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
Q02152 UniProt NPD GO	5HT2B_MOUSE	5-hydroxytryptamine 2B receptor (5-HT-2B) (Serotonin receptor 2B) (5-HT-2F) (NP75 protein)	0.09	-	end	7	Membrane; multi-pass membrane protein				479
P36211 UniProt NPD GO	RK122_ARATH	50S ribosomal protein L12-2, chloroplast precursor (CL12-B)	0.09	-	mit	0	Plastid; chloroplast				193
P56379 UniProt NPD GO	68MP_MOUSE	6.8 kDa mitochondrial proteolipid	0.09	-	mit	1 *	Mitochondrion (By similarity)				58
O78419 UniProt NPD GO	CH60_GUITH	60 kDa chaperonin (Protein Cpn60) (groEL protein)	0.09	-	cyt	0	Plastid; chloroplast				529
P16168 UniProt NPD GO	RL11_DICDI	60S ribosomal protein L11 (L5) (Vegetative-specific protein V18) (Fragment)	0.09	-	cyt	0					79
P49666 UniProt NPD GO	RL21_PIG	60S ribosomal protein L21 (Fragment)	0.09	-	mit	0					61
P49690 UniProt NPD GO	RL23_ARATH	60S ribosomal protein L23	0.09	-	mit	0					140
Q9XEK8 UniProt NPD GO	RL23_TORRU	60S ribosomal protein L23 (L17)	0.09	-	cyt	0					139
Q20647 UniProt NPD GO	R23A2_CAEEL	60S ribosomal protein L23a 2	0.09	-	mit	0					146
P61359 UniProt NPD GO	RL27_HIPCM	60S ribosomal protein L27	0.09	-	cyt	0					135
P48160 UniProt NPD GO	RL27A_DICDI	60S ribosomal protein L27a	0.09	+	mit	0					148
O01358 UniProt NPD GO	RL27A_OSCBR	60S ribosomal protein L27a (Ribosomal protein RPL-27)	0.09	+	mit	0					145
P52808 UniProt NPD GO	RL30A_SCHPO	60S ribosomal protein L30-1 (L32)	0.09	-	mit	0					109
P18077 UniProt NPD GO	RL35A_HUMAN	60S ribosomal protein L35a	0.09	-	mit	0			180468		110
P61272 UniProt NPD GO	RL35A_MACFA	60S ribosomal protein L35a	0.09	-	mit	0					110
O55142 UniProt NPD GO	RL35A_MOUSE	60S ribosomal protein L35a	0.09	-	mit	0					110
Q5R8K6 UniProt NPD GO	RL35A_PONPY	60S ribosomal protein L35a	0.09	-	mit	0					110
P04646 UniProt NPD GO	RL35A_RAT	60S ribosomal protein L35a	0.09	-	mit	0		ribosome [TAS]			110
P02434 UniProt NPD GO	RL35A_XENLA	60S ribosomal protein L35a (L32)	0.09	-	mit	0					110
O61462 UniProt NPD GO	RL37A_CRYST	60S ribosomal protein L37a	0.09	-	cyt	0					91
P79071 UniProt NPD GO	RL6_SCHPO	60S ribosomal protein L6	0.09	-	cyt	0					194
O02376 UniProt NPD GO	RL9_HAECO	60S ribosomal protein L9 (Fragment)	0.09	-	cyt	0					141
P80816 UniProt NPD GO	CWP20_LYCES	66 kDa cell wall protein (Fragment)	0.09	-		0	Cell wall				18
P80843 UniProt NPD GO	CWP22_ARATH	68 kDa cell wall protein (Fragment)	0.09	-		0	Cell wall				11
Q43207 UniProt NPD GO	FKB70_WHEAT	70 kDa peptidyl-prolyl isomerase (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotama ...	0.09	-	cyt	0					559
P33434 UniProt NPD GO	MMP2_MOUSE	72 kDa type IV collagenase precursor (EC 3.4.24.24) (72 kDa gelatinase) (Matrix metalloproteinase-2) ...	0.09	-	mit	1 *					662
P50757 UniProt NPD GO	MMP2_RABIT	72 kDa type IV collagenase precursor (EC 3.4.24.24) (72 kDa gelatinase) (Matrix metalloproteinase-2) ...	0.09	-	mit	0					662
P84080 UniProt NPD GO	ARF1_BOVIN	ADP-ribosylation factor 1	0.09	-	cyt	0				1S9D	180
P84077 UniProt NPD GO	ARF1_HUMAN	ADP-ribosylation factor 1	0.09	-	cyt	0		plasma membrane [TAS]	103180	1U81	180
Q4R5P2 UniProt NPD GO	ARF1_MACFA	ADP-ribosylation factor 1	0.09	-	cyt	0					180
