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
Q9SFU1 UniProt NPD GO	R13A1_ARATH	60S ribosomal protein L13a-1	0.49	+	cyt	0					206
O65082 UniProt NPD GO	RL15B_PICMA	60S ribosomal protein L15-2	0.49	-	nuc	0					204
P35980 UniProt NPD GO	RL18_MOUSE	60S ribosomal protein L18	0.49	-	nuc	0	Cytoplasm				187
Q3SZ10 UniProt NPD GO	RL3L_BOVIN	60S ribosomal protein L3-like	0.49	-	mit	0					406
Q9GN74 UniProt NPD GO	RL31_AEDAE	60S ribosomal protein L31	0.49	-	nuc	0					124
Q9LRB8 UniProt NPD GO	RL36_ENTCP	60S ribosomal protein L36	0.49	+	mit	0					101
O23290 UniProt NPD GO	RL36A_ARATH	60S ribosomal protein L36a	0.49	-	nuc	0					104
O96184 UniProt NPD GO	RL37A_PLAF7	60S ribosomal protein L37a	0.49	-	mit	0					96
P63048 UniProt NPD GO	RL40_BOVIN	60S ribosomal protein L40 (CEP52)	0.49	-	nuc	0					52
P63050 UniProt NPD GO	RL40_CANFA	60S ribosomal protein L40 (CEP52)	0.49	-	nuc	0					52
P62985 UniProt NPD GO	RL40_CHICK	60S ribosomal protein L40 (CEP52)	0.49	-	nuc	0					52
P63052 UniProt NPD GO	RL40_FELCA	60S ribosomal protein L40 (CEP52)	0.49	-	nuc	0					52
P62987 UniProt NPD GO	RL40_HUMAN	60S ribosomal protein L40 (CEP52)	0.49	-	nuc	0			191321		52
P62984 UniProt NPD GO	RL40_MOUSE	60S ribosomal protein L40 (CEP52)	0.49	-	nuc	0					52
P68205 UniProt NPD GO	RL40_OPHHA	60S ribosomal protein L40 (CEP52)	0.49	-	nuc	0					52
P63053 UniProt NPD GO	RL40_PIG	60S ribosomal protein L40 (CEP52)	0.49	-	nuc	0					52
P62986 UniProt NPD GO	RL40_RAT	60S ribosomal protein L40 (CEP52)	0.49	-	nuc	0					52
P93779 UniProt NPD GO	RL5_SOLME	60S ribosomal protein L5 (Fragment)	0.49	-	nuc	0					121
Q92667 UniProt NPD GO	AKAP1_HUMAN	A kinase anchor protein 1, mitochondrial precursor (Protein kinase A-anchoring protein 1) (PRKA1) (A ...	0.49	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane (Potential)		602449		903
O75078 UniProt NPD GO	ADA11_HUMAN	ADAM 11 precursor (A disintegrin and metalloproteinase domain 11) (Metalloproteinase-like, disintegr ...	0.49	-	end	1 *	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	155120		769
P59384 UniProt NPD GO	ATS15_MOUSE	ADAMTS-15 (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 15) (ADAM-TS ...	0.49	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				562
Q759E2 UniProt NPD GO	AP3B_ASHGO	AP-3 complex subunit beta (Beta-adaptin) (Adapter-related protein complex 3 beta subunit) (Clathrin ...	0.49	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				781
Q00361 UniProt NPD GO	ATP5I_BOVIN	ATP synthase e chain, mitochondrial (EC 3.6.3.14)	0.49	-	nuc	0					70
P0C1M0 UniProt NPD GO	ATPG_MAIZE	ATP synthase subunit gamma, chloroplast precursor (EC 3.6.3.14) [Contains: Inceptin]	0.49	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane (By similarity)				359
O95477 UniProt NPD GO	ABCA1_HUMAN	ATP-binding cassette sub-family A member 1 (ATP-binding cassette transporter 1) (ATP-binding cassett ...	0.49	-	end	11 *		integral to plasma membrane [NAS] membrane fraction [TAS]	604091		2261
Q9Z129 UniProt NPD GO	RECQ1_MOUSE	ATP-dependent DNA helicase Q1 (EC 3.6.1.-) (DNA-dependent ATPase Q1)	0.49	-	cyt	0	Nucleus (By similarity)				648
Q6CUI6 UniProt NPD GO	DBP9_KLULA	ATP-dependent RNA helicase DBP9 (EC 3.6.1.-)	0.49	-	cyt	0	Nucleus; nucleolus (By similarity)				594
Q74Z73 UniProt NPD GO	HAS1_ASHGO	ATP-dependent RNA helicase HAS1 (EC 3.6.1.-)	0.49	-	nuc	0	Nucleus; nucleolus (By similarity)				504
Q7S5R1 UniProt NPD GO	DBP3_NEUCR	ATP-dependent RNA helicase dbp-3 (EC 3.6.1.-)	0.49	+	nuc	0	Nucleus; nucleolus (By similarity)				614
