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
Q9SA34 UniProt NPD GO	IMDH2_ARATH	Probable inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMPD)	0.01	-	cyt	0					502
Q19420 UniProt NPD GO	IMPA1_CAEEL	Probable inositol monophosphatase (EC 3.1.3.25) (IMPase) (IMP) (Inositol-1(or 4)-monophosphatase)	0.01	-	mit	0	Cytoplasm (By similarity)				341
Q21507 UniProt NPD GO	ILA1_CAEEL	Probable insulin-like peptide alpha-type 1 precursor	0.01	-	mit	1 *	Secreted protein (Potential)				89
Q94425 UniProt NPD GO	SYIM_CIOIN	Probable isoleucyl-tRNA synthetase, mitochondrial (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS) (Fr ...	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				413
P30039 UniProt NPD GO	MAWBP_HUMAN	Probable isomerase MAWBP (EC 5.1.-.-) (MAWD-binding protein) (Unknown protein 32 from 2D-page of liv ...	0.01	-	cyt	0					288
O15432 UniProt NPD GO	COPT2_HUMAN	Probable low-affinity copper uptake protein 2 (hCTR2) (Copper transporter 2) (Solute carrier family ...	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS]	603088		143
O82515 UniProt NPD GO	MTDH_MEDSA	Probable mannitol dehydrogenase (EC 1.1.1.255) (NAD-dependent mannitol dehydrogenase)	0.01	-	cyt	0					359
O42999 UniProt NPD GO	TOM7_SCHPO	Probable mitochondrial import receptor subunit tom7 (Translocase of outer membrane 7 kDa subunit)	0.01	-	mit	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				49
O76534 UniProt NPD GO	MIH_METEN	Probable molt-inhibiting hormone precursor (MEE-MIH)	0.01	-	exc	1 *	Secreted protein				105
P83901 UniProt NPD GO	TX34_PHORI	Probable neurotoxin PRTx34C2	0.01	-	cyt	0	Secreted protein				58
Q9BLM0 UniProt NPD GO	SCXC_ANDAU	Probable neurotoxin pcD-993 precursor	0.01	-	exc	0	Secreted protein (Potential)				72
P26913 UniProt NPD GO	NLTPB_WHEAT	Probable nonspecific lipid-transfer protein (LTP) (Basic protein) (WBP) (Fragment)	0.01	-	cyt	0					40
Q40905 UniProt NPD GO	NLT13_PARJU	Probable nonspecific lipid-transfer protein 1 precursor (LTP) (Major pollen allergen Par j 1.0201) ( ...	0.01	-	gol	1 *					138
P55958 UniProt NPD GO	NLT21_PARJU	Probable nonspecific lipid-transfer protein 2 precursor (LTP 2) (Major pollen allergen Par j 2.0101) ...	0.01	-	exc	0					133
Q43681 UniProt NPD GO	NLTP_VIGUN	Probable nonspecific lipid-transfer protein AKCS9 precursor (LTP)	0.01	-	nuc	0					99
P20145 UniProt NPD GO	NLTP2_HORVU	Probable nonspecific lipid-transfer protein precursor (LTP) (Aleurone-specific 10 kDa protein) (B-FA ...	0.01	-	mit	1 *					102
O23482 UniProt NPD GO	OPT3_ARATH	Probable oligopeptide transporter 3 (AtOPT3)	0.01	-	end	14 *	Membrane; multi-pass membrane protein (Probable)				737
Q9P544 UniProt NPD GO	VDAC_SCHPO	Probable outer mitochondrial membrane protein porin	0.01	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity)				282
Q9HCJ6 UniProt NPD GO	K1576_HUMAN	Probable oxidoreductase KIAA1576 (EC 1.-.-.-)	0.01	-	cyt	0					419
Q80TB8 UniProt NPD GO	K1576_MOUSE	Probable oxidoreductase KIAA1576 (EC 1.-.-.-)	0.01	-	cyt	0					417
Q8WVZ1 UniProt NPD GO	ZDH19_HUMAN	Probable palmitoyltransferase ZDHHC19 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 19) ( ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				282
O97067 UniProt NPD GO	PTH2_DROME	Probable peptidyl-tRNA hydrolase 2 (EC 3.1.1.29) (PTH 2)	0.01	-	cyt	1 *					186
P52572 UniProt NPD GO	REHY_HORVU	Probable peroxiredoxin (EC 1.11.1.15) (Thioredoxin peroxidase) (Rehydrin homolog) (B15C)	0.01	-	cyt	0					218
P52571 UniProt NPD GO	REHY_BROSE	Probable peroxiredoxin (EC 1.11.1.15) (Thioredoxin peroxidase) (Rehydrin homolog) (Dormancy-associat ...	0.01	-	cyt	0					202
P52574 UniProt NPD GO	REHY_TORRU	Probable peroxiredoxin (EC 1.11.1.15) (Thioredoxin peroxidase) (Rehydrin)	0.01	-	cyt	0					218
