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
P21616 UniProt NPD GO	AVP_PHAAU	Pyrophosphate-energized vacuolar membrane proton pump (EC 3.6.1.1) (Pyrophosphate-energized inorgani ...	0.01	-	end	13 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				764
P32263 UniProt NPD GO	P5CR_YEAST	Pyrroline-5-carboxylate reductase (EC 1.5.1.2) (P5CR) (P5C reductase)	0.01	-	end	0		cytoplasm [IDA]			286
Q922W5 UniProt NPD GO	P5CR1_MOUSE	Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) (P5CR 1) (P5C reductase 1)	0.01	-	cyt	0					309
Q4WXX9 UniProt NPD GO	PDC_ASPFU	Pyruvate decarboxylase (EC 4.1.1.1)	0.01	-	cyt	0					569
P33287 UniProt NPD GO	PDC_NEUCR	Pyruvate decarboxylase (EC 4.1.1.1) (8-10 nm cytoplasmic filament-associated protein) (P59NC)	0.01	-	cyt	0	Cytoplasm. Cytoplasmic filaments				570
P51847 UniProt NPD GO	PDC1_ORYSA	Pyruvate decarboxylase isozyme 1 (EC 4.1.1.1) (PDC)	0.01	-	cyt	0					605
P51845 UniProt NPD GO	PDC1_TOBAC	Pyruvate decarboxylase isozyme 1 (EC 4.1.1.1) (PDC) (Fragment)	0.01	-	cyt	1 *					418
P51848 UniProt NPD GO	PDC2_ORYSA	Pyruvate decarboxylase isozyme 2 (EC 4.1.1.1) (PDC)	0.01	-	cyt	0					605
P51851 UniProt NPD GO	PDC2_PEA	Pyruvate decarboxylase isozyme 2 (EC 4.1.1.1) (PDC) (Fragment)	0.01	-	cyt	0					405
P51849 UniProt NPD GO	PDC3_ORYSA	Pyruvate decarboxylase isozyme 3 (EC 4.1.1.1) (PDC)	0.01	-	cyt	0					587
Q05327 UniProt NPD GO	PDC3_MAIZE	Pyruvate decarboxylase isozyme 3 (EC 4.1.1.1) (PDC) (Fragment)	0.01	-	cyt	0					202
Q9MUR4 UniProt NPD GO	ODPB_MESVI	Pyruvate dehydrogenase E1 component subunit beta (EC 1.2.4.1)	0.01	-	mit	0	Plastid; chloroplast				327
P52904 UniProt NPD GO	ODPB_PEA	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial precursor (EC 1.2.4.1) (PDHE1-B)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix				359
Q6BS75 UniProt NPD GO	KPYK_DEBHA	Pyruvate kinase (EC 2.7.1.40) (PK)	0.01	-	nuc	0					504
P52480 UniProt NPD GO	KPYM_MOUSE	Pyruvate kinase isozyme M2 (EC 2.7.1.40)	0.01	-	cyt	0		mitochondrion [IDA]			530
P11980 UniProt NPD GO	KPYM_RAT	Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) (Pyruvate kinase muscle isozyme)	0.01	-	cyt	0					530
P14618 UniProt NPD GO	KPYM_HUMAN	Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) (Pyruvate kinase muscle isozyme) (Cytosolic thyroid hor ...	0.01	-	cyt	0		cytosol [NAS]	179050	1ZJH	530
P00548 UniProt NPD GO	KPYK_CHICK	Pyruvate kinase muscle isozyme (EC 2.7.1.40)	0.01	-	cyt	0					529
Q42806 UniProt NPD GO	KPYC_SOYBN	Pyruvate kinase, cytosolic isozyme (EC 2.7.1.40) (PK)	0.01	-	cyt	0	Cytoplasm				511
Q9FK25 UniProt NPD GO	OMT1_ARATH	Quercetin 3-O-methyltransferase 1 (EC 2.1.1.76) (AtOMT1) (Flavonol 3-O-methyltransferase 1)	0.01	-	cyt	0				1NII	363
P11635 UniProt NPD GO	DHQA_NEUCR	Quinate dehydrogenase (EC 1.1.1.24)	0.01	-	cyt	0					321
P59858 UniProt NPD GO	PHCA_POLUR	R-phycocyanin alpha chain	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen. Phycobilisome rod			1F99	162
P51368 UniProt NPD GO	PHEA_PORPU	R-phycoerythrin alpha chain	0.01	-	cyt	0	Periphery of the rods of the phycobilisome				164
