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
P52822 UniProt NPD GO	RL5A_SCHPO	60S ribosomal protein L5-A	0.46	-	mit	0					294
O74306 UniProt NPD GO	RL5B_SCHPO	60S ribosomal protein L5-B	0.46	-	mit	0					294
P25457 UniProt NPD GO	RL7B_SCHPO	60S ribosomal protein L7-B	0.46	-	cyt	0					250
O88884 UniProt NPD GO	AKAP1_RAT	A kinase anchor protein 1, mitochondrial precursor (Protein kinase A-anchoring protein 1) (PRKA1) (A ...	0.46	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane (By similarity)				854
Q06811 UniProt NPD GO	ABA1_ASCSU	ABA-1 polyprotein precursor (Body fluid allergen 1) (Allergen Asc s 1) (Nematode polyprotein allerge ...	0.46	+	nuc	0					1365
Q99PE9 UniProt NPD GO	ARL4D_MOUSE	ADP-ribosylation factor-like protein 4D (ADP-ribosylation factor-like protein 4L) (ADP-ribosylation ...	0.46	-	cyt	0	Nucleus; nucleolus	nucleus [IDA]			201
O94973 UniProt NPD GO	AP2A2_HUMAN	AP-2 complex subunit alpha-2 (Adapter-related protein complex 2 alpha-2 subunit) (Alpha-adaptin C) ( ...	0.46	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane (By ...	AP-2 adaptor complex [NAS]	607242		939
Q2WGJ0 UniProt NPD GO	ATPA_SELUN	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.46	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P16970 UniProt NPD GO	ABCD3_RAT	ATP-binding cassette sub-family D member 3 (70 kDa peroxisomal membrane protein) (PMP70)	0.46	-	mit	3	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to membrane [NAS] peroxisomal membrane [IMP] peroxisome [NAS]			658
Q6BZ77 UniProt NPD GO	DBP3_DEBHA	ATP-dependent RNA helicase DBP3 (EC 3.6.1.-)	0.46	+	nuc	0	Nucleus; nucleolus (By similarity)				527
Q5K7L2 UniProt NPD GO	DBP9_CRYNE	ATP-dependent RNA helicase DBP9 (EC 3.6.1.-)	0.46	-	nuc	0	Nucleus; nucleolus (By similarity)				627
Q4IAA0 UniProt NPD GO	FAL1_GIBZE	ATP-dependent RNA helicase FAL1 (EC 3.6.1.-)	0.46	-	nuc	0	Nucleus; nucleolus (By similarity)				401
Q4P184 UniProt NPD GO	FAL1_USTMA	ATP-dependent RNA helicase FAL1 (EC 3.6.1.-)	0.46	-	nuc	0	Nucleus; nucleolus (By similarity)				397
Q7SBR1 UniProt NPD GO	MRH4_NEUCR	ATP-dependent RNA helicase mrh-4, mitochondrial precursor (EC 3.6.1.-)	0.46	-	mit	0	Mitochondrion (By similarity)				625
Q503W7 UniProt NPD GO	ATD1B_BRARE	ATPase family AAA domain-containing protein 1-B	0.46	-	cyt	1 *					362
P48937 UniProt NPD GO	ACCD_BRANA	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.46	-	nuc	0	Plastid; chloroplast				489
Q4W9M3 UniProt NPD GO	ARP6_ASPFU	Actin-like protein arp6	0.46	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				468
P97562 UniProt NPD GO	ACOX2_RAT	Acyl-coenzyme A oxidase 2, peroxisomal (EC 1.17.99.3) (3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-ch ...	0.46	-	cyt	0	Peroxisome	peroxisome [IDA]			681
Q8HXY5 UniProt NPD GO	PUR8_MACFA	Adenylosuccinate lyase (EC 4.3.2.2) (Adenylosuccinase) (ASL) (ASASE)	0.46	-	mit	0					484
Q80WT5 UniProt NPD GO	AFTIN_MOUSE	Aftiphilin	0.46	-	nuc	0	Cytoplasm (By similarity). Colocalizes with AP1G1 and clathrin (By similarity)				931
P29386 UniProt NPD GO	AGL6_ARATH	Agamous-like MADS-box protein AGL6	0.46	-	nuc	0	Nucleus				252
P51652 UniProt NPD GO	AKC1H_RAT	Aldo-keto reductase family 1 member C18 (EC 1.1.-.-) (20-alpha-hydroxysteroid dehydrogenase) (EC 1.1 ...	0.46	-	cyt	0	Cytoplasm	cytosol [IDA] soluble fraction [IDA]			323
Q9D6Z0 UniProt NPD GO	ALKB7_MOUSE	Alkylated repair protein alkB homolog 7 precursor	0.46	-	exc	0					221
Q9BDK2 UniProt NPD GO	AIF1_BOVIN	Allograft inflammatory factor 1 (AIF-1)	0.46	-	nuc	0					147
Q05713 UniProt NPD GO	CRYAB_CHICK	Alpha crystallin B chain (Alpha(B)-crystallin)	0.46	-	nuc	0					174
