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
O65314 UniProt NPD GO	ACT_SCHDU	Actin	0.03	-	cyt	0	Cytoplasm				378
P53476 UniProt NPD GO	ACT_TOXGO	Actin	0.03	-	cyt	0	Cytoplasm				376
Q99023 UniProt NPD GO	ACT_TRIRE	Actin	0.03	-	cyt	0	Cytoplasm				376
P20904 UniProt NPD GO	ACT_VOLCA	Actin	0.03	-	cyt	0	Cytoplasm				377
P60010 UniProt NPD GO	ACT_YEAST	Actin	0.03	-	cyt	0	Cytoplasm	actin cable [TAS] actin cortical patch [TAS] contractile ring (sensu Saccharomyces) [TAS] H4/H2A histone acetyltransferase complex [IPI] INO80 complex [IPI] SWR1 complex [IPI]		1YVN	375
P30161 UniProt NPD GO	ACT_COSCS	Actin (Fragment)	0.03	-	cyt	0	Cytoplasm				331
P30164 UniProt NPD GO	ACT1_PEA	Actin-1	0.03	-	cyt	0	Cytoplasm				376
P22131 UniProt NPD GO	ACT1_PHYIN	Actin-1	0.03	-	cyt	0	Cytoplasm				376
P53504 UniProt NPD GO	ACT1_SORBI	Actin-1	0.03	-	cyt	0	Cytoplasm				377
P30165 UniProt NPD GO	ACT2_PEA	Actin-2	0.03	-	cyt	0	Cytoplasm				376
P22132 UniProt NPD GO	ACT2_PHYIN	Actin-2	0.03	-	cyt	0	Cytoplasm				375
Q9Y896 UniProt NPD GO	ACT2_SCHCO	Actin-2	0.03	-	cyt	0	Cytoplasm				375
Q61WW9 UniProt NPD GO	ARP3_CAEBR	Actin-like protein 3 (Actin-related protein 3)	0.03	-	cyt	0					426
Q9N4I0 UniProt NPD GO	ARP3_CAEEL	Actin-like protein 3 (Actin-related protein 3)	0.03	-	cyt	0					425
Q9QY84 UniProt NPD GO	ACL7A_MOUSE	Actin-like protein 7A (Actin-like-7-alpha) (T-actin-2) (Testis-specific actin-2)	0.03	-	cyt	0		flagellum (sensu Eukaryota) [IDA] male germ cell nucleus [IDA]			440
Q5AW89 UniProt NPD GO	ARP4_EMENI	Actin-like protein arp4	0.03	-	cyt	0	Nucleus (By similarity)				472
Q9CVB6 UniProt NPD GO	ARPC2_MOUSE	Actin-related protein 2/3 complex subunit 2 (ARP2/3 complex 34 kDa subunit) (p34-ARC)	0.03	-	cyt	0		Arp2/3 protein complex [TAS] focal adhesion [IDA]			300
Q8BXF8 UniProt NPD GO	ARPM1_MOUSE	Actin-related protein M1 homolog	0.03	-	nuc	0					369
P00785 UniProt NPD GO	ACTN_ACTCH	Actinidain precursor (EC 3.4.22.14) (Actinidin) (Allergen Act c 1)	0.03	-	exc	1 *				2ACT	380
Q61271 UniProt NPD GO	ACV1B_MOUSE	Activin receptor type 1B precursor (EC 2.7.11.30) (ACTR-IB) (Serine/threonine-protein kinase recepto ...	0.03	-	nuc	1 *	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]			505
P80202 UniProt NPD GO	ACV1B_RAT	Activin receptor type 1B precursor (EC 2.7.11.30) (ACTR-IB) (Serine/threonine-protein kinase recepto ...	0.03	-	nuc	1 *	Membrane; single-pass type I membrane protein				505
P37167 UniProt NPD GO	ACTP_ACACA	Actophorin	0.03	-	cyt	0	Cytoplasm			1CNU	137
Q12618 UniProt NPD GO	ACO1_AJECA	Acyl-CoA desaturase (EC 1.14.19.1) (Stearoyl-CoA desaturase) (Fatty acid desaturase) (Delta(9)-desat ...	0.03	-	mit	4	Membrane; multi-pass membrane protein (By similarity)				476
Q8BWN8 UniProt NPD GO	ACOT4_MOUSE	Acyl-coenzyme A thioesterase 4 (EC 3.1.2.2) (Acyl-CoA thioesterase 4) (Peroxisomal acyl coenzyme A t ...	0.03	-	mit	0	Peroxisome (Potential)	peroxisome [TAS]			421
Q6CGL4 UniProt NPD GO	APTH1_YARLI	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.03	-	cyt	0	Cytoplasm (By similarity)				227
Q5RBR7 UniProt NPD GO	LYPA1_PONPY	Acyl-protein thioesterase 1 (EC 3.1.2.-) (Lysophospholipase 1) (Lysophospholipase I)	0.03	-	cyt	0	Cytoplasm (By similarity)				230
P25154 UniProt NPD GO	ACPH_RABIT	Acylamino-acid-releasing enzyme (EC 3.4.19.1) (AARE) (Acyl-peptide hydrolase) (APH) (Acylaminoacyl-p ...	0.03	-		0	Cytoplasm				6
P56376 UniProt NPD GO	ACYP1_MOUSE	Acylphosphatase-1 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 1) (Acylphosphatase, organ-common typ ...	0.03	-	cyt	0					98
