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
Q9T043 UniProt NPD GO	RL142_ARATH	60S ribosomal protein L14-2	0.21	-	cyt	0		cytosolic ribosome (sensu Eukaryota) [IDA]			134
Q8SRA7 UniProt NPD GO	RL23_ENCCU	60S ribosomal protein L23	0.21	-	nuc	0					146
Q9AT35 UniProt NPD GO	RL23A_DAUCA	60S ribosomal protein L23a	0.21	-	nuc	0					154
Q9VMU4 UniProt NPD GO	RL37A_DROME	60S ribosomal protein L37a	0.21	-	nuc	0					91
P63173 UniProt NPD GO	RL38_HUMAN	60S ribosomal protein L38	0.21	-	nuc	0			604182		69
Q9JJI8 UniProt NPD GO	RL38_MOUSE	60S ribosomal protein L38	0.21	-	nuc	0					69
O61570 UniProt NPD GO	RL38_OSTOS	60S ribosomal protein L38	0.21	-	nuc	0					70
P63174 UniProt NPD GO	RL38_RAT	60S ribosomal protein L38	0.21	-	nuc	0					69
P49691 UniProt NPD GO	RL4B_ARATH	60S ribosomal protein L4-2 (L1)	0.21	-	mit	0					407
O94686 UniProt NPD GO	RL43B_SCHPO	60S ribosomal protein L43-B (L37B)	0.21	-	mit	0					94
Q9XVF7 UniProt NPD GO	RL8_CAEEL	60S ribosomal protein L8	0.21	-	mit	0	Cytoplasm				260
Q9R158 UniProt NPD GO	AD26A_MOUSE	ADAM 26A precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 26A) (Testase-3)	0.21	-	nuc	1	Membrane; single-pass type I membrane protein				697
P78325 UniProt NPD GO	ADAM8_HUMAN	ADAM 8 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 8) (Cell surface antigen ...	0.21	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	602267		824
P04710 UniProt NPD GO	ADT1_YEAST	ADP,ATP carrier protein 1 (ADP/ATP translocase 1) (Adenine nucleotide translocator 1) (ANT 1)	0.21	-	cyt	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [TAS]			309
Q6P5E6 UniProt NPD GO	GGA2_MOUSE	ADP-ribosylation factor-binding protein GGA2 (Golgi-localized, gamma ear-containing, ARF-binding pro ...	0.21	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein (By ...				603
O00170 UniProt NPD GO	AIP_HUMAN	AH receptor-interacting protein (AIP) (Aryl-hydrocarbon receptor-interacting protein) (Immunophilin ...	0.21	-	cyt	0	Cytoplasm	cytoplasm [TAS]	605555		330
P35602 UniProt NPD GO	AP1M_CAEEL	AP-1 complex subunit mu (Clathrin coat assembly protein AP47) (Clathrin coat-associated protein AP47 ...	0.21	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	AP-1 adaptor complex [NAS]			422
Q15041 UniProt NPD GO	AR6P1_HUMAN	ARL-6-interacting protein 1 (ADP-ribosylation-like factor 6-interacting protein 1) (Aip-1)	0.21	-	end	4 *	Intracytoplasmic membrane; multi-pass membrane protein. Predominantly localized to intracytoplasmic ...		607669		203
Q5R454 UniProt NPD GO	AR6P1_PONPY	ARL-6-interacting protein 1 (ADP-ribosylation-like factor 6-interacting protein 1) (Aip-1)	0.21	-	end	4 *	Membrane; multi-pass membrane protein (By similarity). Predominantly localized to intracytoplasmic m ...				203
P33204 UniProt NPD GO	ARPC4_YEAST	ARP2/3 complex 20 kDa subunit (p20-ARC)	0.21	-	mit	0		Arp2/3 protein complex [IDA]			171
O13350 UniProt NPD GO	ATP7_KLULA	ATP synthase D chain, mitochondrial (EC 3.6.3.14)	0.21	-	mit	0					173
P51243 UniProt NPD GO	ATPD_PORPU	ATP synthase delta chain, chloroplast (EC 3.6.3.14)	0.21	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane				186
P22778 UniProt NPD GO	ATPO_IPOBA	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral pr ...	0.21	-	mit	0	Mitochondrion				244
O63902 UniProt NPD GO	ATP8_MYOGL	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.21	-	nuc	0	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q35914 UniProt NPD GO	ATP8_PIG	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.21	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q3V549 UniProt NPD GO	ATPA_ACOCL	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.21	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P00823 UniProt NPD GO	ATPA_TOBAC	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.21	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P19482 UniProt NPD GO	ATPA2_BOVIN	ATP synthase subunit alpha liver isoform, mitochondrial precursor (EC 3.6.3.14) (Fragment)	0.21	-	mit	0	Mitochondrion; mitochondrial inner membrane				359
