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
O59852 UniProt NPD GO	INV1_SCHPO	Invertase precursor (EC 3.2.1.26) (Beta-fructofuranosidase) (Saccharase)	0.01	-	exc	0		vacuole [IDA]			581
Q6CRQ9 UniProt NPD GO	ISU1_KLULA	Iron sulfur cluster assembly protein 1, mitochondrial precursor (Iron sulfur cluster scaffold protei ...	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				180
Q09920 UniProt NPD GO	FIO1_SCHPO	Iron transport multicopper oxidase fio1 precursor (EC 1.-.-.-)	0.01	-	end	0	Cell membrane; single-pass type I membrane protein; extracellular side (By similarity)				622
Q28207 UniProt NPD GO	IAPP_BOVIN	Islet amyloid polypeptide (Amylin) (Fragment)	0.01	-	nuc	0	Secreted protein				32
Q28605 UniProt NPD GO	IAPP_SHEEP	Islet amyloid polypeptide (Amylin) (Fragment)	0.01	-	nuc	0	Secreted protein				32
P50217 UniProt NPD GO	IDHC_SOLTU	Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) (Oxalosuccinate decarboxylase) (IDH) (NADP(+)-specific ...	0.01	-	cyt	0	Cytoplasm (By similarity)				416
Q06197 UniProt NPD GO	IDHC_SOYBN	Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) (Oxalosuccinate decarboxylase) (IDH) (NADP(+)-specific ...	0.01	-	cyt	0	Cytoplasm				413
P41939 UniProt NPD GO	IDHC_YEAST	Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) (Oxalosuccinate decarboxylase) (IDH) (NADP ...	0.01	-	cyt	0	Cytoplasm	cytosol [IDA]			412
P56574 UniProt NPD GO	IDHP_RAT	Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42) (Oxalosuccinate decarboxylase) (IDH) (N ...	0.01	-		0	Mitochondrion				13
O94230 UniProt NPD GO	IDH2_KLULA	Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydroge ...	0.01	-	mit	0	Mitochondrion (By similarity)				368
Q9USP8 UniProt NPD GO	IDH2_SCHPO	Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydroge ...	0.01	-	mit	0	Mitochondrion (By similarity)				378
P50213 UniProt NPD GO	IDH3A_HUMAN	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehyd ...	0.01	-	cyt	0	Mitochondrion		601149		366
Q9D6R2 UniProt NPD GO	IDH3A_MOUSE	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehyd ...	0.01	-	cyt	0	Mitochondrion (By similarity)	mitochondrion [IDA]			366
Q5R678 UniProt NPD GO	IDH3A_PONPY	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehyd ...	0.01	-	cyt	0	Mitochondrion (By similarity)				366
Q99NA5 UniProt NPD GO	IDH3A_RAT	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehyd ...	0.01	-	cyt	0	Mitochondrion (By similarity)				366
Q28480 UniProt NPD GO	IDH3A_MACFA	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehyd ...	0.01	-	cyt	0	Mitochondrion				347
P41563 UniProt NPD GO	IDH3A_BOVIN	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehyd ...	0.01	-	cyt	0	Mitochondrion				366
P41566 UniProt NPD GO	IDH3G_PIG	Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial (EC 1.1.1.41) (Isocitric dehydrogenase) ...	0.01	-	cyt	0	Mitochondrion				106
P51553 UniProt NPD GO	IDH3G_HUMAN	Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehyd ...	0.01	-	cyt	0	Mitochondrion		300089		393
P52579 UniProt NPD GO	IFRH_TOBAC	Isoflavone reductase homolog A622 (EC 1.3.1.-)	0.01	-	cyt	0	Cytoplasm (By similarity)				310
P83974 UniProt NPD GO	JZTX1_CHIJI	Jingzhaotoxin-1 precursor (Jingzhaotoxin-I) (JZTX-I)	0.01	-	exc	1 *	Secreted protein				62
P62520 UniProt NPD GO	JZTX3_CHIJI	Jingzhaotoxin-3 precursor (Jingzhaotoxin-III) (JZTX-III)	0.01	-	exc	1 *	Secreted protein				63