Q21824 UniProt NPD GO	TDX1_CAEEL	Probable peroxiredoxin (EC 1.11.1.15) (Thioredoxin peroxidase) (Thioredoxin-dependent peroxide reduc ...	0.01	-	mit	0	Cytoplasm (By similarity)				226
O64792 UniProt NPD GO	PIGP_ARATH	Probable phosphatidylinositol N-acetylglucosaminyltransferase subunit P (EC 2.4.1.198)	0.01	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				137
O49069 UniProt NPD GO	GPX4_GOSHI	Probable phospholipid hydroperoxide glutathione peroxidase (EC 1.11.1.12) (PHGPx)	0.01	-	cyt	0	Cytoplasm (Potential)				170
O23814 UniProt NPD GO	GPX4_SPIOL	Probable phospholipid hydroperoxide glutathione peroxidase (EC 1.11.1.12) (PHGPx)	0.01	-	mit	0	Cytoplasm (Potential)				171
P30708 UniProt NPD GO	GPX4_NICSY	Probable phospholipid hydroperoxide glutathione peroxidase (EC 1.11.1.12) (PHGPx) (6P229)	0.01	-	cyt	0	Cytoplasm (Potential)				169
Q9FXS3 UniProt NPD GO	GPX4_TOBAC	Probable phospholipid hydroperoxide glutathione peroxidase (EC 1.11.1.12) (PHGPx) (Nt-SubC08)	0.01	-	cyt	0	Cytoplasm (Potential)				169
Q9M330 UniProt NPD GO	PSMF1_ARATH	Probable proteasome inhibitor	0.01	-	mit	0					302
O94579 UniProt NPD GO	PSA2_SCHPO	Probable proteasome subunit alpha type 2 (EC 3.4.25.1)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				245
O59770 UniProt NPD GO	PSA3_SCHPO	Probable proteasome subunit alpha type 3 (EC 3.4.25.1)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]			253
O43063 UniProt NPD GO	PSB6_SCHPO	Probable proteasome subunit beta type 6 precursor (EC 3.4.25.1)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]			226
Q84VA7 UniProt NPD GO	BRK1_ORYSA	Probable protein BRICK1	0.01	-	cyt	0					86
Q41348 UniProt NPD GO	PDX1_STELP	Probable pyridoxin biosynthesis H47 (PDX1 homolog) (Fragment)	0.01	-	cyt	0					235
O14027 UniProt NPD GO	PDX1_SCHPO	Probable pyridoxin biosynthesis PDX1-like protein	0.01	-	cyt	0					296
O80448 UniProt NPD GO	PDXL1_ARATH	Probable pyridoxin biosynthesis PDX1-like protein 1 (HEVER-like protein)	0.01	-	cyt	0		cytosol [IDA]			309
P53824 UniProt NPD GO	SNZ2_YEAST	Probable pyridoxin biosynthesis protein SNZ2 (PDX1 homolog 2)	0.01	-	cyt	0					298
P43545 UniProt NPD GO	SNZ3_YEAST	Probable pyridoxin biosynthesis protein SNZ3 (PDX1 homolog 3)	0.01	-	cyt	0					298
Q9C1K6 UniProt NPD GO	PDX1_NEUCR	Probable pyridoxin biosynthesis protein pdx-1	0.01	-	cyt	0					308
P38230 UniProt NPD GO	QOR_YEAST	Probable quinone oxidoreductase (EC 1.6.5.5) (NADPH:quinone reductase)	0.01	-	mit	0		cytoplasm [IDA] nucleus [IDA]			334
P22045 UniProt NPD GO	P100_LEIMA	Probable reductase (EC 1.1.-.-)	0.01	-	cyt	0					284
Q9P5X8 UniProt NPD GO	RNHL_NEUCR	Probable ribonuclease HI large subunit (EC 3.1.26.4) (RNase HI large subunit) (RNase H(35))	0.01	-	cyt	0					317
Q9XWW1 UniProt NPD GO	SPCS2_CAEEL	Probable signal peptidase complex subunit 2 (EC 3.4.-.-) (Microsomal signal peptidase 25 kDa subunit ...	0.01	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				180
Q8LSQ2 UniProt NPD GO	SR43C_ORYSA	Probable signal recognition particle 43 kDa protein, chloroplast precursor	0.01	-	mit	0	Plastid; chloroplast (Potential)				388
Q9SUM2 UniProt NPD GO	RUXF_ARATH	Probable small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF)	0.01	-	cyt	0	Nucleus (By similarity)				88
Q9P5Z8 UniProt NPD GO	RUXF_NEUCR	Probable small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF)	0.01	-	cyt	0	Nucleus (By similarity)				90
O59734 UniProt NPD GO	RUXF_SCHPO	Probable small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF)	0.01	-	cyt	0	Nucleus (By similarity)				78

You are viewing entries 90751 to 90800 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.