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
P10816 UniProt NPD GO	LGB3_SESRO	Leghemoglobin 3 (Srglb3)	0.00	-	cyt	0					147
P02234 UniProt NPD GO	LGBA_PHAVU	Leghemoglobin A	0.00	-	cyt	0					145
P02238 UniProt NPD GO	LGBA_SOYBN	Leghemoglobin A (Nodulin 2)	0.00	-	cyt	0				1FSL	143
P02235 UniProt NPD GO	LGB1_SOYBN	Leghemoglobin C1 (Nodulin 50)	0.00	-	cyt	0					143
P02236 UniProt NPD GO	LGB2_SOYBN	Leghemoglobin C2	0.00	-	cyt	0					144
P02237 UniProt NPD GO	LGB3_SOYBN	Leghemoglobin C3	0.00	-	cyt	0					144
O80405 UniProt NPD GO	LGB3_PEA	Leghemoglobin Lb120-1	0.00	-	cyt	0					145
O48665 UniProt NPD GO	LGB5_PEA	Leghemoglobin Lb120-29	0.00	-	cyt	0					145
Q9SAZ0 UniProt NPD GO	LGB6_PEA	Leghemoglobin Lb120-34	0.00	-	cyt	0					145
Q9SAZ1 UniProt NPD GO	LGB4_PEA	Leghemoglobin Lb120-8	0.00	-	cyt	0					145
O48668 UniProt NPD GO	LGB2_PEA	Leghemoglobin Lb5-10	0.00	-	cyt	0					146
P02239 UniProt NPD GO	LGB1_LUPLU	Leghemoglobin-1 (Leghemoglobin I)	0.00	-	cyt	0					153
P09187 UniProt NPD GO	LGB1_MEDSA	Leghemoglobin-1 (Leghemoglobin I)	0.00	-	cyt	0					147
P02233 UniProt NPD GO	LGB1_PEA	Leghemoglobin-1 (Leghemoglobin I)	0.00	-	cyt	0					147
P02232 UniProt NPD GO	LGB1_VICFA	Leghemoglobin-1 (Leghemoglobin I)	0.00	-	cyt	0					143
Q43236 UniProt NPD GO	LGB1_VIGUN	Leghemoglobin-1 (Leghemoglobin I) (LbI)	0.00	-	cyt	0					145
P02240 UniProt NPD GO	LGB2_LUPLU	Leghemoglobin-2 (Leghemoglobin II)	0.00	-	cyt	0				2LH7	153
Q43296 UniProt NPD GO	LGB2_VIGUN	Leghemoglobin-2 (Leghemoglobin II) (LbII)	0.00	-	cyt	0					145
P14962 UniProt NPD GO	LGB3_MEDSA	Leghemoglobin-3 (Leghemoglobin III)	0.00	-	cyt	0					146
P45661 UniProt NPD GO	SCK3_LEIQU	Leiurutoxin-3 (Leiurutoxin III) (Fragment)	0.00	-		0	Secreted protein				14
Q6J8I9 UniProt NPD GO	MIP_SHEEP	Lens fiber major intrinsic protein (Aquaporin-0)	0.00	-	end	6 *	Membrane; multi-pass membrane protein			2B6O	263
P06624 UniProt NPD GO	MIP_BOVIN	Lens fiber major intrinsic protein (Aquaporin-0) (MIP26) (MP26)	0.00	-	end	6 *	Membrane; multi-pass membrane protein			2C32	263
P30301 UniProt NPD GO	MIP_HUMAN	Lens fiber major intrinsic protein (Aquaporin-0) (MIP26) (MP26)	0.00	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	154050		263
Q06019 UniProt NPD GO	MIP_RANPI	Lens fiber major intrinsic protein (MIP26) (MP26)	0.00	-	end	6 *	Membrane; multi-pass membrane protein				263
P55344 UniProt NPD GO	LMIP_HUMAN	Lens fiber membrane intrinsic protein (MP18) (MP19) (MP20)	0.00	-	end	4 *	Membrane; multi-pass membrane protein	cell junction [NAS]	154045		173
O95214 UniProt NPD GO	LERL1_HUMAN	Leptin receptor overlapping transcript-like 1	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)		607338		131
Q9CQ74 UniProt NPD GO	LERL1_MOUSE	Leptin receptor overlapping transcript-like 1	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				131
Q5RDE9 UniProt NPD GO	LERL1_PONPY	Leptin receptor overlapping transcript-like 1	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				131
