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
P0C0T4 UniProt NPD GO	RS25B_YEAST	40S ribosomal protein S25-B precursor (S31) (YS23) (RP45)	0.34	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			108
Q2LL38 UniProt NPD GO	AAKG3_BOVIN	5'-AMP-activated protein kinase subunit gamma-3 (AMPK gamma-3 chain) (AMPK gamma3)	0.34	-	end	0					497
Q5IS66 UniProt NPD GO	5HT2C_PANTR	5-hydroxytryptamine 2C receptor (5-HT-2C) (Serotonin receptor 2C) (5-HT2C) (5-HTR2C)	0.34	+	end	8 *	Membrane; multi-pass membrane protein				458
P28335 UniProt NPD GO	5HT2C_HUMAN	5-hydroxytryptamine 2C receptor (5-HT-2C) (Serotonin receptor 2C) (5-HT2C) (5-HTR2C) (5HT-1C)	0.34	+	end	8 *	Membrane; multi-pass membrane protein		312861		458
P12629 UniProt NPD GO	RK13_SPIOL	50S ribosomal protein L13, chloroplast precursor (CL13)	0.34	-	mit	0	Plastid; chloroplast				250
Q4W9B8 UniProt NPD GO	K6PF_ASPFU	6-phosphofructokinase (EC 2.7.1.11) (Phosphofructokinase) (Phosphohexokinase) (6PF-1-K)	0.34	+	cyt	0	Cytoplasm (By similarity)				808
P24119 UniProt NPD GO	RL11_TETTH	60S ribosomal protein L11 (L21)	0.34	-	cyt	0					172
O57561 UniProt NPD GO	RL18A_SALSA	60S ribosomal protein L18a	0.34	-	mit	0					176
Q75ET6 UniProt NPD GO	RM02_ASHGO	60S ribosomal protein L2, mitochondrial precursor	0.34	-	mit	0	Mitochondrion (By similarity)				359
P34334 UniProt NPD GO	RL21_CAEEL	60S ribosomal protein L21	0.34	-	nuc	0					160
Q6QN05 UniProt NPD GO	RL21_CHILA	60S ribosomal protein L21	0.34	-	nuc	0					159
Q90YU6 UniProt NPD GO	RL22_ICTPU	60S ribosomal protein L22	0.34	-	nuc	0					127
Q9BI14 UniProt NPD GO	R27A3_ENTHI	60S ribosomal protein L27a-3	0.34	-	mit	0					149
Q962T2 UniProt NPD GO	RL28_SPOFR	60S ribosomal protein L28	0.34	-	nuc	0					139
P47915 UniProt NPD GO	RL29_MOUSE	60S ribosomal protein L29	0.34	-	nuc	0					159
P25886 UniProt NPD GO	RL29_RAT	60S ribosomal protein L29 (P23)	0.34	-	nuc	0					155
Q9MAV7 UniProt NPD GO	RL31_PANGI	60S ribosomal protein L31	0.34	-	nuc	0					121
P49692 UniProt NPD GO	RL7A1_ARATH	60S ribosomal protein L7a-1	0.34	-	nuc	0					257
P41569 UniProt NPD GO	RL8_AEDAL	60S ribosomal protein L8	0.34	-	mit	0	Cytoplasm				261
Q9U9L2 UniProt NPD GO	RL8_ANOGA	60S ribosomal protein L8	0.34	-	mit	0	Cytoplasm				261
P51410 UniProt NPD GO	RL9_MOUSE	60S ribosomal protein L9	0.34	-	cyt	0					192
Q94738 UniProt NPD GO	HSP97_STRFN	97 kDa heat shock protein (Heat shock protein 110)	0.34	-	nuc	0	Cytoplasm (Potential)				886
Q9VAC5 UniProt NPD GO	ADA17_DROME	ADAM 17-like protease precursor (EC 3.4.24.-)	0.34	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				732
Q9WUL7 UniProt NPD GO	ARL3_MOUSE	ADP-ribosylation factor-like protein 3	0.34	-	cyt	0				1FZQ	182
P38153 UniProt NPD GO	AP3M_YEAST	AP-3 complex subunit mu (Adapter-related protein complex 3 mu subunit) (Mu-adaptin 3A) (AP-3 adapter ...	0.34	+	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				483
Q7SI16 UniProt NPD GO	ATP7_NEUCR	ATP synthase D chain, mitochondrial (EC 3.6.3.14)	0.34	-	mit	0					173
Q6FLF3 UniProt NPD GO	DBP2_CANGA	ATP-dependent RNA helicase DBP2 (EC 3.6.1.-)	0.34	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				544
Q2UKX3 UniProt NPD GO	DBP8_ASPOR	ATP-dependent RNA helicase dbp8 (EC 3.6.1.-)	0.34	-	mit	0	Nucleus; nucleolus (By similarity)				443
