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
Q6A1I3 UniProt NPD GO	AN32B_SHEEP	Acidic leucine-rich nuclear phosphoprotein 32 family member B (Leucine-rich acidic nuclear protein) ...	0.24	-	nuc	0	Nucleus. Accumulates in the nuclei at the S phase				261
P48038 UniProt NPD GO	ACRO_RABIT	Acrosin precursor (EC 3.4.21.10) [Contains: Acrosin light chain; Acrosin heavy chain]	0.24	-	nuc	0					431
P10994 UniProt NPD GO	ACTS_PLEWA	Actin, alpha skeletal muscle (Fragment)	0.24	-	nuc	0	Cytoplasm				125
Q9P7X7 UniProt NPD GO	ARP4_SCHPO	Actin-like protein arp4	0.24	-	cyt	0	Nucleus (By similarity)	H4/H2A histone acetyltransferase complex [IDA] nucleus [IDA]			433
P27039 UniProt NPD GO	AVR2A_XENLA	Activin receptor type 2A precursor (EC 2.7.11.30) (Activin receptor type II) (ACTR-II)	0.24	-	end	1	Membrane; single-pass type I membrane protein				514
P27038 UniProt NPD GO	AVR2A_MOUSE	Activin receptor type 2A precursor (EC 2.7.11.30) (Activin receptor type IIA) (ACTR-IIA)	0.24	-	end	1	Membrane; single-pass type I membrane protein			1LX5	513
P38444 UniProt NPD GO	AVR2A_RAT	Activin receptor type 2A precursor (EC 2.7.11.30) (Activin receptor type IIA) (ACTR-IIA)	0.24	-	end	1	Membrane; single-pass type I membrane protein	activin receptor complex [TAS]		1NYU	513
P27037 UniProt NPD GO	AVR2A_HUMAN	Activin receptor type 2A precursor (EC 2.7.11.30) (Activin receptor type IIA) (ACTR-IIA) (ACTRIIA)	0.24	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	102581		513
P13011 UniProt NPD GO	ACOD2_MOUSE	Acyl-CoA desaturase 2 (EC 1.14.19.1) (Stearoyl-CoA desaturase 2) (Fatty acid desaturase 2) (Delta(9) ...	0.24	-	nuc	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum [IDA]			358
P32062 UniProt NPD GO	STAD_LINUS	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.24	-	mit	0	Plastid; chloroplast. In green tissue, found in chloroplasts. Plastid. In non-photosynthetic tissue, ...				396
Q6FY63 UniProt NPD GO	ACOX_CANGA	Acyl-coenzyme A oxidase (EC 1.3.3.6) (Acyl-CoA oxidase)	0.24	-	cyt	0	Peroxisome (By similarity)				748
P06598 UniProt NPD GO	ACOX4_CANTR	Acyl-coenzyme A oxidase 4 (EC 1.3.3.6) (Acyl-CoA oxidase 4) (PXP-4) (Peroxisomal fatty acyl-CoA oxid ...	0.24	-	cyt	0	Peroxisome				708
P13676 UniProt NPD GO	ACPH_RAT	Acylamino-acid-releasing enzyme (EC 3.4.19.1) (AARE) (Acyl-peptide hydrolase) (APH) (Acylaminoacyl-p ...	0.24	-	nuc	0	Cytoplasm				732
Q8N142 UniProt NPD GO	PURA1_HUMAN	Adenylosuccinate synthetase isozyme 1 (EC 6.3.4.4) (IMP--aspartate ligase 1) (AdSS 1) (AMPSase 1)	0.24	-	cyt	0	Cytoplasm (By similarity)			2GJO	457
Q39529 UniProt NPD GO	LEC2_CLALU	Agglutinin-2 precursor (Agglutinin II) (ClAII) (LecClAII)	0.24	-	nuc	0					290
Q8BGQ7 UniProt NPD GO	SYA_MOUSE	Alanyl-tRNA synthetase (EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS)	0.24	-	cyt	0	Cytoplasm (Potential)				968
Q80VQ0 UniProt NPD GO	AL3B1_MOUSE	Aldehyde dehydrogenase 3B1 (EC 1.2.1.5) (Aldehyde dehydrogenase 7)	0.24	-	mit	0					468
Q8K023 UniProt NPD GO	AKC1H_MOUSE	Aldo-keto reductase family 1 member C18 (EC 1.1.-.-) (20-alpha-hydroxysteroid dehydrogenase) (EC 1.1 ...	0.24	-	cyt	0	Cytoplasm (By similarity)				323
Q6P6J4 UniProt NPD GO	ALKB2_MOUSE	Alkylated repair protein alkB homolog 2	0.24	-	cyt	0					239
O12988 UniProt NPD GO	CRYAA_COLLI	Alpha crystallin A chain (Fragment)	0.24	-	cyt	0					149
P02500 UniProt NPD GO	CRYAA_TRIIN	Alpha crystallin A chain (Fragments)	0.24	-	cyt	0					161
P68280 UniProt NPD GO	CRYAA_CANFA	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.24	-	cyt	0					173
P82533 UniProt NPD GO	CRYAA_ERIEU	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.24	-	cyt	0					173
P68282 UniProt NPD GO	CRYAA_FELCA	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.24	-	cyt	0					173
P02475 UniProt NPD GO	CRYAA_PIG	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.24	-	cyt	0					173