P10081 UniProt NPD GO	IF4A_YEAST	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.49	-	cyt	0	Cytoplasm	cytoplasm [IDA] eukaryotic translation initiation factor 4F... [IGI] ribosome [TAS]		1QVA	394
O46197 UniProt NPD GO	A29AB_DROME	Accessory gland protein Acp29AB precursor	0.49	-	nuc	0	Secreted protein (Probable)				234
Q6NUW5 UniProt NPD GO	AN32E_BRARE	Acidic leucine-rich nuclear phosphoprotein 32 family member E	0.49	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				250
Q9BTT0 UniProt NPD GO	AN32E_HUMAN	Acidic leucine-rich nuclear phosphoprotein 32 family member E (LANP-like protein) (LANP-L)	0.49	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasmic membrane-bound vesicle [ISS] nucleus [ISS]	609611		268
Q5AP59 UniProt NPD GO	ARP6_CANAL	Actin-like protein ARP6	0.49	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				446
Q5KAQ4 UniProt NPD GO	ARP6_CRYNE	Actin-like protein ARP6	0.49	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				490
Q8WXI4 UniProt NPD GO	ACO11_HUMAN	Acyl-coenzyme A thioesterase 11 (EC 3.1.2.-) (Acyl-CoA thioesterase 11) (Acyl-CoA thioester hydrolas ...	0.49	-	mit	0	Cytoplasm	cytoplasm [IC]	606803		607
P40146 UniProt NPD GO	ADCY8_RAT	Adenylate cyclase type 8 (EC 4.6.1.1) (Adenylate cyclase type VIII) (ATP pyrophosphate-lyase 8) (Ca( ...	0.49	-	end	10	Membrane; multi-pass membrane protein				1248
Q9TUM6 UniProt NPD GO	ADFP_BOVIN	Adipophilin (Adipose differentiation-related protein) (ADRP)	0.49	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				450
Q9VYV5 UniProt NPD GO	FUT8_DROME	Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) (Glycoprotein 6-alpha-L-fucosyltransferase) (GDP-fucose ...	0.49	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				619
Q8JG70 UniProt NPD GO	AA2DA_BRARE	Alpha-2Da adrenergic receptor (Alpha-2Da adrenoceptor) (Alpha-2Da adrenoreceptor) (Alpha(2Da)AR)	0.49	+	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IC]			408
Q9BVH7 UniProt NPD GO	SIA7E_HUMAN	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5 (EC 2.4.99.-) (GalNAc alpha-2,6-sialyltr ...	0.49	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				336
O13728 UniProt NPD GO	AIN1_SCHPO	Alpha-actinin-like protein 1	0.49	-	mit	0	Localizes to the medial ring in an F-actin-dependent manner	contractile ring (sensu Fungi) [IDA]			621
Q5EGZ1 UniProt NPD GO	ACE2_RAT	Angiotensin-converting enzyme 2 precursor (EC 3.4.17.-) (ACE-related carboxypeptidase)	0.49	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				805
O08764 UniProt NPD GO	ABTB2_RAT	Ankyrin repeat and BTB/POZ domain-containing protein 2 (Confluent 3Y1 cell-associated protein) (CCA3 ...	0.49	-	nuc	0					1009
Q9H560 UniProt NPD GO	ANR19_HUMAN	Ankyrin repeat domain-containing protein 19	0.49	-	mit	0					264
Q04749 UniProt NPD GO	YMV8_YEAST	Ankyrin repeat-containing protein YMR068W	0.49	-	nuc	0		cytoplasm [IDA] TORC 2 complex [IPI]			426
P18649 UniProt NPD GO	APOE_CANFA	Apolipoprotein E (Apo-E)	0.49	-	nuc	0	Secreted protein	cytoplasm [ISS] extracellular region [ISS]			305
Q03247 UniProt NPD GO	APOE_BOVIN	Apolipoprotein E precursor (Apo-E)	0.49	-	exc	0	Secreted protein	cytoplasm [ISS] extracellular region [ISS]			316
P18650 UniProt NPD GO	APOE_PIG	Apolipoprotein E precursor (Apo-E)	0.49	-	exc	0	Secreted protein	cytoplasm [ISS] extracellular region [ISS]			317
O42364 UniProt NPD GO	APOEB_BRARE	Apolipoprotein Eb precursor (Apo-Eb)	0.49	-	exc	0	Secreted protein				281

You are viewing entries 25401 to 25450 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.