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
Q6EV21 UniProt NPD GO	RS28_PAPDA	40S ribosomal protein S28	0.13	-	cyt	0					65
Q962Q2 UniProt NPD GO	RS28_SPOFR	40S ribosomal protein S28	0.13	-	cyt	0					65
P41058 UniProt NPD GO	RS29B_YEAST	40S ribosomal protein S29-B (S36) (YS29)	0.13	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]		1K5X	55
P49398 UniProt NPD GO	RS4_ORYSA	40S ribosomal protein S4 (SCAR protein SS620)	0.13	-	mit	0	Cytoplasm (By similarity)				265
O15587 UniProt NPD GO	RS5_ENTHI	40S ribosomal protein S5 (Fragment)	0.13	-	nuc	0					148
P80753 UniProt NPD GO	CWP03_DAUCA	46 kDa cell wall protein (Fragment)	0.13	-		0	Cell wall				15
P92981 UniProt NPD GO	APR2_ARATH	5'-adenylylsulfate reductase 2, chloroplast precursor (EC 1.8.4.9) (Adenosine 5'-phosphosulfate 5'-a ...	0.13	-	mit	0	Plastid; chloroplast (Potential)				454
O46635 UniProt NPD GO	5HT2A_CANFA	5-hydroxytryptamine 2A receptor (5-HT-2A) (Serotonin receptor 2A) (5-HT-2) (5-hydroxytryptamine rece ...	0.13	-	end	7	Cell membrane; multi-pass membrane protein. Localizes to the post-synaptic thickening of axo-dendrit ...				470
O70212 UniProt NPD GO	5HT3R_CAVPO	5-hydroxytryptamine 3 receptor precursor (5-HT-3) (Serotonin-gated ion channel receptor) (5-HT3R)	0.13	-	end	4	Membrane; multi-pass membrane protein	integral to synaptic vesicle membrane [IDA]			490
Q39586 UniProt NPD GO	METE_CHLRE	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) (Methionine synt ...	0.13	-	nuc	0					814
Q9SX68 UniProt NPD GO	RK18_ARATH	50S ribosomal protein L18, chloroplast precursor	0.13	-	nuc	0	Plastid; chloroplast				170
Q03216 UniProt NPD GO	K6PF2_KLULA	6-phosphofructokinase subunit beta (EC 2.7.1.11) (Phosphofructokinase 2) (Phosphohexokinase) (6PF-1- ...	0.13	-	mit	0	Cytoplasm (By similarity)				938
P12382 UniProt NPD GO	K6PL_MOUSE	6-phosphofructokinase, liver type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phospho ...	0.13	-	cyt	0		6-phosphofructokinase complex [ISS]			779
P30835 UniProt NPD GO	K6PL_RAT	6-phosphofructokinase, liver type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phospho ...	0.13	-	cyt	0		6-phosphofructokinase complex [ISS]			779
P14332 UniProt NPD GO	6PGD_PIG	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) (Fragment)	0.13	-	nuc	0					250
O42848 UniProt NPD GO	RL16A_SCHPO	60S ribosomal protein L16-A	0.13	-	cyt	0					197
O62581 UniProt NPD GO	RL27A_ENCCU	60S ribosomal protein L27a	0.13	-	mit	0					147
P14115 UniProt NPD GO	RL27A_MOUSE	60S ribosomal protein L27a (L29)	0.13	+	mit	0					147
Q8VZ19 UniProt NPD GO	RL302_ARATH	60S ribosomal protein L30-2	0.13	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [IDA]			112
Q9Y0H7 UniProt NPD GO	RL37A_MYXGL	60S ribosomal protein L37a (Fragment)	0.13	-	cyt	0					85
P13023 UniProt NPD GO	RL8_DICDI	60S ribosomal protein L8 (60S ribosomal protein L2)	0.13	-	mit	0					255
P29766 UniProt NPD GO	RL8_LYCES	60S ribosomal protein L8 (L2) (Ribosomal protein TL2)	0.13	-	mit	0	Cytoplasm				260
P29453 UniProt NPD GO	RL8B_YEAST	60S ribosomal protein L8-B (L7A-1) (L4-1) (YL5) (RP6)	0.13	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			255
P53744 UniProt NPD GO	BIO5_YEAST	7-keto 8-aminopelargonic acid transporter (KAPA transporter)	0.13	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				561
Q99170 UniProt NPD GO	GRP78_YARLI	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.13	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum lumen [ISS]			670
P13994 UniProt NPD GO	9KD_HUMAN	9 kDa protein	0.13	-	nuc	0					82
Q1PEH6 UniProt NPD GO	ATH2_ARATH	ABC2 homolog 2	0.13	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				578
