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
O42451 UniProt NPD GO	OPSD_PROJE	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				289
O16020 UniProt NPD GO	OPSD_PROML	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				301
O18485 UniProt NPD GO	OPSD_PROOR	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				298
O18486 UniProt NPD GO	OPSD_PROSE	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				301
P79901 UniProt NPD GO	OPSD_SARMI	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P79902 UniProt NPD GO	OPSD_SARPU	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P79903 UniProt NPD GO	OPSD_SARSP	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				347
P79911 UniProt NPD GO	OPSD_SARTI	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				347
P79914 UniProt NPD GO	OPSD_SARXA	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
O42466 UniProt NPD GO	OPSD_TAUBU	Rhodopsin (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				287
P87369 UniProt NPD GO	OPSD_ORYLA	Rhodopsin (KFH-RH)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
Q90215 UniProt NPD GO	OPSD2_ANGAN	Rhodopsin, freshwater form	0.00	-	end	7 *	Membrane; multi-pass membrane protein				352
Q755H8 UniProt NPD GO	RBD2_ASHGO	Rhomboid protein 2 (EC 3.4.21.-)	0.00	-	end	5 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). Golgi apparatus; cis-G ...				261
Q4WLP9 UniProt NPD GO	RBD2_ASPFU	Rhomboid protein 2 (EC 3.4.21.-)	0.00	-	end	5 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). Golgi apparatus; cis-G ...				272
Q6FSG0 UniProt NPD GO	RBD2_CANGA	Rhomboid protein 2 (EC 3.4.21.-)	0.00	-	end	6 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). Golgi apparatus; cis-G ...				266
Q695T9 UniProt NPD GO	RHBL2_TOXGO	Rhomboid-like protease 2 (EC 3.4.21.105)	0.00	-	end	7	Membrane; multi-pass membrane protein (Potential)				283
Q6IUY1 UniProt NPD GO	RHBL3_TOXGO	Rhomboid-like protease 3 (EC 3.4.21.105)	0.00	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				263
Q8CFV9 UniProt NPD GO	RIFK_MOUSE	Riboflavin kinase (EC 2.7.1.26) (ATP:riboflavin 5'-phosphotransferase) (Flavokinase) (KOI-4)	0.00	-	mit	0	Cytoplasm (By similarity)				155
Q9Y7P0 UniProt NPD GO	RISA_SCHPO	Riboflavin synthase alpha chain (EC 2.5.1.9)	0.00	-	cyt	0				1KZL	208
P84784 UniProt NPD GO	RNHI1_THEGA	Ribonuclease (EC 3.1.-.-) (Fragment)	0.00	-		0					15
P80889 UniProt NPD GO	RNS1_PANGI	Ribonuclease 1 (EC 3.1.-.-)	0.00	-	cyt	0	Cytoplasm (Potential)				154
P80890 UniProt NPD GO	RNS2_PANGI	Ribonuclease 2 (EC 3.1.-.-)	0.00	-	cyt	0					153
O95059 UniProt NPD GO	RPP14_HUMAN	Ribonuclease P protein subunit p14 (EC 3.1.26.5)	0.00	-	cyt	0	Nucleus (Potential)	nucleus [TAS]	606112		123
Q5RB79 UniProt NPD GO	RPP14_PONPY	Ribonuclease P protein subunit p14 (EC 3.1.26.5)	0.00	-	cyt	0	Nucleus (Potential)				123
P52759 UniProt NPD GO	UK114_RAT	Ribonuclease UK114 (EC 3.1.-.-) (14.5 kDa translational inhibitor protein) (Perchloric acid soluble ...	0.00	-	mit	0	Mitochondrion. Cytoplasm. Nucleus			1QAH	136
P52758 UniProt NPD GO	UK114_HUMAN	Ribonuclease UK114 (EC 3.1.-.-) (14.5 kDa translational inhibitor protein) (p14.5) (UK114 antigen ho ...	0.00	-	mit	0	Cytoplasm. Nucleus. Mostly cytoplasmic but, in less differentiated cells occasionally nuclear	cytoplasm [TAS] nucleus [TAS]	602487	1ONI	137
P52760 UniProt NPD GO	UK114_MOUSE	Ribonuclease UK114 (EC 3.1.-.-) (Heat-responsive protein 12)	0.00	-	mit	0					134
P83145 UniProt NPD GO	UK114_CHICK	Ribonuclease UK114 (EC 3.1.-.-) (Perchloric acid-soluble protein) (PSP) (Fragments)	0.00	-	cyt	0	Cytoplasm	cytoplasm [TAS]			39
P80750 UniProt NPD GO	RIPX_CUCPE	Ribosome-inactivating protein (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.00	-		0					20
P98184 UniProt NPD GO	RIP2_BRYDI	Ribosome-inactivating protein bryodin II precursor (EC 3.2.2.22) (rRNA N-glycosidase) (BD2)	0.00	-	cyt	0					282
P84530 UniProt NPD GO	RIP_LUFAC	Ribosome-inactivating protein luffaculin 1 (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.00	-		0					10
P16093 UniProt NPD GO	RIPK_TRIKI	Ribosome-inactivating protein trichokirin (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.00	-		0					16
P16083 UniProt NPD GO	NQO2_HUMAN	Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.99.2) (NRH dehydrogenase [quinone] 2) (Q ...	0.00	-	cyt	0	Cytoplasm		160998	2QR2	230
Q5RBB9 UniProt NPD GO	NQO2_PONPY	Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.99.2) (NRH dehydrogenase [quinone] 2) (Q ...	0.00	-	cyt	0	Cytoplasm (By similarity)				230
P24624 UniProt NPD GO	RBL_ANTSP	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	mit	1	Plastid; chloroplast				488
P14957 UniProt NPD GO	RBL_GUITH	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.00	-	nuc	0	Plastid; chloroplast				488
O78258 UniProt NPD GO	RBL_ABIFI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	nuc	0	Plastid; chloroplast				443
O78259 UniProt NPD GO	RBL_ABIHO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	nuc	0	Plastid; chloroplast				443
O78261 UniProt NPD GO	RBL_ABIMR	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	nuc	0	Plastid; chloroplast				443
O78262 UniProt NPD GO	RBL_ABISA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	nuc	0	Plastid; chloroplast				443
O78260 UniProt NPD GO	RBL_ABIVE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	nuc	0	Plastid; chloroplast				443
O99000 UniProt NPD GO	RBL_ADEOB	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
Q31827 UniProt NPD GO	RBL_AESPA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				466
Q07209 UniProt NPD GO	RBL_AILAL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				465
Q07281 UniProt NPD GO	RBL_AKABI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				469
P34767 UniProt NPD GO	RBL_ALIPL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				394
Q31669 UniProt NPD GO	RBL_ANTHE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				468
Q31672 UniProt NPD GO	RBL_ANTLU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				469
Q05554 UniProt NPD GO	RBL_ANTMA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				443
Q31859 UniProt NPD GO	RBL_ANTVS	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				468

You are viewing entries 97651 to 97700 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.