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
Q68S21 UniProt NPD GO	ATPA_PANGI	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
O99015 UniProt NPD GO	ATPA_PROWI	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; plastid membrane; peripheral membrane protein (By similarity)				506
Q8WI30 UniProt NPD GO	ATPA_PSINU	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				508
Q6L3A1 UniProt NPD GO	ATPA_SACHY	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q589B3 UniProt NPD GO	ATPA_SILLA	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q2MIK2 UniProt NPD GO	ATPA_SOLBU	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q27S65 UniProt NPD GO	ATPA_SOLTU	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q2PMS8 UniProt NPD GO	ATPA_SOYBN	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.22	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				510
P46523 UniProt NPD GO	CLPA_BRANA	ATP-dependent Clp protease ATP-binding subunit clpA homolog, chloroplast precursor (Fragment)	0.22	-	cyt	0	Plastid; chloroplast				874
Q6C9P3 UniProt NPD GO	DBP3_YARLI	ATP-dependent RNA helicase DBP3 (EC 3.6.1.-)	0.22	+	cyt	0	Nucleus; nucleolus (By similarity)				532
Q5KNA3 UniProt NPD GO	SUB2_CRYNE	ATP-dependent RNA helicase SUB2 (EC 3.6.1.-)	0.22	-	cyt	0	Nucleus (By similarity)				442
Q9UNX9 UniProt NPD GO	IRK14_HUMAN	ATP-sensitive inward rectifier potassium channel 14 (Potassium channel, inwardly rectifying subfamil ...	0.22	-	end	3	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	603953		436
Q9LY32 UniProt NPD GO	PMA7_ARATH	ATPase 7, plasma membrane-type (EC 3.6.3.6) (Proton pump 7)	0.22	-	end	7	Membrane; multi-pass membrane protein				961
Q95JK8 UniProt NPD GO	ACL7B_MACFA	Actin-like protein 7B (Actin-like-7-beta)	0.22	-	cyt	0					415
Q28560 UniProt NPD GO	AVR2A_SHEEP	Activin receptor type 2A precursor (EC 2.7.11.30) (Activin receptor type IIA) (ACTR-IIA)	0.22	-	end	1	Membrane; single-pass type I membrane protein				513
P07854 UniProt NPD GO	ACP1_SPIOL	Acyl carrier protein 1, chloroplast precursor (Acyl carrier protein I) (ACP I)	0.22	-	mit	0	Plastid; chloroplast			2FVF	138
P22243 UniProt NPD GO	STAD_CARTI	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.22	-	mit	0	Plastid; chloroplast. In green tissue, found in chloroplasts. Plastid. In non-photosynthetic tissue, ...				396
Q96456 UniProt NPD GO	STAD_HELAN	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.22	-	mit	0	Plastid; chloroplast (By similarity). In green tissue, found in chloroplasts. Plastid (By similarity ...				396
O74934 UniProt NPD GO	ACOX1_YARLI	Acyl-coenzyme A oxidase 1 (EC 1.3.3.6) (Acyl-CoA oxidase 1)	0.22	-	cyt	0	Peroxisome				689
Q9D5U0 UniProt NPD GO	AYT1B_MOUSE	Acyltransferase-like 1-B (EC 2.3.1.-)	0.22	-	vac	2	Membrane; multi-pass membrane protein (Potential)				516
P84309 UniProt NPD GO	ADCY5_MOUSE	Adenylate cyclase type 5 (EC 4.6.1.1) (Adenylate cyclase type V) (ATP pyrophosphate-lyase 5) (Adenyl ...	0.22	-	vac	6	Membrane; multi-pass membrane protein (By similarity)	plasma membrane [IDA]			795
P51828 UniProt NPD GO	ADCY7_HUMAN	Adenylate cyclase type 7 (EC 4.6.1.1) (Adenylate cyclase type VII) (ATP pyrophosphate-lyase 7) (Aden ...	0.22	-	end	12 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	600385		1080
P08166 UniProt NPD GO	KAD2_BOVIN	Adenylate kinase isoenzyme 2, mitochondrial (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.22	-	nuc	0	Mitochondrion; mitochondrial intermembrane space			2AK2	240
Q05911 UniProt NPD GO	PUR8_YEAST	Adenylosuccinate lyase (EC 4.3.2.2) (Adenylosuccinase) (ASL) (ASASE)	0.22	-	cyt	0					482
P28650 UniProt NPD GO	PURA1_MOUSE	Adenylosuccinate synthetase isozyme 1 (EC 6.3.4.4) (Adenylosuccinate synthetase, muscle isozyme) (IM ...	0.22	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Partially associated with particulate fractions			1MF1	457
O74623 UniProt NPD GO	ALS3_CANAL	Agglutinin-like protein 3 precursor	0.22	-	exc	0					1119
