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
O62792 UniProt NPD GO	OPSD_GLOME	Rhodopsin	0.02	-	end	7 *	Membrane; multi-pass membrane protein				348
O62798 UniProt NPD GO	OPSD_TURTR	Rhodopsin	0.02	-	end	7 *	Membrane; multi-pass membrane protein			1RY1	348
O16018 UniProt NPD GO	OPSD_CAMSC	Rhodopsin (Fragment)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				301
Q90214 UniProt NPD GO	OPSD1_ANGAN	Rhodopsin, deep-sea form	0.02	-	end	7 *	Membrane; multi-pass membrane protein				352
Q17053 UniProt NPD GO	OPSD_APIME	Rhodopsin, long-wavelength (Opsin, green-sensitive)	0.02	-	end	7	Membrane; multi-pass membrane protein				377
Q12270 UniProt NPD GO	RBD2_YEAST	Rhomboid protein 2 (EC 3.4.21.-)	0.02	-	end	5 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein. Golgi apparatus; cis-Golgi network; ci ...	Golgi apparatus [IDA]			262
Q695U0 UniProt NPD GO	RHBL1_TOXGO	Rhomboid-like protease 1 (EC 3.4.21.105)	0.02	-	end	6	Membrane; multi-pass membrane protein. Detected in micronemes in intracellular and extracellular tac ...				293
Q9NX52 UniProt NPD GO	RHBD2_HUMAN	Rhomboid-related protein 2 (EC 3.4.21.105) (RRP2) (Rhomboid-like protein 2)	0.02	-	end	6	Membrane; multi-pass membrane protein		608962		303
Q03778 UniProt NPD GO	RIFK_YEAST	Riboflavin kinase precursor (EC 2.7.1.26) (Flavin mononucleotide kinase 1)	0.02	-	mit	1 *	Microsome. 90%. Mitochondrion; mitochondrial inner membrane. 10%. Found to be present in the inner m ...	microsome [IDA] mitochondrial inner membrane [IDA]			218
P83618 UniProt NPD GO	RN28_PANGI	Ribonuclease-like storage protein precursor (Root 28 kDa major protein)	0.02	-	exc	1 *					238
Q8SRR2 UniProt NPD GO	RIR2_ENCCU	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.02	-	nuc	0					325
P33186 UniProt NPD GO	RIPG_GELMU	Ribosome-inactivating protein gelonin precursor (EC 3.2.2.22) (rRNA N-glycosidase)	0.02	-	exc	1 *					316
P83323 UniProt NPD GO	RIP_SIRGR	Ribosome-inactivating protein momorgrosvin (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.02	-		0					18
P26490 UniProt NPD GO	RBL_ASTLO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid				475
P43222 UniProt NPD GO	RBL_ACRAU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				417
P25413 UniProt NPD GO	RBL_AEGCR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				421
P25414 UniProt NPD GO	RBL_AEGTA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				421
Q31674 UniProt NPD GO	RBL_ANEME	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				420
P36478 UniProt NPD GO	RBL_ANTGA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				471
P43226 UniProt NPD GO	RBL_BLEOR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				414
P28386 UniProt NPD GO	RBL_BYBLI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				436
Q05986 UniProt NPD GO	RBL_CALHE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				443
P48687 UniProt NPD GO	RBL_CALSH	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	nuc	0	Plastid; chloroplast				459
Q95694 UniProt NPD GO	RBL_CAMLE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				447
P28390 UniProt NPD GO	RBL_CEPFO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				459
P48701 UniProt NPD GO	RBL_DICAN	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				440
P28401 UniProt NPD GO	RBL_DIOMU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				466
P28406 UniProt NPD GO	RBL_DRODC	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				441
Q37227 UniProt NPD GO	RBL_IRIGE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				443
P48707 UniProt NPD GO	RBL_MATST	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				440
Q32663 UniProt NPD GO	RBL_NOTDE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				441
P48710 UniProt NPD GO	RBL_ONOSE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				440
P33536 UniProt NPD GO	RBL_OSMCI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				444
Q8WKC9 UniProt NPD GO	RBL_PINVI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				418
Q33015 UniProt NPD GO	RBL_PTEVI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				440
O98360 UniProt NPD GO	RBL_PTYGA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast	ribulose bisphosphate carboxylase complex (... [NAS]			440
P28448 UniProt NPD GO	RBL_RORGO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				459
P28451 UniProt NPD GO	RBL_SARFL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				465
P36490 UniProt NPD GO	RBL_VERBO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				443
P81080 UniProt NPD GO	RBL_PINPS	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Water stress-re ...	0.02	-	cyt	0	Plastid; chloroplast				48
P16306 UniProt NPD GO	RBL_AMAHP	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				475
Q31795 UniProt NPD GO	RBL_ANTFO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				475
Q8SN66 UniProt NPD GO	RBL_CHAGL	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				475
P14958 UniProt NPD GO	RBL_GOSHI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				475
P28260 UniProt NPD GO	RBL_IPOPU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				480
P30827 UniProt NPD GO	RBL_LIRTU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				476
P00874 UniProt NPD GO	RBL_MAIZE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				476
P25831 UniProt NPD GO	RBL_MIRJA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				480
Q6ENG6 UniProt NPD GO	RBL_ORYNI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				477
P12089 UniProt NPD GO	RBL_ORYSA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast			1WDD	477

You are viewing entries 85601 to 85650 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.