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
P19511 UniProt NPD GO	AT5F1_RAT	ATP synthase B chain, mitochondrial precursor (EC 3.6.3.14)	0.20	-	mit	0	Mitochondrion				256
Q00823 UniProt NPD GO	ATPX_ODOSI	ATP synthase B' chain (EC 3.6.3.14) (Subunit II)	0.20	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				156
P18859 UniProt NPD GO	ATP5J_HUMAN	ATP synthase coupling factor 6, mitochondrial precursor (EC 3.6.3.14) (ATPase subunit F6)	0.20	-	mit	0		mitochondrial inner membrane [TAS] mitochondrion [TAS]	603152		108
P28552 UniProt NPD GO	ATPG_PEA	ATP synthase gamma chain, chloroplast precursor (EC 3.6.3.14)	0.20	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				376
Q94NW9 UniProt NPD GO	ATP8_FELLI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.20	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q870C4 UniProt NPD GO	ATPF_PARBR	ATP synthase subunit 4, mitochondrial precursor (EC 3.6.3.14)	0.20	-	nuc	0	Mitochondrion (By similarity)				244
Q9TM26 UniProt NPD GO	ATPA_CYACA	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.20	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				504
Q6B8Q8 UniProt NPD GO	ATPA_GRATL	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.20	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				503
Q9MTL7 UniProt NPD GO	ATPA_OENHO	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.20	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				505
O89016 UniProt NPD GO	ABCD4_MOUSE	ATP-binding cassette sub-family D member 4 (Peroxisomal membrane protein 69) (PMP69) (Peroxisomal me ...	0.20	-	end	2 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein				606
P51332 UniProt NPD GO	CLPC_PORPU	ATP-dependent Clp protease ATP-binding subunit clpA homolog	0.20	-	nuc	0	Plastid; chloroplast				821
Q4PHU9 UniProt NPD GO	DBP2_USTMA	ATP-dependent RNA helicase DBP2 (EC 3.6.1.-)	0.20	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				552
Q5AJD0 UniProt NPD GO	DBP5_CANAL	ATP-dependent RNA helicase DBP5 (EC 3.6.1.-)	0.20	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				540
Q6BT27 UniProt NPD GO	FAL1_DEBHA	ATP-dependent RNA helicase FAL1 (EC 3.6.1.-)	0.20	-	cyt	0	Nucleus; nucleolus (By similarity)				399
Q759L6 UniProt NPD GO	SUB2_ASHGO	ATP-dependent RNA helicase SUB2 (EC 3.6.1.-)	0.20	-	cyt	0	Nucleus (By similarity)				438
Q6BME5 UniProt NPD GO	SUB2_DEBHA	ATP-dependent RNA helicase SUB2 (EC 3.6.1.-)	0.20	-	cyt	0	Nucleus (By similarity)				435
Q6CM95 UniProt NPD GO	SUB2_KLULA	ATP-dependent RNA helicase SUB2 (EC 3.6.1.-)	0.20	-	cyt	0	Nucleus (By similarity)				437
Q95YF3 UniProt NPD GO	CGH1_CAEEL	ATP-dependent RNA helicase cgh-1 (EC 3.6.1.-) (Conserved germline helicase 1)	0.20	-	nuc	0	Cytoplasm. Cytoplasmic when associated with pgl-1	cytoplasm [IDA]			430
Q9DBL9 UniProt NPD GO	ABHD5_MOUSE	Abhydrolase domain-containing protein 5 (Lipid droplet-binding protein CGI-58)	0.20	-	cyt	0	Cytoplasm. Colocalizated with PLIN and ADRP on the surface of lipid droplets. The localization is de ...	cytosol [IDA] lipid particle [IDA]			351
Q6QA69 UniProt NPD GO	ABHD5_RAT	Abhydrolase domain-containing protein 5 (Lipid droplet-binding protein CGI-58)	0.20	-	cyt	0	Cytoplasm. Colocalizated with PLIN and ADRP on the surface of lipid droplets. The localization is de ...				351
Q41768 UniProt NPD GO	ILV1_MAIZE	Acetolactate synthase 1, chloroplast precursor (EC 2.2.1.6) (Acetohydroxy-acid synthase 1)	0.20	-	mit	0	Plastid; chloroplast (By similarity)				638
Q41769 UniProt NPD GO	ILV2_MAIZE	Acetolactate synthase 2, chloroplast precursor (EC 2.2.1.6) (Acetohydroxy-acid synthase 2)	0.20	-	mit	0	Plastid; chloroplast (By similarity)				638
Q5KPJ5 UniProt NPD GO	ILVB_CRYNE	Acetolactate synthase, mitochondrial precursor (EC 2.2.1.6) (Acetohydroxy-acid synthase) (ALS) (AHAS ...	0.20	-	mit	0	Mitochondrion (By similarity)				718
Q6FLU2 UniProt NPD GO	ACS1_CANGA	Acetyl-coenzyme A synthetase 1 (EC 6.2.1.1) (Acetate--CoA ligase 1) (Acyl-activating enzyme 1)	0.20	-	nuc	0	Microsome (Potential)				704
P91766 UniProt NPD GO	ACH1_MANSE	Acetylcholine receptor protein subunit alpha-like precursor (MARA1)	0.20	-	end	4	Membrane; multi-pass membrane protein				516
