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
P54248 UniProt NPD GO	ACHA_CRORS	Acetylcholine receptor protein subunit alpha (Fragment)	0.01	-	cyt	0	Membrane; multi-pass membrane protein (By similarity)				84
P09688 UniProt NPD GO	ACHA_ELEEL	Acetylcholine receptor protein subunit alpha (Fragment)	0.01	-	cyt	0	Membrane; multi-pass membrane protein				24
P09689 UniProt NPD GO	ACHB_ELEEL	Acetylcholine receptor protein subunit beta (Fragment)	0.01	-	nuc	0	Membrane; multi-pass membrane protein				24
P09692 UniProt NPD GO	ACHG_ELEEL	Acetylcholine receptor protein subunit gamma (Fragment)	0.01	-	nuc	0	Membrane; multi-pass membrane protein				23
Q6B8Z0 UniProt NPD GO	ARGB_GRATL	Acetylglutamate kinase (EC 2.7.2.8) (NAG kinase) (AGK) (N-acetyl-L-glutamate 5-phosphotransferase)	0.01	-	end	0	Plastid; chloroplast				285
P69365 UniProt NPD GO	ARGB_PORPU	Acetylglutamate kinase (EC 2.7.2.8) (NAG kinase) (AGK) (N-acetyl-L-glutamate 5-phosphotransferase)	0.01	-	cyt	0	Plastid; chloroplast				283
P69366 UniProt NPD GO	ARGB_PORUM	Acetylglutamate kinase (EC 2.7.2.8) (NAG kinase) (AGK) (N-acetyl-L-glutamate 5-phosphotransferase)	0.01	-	cyt	0	Plastid; chloroplast				283
O14433 UniProt NPD GO	ARGD_KLULA	Acetylornithine aminotransferase, mitochondrial precursor (EC 2.6.1.11) (ACOAT)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				423
Q6C846 UniProt NPD GO	ARGD_YARLI	Acetylornithine aminotransferase, mitochondrial precursor (EC 2.6.1.11) (ACOAT)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				411
P30887 UniProt NPD GO	PHO2_YARLI	Acid phosphatase precursor (EC 3.1.3.2)	0.01	-	exc	0	Secreted protein				358
Q641Z7 UniProt NPD GO	ASM3A_RAT	Acid sphingomyelinase-like phosphodiesterase 3a precursor (EC 3.1.4.-) (ASM-like phosphodiesterase 3 ...	0.01	-	exc	0	Secreted protein (By similarity)				445
Q92485 UniProt NPD GO	ASM3B_HUMAN	Acid sphingomyelinase-like phosphodiesterase 3b precursor (EC 3.1.4.-) (ASM-like phosphodiesterase 3 ...	0.01	-	exc	0	Secreted protein (By similarity)				455
P29032 UniProt NPD GO	CHIC_POPTR	Acidic endochitinase WIN6.2C precursor (EC 3.2.1.14) (Fragment)	0.01	-	exc	0					121
O04916 UniProt NPD GO	ACOC_SOLTU	Aconitate hydratase, cytoplasmic (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase) (Fragment)	0.01	-	cyt	0	Cytoplasm				616
Q3C256 UniProt NPD GO	ACR2_ACTEQ	Acrorhagin-2 precursor (Acrorhagin II)	0.01	-	exc	0	Secreted protein. Found in nematocyst				83
Q3C255 UniProt NPD GO	ACR2A_ACTEQ	Acrorhagin-2a precursor (Acrorhagin IIa)	0.01	-	exc	0	Secreted protein. Found in nematocyst				83
P17128 UniProt NPD GO	ACT_KLULA	Actin	0.01	-	cyt	0	Cytoplasm				375
P80709 UniProt NPD GO	ACT_CARMA	Actin (Fragment)	0.01	-		0	Cytoplasm				8
Q92193 UniProt NPD GO	ACT_CRAVI	Actin (Fragment)	0.01	-	cyt	0	Cytoplasm				266
P12432 UniProt NPD GO	ACT1_TRYBB	Actin A	0.01	-	cyt	0	Cytoplasm				376
P30173 UniProt NPD GO	ACT13_SOLTU	Actin-101	0.01	-	cyt	0	Cytoplasm				377
Q96484 UniProt NPD GO	ACT3_LYCES	Actin-52 (Fragment)	0.01	-	cyt	0	Cytoplasm				336
P93373 UniProt NPD GO	ACT3_TOBAC	Actin-54 (Fragment)	0.01	-	cyt	0	Cytoplasm				339
P93585 UniProt NPD GO	ACT4_SOLTU	Actin-65 (Fragment)	0.01	-	cyt	0	Cytoplasm				337
P93371 UniProt NPD GO	ACT5_TOBAC	Actin-93 (Fragment)	0.01	-	cyt	0	Cytoplasm				336