P84078 UniProt NPD GO	ARF1_MOUSE	ADP-ribosylation factor 1	0.09	-	cyt	0		cytosol [IDA] endomembrane system [IDA] Golgi apparatus [IDA] sarcomere [IDA]		1O3Y	180
P84079 UniProt NPD GO	ARF1_RAT	ADP-ribosylation factor 1	0.09	-	cyt	0				1RRG	180
P51643 UniProt NPD GO	ARF1_XENLA	ADP-ribosylation factor 1	0.09	-	cyt	0					180
P18085 UniProt NPD GO	ARF4_HUMAN	ADP-ribosylation factor 4	0.09	-	mit	0			601177	1Z6X	179
Q5RCF1 UniProt NPD GO	ARF4_PONPY	ADP-ribosylation factor 4	0.09	-	mit	0					179
P84085 UniProt NPD GO	ARF5_HUMAN	ADP-ribosylation factor 5	0.09	-	mit	0			103188	2B6H	179
P84084 UniProt NPD GO	ARF5_MOUSE	ADP-ribosylation factor 5	0.09	-	mit	0		cytoplasm [IDA] plasma membrane [IDA]			179
P84083 UniProt NPD GO	ARF5_RAT	ADP-ribosylation factor 5	0.09	-	mit	0					179
Q02804 UniProt NPD GO	ARL3_YEAST	ADP-ribosylation factor-like protein 3 (Arf-like GTPase 3)	0.09	-	cyt	0		Golgi apparatus [IDA] nuclear envelope-endoplasmic reticulum network [IDA] soluble fraction [IDA]			198
Q9VHV5 UniProt NPD GO	ARL8_DROME	ADP-ribosylation factor-like protein 8 (Novel small G protein indispensable for equal chromosome seg ...	0.09	-	cyt	0	Endosome; late endosome. Lysosome	cytoplasm [ISS] midbody [ISS] spindle midzone [ISS]			186
P51881 UniProt NPD GO	ADT2_MOUSE	ADP/ATP translocase 2 (Adenine nucleotide translocator 2) (ANT 2) (ADP,ATP carrier protein 2) (Solut ...	0.09	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA] mitochondrion [IDA]			297
Q09073 UniProt NPD GO	ADT2_RAT	ADP/ATP translocase 2 (Adenine nucleotide translocator 2) (ANT 2) (ADP,ATP carrier protein 2) (Solut ...	0.09	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				297
P05141 UniProt NPD GO	ADT2_HUMAN	ADP/ATP translocase 2 (Adenine nucleotide translocator 2) (ANT 2) (ADP,ATP carrier protein 2) (Solut ...	0.09	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	300150		297
P32007 UniProt NPD GO	ADT3_BOVIN	ADP/ATP translocase 3 (Adenine nucleotide translocator 2) (ANT 3) (ADP,ATP carrier protein 3) (Solut ...	0.09	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				297
P63009 UniProt NPD GO	AP2B1_BOVIN	AP-2 complex subunit beta-1 (Adapter-related protein complex 2 beta-1 subunit) (Beta-adaptin) (Plasm ...	0.09	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane				236
P47064 UniProt NPD GO	AP3S_YEAST	AP-3 complex subunit sigma (Adapter-related protein complex 3 sigma subunit) (Sigma-adaptin 3A) (AP- ...	0.09	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				194
Q40610 UniProt NPD GO	ATPD_OCHNE	ATP synthase delta chain, chloroplast (EC 3.6.3.14)	0.09	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane				179
Q12165 UniProt NPD GO	ATPD_YEAST	ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)	0.09	-	mit	0	Mitochondrion	proton-transporting ATP synthase, central s... [IMP]			160
P31477 UniProt NPD GO	ATPE_EUGGR	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.09	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				135
O78492 UniProt NPD GO	ATPE_GUITH	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.09	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				131

You are viewing entries 65551 to 65600 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.