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
P62832 UniProt NPD GO	RL23_RAT	60S ribosomal protein L23	0.10	-	mit	0					140
O42867 UniProt NPD GO	RL23_SCHPO	60S ribosomal protein L23	0.10	-	mit	0					139
P62829 UniProt NPD GO	RL23_HUMAN	60S ribosomal protein L23 (Ribosomal protein L17)	0.10	-	mit	0		ribosome [NAS]	603662		140
P62831 UniProt NPD GO	RL23_PIG	60S ribosomal protein L23 (Ribosomal protein L17)	0.10	-	mit	0					140
P41101 UniProt NPD GO	RL27_SOLTU	60S ribosomal protein L27	0.10	-	cyt	0					138
P48161 UniProt NPD GO	RL27A_EUPCR	60S ribosomal protein L27a (L29)	0.10	+	mit	0					148
Q00454 UniProt NPD GO	RL27A_TETTH	60S ribosomal protein L27a (L29)	0.10	-	nuc	0					149
P36585 UniProt NPD GO	RL28A_SCHPO	60S ribosomal protein L28-A (L27A) (L29)	0.10	+	mit	0					148
Q29293 UniProt NPD GO	RL3_PIG	60S ribosomal protein L3 (Fragment)	0.10	-	mit	0	Cytoplasm				130
Q3T0D5 UniProt NPD GO	RL30_BOVIN	60S ribosomal protein L30	0.10	-	mit	0					114
P62888 UniProt NPD GO	RL30_HUMAN	60S ribosomal protein L30	0.10	-	mit	0			180467		114
Q76KA2 UniProt NPD GO	RL30_MACFA	60S ribosomal protein L30	0.10	-	mit	0					114
P62889 UniProt NPD GO	RL30_MOUSE	60S ribosomal protein L30	0.10	-	mit	0					114
P62890 UniProt NPD GO	RL30_RAT	60S ribosomal protein L30	0.10	-	mit	0					114
Q56JY1 UniProt NPD GO	RL35A_BOVIN	60S ribosomal protein L35a	0.10	-	mit	0					110
O61598 UniProt NPD GO	RL37A_OSTOS	60S ribosomal protein L37a	0.10	-	cyt	0					90
P49631 UniProt NPD GO	RL43_YEAST	60S ribosomal protein L43 (L37A) (YL35)	0.10	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	91
P33436 UniProt NPD GO	MMP2_RAT	72 kDa type IV collagenase precursor (EC 3.4.24.24) (72 kDa gelatinase) (Matrix metalloproteinase-2) ...	0.10	-	mit	1 *					662
Q24798 UniProt NPD GO	GRP78_ECHGR	78 kDa glucose-regulated protein precursor (GRP 78)	0.10	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				651
Q24895 UniProt NPD GO	GRP78_ECHMU	78 kDa glucose-regulated protein precursor (GRP 78)	0.10	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				649
P70505 UniProt NPD GO	ADAM1_RAT	ADAM 1 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 1) (Fertilin subunit alph ...	0.10	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			789
P34728 UniProt NPD GO	ARF_CRYNE	ADP-ribosylation factor	0.10	-	mit	0					181
P51824 UniProt NPD GO	ARF1_SOLTU	ADP-ribosylation factor 1	0.10	-	cyt	0					196
P61750 UniProt NPD GO	ARF4_MOUSE	ADP-ribosylation factor 4	0.10	-	mit	0		cytoplasm [IDA] plasma membrane [IDA]			179
P61751 UniProt NPD GO	ARF4_RAT	ADP-ribosylation factor 4	0.10	-	mit	0					179
P26990 UniProt NPD GO	ARF6_CHICK	ADP-ribosylation factor 6	0.10	-	cyt	0		cell cortex [ISS] cytoplasm [ISS] endosome [ISS] plasma membrane [ISS] ruffle [ISS]			174
P62330 UniProt NPD GO	ARF6_HUMAN	ADP-ribosylation factor 6	0.10	-	cyt	0		cell cortex [IDA] endosome [TAS] plasma membrane [IDA] ruffle [IDA]	600464	2A5G	174
P62331 UniProt NPD GO	ARF6_MOUSE	ADP-ribosylation factor 6	0.10	-	cyt	0		cytoplasm [IDA] endosome [TAS] plasma membrane [IDA]			174
P62332 UniProt NPD GO	ARF6_RAT	ADP-ribosylation factor 6	0.10	-	cyt	0					174
O45379 UniProt NPD GO	ARL3_CAEEL	ADP-ribosylation factor-like protein 3	0.10	-	cyt	0					184
Q9UKK9 UniProt NPD GO	NUDT5_HUMAN	ADP-sugar pyrophosphatase (EC 3.6.1.13) (EC 3.6.1.-) (Nucleoside diphosphate-linked moiety X motif 5 ...	0.10	-	cyt	0		intracellular [NAS]	609230		219
P02760 UniProt NPD GO	AMBP_HUMAN	AMBP protein precursor [Contains: Alpha-1-microglobulin (Protein HC) (Complex-forming glycoprotein h ...	0.10	-	exc	0	Secreted protein	extracellular region [NAS] plasma membrane [IDA]	176870	1BIK	352
Q9CXI5 UniProt NPD GO	ARMET_MOUSE	ARMET protein precursor	0.10	-	exc	0	Secreted protein (Potential)				179
P55145 UniProt NPD GO	ARMET_HUMAN	ARMET protein precursor (Arginine-rich protein)	0.10	-	exc	0	Secreted protein (Potential)		601916		179
P80497 UniProt NPD GO	ATPY_SOLTU	ATP synthase 6 kDa subunit, mitochondrial (EC 3.6.3.14) (Fragment)	0.10	-	cyt	0	Mitochondrion				25
O21330 UniProt NPD GO	ATP6_DASNO	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.10	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
Q34946 UniProt NPD GO	ATP6_LUMTE	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.10	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				231
Q00821 UniProt NPD GO	ATPD_ODOSI	ATP synthase delta chain, chloroplast (EC 3.6.3.14)	0.10	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				187
P07926 UniProt NPD GO	AT5G2_BOVIN	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.10	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				143
Q5RAP9 UniProt NPD GO	AT5G2_PONPY	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.10	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				141
Q9XKZ5 UniProt NPD GO	ATP8_AYTAM	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.10	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q9MDB7 UniProt NPD GO	ATP8_COLPA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.10	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
P84344 UniProt NPD GO	ATP8_DROMA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.10	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
P84345 UniProt NPD GO	ATP8_DROME	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.10	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
P50270 UniProt NPD GO	ATP8_DROSI	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.10	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
Q9TBJ1 UniProt NPD GO	ATP8_GUIGU	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.10	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
O63913 UniProt NPD GO	ATP8_MYXGL	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.10	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				54
Q36453 UniProt NPD GO	ATP8_ORNAN	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.10	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				69
P92694 UniProt NPD GO	ATP8_PONPA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.10	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68
Q35584 UniProt NPD GO	ATP8_PONPY	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.10	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68

You are viewing entries 63851 to 63900 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.