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
P84358 UniProt NPD GO	PPK4_PERBR	Pyrokinin-4 (Peb-PK-4) (YXPRL-amide)	0.02	-		0	Secreted protein				12
P82690 UniProt NPD GO	PPK4_PERFU	Pyrokinin-4 (Pef-PK-4) (YXPRL-amide)	0.02	-		0	Secreted protein				12
P84672 UniProt NPD GO	PPK5_DERCR	Pyrokinin-5 (Dercr-PK-5) (FXPRL-amide)	0.02	-		0	Secreted protein				17
P84671 UniProt NPD GO	PPK5_DERVE	Pyrokinin-5 (Derve-PK-5) (FXPRL-amide)	0.02	-		0	Secreted protein				17
P84665 UniProt NPD GO	PPK5_DIPPU	Pyrokinin-5 (Dippu-PK-5) (FXPRL-amide)	0.02	-		0	Secreted protein				17
P84595 UniProt NPD GO	PPK5_ARCTE	Pyrokinin-5 (FXPRL-amide)	0.02	-		0	Secreted protein				17
P84594 UniProt NPD GO	PPK5_BLADU	Pyrokinin-5 (FXPRL-amide)	0.02	-		0	Secreted protein				17
P84669 UniProt NPD GO	PPK5_LAXSP	Pyrokinin-5 (Lax-PK-5) (FXPRL-amide)	0.02	-		0	Secreted protein				17
P84664 UniProt NPD GO	PPK5_LEUMA	Pyrokinin-5 (Leuma-PK-5) (FXPRL-amide)	0.02	-		0	Secreted protein				17
P82617 UniProt NPD GO	PPK5_PERAM	Pyrokinin-5 (Pea-PK-5) (FXPRL-amide)	0.02	-		0	Secreted protein				17
P84667 UniProt NPD GO	PPK5A_PYCSU	Pyrokinin-5a (Pycsu-PK-5a) (FXPRL-amide)	0.02	-		0	Secreted protein				17
P84668 UniProt NPD GO	PPK5B_PYCSU	Pyrokinin-5b (Pycsu-PK-5b) (FXPRL-amide)	0.02	-		0	Secreted protein				17
P31414 UniProt NPD GO	AVP1_ARATH	Pyrophosphate-energized vacuolar membrane proton pump 1 (EC 3.6.1.1) (Pyrophosphate-energized inorga ...	0.02	-	end	14 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Endosome; endosomal membrane; multi-pass me ...				770
P54904 UniProt NPD GO	P5CR1_ARATH	Pyrroline-5-carboxylate reductase (EC 1.5.1.2) (P5CR) (P5C reductase)	0.02	-	cyt	0	Cytoplasm				276
Q9P7Y7 UniProt NPD GO	P5CR_SCHPO	Pyrroline-5-carboxylate reductase (EC 1.5.1.2) (P5CR) (P5C reductase)	0.02	-	cyt	0					282
P17817 UniProt NPD GO	P5CR_SOYBN	Pyrroline-5-carboxylate reductase (EC 1.5.1.2) (P5CR) (P5C reductase)	0.02	-	cyt	0	Cytoplasm				274
Q12740 UniProt NPD GO	P5CR_ZALAR	Pyrroline-5-carboxylate reductase (EC 1.5.1.2) (P5CR) (P5C reductase)	0.02	-	end	1 *					320
P32322 UniProt NPD GO	P5CR1_HUMAN	Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) (P5CR 1) (P5C reductase 1)	0.02	-	cyt	0			179035		319
Q5R9X6 UniProt NPD GO	P5CR1_PONPY	Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) (P5CR 1) (P5C reductase 1)	0.02	-	cyt	0					319
Q2UKV4 UniProt NPD GO	PDC_ASPOR	Pyruvate decarboxylase (EC 4.1.1.1)	0.02	-	cyt	0					570
P28516 UniProt NPD GO	PDC1_MAIZE	Pyruvate decarboxylase isozyme 1 (EC 4.1.1.1) (PDC)	0.02	-	cyt	0					610
P51850 UniProt NPD GO	PDC1_PEA	Pyruvate decarboxylase isozyme 1 (EC 4.1.1.1) (PDC)	0.02	-	mit	0					593
P26263 UniProt NPD GO	PDC6_YEAST	Pyruvate decarboxylase isozyme 3 (EC 4.1.1.1) (EC 4.1.1.-)	0.02	-	cyt	0	Cytoplasm	cytoplasm [IDA]			562
P51266 UniProt NPD GO	ODPB_PORPU	Pyruvate dehydrogenase E1 component subunit beta (EC 1.2.4.1)	0.02	-	cyt	0	Plastid; chloroplast				331
O62619 UniProt NPD GO	KPYK_DROME	Pyruvate kinase (EC 2.7.1.40) (PK)	0.02	-	cyt	0		cytosol [IDA]			533
O44006 UniProt NPD GO	KPYK_EIMTE	Pyruvate kinase (EC 2.7.1.40) (PK)	0.02	-	mit	0					531
