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
P29001 UniProt NPD GO	INVA_PHAAU	Acid beta-fructofuranosidase precursor (EC 3.2.1.26) (Acid sucrose hydrolase) (Acid invertase) (AI) ...	0.06	-	nuc	1 *	Vacuole (Probable)				649
Q60HH4 UniProt NPD GO	ASAH1_MACFA	Acid ceramidase precursor (EC 3.5.1.23) (Acylsphingosine deacylase) (N-acylsphingosine amidohydrolas ...	0.06	-	exc	0	Lysosome (By similarity)				395
P35842 UniProt NPD GO	PPAB_YEAST	Acid phosphatase PHO11 precursor (EC 3.1.3.2) (P56)	0.06	-	exc	0		extracellular region [IDA]			467
P38693 UniProt NPD GO	PPAC_YEAST	Acid phosphatase PHO12 precursor (EC 3.1.3.2)	0.06	-	exc	0		vacuole (sensu Fungi) [IDA]			467
Q05540 UniProt NPD GO	CHIB_LYCES	Acidic 27 kDa endochitinase precursor (EC 3.2.1.14)	0.06	-	exc	0	Secreted protein; extracellular space				247
P42820 UniProt NPD GO	CHIP_BETVU	Acidic endochitinase SP2 precursor (EC 3.2.1.14)	0.06	-	exc	0	Secreted protein; extracellular space				288
P02577 UniProt NPD GO	ACT1_DICDI	Actin	0.06	-	cyt	0	Cytoplasm			1NMD	375
Q9UVZ8 UniProt NPD GO	ACT_CANDU	Actin	0.06	-	cyt	0	Cytoplasm				376
O17320 UniProt NPD GO	ACT_CRAGI	Actin	0.06	-	cyt	0	Cytoplasm				376
Q8SWN8 UniProt NPD GO	ACT_ENCCU	Actin	0.06	-	cyt	0	Cytoplasm (By similarity)				375
Q8X119 UniProt NPD GO	ACT_EXODE	Actin	0.06	-	cyt	0	Cytoplasm				375
O16808 UniProt NPD GO	ACT_MAYDE	Actin	0.06	-	cyt	0	Cytoplasm				376
P10989 UniProt NPD GO	ACT_SCHPO	Actin	0.06	-	cyt	0	Cytoplasm	actin filament [TAS] contractile ring (sensu Fungi) [TAS]			375
P68555 UniProt NPD GO	ACT_TAESO	Actin	0.06	-	cyt	0	Cytoplasm				376
P41339 UniProt NPD GO	ACTA_LIMPO	Actin, acrosomal process isoform (Actin-5)	0.06	-	cyt	0	Cytoplasm				376
Q26065 UniProt NPD GO	ACT_PLAMG	Actin, adductor muscle	0.06	-	cyt	0	Cytoplasm				376
P49055 UniProt NPD GO	ACTS_CARAU	Actin, alpha skeletal muscle (Alpha-actin-1)	0.06	-	cyt	0	Cytoplasm				377
P12716 UniProt NPD GO	ACTC_PISOC	Actin, cytoplasmic	0.06	-	cyt	0	Cytoplasm				376
P20360 UniProt NPD GO	ACT_EUPCR	Actin, cytoplasmic	0.06	-	cyt	0	Cytoplasm				379
P53468 UniProt NPD GO	ACT1_OXYTR	Actin, cytoplasmic (Actin, macronuclear)	0.06	-	cyt	0	Cytoplasm				375
P53469 UniProt NPD GO	ACT2_OXYTR	Actin, cytoplasmic (Actin, micronuclear)	0.06	-	cyt	0	Cytoplasm				375
Q25010 UniProt NPD GO	ACT3A_HELAM	Actin, cytoplasmic A3a	0.06	-	cyt	0	Cytoplasm				376
P84183 UniProt NPD GO	ACT4_BOMMO	Actin, cytoplasmic A4	0.06	-	cyt	0	Cytoplasm				376
Q07903 UniProt NPD GO	ACTC_STRPU	Actin, cytoskeletal IIA	0.06	-	cyt	0	Cytoplasm. Cytoskeleton				376