O49843 UniProt NPD GO	PHEA_PORTE	R-phycoerythrin alpha chain	0.01	-	cyt	0	Periphery of the rods of the phycobilisome				164
O20206 UniProt NPD GO	PHEA_PORYE	R-phycoerythrin alpha chain	0.01	-	cyt	0	Periphery of the rods of the phycobilisome				164
P28560 UniProt NPD GO	PHEB_AGLNE	R-phycoerythrin beta chain	0.01	-	cyt	0	Periphery of the rods of the phycobilisome				176
Q28849 UniProt NPD GO	RHL_MACMU	RH-like protein (Rhesus-like protein)	0.01	-	end	10 *	Membrane; multi-pass membrane protein				416
Q6IV56 UniProt NPD GO	RN141_BRARE	RING finger protein 141	0.01	-	cyt	0					222
Q9NHX0 UniProt NPD GO	RBX1B_DROME	RING-box protein 1B (Regulator of cullins 1b)	0.01	-	cyt	0	Cytoplasm. Nucleus	nucleus [ISS] SCF ubiquitin ligase complex [ISS]			122
P0C0X3 UniProt NPD GO	TFB5_CANAL	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.01	-	cyt	0	Nucleus (By similarity)				69
Q4HYI0 UniProt NPD GO	TFB5_GIBZE	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.01	-	cyt	0	Nucleus (By similarity)				73
P11745 UniProt NPD GO	RNA1_YEAST	Ran GTPase-activating protein 1 (Protein involved in RNA production/processing)	0.01	-	cyt	0	Cytoplasm	cytosol [IDA] nucleus [IDA]			407
P82876 UniProt NPD GO	RLCA_RANCL	Ranalexin-1Ca	0.01	-		0	Secreted protein				20
P82877 UniProt NPD GO	RLCB_RANCL	Ranalexin-1Cb	0.01	-		0	Secreted protein				20
P40951 UniProt NPD GO	TKNM_RANMA	Ranamargarin	0.01	-		0	Secreted protein				14
P22688 UniProt NPD GO	TKNA_RANCA	Ranatachykinin-A (RTK A)	0.01	-		0	Secreted protein				11
P22690 UniProt NPD GO	TKNC_RANCA	Ranatachykinin-C (RTK C)	0.01	-		0	Secreted protein				10
P08951 UniProt NPD GO	RANC_RANPI	Ranatensin-C	0.01	-		0	Secreted protein				11
P82840 UniProt NPD GO	RAN2_RANBE	Ranatuerin-2B	0.01	-	cyt	0	Secreted protein				28
P84115 UniProt NPD GO	RA2BB_RANBO	Ranatuerin-2BYb	0.01	-	nuc	0	Secreted protein				28
P82780 UniProt NPD GO	RAN3_RANCA	Ranatuerin-3	0.01	-	cyt	0	Secreted protein				32
P82821 UniProt NPD GO	RAN6_RANCA	Ranatuerin-6	0.01	-		0	Secreted protein				13
P82822 UniProt NPD GO	RAN7_RANCA	Ranatuerin-7	0.01	-		0	Secreted protein				13
P22127 UniProt NPD GO	RAB10_DISOM	Ras-related protein Rab-10 (ORA1)	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200
Q921E2 UniProt NPD GO	RAB31_MOUSE	Ras-related protein Rab-31	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				194
Q6GQP4 UniProt NPD GO	RAB31_RAT	Ras-related protein Rab-31 (GTP-binding protein Rab0)	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				194
P20337 UniProt NPD GO	RAB3B_HUMAN	Ras-related protein Rab-3B	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		179510		219
P10948 UniProt NPD GO	RAB3B_BOVIN	Ras-related protein Rab-3B (SMG P25B)	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				219
Q8BHH2 UniProt NPD GO	RAB9B_MOUSE	Ras-related protein Rab-9B	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
Q5R4W9 UniProt NPD GO	RAB9B_PONPY	Ras-related protein Rab-9B	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201

You are viewing entries 91101 to 91150 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.