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
Q6DE05 UniProt NPD GO	ACYP1_XENLA	Acylphosphatase-1 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 1)	0.11	-	cyt	0					99
Q9CR95 UniProt NPD GO	NECP1_MOUSE	Adaptin ear-binding coat-associated protein 1 (NECAP-1)	0.11	-	nuc	0	Membrane-associated; with clathrin-coated vesicles. Colocalizes with AP-2 at the plasma membrane	clathrin vesicle coat [IDA] coated pit [IDA]		1TQZ	275
P47952 UniProt NPD GO	APT_CRIGR	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.11	-	cyt	0	Cytoplasm				180
Q91ZN5 UniProt NPD GO	S35B2_MOUSE	Adenosine 3'-phospho 5'-phosphosulfate transporter 1 (PAPS transporter 1) (Solute carrier family 35 ...	0.11	-	end	10 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				431
P56658 UniProt NPD GO	ADA_BOVIN	Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase)	0.11	-	cyt	0				2BGN	362
P00813 UniProt NPD GO	ADA_HUMAN	Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase)	0.11	-	cyt	0			102700	1M7M	362
Q64640 UniProt NPD GO	ADK_RAT	Adenosine kinase (EC 2.7.1.20) (AK) (Adenosine 5'-phosphotransferase)	0.11	-	cyt	0				1LNJ	361
P33075 UniProt NPD GO	KAD1_SCHPO	Adenylate kinase (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.11	-	cyt	0					220
O24464 UniProt NPD GO	KAD_PRUAR	Adenylate kinase (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.11	-	mit	0					231
O82514 UniProt NPD GO	KAD1_ARATH	Adenylate kinase 1 (EC 2.7.4.3) (ATP-AMP transphosphorylase 1)	0.11	-	cyt	0					246
P07170 UniProt NPD GO	KAD1_YEAST	Adenylate kinase cytosolic (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.11	-	cyt	0	Cytoplasm	cytoplasm [TAS] mitochondrial intermembrane space [TAS]		3AKY	222
P00569 UniProt NPD GO	KAD1_RABIT	Adenylate kinase isoenzyme 1 (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK1) (Myokinase)	0.11	-	cyt	0	Cytoplasm				194
Q5Y4Y5 UniProt NPD GO	TXAG_AGEOR	Agelenin precursor	0.11	-	exc	0	Secreted protein				70
Q29011 UniProt NPD GO	PGCA_PIG	Aggrecan core protein (Cartilage-specific proteoglycan core protein) (CSPCP) (Fragments)	0.11	-	cyt	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				537
Q9NRG9 UniProt NPD GO	AAAS_HUMAN	Aladin (Adracalin)	0.11	-	cyt	0		nuclear pore [IDA]	605378		546
P81113 UniProt NPD GO	ABA3_TRIAB	Alboaggregin-A subunit 3	0.11	-	cyt	0	Secreted protein				125
P30907 UniProt NPD GO	AL3A1_BOVIN	Aldehyde dehydrogenase, dimeric NADP-preferring (EC 1.2.1.5) (ALDH class 3) (Corneal 15.8 kDa protei ...	0.11	-	cyt	0	Cytoplasm (By similarity)				239
Q04828 UniProt NPD GO	AK1C1_HUMAN	Aldo-keto reductase family 1 member C1 (EC 1.1.1.-) (20-alpha-hydroxysteroid dehydrogenase) (EC 1.1. ...	0.11	-	cyt	0	Cytoplasm	cytosol [IDA]	600449	1MRQ	323
Q8R4X1 UniProt NPD GO	ASAH3_MOUSE	Alkaline ceramidase 1 (EC 3.5.1.23) (Alkaline CDase-1) (AlkCDase 1) (maCER1) (Acylsphingosine deacyl ...	0.11	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			273
O97157 UniProt NPD GO	ADAS_TRYBB	Alkyldihydroxyacetonephosphate synthase (EC 2.5.1.26) (Alkyl-DHAP synthase) (Alkylglycerone-phosphat ...	0.11	-	cyt	0	Peroxisome (By similarity)				613
Q64FG0 UniProt NPD GO	RETST_MACFA	All-trans-retinol 13,14-reductase precursor (EC 1.3.99.23) (All-trans-13,14-dihydroretinol saturase) ...	0.11	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)	endoplasmic reticulum membrane [ISS] nuclear outer membrane [ISS]			610
Q00075 UniProt NPD GO	TPSA_ASPNG	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] 1 (EC 2.4.1.15) (Trehalose-6-phosphate syntha ...	0.11	-	cyt	0					517
Q5BKT4 UniProt NPD GO	AG10A_HUMAN	Alpha-1,2-glucosyltransferase ALG10-A (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10-A) (Asparagine ...	0.11	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				473
P53954 UniProt NPD GO	ALG11_YEAST	Alpha-1,2-mannosyltransferase ALG11 (EC 2.4.1.-) (Asparagine-linked glycosylation protein 11)	0.11	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	endoplasmic reticulum [IDA]			548