P18499 UniProt NPD GO	ACTF_STRPU	Actin, cytoskeletal IIIB	0.06	-	cyt	0	Cytoplasm. Cytoskeleton				376
P49871 UniProt NPD GO	ACT_MANSE	Actin, muscle	0.06	-	cyt	0	Cytoplasm				376
P02578 UniProt NPD GO	ACT1_ACACA	Actin-1	0.06	-	cyt	0	Cytoplasm				375
P49128 UniProt NPD GO	ACT1_AEDAE	Actin-1	0.06	-	cyt	0	Cytoplasm				376
Q4Z1L3 UniProt NPD GO	ACT1_PLABA	Actin-1 (Actin I)	0.06	-	cyt	0	Cytoplasm				375
Q8I4X0 UniProt NPD GO	ACT1_PLAF7	Actin-1 (Actin I)	0.06	-	cyt	0	Cytoplasm				376
P10988 UniProt NPD GO	ACT1_PLAFA	Actin-1 (Actin I)	0.06	-	cyt	0	Cytoplasm				376
Q7RME1 UniProt NPD GO	ACT1_PLAYO	Actin-1 (Actin I)	0.06	-	cyt	0	Cytoplasm				376
P68556 UniProt NPD GO	ACT1_DIPDE	Actin-1/4	0.06	-	cyt	0	Cytoplasm				376
P07830 UniProt NPD GO	ACT8_DICDI	Actin-15 (Actin A8) (Actin-1/100/103)	0.06	-	cyt	0	Cytoplasm			1DEJ	375
P53456 UniProt NPD GO	ACT2_DIPDE	Actin-2	0.06	-	cyt	0	Cytoplasm				376
Q9Y707 UniProt NPD GO	ACT2_SUIBO	Actin-2	0.06	-	cyt	0	Cytoplasm				375
P45885 UniProt NPD GO	ACT2_BACDO	Actin-2, muscle-specific	0.06	-	cyt	0	Cytoplasm				376
P53457 UniProt NPD GO	ACT3_DIPDE	Actin-3	0.06	-	cyt	0	Cytoplasm				377
P10987 UniProt NPD GO	ACT1_DROME	Actin-5C	0.06	-	cyt	0	Cytoplasm			1N58	376
P84185 UniProt NPD GO	ACT5C_ANOGA	Actin-5C (Actin-1D, cytoplasmic)	0.06	-	cyt	0	Cytoplasm				376
P84184 UniProt NPD GO	ACT3B_HELAM	Actin-A3b, cytoplasmic	0.06	-	cyt	0	Cytoplasm				376
Q61JZ2 UniProt NPD GO	ARP2_CAEBR	Actin-like protein 2 (Actin-related protein 2)	0.06	-	cyt	0					393
Q4IPI4 UniProt NPD GO	ARP4_GIBZE	Actin-like protein ARP4	0.06	-	cyt	0	Nucleus (By similarity)				471
Q7SHR0 UniProt NPD GO	ARP4_NEUCR	Actin-like protein arp-4	0.06	-	cyt	0	Nucleus (By similarity)				469
Q9BR61 UniProt NPD GO	ACBD6_HUMAN	Acyl-CoA-binding domain-containing protein 6	0.06	-	cyt	0				2COP	282
P05335 UniProt NPD GO	ACOX4_CANMA	Acyl-coenzyme A oxidase 4 (EC 1.3.3.6) (Acyl-CoA oxidase 4) (AOX 4)	0.06	-	cyt	0	Peroxisome				708
Q8VHK0 UniProt NPD GO	ACOT8_RAT	Acyl-coenzyme A thioesterase 8 (EC 3.1.2.2) (Acyl-CoA thioesterase 8) (Peroxisomal acyl-coenzyme A t ...	0.06	-	pox	0	Peroxisome				320
Q4WCX7 UniProt NPD GO	APTH1_ASPFU	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.06	-	cyt	0	Cytoplasm (By similarity)				241
O42842 UniProt NPD GO	APT_SCHPO	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				188
P46616 UniProt NPD GO	AA2AR_CAVPO	Adenosine A2a receptor	0.06	-	end	7 *	Membrane; multi-pass membrane protein				409

You are viewing entries 71451 to 71500 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.