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
P07635 UniProt NPD GO	INV7_YEAST	Invertase 7 precursor (EC 3.2.1.26) (Beta-fructofuranosidase 7) (Saccharase) (Fragments)	0.00	-	cyt	0					96
P50218 UniProt NPD GO	IDHC_TOBAC	Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) (Oxalosuccinate decarboxylase) (IDH) (NADP(+)-specific ...	0.00	-	cyt	0	Cytoplasm (By similarity)				415
P83726 UniProt NPD GO	IDHC_NAEFO	Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) (Oxalosuccinate decarboxylase) (IDH) (NADP(+)-specific ...	0.00	-		0	Cytoplasm (By similarity)				20
O75874 UniProt NPD GO	IDHC_HUMAN	Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) (Cytosolic NADP-isocitrate dehydrogenase) ...	0.00	-	pox	0	Cytoplasm. Peroxisome	cytosol [TAS]	147700	1T0L	414
Q5R9C5 UniProt NPD GO	IDHC_PONPY	Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) (Cytosolic NADP-isocitrate dehydrogenase) ...	0.00	-	pox	0	Cytoplasm (By similarity)				414
P20304 UniProt NPD GO	IDHC_PIG	Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) (Cytosolic NADP-isocitrate dehydrogenase) ...	0.00	-		0					13
Q40345 UniProt NPD GO	IDHP_MEDSA	Isocitrate dehydrogenase [NADP], chloroplast precursor (EC 1.1.1.42) (Oxalosuccinate decarboxylase) ...	0.00	-	cyt	0	Plastid; chloroplast (Potential)				433
P56471 UniProt NPD GO	IDH3A_PIG	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) (Isocitric dehydrogenase) ...	0.00	-	cyt	0	Mitochondrion	mitochondrion [IDA]			90
P56472 UniProt NPD GO	IDH3B_PIG	Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial (EC 1.1.1.41) (Isocitric dehydrogenase) ( ...	0.00	-	cyt	0	Mitochondrion				103
Q00016 UniProt NPD GO	IFR_CICAR	Isoflavone reductase (EC 1.3.1.45) (IFR) (2'-hydroxyisoflavone reductase) (NADPH:isoflavone oxidored ...	0.00	-	mit	0					318
P52575 UniProt NPD GO	IFR_MEDSA	Isoflavone reductase (EC 1.3.1.45) (IFR) (2'-hydroxyisoflavone reductase) (NADPH:isoflavone oxidored ...	0.00	-	cyt	0				2GAS	318
P52576 UniProt NPD GO	IFR_PEA	Isoflavone reductase (EC 1.3.1.45) (IFR) (2'-hydroxyisoflavone reductase) (NADPH:isoflavone oxidored ...	0.00	-	cyt	0					318
P52581 UniProt NPD GO	IFRH_LUPAL	Isoflavone reductase homolog (EC 1.3.1.-)	0.00	-	cyt	0					312
P52578 UniProt NPD GO	IFRH_SOLTU	Isoflavone reductase homolog (EC 1.3.1.-) (CP100)	0.00	-	cyt	0	Cytoplasm (By similarity)				308
P52580 UniProt NPD GO	IFRH_MAIZE	Isoflavone reductase homolog IRL (EC 1.3.1.-)	0.00	-	cyt	0	Cytoplasm				309
P42993 UniProt NPD GO	ISOT_CYPCA	Isotocin	0.00	-		0	Secreted protein				9
P83305 UniProt NPD GO	JAP1_RANJA	Japonicin-1	0.00	-		0	Secreted protein				14
P84759 UniProt NPD GO	JELL3_APIME	Jellein-3 (Jelleine-III)	0.00	-		0	Secreted protein	extracellular region [IDA]			9
P56675 UniProt NPD GO	JHBP_PLAVG	Juvenile hormone-binding protein (Fragment)	0.00	-		0	Secreted protein				17
P58456 UniProt NPD GO	KAB5_OLDAF	Kalata-B5	0.00	-	nuc	0					30
P15946 UniProt NPD GO	K1B11_MOUSE	Kallikrein 1-related peptidase b11 precursor (EC 3.4.21.35) (Tissue kallikrein-11) (Glandular kallik ...	0.00	-	exc	0					261
P04071 UniProt NPD GO	K1B16_MOUSE	Kallikrein 1-related peptidase b16 precursor (EC 3.4.21.54) (Gamma-renin, submandibular gland) (mGK- ...	0.00	-	end	0					261
P00756 UniProt NPD GO	K1KB3_MOUSE	Kallikrein 1-related peptidase b3 precursor (EC 3.4.21.35) (Glandular kallikrein K3) (Tissue kallikr ...	0.00	-	exc	0				1SGF	261
P15945 UniProt NPD GO	K1KB5_MOUSE	Kallikrein 1-related peptidase b5 precursor (EC 3.4.21.35) (Glandular kallikrein K5) (Tissue kallikr ...	0.00	-	end	0					261
