.