P38673 UniProt NPD GO	ACTZ_NEUCR	Actin-like protein (Centractin)	0.01	-	cyt	0					380
Q6FKE7 UniProt NPD GO	ARP6_CANGA	Actin-like protein ARP6	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				421
Q4WHA3 UniProt NPD GO	ARP4_ASPFU	Actin-like protein arp4	0.01	-	cyt	0	Nucleus (By similarity)				466
O15143 UniProt NPD GO	ARC1B_HUMAN	Actin-related protein 2/3 complex subunit 1B (ARP2/3 complex 41 kDa subunit) (p41-ARC)	0.01	-	cyt	0		Arp2/3 protein complex [TAS]	604223		371
O88656 UniProt NPD GO	ARC1B_RAT	Actin-related protein 2/3 complex subunit 1B (ARP2/3 complex 41 kDa subunit) (p41-ARC)	0.01	-	cyt	0					371
O95433 UniProt NPD GO	AHSA1_HUMAN	Activator of 90 kDa heat shock protein ATPase homolog 1 (AHA1) (p38)	0.01	-	nuc	0	Cytoplasm; cytosol. Endoplasmic reticulum. May transiently interact with the endoplasmic reticulum	cytoplasm [ISS]	608466	1X53	338
O15602 UniProt NPD GO	ACTO_ENTHI	Actobindin homolog (Fragment)	0.01	-	nuc	0					85
P49517 UniProt NPD GO	ACP_ODOSI	Acyl carrier protein (ACP)	0.01	-	cyt	0	Plastid; chloroplast				80
P08817 UniProt NPD GO	ACP2_HORVU	Acyl carrier protein 2, chloroplast precursor (Acyl carrier protein II) (ACP II)	0.01	-	mit	0	Plastid; chloroplast				129
Q92038 UniProt NPD GO	ACOD_CYPCA	Acyl-CoA desaturase (EC 1.14.19.1) (Stearoyl-CoA desaturase) (Fatty acid desaturase) (Delta(9)-desat ...	0.01	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				327
P57752 UniProt NPD GO	ACBP_ARATH	Acyl-CoA-binding protein (ACBP)	0.01	-	cyt	0					92
Q39315 UniProt NPD GO	ACBP_BRANA	Acyl-CoA-binding protein (ACBP)	0.01	-	cyt	0					92
O22643 UniProt NPD GO	ACBP_FRIAG	Acyl-CoA-binding protein (ACBP)	0.01	-	cyt	0					87
Q39779 UniProt NPD GO	ACBP_GOSHI	Acyl-CoA-binding protein (ACBP)	0.01	-	cyt	0					89
O04066 UniProt NPD GO	ACBP_RICCO	Acyl-CoA-binding protein (ACBP)	0.01	-	cyt	0					90
P31787 UniProt NPD GO	ACBP_YEAST	Acyl-CoA-binding protein (ACBP)	0.01	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		1ST7	86
P07107 UniProt NPD GO	ACBP_BOVIN	Acyl-CoA-binding protein (ACBP) (Diazepam-binding inhibitor) (DBI) (Endozepine) (EP)	0.01	-	cyt	0				2ABD	86
Q9TQX6 UniProt NPD GO	ACBP_CANFA	Acyl-CoA-binding protein (ACBP) (Diazepam-binding inhibitor) (DBI) (Endozepine) (EP)	0.01	-	cyt	0					86
P07108 UniProt NPD GO	ACBP_HUMAN	Acyl-CoA-binding protein (ACBP) (Diazepam-binding inhibitor) (DBI) (Endozepine) (EP)	0.01	-	cyt	0			125950		86
P12026 UniProt NPD GO	ACBP_PIG	Acyl-CoA-binding protein (ACBP) (Diazepam-binding inhibitor) (DBI) (Endozepine) (EP) [Contains: DBI( ...	0.01	-	cyt	0					86
P82934 UniProt NPD GO	ACBP_CHAVI	Acyl-CoA-binding protein (ACBP) (EP)	0.01	-	cyt	0					86
P42281 UniProt NPD GO	ACBP_DROME	Acyl-CoA-binding protein homolog (ACBP) (Diazepam-binding inhibitor homolog) (DBI)	0.01	-	cyt	0					86
Q9TLX4 UniProt NPD GO	LPXA_CYACA	Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase (EC 2.3.1.129) (UDP-N-acetylg ...	0.01	-	cyt	0	Plastid; chloroplast				269
Q6Q2Z6 UniProt NPD GO	ACOT5_MOUSE	Acyl-coenzyme A thioesterase 5 (EC 3.1.2.2) (Acyl-CoA thioesterase 5) (Peroxisomal acyl-coenzyme A t ...	0.01	-	pox	0	Peroxisome				421
Q6CJK6 UniProt NPD GO	APTH1_KLULA	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.01	-	mit	0	Cytoplasm (By similarity)				228

You are viewing entries 86551 to 86600 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.