P58454 UniProt NPD GO	KAB2_OLDAF	Kalata-B2 precursor	0.01	-	exc	1 *				1PT4	210
P58457 UniProt NPD GO	KAB7_OLDAF	Kalata-B7 precursor	0.01	-	exc	0					111
P00755 UniProt NPD GO	K1KB1_MOUSE	Kallikrein 1-related peptidase b1 precursor (EC 3.4.21.35) (Glandular kallikrein K1) (Tissue kallikr ...	0.01	-	exc	0					261
Q61759 UniProt NPD GO	K1B21_MOUSE	Kallikrein 1-related peptidase b21 precursor (EC 3.4.21.35) (Tissue kallikrein 21) (Glandular kallik ...	0.01	-	end	0		extracellular space [IDA]			261
P20151 UniProt NPD GO	KLK2_HUMAN	Kallikrein-2 precursor (EC 3.4.21.35) (Tissue kallikrein-2) (Glandular kallikrein-1) (hGK-1)	0.01	-	nuc	0			147960		261
P0C010 UniProt NPD GO	KAS1_KASSE	Kassinatuerin-1	0.01	-	cyt	0	Secreted protein				21
P42986 UniProt NPD GO	TKN1_PSEGU	Kassinin-like peptide K-I (PG-KI)	0.01	-		0	Secreted protein				11
P42987 UniProt NPD GO	TKN2_PSEGU	Kassinin-like peptide K-II (PG-KII)	0.01	-		0	Secreted protein				11
O60662 UniProt NPD GO	KBTBA_HUMAN	Kelch repeat and BTB domain-containing protein 10 (Kelch-related protein 1) (Kel-like protein 23) (S ...	0.01	-	pox	0	Cytoplasm. Predominantly cytoplasmic but can co-localize with F-actin at the membrane ruffle-like st ...		607701		606
Q9P2J3 UniProt NPD GO	KLHL9_HUMAN	Kelch-like protein 9	0.01	-	cyt	0					617
Q6ZPT1 UniProt NPD GO	KLHL9_MOUSE	Kelch-like protein 9	0.01	-	cyt	0					617
Q8IUC2 UniProt NPD GO	KRA81_HUMAN	Keratin-associated protein 8-1 (High glycine-tyrosine keratin-associated protein 8.1)	0.01	-	cyt	0					63
P84534 UniProt NPD GO	ILV5_POPEU	Ketol-acid reductoisomerase, chloroplast (EC 1.1.1.86) (Acetohydroxy-acid reductoisomerase) (Alpha-k ...	0.01	-		0	Plastid; chloroplast (By similarity)				14
P80326 UniProt NPD GO	KT395_PICKL	Killer toxin KT395 (Fragment)	0.01	-	cyt	0	Secreted protein				27
P82689 UniProt NPD GO	KINI5_PERAM	Kinin-5 (Pea-K-5)	0.01	-		0	Secreted protein				8
P84555 UniProt NPD GO	TIQ7_RHISA	Kunitz-type serine protease inhibitor RsTIQ7 (Fragment)	0.01	-	cyt	0					29
P84556 UniProt NPD GO	TIS5_RHISA	Kunitz-type serine protease inhibitor RsTIS5 (Fragment)	0.01	-	nuc	0					25
P25272 UniProt NPD GO	KTI1_SOYBN	Kunitz-type trypsin inhibitor KTI1 precursor	0.01	-	cyt	1 *					203
P56742 UniProt NPD GO	OXLA_CROAT	L-amino-acid oxidase (EC 1.4.3.2) (LAO) (LAAO) (Apoxin I) (Fragment)	0.01	-		0	Secreted protein				20
Q40588 UniProt NPD GO	ASO_TOBAC	L-ascorbate oxidase precursor (EC 1.10.3.3) (Ascorbase) (ASO)	0.01	-	end	0					578
P33571 UniProt NPD GO	LDH_PETMA	L-lactate dehydrogenase (EC 1.1.1.27) (LDH)	0.01	-	mit	0	Cytoplasm (By similarity)				333
Q9P4B6 UniProt NPD GO	LDHA_RHIOR	L-lactate dehydrogenase A (EC 1.1.1.27) (L-LDH A)	0.01	-	nuc	1 *	Cytoplasm (By similarity)				320
Q9W7M6 UniProt NPD GO	LDHA_AMBME	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				333
Q9PVK5 UniProt NPD GO	LDHA_BRARE	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				332
Q98SL2 UniProt NPD GO	LDHA_CAICA	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				331
P69080 UniProt NPD GO	LDHA_CHAAC	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
O93541 UniProt NPD GO	LDHA_CHAGU	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm (By similarity)				330
P00340 UniProt NPD GO	LDHA_CHICK	L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A)	0.01	-	cyt	0	Cytoplasm				331

You are viewing entries 89251 to 89300 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.