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
Q6AYY8 UniProt NPD GO	ACATN_RAT	Acetyl-coenzyme A transporter 1 (AT-1) (Acetyl-CoA transporter) (Solute carrier family 33 member 1)	0.12	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				550
P04758 UniProt NPD GO	ACHB_BOVIN	Acetylcholine receptor protein subunit beta precursor	0.12	-	end	4	Membrane; multi-pass membrane protein				505
P11230 UniProt NPD GO	ACHB_HUMAN	Acetylcholine receptor protein subunit beta precursor	0.12	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	608931		501
Q86GC8 UniProt NPD GO	ACES_CULPI	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.12	-	nuc	0					702
Q92484 UniProt NPD GO	ASM3A_HUMAN	Acid sphingomyelinase-like phosphodiesterase 3a precursor (EC 3.1.4.-) (ASM-like phosphodiesterase 3 ...	0.12	-	mit	0	Secreted protein (By similarity)	extracellular region [NAS]			453
P41802 UniProt NPD GO	ELI1_PHYCR	Acidic elicitin A1 precursor	0.12	-	exc	0	Secreted protein				118
P24902 UniProt NPD GO	ACT_PINCO	Actin (Fragment)	0.12	-	cyt	0	Cytoplasm				161
P08023 UniProt NPD GO	ACTA_CHICK	Actin, aortic smooth muscle (Alpha-actin)	0.12	-	cyt	0	Cytoplasm			1LVT	377
P84336 UniProt NPD GO	ACTB_CAMDR	Actin, cytoplasmic 1 (Beta-actin)	0.12	-	cyt	0	Cytoplasm				375
P12717 UniProt NPD GO	ACTM_PISOC	Actin, muscle	0.12	-	cyt	0	Cytoplasm				376
P53459 UniProt NPD GO	ACT6_DIPDE	Actin-6 (Fragment)	0.12	-	cyt	0	Cytoplasm				373
P45888 UniProt NPD GO	ARP2_DROME	Actin-like protein 2 (Actin-related protein 2) (Actin-like protein 14D)	0.12	-	cyt	0					394
Q9Z2N8 UniProt NPD GO	ACL6A_MOUSE	Actin-like protein 6A (53 kDa BRG1-associated factor A) (Actin-related protein Baf53a)	0.12	-	cyt	0	Nucleus (By similarity)	chromatin remodeling complex [IDA] nucleus [IDA]			429
O96019 UniProt NPD GO	ACL6A_HUMAN	Actin-like protein 6A (53 kDa BRG1-associated factor A) (Actin-related protein Baf53a) (ArpNbeta)	0.12	-	cyt	0	Nucleus	TIP60 histone acetyltransferase complex [IDA]	604958		429
Q12509 UniProt NPD GO	ARP6_YEAST	Actin-like protein ARP6	0.12	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] SWR1 complex [IPI]			438
Q92747 UniProt NPD GO	ARC1A_HUMAN	Actin-related protein 2/3 complex subunit 1A (SOP2-like protein)	0.12	-	cyt	0		actin cytoskeleton [TAS]	604220		370
Q8K348 UniProt NPD GO	ACV1C_MOUSE	Activin receptor type 1C precursor (EC 2.7.11.30) (ACTR-IC) (Activin receptor-like kinase 7) (ALK-7) ...	0.12	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)	activin receptor complex [ISS]			493
P17650 UniProt NPD GO	ACP2_BRANA	Acyl carrier protein, chloroplast precursor (ACP) (ACP09) (Clone 22C01)	0.12	-	mit	0	Plastid; chloroplast				134
Q6BRD5 UniProt NPD GO	ACOX_DEBHA	Acyl-coenzyme A oxidase (EC 1.3.3.6) (Acyl-CoA oxidase)	0.12	-	cyt	0	Peroxisome (By similarity)				706
P21133 UniProt NPD GO	AAAA_EMENI	Acyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase 40 kDa form (EC 2.3.1.164) (Isopenicillin-N ...	0.12	-	cyt	0					357
Q28FK7 UniProt NPD GO	ACYP1_XENTR	Acylphosphatase-1 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 1)	0.12	-	cyt	0					98
Q5R630 UniProt NPD GO	NECP1_PONPY	Adaptin ear-binding coat-associated protein 1 (NECAP-1)	0.12	-	nuc	0	Membrane-associated; with clathrin-coated vesicles. Colocalizes with AP-2 at the plasma membrane (By ...				275
Q64414 UniProt NPD GO	APT_GERCA	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.12	-	cyt	0	Cytoplasm				180
P47958 UniProt NPD GO	APT_STOLO	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.12	-	cyt	0	Cytoplasm				180
P21900 UniProt NPD GO	PURA_DICDI	Adenylosuccinate synthetase (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPSase)	0.12	-	cyt	0	Cytoplasm (By similarity)				427
Q96529 UniProt NPD GO	PURA_ARATH	Adenylosuccinate synthetase, chloroplast precursor (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPS ...	0.12	-	mit	0	Plastid; chloroplast			1DJ2	490
