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
P84841 UniProt NPD GO	ES1B_RANSA	Esculentin-1B	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			46
P40845 UniProt NPD GO	ES2A_RANES	Esculentin-2A	0.00	-	cyt	0	Secreted protein				37
P82839 UniProt NPD GO	ES2B_RANBE	Esculentin-2B	0.00	-	cyt	0	Secreted protein				37
P40846 UniProt NPD GO	ES2B_RANES	Esculentin-2B	0.00	-	cyt	0	Secreted protein				37
P82827 UniProt NPD GO	ES2L_RANLU	Esculentin-2L	0.00	-	mit	0	Secreted protein				37
P82846 UniProt NPD GO	ES2P_RANPI	Esculentin-2P	0.00	-	cyt	0	Secreted protein				37
P81012 UniProt NPD GO	ESTA_SCHGA	Esterase 52 kDa subunit (EC 3.1.1.1) (Carboxylic-ester hydrolase) (Fragment)	0.00	-		0	Cytoplasm				10
P10094 UniProt NPD GO	EST4_DROMO	Esterase-4 (EC 3.1.1.1) (Fragment)	0.00	-	cyt	0					40
Q93WU2 UniProt NPD GO	EOMT1_OCIBA	Eugenol O-methyltransferase (EC 2.1.1.146) ((Iso)eugenol O-methyltransferase EOMT1) (S-adenosysl-L-m ...	0.00	-	cyt	0					357
P83268 UniProt NPD GO	IF2A_RABIT	Eukaryotic translation initiation factor 2 subunit 1 (Eukaryotic translation initiation factor 2 sub ...	0.00	-	nuc	0					52
Q09130 UniProt NPD GO	IF2G_SCHPO	Eukaryotic translation initiation factor 2 subunit gamma (eIF-2-gamma)	0.00	-	cyt	0					446
P79083 UniProt NPD GO	IF32_SCHPO	Eukaryotic translation initiation factor 3 39 kDa subunit (eIF3 p39) (Translation initiation factor ...	0.00	-	cyt	0		eukaryotic translation initiation factor 3 ... [TAS]			328
Q5E966 UniProt NPD GO	IF32_BOVIN	Eukaryotic translation initiation factor 3 subunit 2 (eIF-3 beta) (eIF3 p36)	0.00	-	cyt	0					325
Q13347 UniProt NPD GO	IF32_HUMAN	Eukaryotic translation initiation factor 3 subunit 2 (eIF-3 beta) (eIF3 p36) (eIF3i) (TGF-beta recep ...	0.00	-	cyt	0		eukaryotic translation initiation factor 3 ... [TAS]	603911		325
Q9QZD9 UniProt NPD GO	IF32_MOUSE	Eukaryotic translation initiation factor 3 subunit 2 (eIF-3 beta) (eIF3 p36) (eIF3i) (TGF-beta recep ...	0.00	-	cyt	0					325
O04202 UniProt NPD GO	IF35_ARATH	Eukaryotic translation initiation factor 3 subunit 5 (eIF-3 epsilon) (eIF3 p32 subunit) (eIF3f)	0.00	-	mit	0					293
Q9SC12 UniProt NPD GO	IF5A_SENVE	Eukaryotic translation initiation factor 5A (eIF-5A)	0.00	-	cyt	0					159
O94083 UniProt NPD GO	IF5A_CANAL	Eukaryotic translation initiation factor 5A (eIF-5A) (eIF-4D)	0.00	-	mit	0					157
P80639 UniProt NPD GO	IF5A_MAIZE	Eukaryotic translation initiation factor 5A (eIF-5A) (eIF-4D)	0.00	-	cyt	0					160
Q9AXQ6 UniProt NPD GO	IF5A1_LYCES	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1)	0.00	-	cyt	0					159
P69039 UniProt NPD GO	IF5A1_NICPL	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (eIF-4D)	0.00	-	cyt	0					159
P69040 UniProt NPD GO	IF5A1_TOBAC	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (eIF-4D)	0.00	-	cyt	0					159
P56333 UniProt NPD GO	IF5A1_SOLTU	Eukaryotic translation initiation factor 5A-1/2 (eIF-5A-1/2) (eIF-4D)	0.00	-	cyt	0					160
Q93VP3 UniProt NPD GO	IF5A2_ARATH	Eukaryotic translation initiation factor 5A-2 (eIF-5A-2)	0.00	-	cyt	0					159
Q9AXQ5 UniProt NPD GO	IF5A2_LYCES	Eukaryotic translation initiation factor 5A-2 (eIF-5A-2)	0.00	-	cyt	0					160
P24922 UniProt NPD GO	IF5A2_NICPL	Eukaryotic translation initiation factor 5A-2 (eIF-5A-2) (eIF-4D)	0.00	-	cyt	0					159
Q9AXQ4 UniProt NPD GO	IF5A3_LYCES	Eukaryotic translation initiation factor 5A-3 (eIF-5A-3)	0.00	-	cyt	0					159
P56335 UniProt NPD GO	IF5A3_SOLTU	Eukaryotic translation initiation factor 5A-3 (eIF-5A-3) (eIF-4D)	0.00	-	cyt	0					160