Q28660 UniProt NPD GO	ADAM2_RABIT	ADAM 2 precursor (A disintegrin and metalloproteinase domain 2) (Fertilin subunit beta) (PH-30) (PH3 ...	0.13	-	end	1	Membrane; single-pass type I membrane protein				751
Q99393 UniProt NPD GO	IZH4_YEAST	ADIPOR-like receptor IZH4 (Implicated in zinc homeostasis protein 4)	0.13	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	membrane [TAS]			312
Q12442 UniProt NPD GO	PHO36_YEAST	ADIPOR-like receptor PHO36 (Phosphate metabolism protein 36)	0.13	-	end	7	Membrane; multi-pass membrane protein (Potential)	membrane [TAS]			327
P18238 UniProt NPD GO	ADT3_YEAST	ADP,ATP carrier protein 3 (ADP/ATP translocase 3) (Adenine nucleotide translocator 3) (ANT 3)	0.13	-	cyt	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				307
P40945 UniProt NPD GO	ARF2_DROME	ADP-ribosylation factor 2 (dARF II)	0.13	-	mit	0					179
Q3SZF2 UniProt NPD GO	ARF4_BOVIN	ADP-ribosylation factor 4	0.13	-	mit	0					179
Q20758 UniProt NPD GO	ARL1_CAEEL	ADP-ribosylation factor-like protein 1	0.13	-	cyt	0					179
Q8SQH5 UniProt NPD GO	ADT2_BOVIN	ADP/ATP translocase 2 (Adenine nucleotide translocator 2) (ANT 2) (ADP,ATP carrier protein 2) (Solut ...	0.13	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				297
Q2KJ81 UniProt NPD GO	AP1M1_BOVIN	AP-1 complex subunit mu-1 (Adaptor-related protein complex 1 mu-1 subunit) (Mu-adaptin 1) (Adaptor p ...	0.13	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				422
Q9BXS5 UniProt NPD GO	AP1M1_HUMAN	AP-1 complex subunit mu-1 (Adaptor-related protein complex 1 mu-1 subunit) (Mu-adaptin 1) (Adaptor p ...	0.13	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...		603535		422
Q84QC0 UniProt NPD GO	ASCL3_ORYSA	ASC1-like protein 3 (Alternaria stem canker resistance-like protein 3)	0.13	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				284
P13620 UniProt NPD GO	ATP5H_BOVIN	ATP synthase D chain, mitochondrial (EC 3.6.3.14)	0.13	-	cyt	0					160
P48047 UniProt NPD GO	ATPO_HUMAN	ATP synthase O subunit, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.13	-	mit	0	Mitochondrion; mitochondrial matrix	proton-transporting ATP synthase complex (s... [TAS]	600828		213
O47872 UniProt NPD GO	ATP6_ALLMI	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.13	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				225
Q9ZXX9 UniProt NPD GO	ATP6_PAPHA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.13	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q01909 UniProt NPD GO	ATPG2_ARATH	ATP synthase gamma chain 2, chloroplast precursor (EC 3.6.3.14)	0.13	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				386
P05435 UniProt NPD GO	ATPG_SPIOL	ATP synthase gamma chain, chloroplast precursor (EC 3.6.3.14)	0.13	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				364
P48202 UniProt NPD GO	AT5G1_MOUSE	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.13	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			136
Q8HG02 UniProt NPD GO	ATP8_ALOSA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.13	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				66
Q9ZZ63 UniProt NPD GO	ATP8_CANFA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.13	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q2I3H0 UniProt NPD GO	ATP8_ELEMA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.13	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				66
P48663 UniProt NPD GO	ATP8_HORSE	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.13	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q95705 UniProt NPD GO	ATP8_HYLLA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.13	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68

You are viewing entries 59301 to 59350 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.