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
P41315 UniProt NPD GO	NU6M_DIDMA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					168
Q8W9M5 UniProt NPD GO	NU6M_DUGDU	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
P92486 UniProt NPD GO	NU6M_EQUAS	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
P48926 UniProt NPD GO	NU6M_FELCA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
Q34573 UniProt NPD GO	NU6M_GORGO	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					174
P38603 UniProt NPD GO	NU6M_HALGR	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
Q9ZZY0 UniProt NPD GO	NU6M_HIPAM	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	6 *					175
P48657 UniProt NPD GO	NU6M_HORSE	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
P03923 UniProt NPD GO	NU6M_HUMAN	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	6 *		respiratory chain complex I (sensu Eukaryota) [NAS]	540000		174
Q95710 UniProt NPD GO	NU6M_HYLLA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					174
Q8LX23 UniProt NPD GO	NU6M_LEMCA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					171
O47478 UniProt NPD GO	NU6M_LOLBL	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	4 *					168
P26850 UniProt NPD GO	NU6M_MARPO	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					199
O47498 UniProt NPD GO	NU6M_METSE	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					202
Q00570 UniProt NPD GO	NU6M_MYTED	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	3 *					158
Q36460 UniProt NPD GO	NU6M_ORNAN	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					166
Q9T9W5 UniProt NPD GO	NU6M_PANPA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	6 *					174
Q9T9V6 UniProt NPD GO	NU6M_PANTR	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					174
Q9ZXX5 UniProt NPD GO	NU6M_PAPHA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					174
Q00543 UniProt NPD GO	NU6M_PHOVI	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
O79882 UniProt NPD GO	NU6M_PIG	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
P92700 UniProt NPD GO	NU6M_PONPA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	6 *					174
Q9T9X3 UniProt NPD GO	NU6M_PONPY	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	6 *					174
Q94VK5 UniProt NPD GO	NU6M_RHIMO	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
Q96070 UniProt NPD GO	NU6M_RHIUN	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
O78757 UniProt NPD GO	NU6M_SHEEP	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
Q953I3 UniProt NPD GO	NU6M_SORFM	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					178
Q7Y8D2 UniProt NPD GO	NU6M_UROTA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.01	-	end	5 *					175
Q96VJ7 UniProt NPD GO	DHE4_GIBFU	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.01	-	cyt	0					451
Q8TFF6 UniProt NPD GO	DHE4_SACBA	NADP-specific glutamate dehydrogenase 1 (EC 1.4.1.4) (NADP-GDH 1) (NADP-dependent glutamate dehydrog ...	0.01	-	cyt	0					454
Q03558 UniProt NPD GO	OYE2_YEAST	NADPH dehydrogenase 2 (EC 1.6.99.1) (Old yellow enzyme 2)	0.01	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			399
O94735 UniProt NPD GO	XYL1_PICGU	NADPH-dependent D-xylose reductase (EC 1.1.1.-) (XR)	0.01	-	cyt	0					317
O65041 UniProt NPD GO	UBA3_ARATH	NEDD8-activating enzyme E1 catalytic subunit (EC 6.3.2.-) (RUB-activating enzyme) (Ubiquitin-activat ...	0.01	-	cyt	0	Nucleus (Probable)				454
Q9SDY5 UniProt NPD GO	UBC12_ARATH	NEDD8-conjugating enzyme Ubc12 (EC 6.3.2.-) (RUB1-conjugating enzyme 1) (RUB1-protein ligase 1) (RUB ...	0.01	-	nuc	0					184
Q9NYS0 UniProt NPD GO	KBRS1_HUMAN	NF-kappa-B inhibitor-interacting Ras-like protein 1 (I-kappa-B-interacting Ras-like protein 1) (Kapp ...	0.01	-	cyt	0	Cytoplasm		604496		192
Q9BH04 UniProt NPD GO	KBRS1_MACFA	NF-kappa-B inhibitor-interacting Ras-like protein 1 (I-kappa-B-interacting Ras-like protein 1) (Kapp ...	0.01	-	cyt	0	Cytoplasm (By similarity)				192
O95865 UniProt NPD GO	DDAH2_HUMAN	NG,NG-dimethylarginine dimethylaminohydrolase 2 (EC 3.5.3.18) (Dimethylargininase-2) (Dimethylargini ...	0.01	-	cyt	0			604744		285
P61483 UniProt NPD GO	NCTR3_MACFA	Natural cytotoxicity triggering receptor 3 precursor (Natural killer cell p30-related protein) (NKp3 ...	0.01	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				176
Q9XT74 UniProt NPD GO	NRAM1_CANFA	Natural resistance-associated macrophage protein 1 (NRAMP 1)	0.01	-	end	11	Membrane; multi-pass membrane protein (Probable)	integral to membrane [NAS]			547
P49279 UniProt NPD GO	NRAM1_HUMAN	Natural resistance-associated macrophage protein 1 (NRAMP 1)	0.01	-	end	10	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS] membrane fraction [TAS]	600266		550
Q09148 UniProt NPD GO	COOT_SARBU	Neb-colloostatin (Folliculostatin)	0.01	-		0					19
P61850 UniProt NPD GO	NEMS_SARBU	Neomyosuppressin (Neb-MS) (TDVDHVFLRFamide)	0.01	-		0	Secreted protein				10
P41493 UniProt NPD GO	NSK2_SARBU	Neosulfakinin-2 (Neosulfakinin-II) (Neb-SK-II)	0.01	-		0	Secreted protein				14
P00758 UniProt NPD GO	KLK1_RAT	Nerve growth factor gamma chain precursor (EC 3.4.21.35) (Gamma-NGF) (Tissue kallikrein) (True tissu ...	0.01	-	end	0					261
P59742 UniProt NPD GO	NGB1_ONCMY	Neuroglobin 1	0.01	-	cyt	0					159
P59743 UniProt NPD GO	NGB2_ONCMY	Neuroglobin 2	0.01	-	cyt	0					159
P29135 UniProt NPD GO	TKNB_RANRI	Neurokinin-A	0.01	-		0	Secreted protein				10
P69144 UniProt NPD GO	TKNB_GADMO	Neurokinin-A (Substance K) (Neuromedin-L)	0.01	-		0	Secreted protein				10
P69143 UniProt NPD GO	TKNB_ONCMY	Neurokinin-A (Substance K) (Neuromedin-L)	0.01	-		0	Secreted protein				10
P81872 UniProt NPD GO	NEUU_LITCE	Neuromedin U-23 (NmU-23)	0.01	-	cyt	0	Secreted protein				23

You are viewing entries 89851 to 89900 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.