Q6FJJ9 UniProt NPD GO	ALG2_CANGA	Alpha-1,3-mannosyltransferase ALG2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransfe ...	0.11	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				458
Q8X0H8 UniProt NPD GO	ALG2_NEUCR	Alpha-1,3-mannosyltransferase alg-2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransf ...	0.11	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				471
Q9WUV2 UniProt NPD GO	SIA7C_MOUSE	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 (EC 2.4.99.-) (GalNAc alpha-2,6-sialyltr ...	0.11	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				305
Q92455 UniProt NPD GO	ABF1_TRIRE	Alpha-N-arabinofuranosidase precursor (EC 3.2.1.55) (Arabinosidase)	0.11	-	mit	0					500
P83186 UniProt NPD GO	BRA_BASAL	Alpha-basrubrin (Fragment)	0.11	-		0					20
P50982 UniProt NPD GO	CXA1_CONER	Alpha-conotoxin EI	0.11	-		0	Secreted protein				18
P04824 UniProt NPD GO	MEL1_YEAST	Alpha-galactosidase 1 precursor (EC 3.2.1.22) (Melibiase 1) (Alpha-D-galactoside galactohydrolase 1) ...	0.11	-	mit	0					471
P56526 UniProt NPD GO	AGLU_ASPNG	Alpha-glucosidase precursor (EC 3.2.1.20) (Maltase)	0.11	-	end	0					985
Q9C0Y4 UniProt NPD GO	AGLU_SCHPO	Alpha-glucosidase precursor (EC 3.2.1.20) (Maltase)	0.11	-	cyt	1 *	Secreted protein	extracellular region [IDA]			969
Q17058 UniProt NPD GO	MAL1_APIME	Alpha-glucosidase precursor (EC 3.2.1.20) (Maltase)	0.11	-	vac	0					567
P00710 UniProt NPD GO	LALBA_CAMDR	Alpha-lactalbumin (Lactose synthase B protein)	0.11	-	nuc	0	Secreted protein				123
O22048 UniProt NPD GO	AOX1C_ARATH	Alternative oxidase 1c, mitochondrial precursor (EC 1.-.-.-)	0.11	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				329
Q26710 UniProt NPD GO	AOX_TRYBB	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.11	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				329
P52418 UniProt NPD GO	PUR1_SOYBN	Amidophosphoribosyltransferase, chloroplast precursor (EC 2.4.2.14) (Glutamine phosphoribosylpyropho ...	0.11	-	mit	0	Plastid; chloroplast				569
Q5NU32 UniProt NPD GO	AOFA_HORSE	Amine oxidase [flavin-containing] A (EC 1.4.3.4) (Monoamine oxidase type A) (MAO-A)	0.11	-	cyt	1	Mitochondrion; mitochondrial outer membrane (By similarity)				527
Q5RE60 UniProt NPD GO	AOFA_PONPY	Amine oxidase [flavin-containing] A (EC 1.4.3.4) (Monoamine oxidase type A) (MAO-A)	0.11	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity)				527
P41948 UniProt NPD GO	MEP2_YEAST	Ammonium transporter MEP2	0.11	-	end	11 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			499
P01019 UniProt NPD GO	ANGT_HUMAN	Angiotensinogen precursor [Contains: Angiotensin-1 (Angiotensin I) (Ang I); Angiotensin-2 (Angiotens ...	0.11	-	mit	0	Secreted protein	extracellular region [NAS] soluble fraction [TAS]	145500		485
Q9GLN8 UniProt NPD GO	ANGT_PANTR	Angiotensinogen precursor [Contains: Angiotensin-1 (Angiotensin I) (Ang I); Angiotensin-2 (Angiotens ...	0.11	-	mit	0	Secreted protein (By similarity)				485
Q9Y576 UniProt NPD GO	ASB1_HUMAN	Ankyrin repeat and SOCS box protein 1 (ASB-1)	0.11	-	cyt	0		intracellular [IC]	605758		335
Q8N8A2 UniProt NPD GO	ANR44_HUMAN	Ankyrin repeat domain-containing protein 44	0.11	-	cyt	0					944
P18483 UniProt NPD GO	TRPG_ASPAW	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.11	-	nuc	0					768
Q5KC22 UniProt NPD GO	TRPG_CRYNE	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.11	-	mit	0					752
P58335 UniProt NPD GO	ANTR2_HUMAN	Anthrax toxin receptor 2 precursor (Capillary morphogenesis gene 2 protein) (CMG-2)	0.11	-	end	1 *	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Endoplasmic reticulum; end ...		228600	1TZN	489
P82010 UniProt NPD GO	AX2_BETVU	Antifungal protein AX2	0.11	-	nuc	0					46
Q27001 UniProt NPD GO	AH4_TOXGO	Antigen H4 (Fragment)	0.11	-	nuc	0					96

You are viewing entries 62301 to 62350 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.