Q75B12 UniProt NPD GO	ALG11_ASHGO	Alpha-1,2-mannosyltransferase ALG11 (EC 2.4.1.-) (Asparagine-linked glycosylation protein 11)	0.24	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				582
P01011 UniProt NPD GO	AACT_HUMAN	Alpha-1-antichymotrypsin precursor (ACT) [Contains: Alpha-1-antichymotrypsin His-Pro-less]	0.24	-	end	0	Secreted protein	extracellular region [NAS] intracellular [NAS]	107280	4CAA	423
P17475 UniProt NPD GO	A1AT_RAT	Alpha-1-antiproteinase precursor (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor)	0.24	-	exc	0	Secreted protein				411
P22599 UniProt NPD GO	A1AT2_MOUSE	Alpha-1-antitrypsin 1-2 precursor (Serine protease inhibitor 1-2) (Alpha-1 protease inhibitor 2) (Al ...	0.24	-	end	0	Secreted protein				413
O35696 UniProt NPD GO	SIA8B_MOUSE	Alpha-2,8-sialyltransferase 8B (EC 2.4.99.-) (ST8Sia II) (Sialyltransferase X) (STX) (Polysialic aci ...	0.24	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				375
P81367 UniProt NPD GO	IAA4_SORBI	Alpha-amylase inhibitor 4 (SI alpha-4)	0.24	-	nuc	0	Secreted protein				118
Q8I6R5 UniProt NPD GO	CXA2_CONIM	Alpha-conotoxin ImII precursor (Alpha-CTx ImII) (Fragment)	0.24	-		0	Secreted protein				17
P28351 UniProt NPD GO	AGAL_ASPNG	Alpha-galactosidase A precursor (EC 3.2.1.22) (Melibiase)	0.24	-	cyt	0					545
Q9FXT4 UniProt NPD GO	AGAL_ORYSA	Alpha-galactosidase precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrolase)	0.24	-	mit	1 *				1UAS	417
Q8J1Z2 UniProt NPD GO	AOX_GELSS	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.24	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				362
Q62840 UniProt NPD GO	AMBN_RAT	Ameloblastin precursor (Amelin)	0.24	-	exc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [ISS]			422
Q43077 UniProt NPD GO	AMO_PEA	Amine oxidase [copper-containing] precursor (EC 1.4.3.6)	0.24	-	exc	1 *				1W2Z	674
P58027 UniProt NPD GO	AOFA_CANFA	Amine oxidase [flavin-containing] A (EC 1.4.3.4) (Monoamine oxidase type A) (MAO-A)	0.24	-	cyt	1	Mitochondrion; mitochondrial outer membrane (By similarity)				527
P97449 UniProt NPD GO	AMPN_MOUSE	Aminopeptidase N (EC 3.4.11.2) (mAPN) (Alanyl aminopeptidase) (Microsomal aminopeptidase) (Aminopept ...	0.24	-	exc	1 *	Membrane; single-pass type II membrane protein				965
Q71MJ0 UniProt NPD GO	ANGI_GORGO	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.24	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			147
Q5VI84 UniProt NPD GO	ANGI_HORSE	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.24	-	exc	0	Secreted protein				146
P03950 UniProt NPD GO	ANGI_HUMAN	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.24	-	exc	1 *	Secreted protein	basal lamina [IDA] extracellular space [IDA] nucleolus [ISS] nucleus [IDA]	105850	2ANG	147
Q9BYF1 UniProt NPD GO	ACE2_HUMAN	Angiotensin-converting enzyme 2 precursor (EC 3.4.17.-) (ACE-related carboxypeptidase) (Angiotensin- ...	0.24	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein. Processing by ...	extracellular region [IDA]	300335	2AJF	805
Q9H672 UniProt NPD GO	ASB7_HUMAN	Ankyrin repeat and SOCS box protein 7 (ASB-7)	0.24	-	mit	0					318
Q9BGT9 UniProt NPD GO	ASB7_MACFA	Ankyrin repeat and SOCS box protein 7 (ASB-7)	0.24	-	mit	0					318
Q8WVL7 UniProt NPD GO	ANR49_HUMAN	Ankyrin repeat domain-containing protein 49 (Fetal globin-inducing factor)	0.24	-	nuc	0					239
Q8BH83 UniProt NPD GO	ANKR9_MOUSE	Ankyrin repeat domain-containing protein 9	0.24	-	nuc	0					326
P04083 UniProt NPD GO	ANXA1_HUMAN	Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) (Chromobindin-9) (p35) (Phospholipase A2 inhibi ...	0.24	-	cyt	0		cornified envelope [IDA] cytoplasm [TAS]	151690	1QLS	345
Q29471 UniProt NPD GO	ANX13_CANFA	Annexin A13 (Annexin XIII) (Annexin, intestine-specific) (ISA)	0.24	-	cyt	0	Enriched in apical vesicles (isoform B)				315
Q9VXG4 UniProt NPD GO	ANX11_DROME	Annexin-B11	0.24	-	cyt	0					322

You are viewing entries 46001 to 46050 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.