P41500 UniProt NPD GO	ACYP1_BOVIN	Acylphosphatase-1 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 1) (Acylphosphatase, organ-common typ ...	0.03	-	cyt	0				2ACY	100
P07033 UniProt NPD GO	ACYP2_BOVIN	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (Acylphosphatase, muscle type isoz ...	0.03	-	nuc	0					98
P35744 UniProt NPD GO	ACYP2_CAVPO	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (Acylphosphatase, muscle type isoz ...	0.03	-	cyt	0					98
P14621 UniProt NPD GO	ACYP2_HUMAN	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (Acylphosphatase, muscle type isoz ...	0.03	-	nuc	0			102595		98
P00819 UniProt NPD GO	ACYP2_PIG	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (Acylphosphatase, muscle type isoz ...	0.03	-	nuc	0					98
P49892 UniProt NPD GO	AA1R_CHICK	Adenosine A1 receptor	0.03	-	end	7 *	Membrane; multi-pass membrane protein				324
Q60613 UniProt NPD GO	AA2AR_MOUSE	Adenosine A2a receptor	0.03	-	end	7 *	Membrane; multi-pass membrane protein	membrane fraction [IDA]			410
Q9SF85 UniProt NPD GO	ADK1_ARATH	Adenosine kinase 1 (EC 2.7.1.20) (AK 1) (Adenosine 5'-phosphotransferase 1)	0.03	-	cyt	0					344
Q9LZG0 UniProt NPD GO	ADK2_ARATH	Adenosine kinase 2 (EC 2.7.1.20) (AK 2) (Adenosine 5'-phosphotransferase 2)	0.03	-	cyt	0					345
P35007 UniProt NPD GO	SAHH_CATRO	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)	0.03	-	cyt	0					485
Q12663 UniProt NPD GO	SAHH_PNECA	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) (Fragment)	0.03	-	cyt	0					440
P83783 UniProt NPD GO	SAHH_CANAL	Adenosylhomocysteinase (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) (Fragments)	0.03	-		0	Cytoplasm				20
Q08480 UniProt NPD GO	KAD2_ORYSA	Adenylate kinase B (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.03	-	cyt	0					243
P18829 UniProt NPD GO	AKH1_SCHGR	Adipokinetic prohormone type 1 precursor [Contains: Adipokinetic hormone 1 (Adipokinetic hormone I) ...	0.03	-	exc	1 *	Secreted protein				63
P55319 UniProt NPD GO	AKH1_LOCMI	Adipokinetic prohormone type 1 precursor [Contains: Adipokinetic hormone 1 (Adipokinetic hormone I) ...	0.03	-	exc	1 *	Secreted protein				63
P18830 UniProt NPD GO	AKH1_SCHNI	Adipokinetic prohormone type 1 precursor [Contains: Adipokinetic hormone 1 (Adipokinetic hormone I) ...	0.03	-	exc	1 *	Secreted protein				63
P19872 UniProt NPD GO	AKH3_LOCMI	Adipokinetic prohormone type 3 precursor [Contains: Adipokinetic hormone 3 (Adipokinetic hormone III ...	0.03	-	end	1 *	Secreted protein				77
Q3Y5Z3 UniProt NPD GO	ADIPO_BOVIN	Adiponectin precursor (Adipocyte, C1q and collagen domain-containing protein) (30 kDa adipocyte comp ...	0.03	-	exc	0	Secreted protein (By similarity)				240
Q86V24 UniProt NPD GO	ADR2_HUMAN	Adiponectin receptor protein 2 (Progestin and adipoQ receptor family member II)	0.03	-	end	7	Membrane; multi-pass membrane protein. Localized to the cell membrane and intracellular organelles	integral to membrane [ISS]	607946		386
P34974 UniProt NPD GO	ACTHR_BOVIN	Adrenocorticotropic hormone receptor (ACTH receptor) (ACTH-R) (Melanocortin receptor 2) (MC2-R) (Adr ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein				297
P46656 UniProt NPD GO	ADX_MOUSE	Adrenodoxin, mitochondrial precursor (Adrenal ferredoxin) (Ferredoxin-1)	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			188
P24483 UniProt NPD GO	ADX_RAT	Adrenodoxin, mitochondrial precursor (Adrenal ferredoxin) (Ferredoxin-1)	0.03	-	mit	0	Mitochondrion; mitochondrial matrix				188

You are viewing entries 79051 to 79100 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.