P04759 UniProt NPD GO	ACHD_BOVIN	Acetylcholine receptor protein subunit delta precursor	0.20	-	end	4 *	Membrane; multi-pass membrane protein				516
P09628 UniProt NPD GO	ACHD_XENLA	Acetylcholine receptor protein subunit delta precursor	0.20	-	end	4	Membrane; multi-pass membrane protein				521
O46431 UniProt NPD GO	FIBP_CERAE	Acidic fibroblast growth factor intracellular-binding protein (aFGF intracellular-binding protein) ( ...	0.20	-	cyt	0	Nucleus (By similarity). Intracellular membrane; peripheral membrane protein (By similarity). Also a ...				357
Q9QY83 UniProt NPD GO	ACL7B_MOUSE	Actin-like protein 7B (Actin-like-7-beta) (T-actin-1) (Testis-specific actin-1)	0.20	-	cyt	0		cytoplasm [IDA]			418
Q7S6X6 UniProt NPD GO	ARP6_NEUCR	Actin-like protein arp-6	0.20	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				446
O96624 UniProt NPD GO	ARPC3_DICDI	Actin-related protein 2/3 complex subunit 3 (ARP2/3 complex 21 kDa subunit) (p21-ARC)	0.20	-	cyt	0					174
P37172 UniProt NPD GO	ACVR1_MOUSE	Activin receptor type-1 precursor (EC 2.7.11.30) (Activin receptor type I) (ACTR-I) (Serine/threonin ...	0.20	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [IDA]			509
P25701 UniProt NPD GO	ACP2_ARATH	Acyl carrier protein 2, chloroplast precursor (ACP)	0.20	-	mit	0	Plastid; chloroplast				136
Q9D7B6 UniProt NPD GO	ACAD8_MOUSE	Acyl-CoA dehydrogenase family member 8, mitochondrial precursor (EC 1.3.99.-) (ACAD-8) (Isobutyryl-C ...	0.20	-	mit	0	Mitochondrion (By similarity)				413
P07308 UniProt NPD GO	ACOD1_RAT	Acyl-CoA desaturase 1 (EC 1.14.19.1) (Stearoyl-CoA desaturase 1) (Fatty acid desaturase 1) (Delta(9) ...	0.20	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				358
Q41319 UniProt NPD GO	STAD_SOLCO	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.20	-	mit	0	Plastid; chloroplast (By similarity). In green tissue, found in chloroplasts. Plastid (By similarity ...				393
Q8R146 UniProt NPD GO	APEH_MOUSE	Acylamino-acid-releasing enzyme (EC 3.4.19.1) (AARE) (Acyl-peptide hydrolase) (APH) (Acylaminoacyl-p ...	0.20	-	nuc	0	Cytoplasm (By similarity)				732
P0C1Q3 UniProt NPD GO	AYT1A_RAT	Acyltransferase-like 1-A (EC 2.3.1.-)	0.20	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)				544
Q9D1J1 UniProt NPD GO	NECP2_MOUSE	Adaptin ear-binding coat-associated protein 2 (NECAP-2)	0.20	-	cyt	0	Membrane-associated; membranes of clathrin-coated vesicles. Colocalizes with AP-2 at the plasma memb ...	clathrin vesicle coat [IDA]			266
Q29450 UniProt NPD GO	ADCY7_BOVIN	Adenylate cyclase type 7 (EC 4.6.1.1) (Adenylate cyclase type VII) (ATP pyrophosphate-lyase 7) (Aden ...	0.20	-	end	10 *	Membrane; multi-pass membrane protein				1078
Q9D7N9 UniProt NPD GO	APMAP_MOUSE	Adipocyte plasma membrane-associated protein (Protein DD16)	0.20	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				415
P10969 UniProt NPD GO	AGI3_WHEAT	Agglutinin isolectin 3 precursor (WGA3) (Fragment)	0.20	-	nuc	0				1WGT	186
P24298 UniProt NPD GO	ALAT1_HUMAN	Alanine aminotransferase 1 (EC 2.6.1.2) (ALT1) (Glutamic--pyruvic transaminase 1) (GPT 1) (Glutamic- ...	0.20	-	cyt	0	Cytoplasm	cytoplasm [NAS]	138200		495
Q6GM82 UniProt NPD GO	ALAT2_XENLA	Alanine aminotransferase 2 (EC 2.6.1.2) (ALT2) (Glutamic--pyruvic transaminase 2) (GPT 2) (Glutamic- ...	0.20	-	mit	0					540
P81114 UniProt NPD GO	ABA4_TRIAB	Alboaggregin-A subunit 4	0.20	-	cyt	0	Secreted protein				123
Q06278 UniProt NPD GO	ADO_HUMAN	Aldehyde oxidase (EC 1.2.3.1)	0.20	-	cyt	0	Cytoplasm		602841		1338
Q5FB27 UniProt NPD GO	ADO_MACFA	Aldehyde oxidase (EC 1.2.3.1)	0.20	-	cyt	0	Cytoplasm (By similarity)				1338
O60066 UniProt NPD GO	ALKBH_SCHPO	Alkylated DNA repair protein alkB homolog	0.20	-	cyt	0					273
Q01594 UniProt NPD GO	ALLN1_ALLSA	Alliin lyase 1 precursor (EC 4.4.1.4) (Alliinase 1) (Cysteine sulphoxide lyase 1)	0.20	-	mit	0	Vacuole			1LK9	486
P02763 UniProt NPD GO	A1AG1_HUMAN	Alpha-1-acid glycoprotein 1 precursor (AGP 1) (Orosomucoid-1) (OMD 1)	0.20	-	vac	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	138600		201

You are viewing entries 50301 to 50350 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.