P07628 UniProt NPD GO	K1KB8_MOUSE	Kallikrein 1-related peptidase b8 precursor (EC 3.4.21.35) (Tissue kallikrein-8) (Glandular kallikre ...	0.00	-	exc	0					261
P22442 UniProt NPD GO	KARA_BROPL	Karatasin (EC 3.4.22.-) (Fragment)	0.00	-		0					14
P08611 UniProt NPD GO	TKN_KASSE	Kassinin	0.00	-		0	Secreted protein			1MYU	12
P42988 UniProt NPD GO	TKN3_PSEGU	Kassinin-like peptide K-III (PG-KIII)	0.00	-		0	Secreted protein				11
Q9ER30 UniProt NPD GO	KBTBA_RAT	Kelch repeat and BTB domain-containing protein 10 (Kelch-related protein 1) (Kel-like protein 23) (S ...	0.00	-	pox	0	Cytoplasm. Predominantly cytoplasmic but can co-localize with F-actin at the membrane ruffle-like st ...	cytoplasm [IDA] pseudopodium [IDA]			606
P61109 UniProt NPD GO	ANRE_HUMAN	Kidney androgen-regulated protein precursor (KAP) (ARP)	0.00	-	exc	0	Secreted protein (Potential)				121
P61110 UniProt NPD GO	ANRE_MOUSE	Kidney androgen-regulated protein precursor (KAP) (ARP)	0.00	-	exc	0	Secreted protein (Potential)	extracellular space [NAS]			121
P56536 UniProt NPD GO	KIF5C_RAT	Kinesin heavy chain isoform 5C (Kinesin heavy chain neuron-specific 2) (Fragment)	0.00	-	cyt	0				3KIN	238
P82686 UniProt NPD GO	KINI2_PERAM	Kinin-2 (Pea-K-2)	0.00	-		0	Secreted protein				8
P82687 UniProt NPD GO	KINI3_PERAM	Kinin-3 (Pea-K-3)	0.00	-		0	Secreted protein				8
P82688 UniProt NPD GO	KINI4_PERAM	Kinin-4 (Pea-K-4)	0.00	-		0	Secreted protein				8
P83051 UniProt NPD GO	BBCI_BAUBA	Kunitz-type proteinase inhibitor BbCI	0.00	-	cyt	0	Secreted protein				164
P83052 UniProt NPD GO	BBKI_BAUBA	Kunitz-type serine protease inhibitor BbKI	0.00	-	cyt	0	Secreted protein				164
P83604 UniProt NPD GO	BMTI3_BOOMI	Kunitz-type serine protease inhibitor BmTI-3 (Fragment)	0.00	-	cyt	0	Secreted protein				27
P83607 UniProt NPD GO	BMTID_BOOMI	Kunitz-type serine protease inhibitor BmTI-D (Fragment)	0.00	-		0	Secreted protein				17
P84554 UniProt NPD GO	TIQ2_RHISA	Kunitz-type serine protease inhibitor RsTIQ2 (Fragment)	0.00	-	cyt	0					31
P84882 UniProt NPD GO	ITRY1_BAURF	Kunitz-type trypsin inhibitor BrTI	0.00	-	cyt	0					164
P25273 UniProt NPD GO	KTI2_SOYBN	Kunitz-type trypsin inhibitor KTI2 precursor	0.00	-	cyt	1 *					204
O08615 UniProt NPD GO	OXLA_MUSSP	L-amino-acid oxidase (EC 1.4.3.2) (LAAO) (Interleukin-4-induced protein 1) (IL4-induced protein 1) ( ...	0.00	-	nuc	0	Lysosome (By similarity)				46
P81383 UniProt NPD GO	OXLA_OPHHA	L-amino-acid oxidase (EC 1.4.3.2) (LAO) (LAAO) (Fragment)	0.00	-		0	Secreted protein				19
P81375 UniProt NPD GO	OXLA_VIPLE	L-amino-acid oxidase (EC 1.4.3.2) (LAO) (LAAO) (Fragment)	0.00	-	cyt	0	Secreted protein				27
P81530 UniProt NPD GO	MIFH_TRIMR	L-dopachrome-methyl ester tautomerase (EC 5.3.3.12) (Macrophage migration inhibitory factor homolog) ...	0.00	-		0					19
P81529 UniProt NPD GO	MIFH_TRISP	L-dopachrome-methyl ester tautomerase (EC 5.3.3.12) (Macrophage migration inhibitory factor homolog) ...	0.00	-		0					19
P81748 UniProt NPD GO	MIFH_TRITR	L-dopachrome-methyl ester tautomerase (EC 5.3.3.12) (Macrophage migration inhibitory factor homolog) ...	0.00	-	cyt	0					32
Q9PW06 UniProt NPD GO	LDHA_ALLMI	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.00	-	cyt	0	Cytoplasm (By similarity)				331
Q98SL0 UniProt NPD GO	LDHA_PELSJ	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.00	-	mit	0	Cytoplasm (By similarity)				331

You are viewing entries 95351 to 95400 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.