Q9AXQ3 UniProt NPD GO	IF5A4_LYCES	Eukaryotic translation initiation factor 5A-4 (eIF-5A-4)	0.00	-	cyt	0					160
P56337 UniProt NPD GO	IF5A5_SOLTU	Eukaryotic translation initiation factor 5A-5 (eIF-5A-5) (eIF-4D)	0.00	-	cyt	0					159
O55135 UniProt NPD GO	IF6_MOUSE	Eukaryotic translation initiation factor 6 (eIF-6) (B4 integrin interactor) (CAB) (p27(BBP))	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	lamin filament [IDA]			245
O81920 UniProt NPD GO	IF6_BETVU	Eukaryotic translation initiation factor 6 (eIF-6) (Fragment)	0.00	-	cyt	0					193
P0C022 UniProt NPD GO	MAST_ANTFM	Eumenine mastoparan-AF (EMP-AF)	0.00	-		0	Secreted protein				14
O61668 UniProt NPD GO	SIX1_MESMA	Excitatory insect selective toxin 1 precursor (BmK IT1) (BmKIT1) (BmK IT) (BmKIT) (Bm32-VI)	0.00	-	cyt	0	Secreted protein			1WWN	88
Q9D0M0 UniProt NPD GO	EXOS7_MOUSE	Exosome complex exonuclease RRP42 (EC 3.1.13.-) (Ribosomal RNA-processing protein 42) (Exosome compo ...	0.00	-	cyt	0	Nucleus; nucleolus (By similarity)	exosome (RNase complex) [ISS]			291
P19364 UniProt NPD GO	GLB7_ARTSX	Extracellular globin-E7	0.00	-	cyt	0					152
Q9V6L9 UniProt NPD GO	FBSP1_DROME	F-box/SPRY-domain protein 1	0.00	-	cyt	0		cytoplasm [ISS]			255
Q8IQC1 UniProt NPD GO	FA18_DROME	FAM18-like protein CG5021	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			223
O42993 UniProt NPD GO	FKBP_SCHPO	FK506-binding protein (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (EC 5.2.1.8)	0.00	-	mit	0	Cytoplasm				112
P0C1J3 UniProt NPD GO	FKBP1_RHIOR	FK506-binding protein 1 (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyci ...	0.00	-	cyt	0	Cytoplasm (By similarity)				108
Q754K8 UniProt NPD GO	FKBP_ASHGO	FK506-binding protein 1 (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyci ...	0.00	-	cyt	0	Cytoplasm (By similarity)				114
Q2U316 UniProt NPD GO	FKBP_ASPOR	FK506-binding protein 1 (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyci ...	0.00	-	cyt	0	Cytoplasm (By similarity)				116
Q6FMA3 UniProt NPD GO	FKBP_CANGA	FK506-binding protein 1 (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyci ...	0.00	-	cyt	0	Cytoplasm (By similarity)				114
Q5KMG3 UniProt NPD GO	FKBP_CRYNE	FK506-binding protein 1 (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyci ...	0.00	-	cyt	0	Cytoplasm (By similarity)				108
O94746 UniProt NPD GO	FKBP_CRYNV	FK506-binding protein 1 (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyci ...	0.00	-	cyt	0	Cytoplasm (By similarity)				108
Q6BX45 UniProt NPD GO	FKBP_DEBHA	FK506-binding protein 1 (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyci ...	0.00	-	cyt	0	Cytoplasm (By similarity)				112
Q6CX30 UniProt NPD GO	FKBP_KLULA	FK506-binding protein 1 (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyci ...	0.00	-	cyt	0	Cytoplasm (By similarity)				114
Q6CF41 UniProt NPD GO	FKBP_YARLI	FK506-binding protein 1 (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rapamyci ...	0.00	-	cyt	0	Cytoplasm (By similarity)				108
P20081 UniProt NPD GO	FKBP_YEAST	FK506-binding protein 1 (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (EC 5.2.1.8) (Rapamyci ...	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]		1YAT	114
Q6KBA8 UniProt NPD GO	FKB1A_EMENI	FK506-binding protein 1A (EC 5.2.1.8) (FKBP) (FkbA) (Peptidyl-prolyl cis-trans isomerase) (PPIase) ( ...	0.00	-	cyt	0	Cytoplasm (By similarity)				108

You are viewing entries 94451 to 94500 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.