Q6U1Z4 UniProt NPD GO	CMT1_CRYNE	Alpha-1,3-mannosyltransferase CMT1 (EC 2.4.1.-)	0.46	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				466
P97717 UniProt NPD GO	ADA1B_MOUSE	Alpha-1B adrenergic receptor (Alpha 1B-adrenoceptor) (Alpha 1B-adrenoreceptor)	0.46	+	end	7 *	Membrane; multi-pass membrane protein	integral to membrane of membrane fraction [IDA]			514
O97943 UniProt NPD GO	CAS1_CAMDR	Alpha-S1-casein precursor	0.46	-	exc	0	Secreted protein				222
P80929 UniProt NPD GO	ANG2_BOVIN	Angiogenin-2 (EC 3.1.27.-)	0.46	-	nuc	0					123
Q58DD0 UniProt NPD GO	ACE2_BOVIN	Angiotensin-converting enzyme 2 precursor (EC 3.4.17.-) (ACE-related carboxypeptidase)	0.46	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				804
Q5BKI6 UniProt NPD GO	ANKR1_XENTR	Ankyrin repeat domain-containing protein 1	0.46	+	nuc	0	Nucleus (By similarity)				318
Q9TU71 UniProt NPD GO	ANKR1_RABIT	Ankyrin repeat domain-containing protein 1 (Cardiac ankyrin repeat protein) (Cardiac adriamycin-resp ...	0.46	+	cyt	0	Nucleus (By similarity)				319
Q3V096 UniProt NPD GO	ANR42_MOUSE	Ankyrin repeat domain-containing protein 42	0.46	-	nuc	0					527
Q8BTI7 UniProt NPD GO	ANR52_MOUSE	Ankyrin repeat domain-containing protein 52	0.46	-	cyt	0					1076
P24639 UniProt NPD GO	ANXA7_DICDI	Annexin A7 (Annexin VII) (Synexin)	0.46	-	nuc	0					462
P49931 UniProt NPD GO	PMP36_PIG	Antibacterial peptide PMAP-36 precursor (Myeloid antibacterial peptide 36)	0.46	+	nuc	1 *	Secreted protein				166
Q26755 UniProt NPD GO	GM6_TRYBG	Antigen GM6 (Fragment)	0.46	-	nuc	0	Located on fibers which connect the microtubules of the membrane skeleton with the flagellum				148
P25230 UniProt NPD GO	CAP18_RABIT	Antimicrobial protein CAP18 precursor (18 kDa lipopolysaccharide-binding protein) (18 kDa cationic p ...	0.46	-	exc	1 *	Secreted protein			1LYP	171
Q9TUI9 UniProt NPD GO	APEL_BOVIN	Apelin precursor (APJ endogenous ligand) [Contains: Apelin-36; Apelin-31; Apelin-28; Apelin-13]	0.46	+	exc	1 *	Secreted protein				77
Q9GLM8 UniProt NPD GO	APOE_GORGO	Apolipoprotein E precursor (Apo-E)	0.46	-	exc	0	Secreted protein	cytoplasm [ISS] extracellular region [ISS]			317
Q9GLM7 UniProt NPD GO	APOE_PONPY	Apolipoprotein E precursor (Apo-E)	0.46	-	exc	0	Secreted protein	cytoplasm [ISS] extracellular region [ISS]			317
Q9Z0L2 UniProt NPD GO	ARTN_MOUSE	Artemin precursor	0.46	-	nuc	0	Secreted protein (By similarity)	extracellular space [IDA]			224
Q6AYE8 UniProt NPD GO	ARTN_RAT	Artemin precursor	0.46	-	nuc	0	Secreted protein (By similarity)				224
Q3SYZ4 UniProt NPD GO	SYD_BOVIN	Aspartyl-tRNA synthetase (EC 6.1.1.12) (Aspartate--tRNA ligase) (AspRS)	0.46	-	nuc	0	Cytoplasm (By similarity)				501
Q6FRU4 UniProt NPD GO	ATG21_CANGA	Autophagy-related protein 21	0.46	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Vacuole; vacuolar ...				453
Q5QJC0 UniProt NPD GO	ATG21_PICAN	Autophagy-related protein 21	0.46	-	end	0	Cytoplasm. Membrane; peripheral membrane protein. Vacuole; vacuolar membrane; peripheral membrane pr ...				388
O95429 UniProt NPD GO	BAG4_HUMAN	BAG family molecular chaperone regulator 4 (BCL2-associated athanogene 4) (BAG-4) (Silencer of death ...	0.46	-	nuc	0	Cytoplasm		603884	1M7K	457
P46736 UniProt NPD GO	BRCC3_HUMAN	BRCA1/BRCA2-containing complex subunit 3	0.46	+	nuc	0		nuclear ubiquitin ligase complex [IDA]			316
Q9DBI2 UniProt NPD GO	BBS10_MOUSE	Bardet-Biedl syndrome 10 protein homolog	0.46	-	nuc	0					713
O43521 UniProt NPD GO	BIM_HUMAN	Bcl-2-like protein 11 (Bcl2-interacting mediator of cell death)	0.46	-	nuc	0	Membrane; peripheral membrane protein. Associated with intracytoplasmic membranes (By similarity)	membrane fraction [TAS]	603827		198

You are viewing entries 27401 to 27450 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.