Q6NYL5 UniProt NPD GO	ALAT2_BRARE	Alanine aminotransferase 2 (EC 2.6.1.2) (ALT2) (Glutamic--pyruvic transaminase 2) (GPT 2) (Glutamic- ...	0.22	-	cyt	0					526
Q5RC02 UniProt NPD GO	SYA_PONPY	Alanyl-tRNA synthetase (EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS)	0.22	-	cyt	0	Cytoplasm (Potential)				968
P81111 UniProt NPD GO	ABA1_TRIAB	Alboaggregin-A subunit 1	0.22	-	cyt	0	Secreted protein				131
P53296 UniProt NPD GO	ATF2_YEAST	Alcohol O-acetyltransferase 2 (EC 2.3.1.84) (AATase 2)	0.22	-	nuc	0	Membrane; peripheral membrane protein (By similarity)	cytoplasm [IDA] endoplasmic reticulum [IDA]			535
Q24803 UniProt NPD GO	ADH2_ENTHI	Aldehyde-alcohol dehydrogenase 2 [Includes: Alcohol dehydrogenase (EC 1.1.1.1) (ADH); Acetaldehyde d ...	0.22	-	cyt	0					870
O16025 UniProt NPD GO	AOSL_PLEHO	Allene oxide synthase-lipoxygenase protein [Includes: Allene oxide synthase (EC 4.2.1.92) (Hydropero ...	0.22	-	cyt	0				1U5U	1066
P68289 UniProt NPD GO	CRYAA_HALGR	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.22	-	cyt	0					173
P68288 UniProt NPD GO	CRYAA_ZALCA	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.22	-	cyt	0					173
Q91518 UniProt NPD GO	CRYAB_TRASC	Alpha crystallin B chain (Alpha(B)-crystallin) (Fragment)	0.22	-	mit	0					52
P20786 UniProt NPD GO	PGFRA_RAT	Alpha platelet-derived growth factor receptor precursor (EC 2.7.10.1) (PDGF-R-alpha)	0.22	-	end	3 *	Membrane; single-pass type I membrane protein				1088
Q659K9 UniProt NPD GO	FUT4_PANTR	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.22	-	gol	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				405
Q659L1 UniProt NPD GO	FUT9_CANFA	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.22	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				359
Q90744 UniProt NPD GO	NAGAB_CHICK	Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) (Alpha-galactosidase B)	0.22	-	cyt	0	Lysosome (By similarity)			1KTC	405
Q92183 UniProt NPD GO	SIA7A_CHICK	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 (EC 2.4.99.3) (GalNAc alpha-2,6-sialyltr ...	0.22	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				566
O57326 UniProt NPD GO	NXSA3_NAJSP	Alpha-neurotoxin NTX-3 precursor	0.22	-	nuc	0	Secreted protein				83
P82350 UniProt NPD GO	SGCA_MOUSE	Alpha-sarcoglycan precursor (Alpha-SG) (Adhalin) (50 kDa dystrophin-associated glycoprotein) (50DAG) ...	0.22	-	end	1	Sarcolemma; sarcolemmal membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]			387
Q9DB05 UniProt NPD GO	SNAA_MOUSE	Alpha-soluble NSF attachment protein (SNAP-alpha) (N-ethylmaleimide-sensitive factor attachment prot ...	0.22	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				295
Q9P414 UniProt NPD GO	AOX_PICST	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-) (SHAM-sensitive terminal oxidase)	0.22	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				357
P21398 UniProt NPD GO	AOFA_BOVIN	Amine oxidase [flavin-containing] A (EC 1.4.3.4) (Monoamine oxidase type A) (MAO-A)	0.22	-	nuc	1	Mitochondrion; mitochondrial outer membrane				527
P79098 UniProt NPD GO	AMPN_BOVIN	Aminopeptidase N (EC 3.4.11.2) (bAPN) (Alanyl aminopeptidase) (Microsomal aminopeptidase) (Aminopept ...	0.22	-	exc	1 *	Membrane; single-pass type II membrane protein				964
P79171 UniProt NPD GO	AMPN_FELCA	Aminopeptidase N (EC 3.4.11.2) (fAPN) (Alanyl aminopeptidase) (Microsomal aminopeptidase) (Aminopept ...	0.22	-	vac	1 *	Membrane; single-pass type II membrane protein				966
Q80ZD5 UniProt NPD GO	AMGO3_RAT	Amphoterin-induced protein 3 precursor (AMIGO-3) (Alivin-3)	0.22	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			508
Q04601 UniProt NPD GO	APC4_YEAST	Anaphase-promoting complex subunit 4	0.22	-	mit	0	Cytoplasm. Nucleus	anaphase-promoting complex [TAS]			652
Q7Z713 UniProt NPD GO	ANR37_HUMAN	Ankyrin repeat domain-containing protein 37 (Low-density lipoprotein receptor-related protein 2-bind ...	0.22	-	nuc	0	Nucleus. Cytoplasm				158

You are viewing entries 48101 to 48150 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.