Q9P6U9 UniProt NPD GO	DED1_NEUCR	ATP-dependent RNA helicase ded-1 (EC 3.6.1.-)	0.34	+	cyt	0	Cytoplasm (By similarity)				688
O76743 UniProt NPD GO	GLH4_CAEEL	ATP-dependent RNA helicase glh-4 (EC 3.6.1.-) (Germline helicase 4)	0.34	-	nuc	0		cytoplasm [IDA] P granule [IDA]			1156
Q750L0 UniProt NPD GO	AEP3_ASHGO	ATPase expression protein 3	0.34	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side (By similarity ...				536
P22240 UniProt NPD GO	TAS14_LYCES	Abscisic acid and environmental stress-inducible protein TAS14 (Dehydrin TAS14)	0.34	-	nuc	0					130
Q8HY67 UniProt NPD GO	AN32A_CANFA	Acidic leucine-rich nuclear phosphoprotein 32 family member A (Inhibitor-1 of protein phosphatase ty ...	0.34	-	nuc	0	Nucleus. Cytoplasm. Shuttles between nucleus and cytoplasm (By similarity)				249
Q9Y7B1 UniProt NPD GO	ACOX_PICPA	Acyl-coenzyme A oxidase (EC 1.3.3.6) (Acyl-CoA oxidase)	0.34	-	cyt	0	Peroxisome				719
Q15067 UniProt NPD GO	ACOX1_HUMAN	Acyl-coenzyme A oxidase 1, peroxisomal (EC 1.3.3.6) (Palmitoyl-CoA oxidase) (AOX) (Straight-chain ac ...	0.34	-	pox	0	Peroxisome	peroxisome [NAS]	609751		660
Q01341 UniProt NPD GO	ADCY6_MOUSE	Adenylate cyclase type 6 (EC 4.6.1.1) (Adenylate cyclase type VI) (ATP pyrophosphate-lyase 6) (Ca(2+ ...	0.34	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [TAS]			1165
Q25460 UniProt NPD GO	FP1_MYTED	Adhesive plaque matrix protein (Polyphenolic adhesive protein) (Foot protein 1) (MEFP1) (Fragment)	0.34	-	nuc	0	Secreted protein				875
P22281 UniProt NPD GO	ALDHX_YEAST	Aldehyde dehydrogenase 1, mitochondrial precursor (EC 1.2.1.3)	0.34	-	mit	0	Mitochondrion; mitochondrial matrix				533
Q7G193 UniProt NPD GO	ALDO1_ARATH	Aldehyde oxidase 1 (EC 1.2.3.1) (AO-1) (AtAO-1) (AtAO1)	0.34	-	cyt	0					1368
P34812 UniProt NPD GO	PHAF_AGLNE	Allophycocyanin B18 subunit	0.34	-	nuc	0	Plastid; chloroplast				171
Q90497 UniProt NPD GO	CRYAA_EUDEL	Alpha crystallin A chain (Fragment)	0.34	-	nuc	0					149
Q91517 UniProt NPD GO	CRYAA_TRASC	Alpha crystallin A chain (Fragment)	0.34	-	nuc	0					149
P02489 UniProt NPD GO	CRYAA_HUMAN	Alpha crystallin A chain (Heat-shock protein beta-4) (HspB4) [Contains: Alpha crystallin A chain, sh ...	0.34	-	cyt	0			604219		173
P02470 UniProt NPD GO	CRYAA_BOVIN	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.34	-	mit	0					173
P02502 UniProt NPD GO	CRYAA_MACRU	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.34	-	nuc	0					173
P02493 UniProt NPD GO	CRYAA_RABIT	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.34	-	cyt	0					173
P02476 UniProt NPD GO	CRYAA_TAPIN	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.34	-	cyt	0					173
Q11127 UniProt NPD GO	FUT4_MOUSE	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.34	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...	cell surface [IDA]			433
Q8HYJ3 UniProt NPD GO	FUT5_HYLLA	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.65) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferas ...	0.34	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				374
Q4X162 UniProt NPD GO	ALG10_ASPFU	Alpha-1,2 glucosyltransferase alg10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase alg10) (Dolichyl-phosp ...	0.34	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				614

You are viewing entries 36401 to 36450 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.