P68542 UniProt NPD GO	ATPAM_BRACM	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.21	-	cyt	0	Mitochondrion				507
P22201 UniProt NPD GO	ATPAM_BRANA	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.21	-	cyt	0	Mitochondrion				507
P68541 UniProt NPD GO	ATPAM_RAPSA	ATP synthase subunit alpha, mitochondrial (EC 3.6.3.14)	0.21	-	cyt	0	Mitochondrion				507
P25705 UniProt NPD GO	ATPA_HUMAN	ATP synthase subunit alpha, mitochondrial precursor (EC 3.6.3.14)	0.21	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [TAS] proton-transporting ATP synthase complex (s... [TAS]	164360		553
Q61285 UniProt NPD GO	ABCD2_MOUSE	ATP-binding cassette sub-family D member 2 (Adrenoleukodystrophy-related protein)	0.21	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				741
O60706 UniProt NPD GO	ABCC9_HUMAN	ATP-binding cassette transporter sub-family C member 9 (Sulfonylurea receptor 2)	0.21	-	end	14 *	Membrane; multi-pass membrane protein (Potential)		608569		1549
P31541 UniProt NPD GO	CLPAA_LYCES	ATP-dependent Clp protease ATP-binding subunit clpA homolog CD4A, chloroplast precursor	0.21	-	cyt	0	Plastid; chloroplast				926
Q4HY71 UniProt NPD GO	DBP5_GIBZE	ATP-dependent RNA helicase DBP5 (EC 3.6.1.-)	0.21	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				488
Q27268 UniProt NPD GO	UAP56_DROME	ATP-dependent RNA helicase WM6 (EC 3.6.1.-) (DEAD box protein UAP56) (HEL/UAP56)	0.21	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle	nucleus [IDA]			424
Q5KN36 UniProt NPD GO	DED1_CRYNE	ATP-dependent RNA helicase ded1 (EC 3.6.1.-)	0.21	-	mit	0	Cytoplasm (By similarity)				637
Q01574 UniProt NPD GO	ACS1_YEAST	Acetyl-coenzyme A synthetase 1 (EC 6.2.1.1) (Acetate--CoA ligase 1) (Acyl-activating enzyme 1)	0.21	-	nuc	0	Microsome (Potential)	cytosol [IDA] mitochondrion [IDA]		1RY2	713
P09478 UniProt NPD GO	ACH1_DROME	Acetylcholine receptor protein subunit alpha-like 1 precursor	0.21	-	end	4	Membrane; multi-pass membrane protein				567
P29031 UniProt NPD GO	CHIB_POPTR	Acidic endochitinase WIN6.2B precursor (EC 3.2.1.14)	0.21	-	exc	0					303
P51614 UniProt NPD GO	CHIT3_VITVI	Acidic endochitinase precursor (EC 3.2.1.14)	0.21	-	exc	0					301
O43423 UniProt NPD GO	AN32C_HUMAN	Acidic leucine-rich nuclear phosphoprotein 32 family member C (Phosphoprotein 32-related protein 1) ...	0.21	-	mit	0			606877		234
Q74ZV8 UniProt NPD GO	ARP6_ASHGO	Actin-like protein ARP6	0.21	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				410
Q04771 UniProt NPD GO	ACVR1_HUMAN	Activin receptor type-1 precursor (EC 2.7.11.30) (Activin receptor type I) (ACTR-I) (Serine/threonin ...	0.21	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	102576		509
Q6P7B9 UniProt NPD GO	ACOD2_RAT	Acyl-CoA desaturase 2 (EC 1.14.19.1) (Stearoyl-CoA desaturase 2) (Fatty acid desaturase 2) (Delta(9) ...	0.21	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				358
Q91YX5 UniProt NPD GO	LGAT1_MOUSE	Acyl-CoA:lysophosphatidylglycerol acyltransferase 1 (EC 2.3.1.-)	0.21	-	mit	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				370
Q756A9 UniProt NPD GO	ACOX_ASHGO	Acyl-coenzyme A oxidase (EC 1.3.3.6) (Acyl-CoA oxidase)	0.21	-	cyt	0	Peroxisome (By similarity)				721
P07032 UniProt NPD GO	ACYP1_CHICK	Acylphosphatase-1 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 1) (Acylphosphatase, organ-common typ ...	0.21	-	cyt	0					98
P80210 UniProt NPD GO	PURA_YEAST	Adenylosuccinate synthetase (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPSase)	0.21	-	cyt	0		cytoplasm [IDA]			432

You are viewing entries 49151 to 49200 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.