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
Q28886 UniProt NPD GO	OPSD_MACFA	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				348
O18766 UniProt NPD GO	OPSD_PIG	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				348
P35356 UniProt NPD GO	OPSD_PROCL	Rhodopsin	0.01	-	end	7	Membrane; multi-pass membrane protein				376
P79863 UniProt NPD GO	OPSD_RAJER	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				354
P56516 UniProt NPD GO	OPSD_RANTE	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				354
P51489 UniProt NPD GO	OPSD_RAT	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				348
Q9YGZ0 UniProt NPD GO	OPSD_SARPI	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				351
O93459 UniProt NPD GO	OPSD_SCYCA	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				354
Q8HY69 UniProt NPD GO	OPSD_SMICR	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				348
Q9YGZ5 UniProt NPD GO	OPSD_SOLSO	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				353
Q90305 UniProt NPD GO	OPSD_CORAU	Rhodopsin (Fragment)	0.01	-	nuc	3 *	Membrane; multi-pass membrane protein				131
O42328 UniProt NPD GO	OPSD_COTGR	Rhodopsin (Fragment)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				289
P35362 UniProt NPD GO	OPSD_SPHSP	Rhodopsin (Opsin)	0.01	-	end	7	Membrane; multi-pass membrane protein				376
P08100 UniProt NPD GO	OPSD_HUMAN	Rhodopsin (Opsin-2)	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	268000		348
Q5AH12 UniProt NPD GO	RBD2_CANAL	Rhomboid protein 2 (EC 3.4.21.-)	0.01	-	end	5 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). Golgi apparatus; cis-G ...				284
Q6BSA9 UniProt NPD GO	RBD2_DEBHA	Rhomboid protein 2 (EC 3.4.21.-)	0.01	-	end	6 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). Golgi apparatus; cis-G ...				286
Q4I4A4 UniProt NPD GO	RBD2_GIBZE	Rhomboid protein 2 (EC 3.4.21.-)	0.01	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). Golgi apparatus; cis-G ...				267
Q6CR06 UniProt NPD GO	RBD2_KLULA	Rhomboid protein 2 (EC 3.4.21.-)	0.01	-	end	5 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). Golgi apparatus; cis-G ...				271
Q7S4V5 UniProt NPD GO	RBD2_NEUCR	Rhomboid protein 2 (EC 3.4.21.-)	0.01	-	end	6 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). Golgi apparatus; cis-G ...				276
Q6CDV6 UniProt NPD GO	RBD2_YARLI	Rhomboid protein 2 (EC 3.4.21.-)	0.01	-	end	6 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity). Golgi apparatus; cis-G ...				297
Q19821 UniProt NPD GO	ROM1_CAEEL	Rhomboid-related protein 1 (EC 3.4.21.105)	0.01	-	end	7	Membrane; multi-pass membrane protein (Potential)				356
O88779 UniProt NPD GO	RHBD1_RAT	Rhomboid-related protein 1 (EC 3.4.21.105) (RRP) (Rhomboid-like protein 1) (Fragment)	0.01	-	cyt	3 *	Membrane; multi-pass membrane protein				164
Q9H477 UniProt NPD GO	RBSK_HUMAN	Ribokinase (EC 2.7.1.15)	0.01	-	end	0				2FV7	322
P84867 UniProt NPD GO	RNAM_PLEOS	Ribonuclease (EC 3.1.-.-) (Fragment)	0.01	-		0					12
Q2TBT5 UniProt NPD GO	RNHL_BOVIN	Ribonuclease HI large subunit (EC 3.1.26.4) (RNase HI large subunit) (Ribonuclease H2) (RNase H2)	0.01	-	cyt	0					299
Q9CQH8 UniProt NPD GO	RPP14_MOUSE	Ribonuclease P protein subunit p14 (EC 3.1.26.5)	0.01	-	mit	0	Nucleus (Potential)				122
Q3T114 UniProt NPD GO	UK114_BOVIN	Ribonuclease UK114 (EC 3.1.-.-)	0.01	-	mit	0					136
P80601 UniProt NPD GO	UK114_CAPHI	Ribonuclease UK114 (EC 3.1.-.-) (14.5 kDa translational inhibitor protein) (UK114 antigen) (14.3 kDa ...	0.01	-	mit	0	Cell surface			1NQ3	136
P49730 UniProt NPD GO	RIR2_TOBAC	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.01	-	cyt	0	Cytoplasm (By similarity)				329
P49247 UniProt NPD GO	RPIA_HUMAN	Ribose-5-phosphate isomerase (EC 5.3.1.6) (Phosphoriboisomerase)	0.01	-	cyt	0		intracellular [NAS]	608611		237
P47968 UniProt NPD GO	RPIA_MOUSE	Ribose-5-phosphate isomerase (EC 5.3.1.6) (Phosphoriboisomerase)	0.01	-	cyt	0					236
P84854 UniProt NPD GO	RIPL2_PHYDI	Ribosome-inactivating protein PD-L3/PD-L4 (EC 3.2.2.22) (rRNA N-glycosidase PD-L3/PD-L4) (Fragment)	0.01	-	nuc	0					45
P20655 UniProt NPD GO	RIPS_MOMCO	Ribosome-inactivating protein momorcochin-S (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.01	-	cyt	0					30
P83245 UniProt NPD GO	RIP_PLETU	Ribosome-inactivating protein pleuturegin (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.01	-	cyt	0					28
P27559 UniProt NPD GO	RIP2_SAPOF	Ribosome-inactivating protein saporin-2 precursor (EC 3.2.2.22) (SAP-2) (SO-2) (rRNA N-glycosidase)	0.01	-	vac	0				1QI7	292
P24313 UniProt NPD GO	RBL_ECTSI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	nuc	0	Plastid; chloroplast				488
Q4G3F4 UniProt NPD GO	RBL_EMIHU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	nuc	0	Plastid; chloroplast				488
Q6B8P0 UniProt NPD GO	RBL_GRATL	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	mit	1	Plastid; chloroplast				488
P49520 UniProt NPD GO	RBL_ODOSI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	mit	1	Plastid; chloroplast				490
P14959 UniProt NPD GO	RBL_OLILU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	mit	1	Plastid; chloroplast				488
Q09119 UniProt NPD GO	RBL_PORAE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	nuc	0	Plastid; chloroplast				488
P51226 UniProt NPD GO	RBL_PORPU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	mit	1	Plastid; chloroplast				488
P23651 UniProt NPD GO	RBL_PYLLI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	nuc	1	Plastid; chloroplast				488
O98947 UniProt NPD GO	RBL_THANO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.01	-	mit	1	Plastid; chloroplast				490
P93998 UniProt NPD GO	RBL_ACAFA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				455
P28376 UniProt NPD GO	RBL_ACESA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465
P28377 UniProt NPD GO	RBL_ACTCH	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				465
P43223 UniProt NPD GO	RBL_ADIPE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				413
P28378 UniProt NPD GO	RBL_ADOMO	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				466
Q8MD78 UniProt NPD GO	RBL_AMOTI	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				473

You are viewing entries 91201 to 91250 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.