P22360 UniProt NPD GO	KPYK_EMENI	Pyruvate kinase (EC 2.7.1.40) (PK)	0.02	-	cyt	0					526
Q7RVA8 UniProt NPD GO	KPYK_NEUCR	Pyruvate kinase (EC 2.7.1.40) (PK)	0.02	-	cyt	0					527
Q875Z9 UniProt NPD GO	KPYK_SACCA	Pyruvate kinase (EC 2.7.1.40) (PK)	0.02	-	mit	0					501
Q875S4 UniProt NPD GO	KPYK_SACKL	Pyruvate kinase (EC 2.7.1.40) (PK)	0.02	-	cyt	0					501
Q10208 UniProt NPD GO	KPYK_SCHPO	Pyruvate kinase (EC 2.7.1.40) (PK)	0.02	-	cyt	0					509
P30614 UniProt NPD GO	KPYK_YARLI	Pyruvate kinase (EC 2.7.1.40) (PK)	0.02	-	cyt	0					515
P46614 UniProt NPD GO	KPYK_CANAL	Pyruvate kinase (EC 2.7.1.40) (PK) (Fragments)	0.02	-	cyt	0	Cytoplasm				92
Q6FIS9 UniProt NPD GO	KPYK1_CANGA	Pyruvate kinase 1 (EC 2.7.1.40) (PK 1)	0.02	-	mit	0					501
P00549 UniProt NPD GO	KPYK1_YEAST	Pyruvate kinase 1 (EC 2.7.1.40) (PK 1)	0.02	-	cyt	0				1A3X	500
Q29536 UniProt NPD GO	KPYR_CANFA	Pyruvate kinase isozyme R (EC 2.7.1.40) (Fragment)	0.02	-	nuc	0					519
Q92122 UniProt NPD GO	KPYK_XENLA	Pyruvate kinase muscle isozyme (EC 2.7.1.40) (Cytosolic thyroid hormone-binding protein) (CTHBP)	0.02	-	cyt	0					527
P22200 UniProt NPD GO	KPYC_SOLTU	Pyruvate kinase, cytosolic isozyme (EC 2.7.1.40) (PK)	0.02	-	nuc	0	Cytoplasm				510
P15325 UniProt NPD GO	QUTD_EMENI	Quinate permease (Quinate transporter)	0.02	-	end	11 *	Membrane; multi-pass membrane protein				533
O95825 UniProt NPD GO	QORL_HUMAN	Quinone oxidoreductase-like 1 (EC 1.-.-.-) (QOH-1) (Zeta-crystallin homolog) (4P11)	0.02	-	cyt	0			603920		349
P37208 UniProt NPD GO	PHCB_PORCR	R-phycocyanin-1 beta chain (R-phycocyanin I beta chain)	0.02	-	nuc	0	Plastid; chloroplast				172
O36004 UniProt NPD GO	PHEB_GRIMO	R-phycoerythrin beta chain	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen. Periphery of the rods of the phycobilisome			1B8D	177
Q01922 UniProt NPD GO	PHEB_POLBO	R-phycoerythrin beta chain	0.02	-	mit	0	Within the thylakoid lumen. Periphery of the rods of the phycobilisome				177
P84862 UniProt NPD GO	PHEB_POLUR	R-phycoerythrin beta chain	0.02	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen. Periphery of the rods of the phycobilisome			1LIA	177
P34146 UniProt NPD GO	RAC1C_DICDI	RAS-related protein rac1C	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				193
Q8NDN9 UniProt NPD GO	RCBT1_HUMAN	RCC1 and BTB domain-containing protein 1 (Regulator of chromosome condensation and BTB domain-contai ...	0.02	-	cyt	0	Nucleus (Potential)		607867		531
Q28813 UniProt NPD GO	RHLA_PANTR	RH-like protein IA (Rhesus-like protein IA)	0.02	-	end	10 *	Membrane; multi-pass membrane protein				416
Q28426 UniProt NPD GO	RHLC_GORGO	RH-like protein IC (Rhesus-like protein IC)	0.02	-	end	10 *	Membrane; multi-pass membrane protein				416
Q28812 UniProt NPD GO	RHLF_PANTR	RH-like protein IIF (Rhesus-like protein IIF)	0.02	-	end	10 *	Membrane; multi-pass membrane protein				416
Q28814 UniProt NPD GO	RHLR_PANTR	RH-like protein IIR (Rhesus-like protein IIR)	0.02	-	end	10 *	Membrane; multi-pass membrane protein				416

You are viewing entries 85501 to 85550 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.