P17727 UniProt NPD GO	TXL1_PHONI	Lethal neurotoxin Tx1 precursor	0.00	-	exc	0	Secreted protein				112
P34629 UniProt NPD GO	AMPL_CAEEL	Leucine aminopeptidase 1 (EC 3.4.11.1)	0.00	-	cyt	0					491
Q84V83 UniProt NPD GO	LAR_DESUN	Leucoanthocyanidin reductase (EC 1.17.1.3) (Leucocyanidin reductase)	0.00	-	cyt	0					382
P21140 UniProt NPD GO	LCK1_LEUMA	Leucokinin-1 (Leucokinin I) (L-I)	0.00	-		0	Secreted protein				8
P21141 UniProt NPD GO	LCK2_LEUMA	Leucokinin-2 (Leucokinin II) (L-II)	0.00	-		0	Secreted protein				8
P21142 UniProt NPD GO	LCK3_LEUMA	Leucokinin-3 (Leucokinin III) (L-III)	0.00	-		0	Secreted protein				8
P19989 UniProt NPD GO	LCK7_LEUMA	Leucokinin-7 (Leucokinin VII) (L-VII)	0.00	-		0	Secreted protein				8
P19990 UniProt NPD GO	LCK8_LEUMA	Leucokinin-8 (Leucokinin VIII) (L-VIII)	0.00	-		0	Secreted protein				8
Q61451 UniProt NPD GO	CD53_MOUSE	Leukocyte surface antigen CD53 (Cell surface glycoprotein CD53)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				218
P24485 UniProt NPD GO	CD53_RAT	Leukocyte surface antigen CD53 (Cell surface glycoprotein CD53) (Leukocyte antigen MRC OX-44)	0.00	-	end	4 *	Membrane; multi-pass membrane protein	cell surface [IDA]			218
Q924U0 UniProt NPD GO	LT4R2_RAT	Leukotriene B4 receptor 2 (LTB4-R2) (LTB4 receptor JULF2)	0.00	-	end	6 *	Membrane; multi-pass membrane protein				358
Q9JJL9 UniProt NPD GO	LT4R2_MOUSE	Leukotriene B4 receptor 2 (LTB4-R2) (Leukotriene B4 receptor BLT2)	0.00	-	end	6 *	Membrane; multi-pass membrane protein				360
P08975 UniProt NPD GO	LH15_EUGGR	Light-harvesting complex I LH35 proteins precursor [Contains: LH35 protein 1; LH35 protein 2] (Fragm ...	0.00	-	cyt	0	Plastid; chloroplast				331
P08976 UniProt NPD GO	LH18_EUGGR	Light-harvesting complex I LH38 proteins precursor [Contains: LH38 protein 1; LH38 protein 2; LH38 p ...	0.00	-	cyt	0	Plastid; chloroplast				530
Q85FG5 UniProt NPD GO	CHLL_ADICA	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.00	-	nuc	0	Plastid; chloroplast				293
Q32067 UniProt NPD GO	CHLB_CIBSC	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.00	-	cyt	0	Plastid; chloroplast				103
Q32450 UniProt NPD GO	CHLB_ISOEC	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.00	-	cyt	0	Plastid; chloroplast				103
P37850 UniProt NPD GO	CHLB_NEPEX	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.00	-	cyt	0	Plastid; chloroplast				103
P37851 UniProt NPD GO	CHLB_OSMCL	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.00	-	cyt	0	Plastid; chloroplast				103
P37855 UniProt NPD GO	CHLB_SALAU	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.00	-	mit	0	Plastid; chloroplast				103
Q33093 UniProt NPD GO	CHLB_STAER	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.00	-	mit	0	Plastid; chloroplast				48
P20011 UniProt NPD GO	LIGA_TRAVE	Ligninase A (EC 1.11.1.14) (Diarylpropane peroxidase) (Lignin peroxidase) (Fragment)	0.00	-		0					13

You are viewing entries 95451 to 95500 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.