P37193 UniProt NPD GO	ADXH_DROME	Adrenodoxin-like protein, mitochondrial precursor	0.12	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				172
P83944 UniProt NPD GO	ALR_PENMO	Alanine racemase (EC 5.1.1.1) (Fragments)	0.12	-	cyt	0					120
Q9SR86 UniProt NPD GO	AGT23_ARATH	Alanine--glyoxylate aminotransferase 2 homolog 3, mitochondrial precursor (EC 2.6.1.44) (Beta-alanin ...	0.12	-	mit	0	Mitochondrion (Potential)				481
Q9QYY9 UniProt NPD GO	ADH4_MOUSE	Alcohol dehydrogenase 4 (EC 1.1.1.1) (Alcohol dehydrogenase class II) (Alcohol dehydrogenase II) (AD ...	0.12	-	mit	0	Cytoplasm (By similarity)			1E3L	376
Q64563 UniProt NPD GO	ADH4_RAT	Alcohol dehydrogenase 4 (EC 1.1.1.1) (Alcohol dehydrogenase class II) (Alcohol dehydrogenase II) (AD ...	0.12	-	mit	0	Cytoplasm (By similarity)				376
Q27640 UniProt NPD GO	ALDH_ENCBU	Aldehyde dehydrogenase (EC 1.2.1.3) (Aldehyde dehydrogenase [NAD+])	0.12	-	cyt	0					497
P30838 UniProt NPD GO	AL3A1_HUMAN	Aldehyde dehydrogenase, dimeric NADP-preferring (EC 1.2.1.5) (ALDH class 3) (ALDHIII)	0.12	-	mit	0	Cytoplasm	cytosol [ISS]	100660		453
Q95JH7 UniProt NPD GO	AK1C1_MACFA	Aldo-keto reductase family 1 member C1 homolog (EC 1.-.-.-) (20-alpha-hydroxysteroid dehydrogenase) ...	0.12	-	cyt	0	Cytoplasm (By similarity)				323
Q95JH6 UniProt NPD GO	AK1C1_MACFU	Aldo-keto reductase family 1 member C1 homolog (EC 1.-.-.-) (20-alpha-hydroxysteroid dehydrogenase) ...	0.12	-	cyt	0	Cytoplasm (By similarity)				323
Q03420 UniProt NPD GO	ALP_TRIAT	Alkaline proteinase precursor (EC 3.4.21.-) (ALP)	0.12	-	exc	1 *	Secreted protein				409
Q68GV9 UniProt NPD GO	ALP_LECPS	Alkaline serine protease ver112 precursor (EC 3.4.21.-)	0.12	-	exc	0	Secreted protein				382
P16282 UniProt NPD GO	PHAC_CYAPA	Allophycocyanin alpha-B chain (Allophycocyanin gamma chain)	0.12	-	cyt	0	Plastid; cyanelle				162
O74878 UniProt NPD GO	ALG11_SCHPO	Alpha-1,2-mannosyltransferase alg11 (EC 2.4.1.-) (Asparagine-linked glycosylation protein 11) (Galac ...	0.12	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				471
Q6CWQ0 UniProt NPD GO	ALG2_KLULA	Alpha-1,3-mannosyltransferase ALG2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransfe ...	0.12	-	cyt	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				503
P43636 UniProt NPD GO	ALG2_YEAST	Alpha-1,3-mannosyltransferase ALG2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransfe ...	0.12	-	cyt	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS]			503
Q91175 UniProt NPD GO	ADA1A_ORYLA	Alpha-1A adrenergic receptor (Alpha 1A-adrenoceptor) (Alpha 1A-adrenoreceptor) (MAR1)	0.12	-	end	7 *	Membrane; multi-pass membrane protein				470
Q64686 UniProt NPD GO	SIA7C_RAT	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 (EC 2.4.99.-) (GalNAc alpha-2,6-sialyltr ...	0.12	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				305
Q6ZXD2 UniProt NPD GO	SIA8A_BOVIN	Alpha-N-acetylneuraminide alpha-2,8-sialyltransferase (EC 2.4.99.8) (Ganglioside GD3 synthase) (Gang ...	0.12	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				356
P02662 UniProt NPD GO	CAS1_BOVIN	Alpha-S1-casein precursor	0.12	-	exc	0	Secreted protein				214
P27932 UniProt NPD GO	AMY3A_ORYSA	Alpha-amylase isozyme 3A precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.12	-	vac	1 *					440
P16969 UniProt NPD GO	IAA_HORVU	Alpha-amylase/trypsin inhibitor precursor	0.12	-	exc	1 *	Secreted protein (Potential)				147
P61162 UniProt NPD GO	ACTZ_CANFA	Alpha-centractin (Centractin) (Centrosome-associated actin homolog) (Actin-RPV) (ARP1)	0.12	-	cyt	0					376
P61163 UniProt NPD GO	ACTZ_HUMAN	Alpha-centractin (Centractin) (Centrosome-associated actin homolog) (Actin-RPV) (ARP1)	0.12	-	cyt	0			605143		376
P61164 UniProt NPD GO	ACTZ_MOUSE	Alpha-centractin (Centractin) (Centrosome-associated actin homolog) (Actin-RPV) (ARP1)	0.12	-	cyt	0					376

You are viewing entries 60801 to 60850 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.