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
O24396 UniProt NPD GO	PURA_WHEAT	Adenylosuccinate synthetase, chloroplast precursor (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPS ...	0.08	-	mit	0	Plastid; chloroplast			1DJ3	476
Q01518 UniProt NPD GO	CAP1_HUMAN	Adenylyl cyclase-associated protein 1 (CAP 1)	0.08	-	nuc	0	Cell membrane (By similarity)			1K8F	474
P35808 UniProt NPD GO	AKH2_SCHGR	Adipokinetic prohormone type 2 precursor [Contains: Adipokinetic hormone 2 (Adipokinetic hormone II) ...	0.08	-	nuc	0	Secreted protein				39
Q9NST1 UniProt NPD GO	ADPN_HUMAN	Adiponutrin (iPLA2-epsilon) (Calcium-independent phospholipase A2-epsilon) (Patatin-like phospholipa ...	0.08	-	cyt	0	Membrane; single-pass membrane protein	integral to membrane [ISS] membrane [ISS]	609567		481
Q15847 UniProt NPD GO	APM2_HUMAN	Adipose most abundant gene transcript 2	0.08	-	cyt	0					76
P10109 UniProt NPD GO	ADX_HUMAN	Adrenodoxin, mitochondrial precursor (Adrenal ferredoxin) (Ferredoxin-1) (Hepatoredoxin)	0.08	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	103260		184
P80515 UniProt NPD GO	CU19_ARADI	Adult-specific rigid cuticular protein 11.9 (ACP 11.9)	0.08	-	cyt	0					120
P07164 UniProt NPD GO	AEQ1_AEQVI	Aequorin-1 precursor	0.08	-	cyt	0				1SL8	196
P38918 UniProt NPD GO	ARK71_RAT	Aflatoxin B1 aldehyde reductase member 1 (EC 1.-.-.-) (AFB1-AR) (rAFAR1)	0.08	-	cyt	0	Cytoplasm			1GVE	327
P43567 UniProt NPD GO	AGX1_YEAST	Alanine--glyoxylate aminotransferase 1 (EC 2.6.1.44)	0.08	-	cyt	0		mitochondrion [IDA]		2BKW	385
P37898 UniProt NPD GO	AAP1_YEAST	Alanine/arginine aminopeptidase (EC 3.4.11.-)	0.08	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			856
P21894 UniProt NPD GO	SYA_BOMMO	Alanyl-tRNA synthetase (EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS)	0.08	-	cyt	0					967
Q9NG42 UniProt NPD GO	ADH_DROEQ	Alcohol dehydrogenase (EC 1.1.1.1)	0.08	-	cyt	0					254
Q9NG40 UniProt NPD GO	ADH_DROIN	Alcohol dehydrogenase (EC 1.1.1.1)	0.08	-	cyt	0					254
Q9U8S9 UniProt NPD GO	ADH_DROPU	Alcohol dehydrogenase (EC 1.1.1.1)	0.08	-	cyt	0					254
Q05114 UniProt NPD GO	ADH_DROWI	Alcohol dehydrogenase (EC 1.1.1.1)	0.08	-	cyt	0					254
P07327 UniProt NPD GO	ADH1A_HUMAN	Alcohol dehydrogenase 1A (EC 1.1.1.1) (Alcohol dehydrogenase alpha subunit)	0.08	-	nuc	0	Cytoplasm	cytoplasm [NAS]	103700	1U3T	374
P54202 UniProt NPD GO	ADH2_EMENI	Alcohol dehydrogenase 2 (EC 1.1.1.1) (Alcohol dehydrogenase II) (ADH II)	0.08	-	mit	0	Cytoplasm (By similarity)				367
P30837 UniProt NPD GO	AL1B1_HUMAN	Aldehyde dehydrogenase X, mitochondrial precursor (EC 1.2.1.3) (ALDH class 2)	0.08	-	mit	0	Mitochondrion; mitochondrial matrix		100670		517
Q9SYG7 UniProt NPD GO	AL7A1_ARATH	Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3) (Antiquitin-1)	0.08	-	nuc	0					508
Q9ZPB7 UniProt NPD GO	AL7A1_MALDO	Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3) (Antiquitin-1) (Matured fruit 60 kDa protein) ...	0.08	-	nuc	0					507
P81178 UniProt NPD GO	ALDH2_MESAU	Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) (ALDH class 2) (ALDH1) (ALDH-E2)	0.08	-	cyt	0	Mitochondrion; mitochondrial matrix				500
P11884 UniProt NPD GO	ALDH2_RAT	Aldehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.3) (ALDH class 2) (ALDH1) (ALDH-E2)	0.08	-	mit	0	Mitochondrion; mitochondrial matrix			1WT4	519
P05091 UniProt NPD GO	ALDH2_HUMAN	Aldehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.3) (ALDH class 2) (ALDHI) (ALDH-E2)	0.08	-	mit	0	Mitochondrion; mitochondrial matrix		100650	1ZUM	517
Q25417 UniProt NPD GO	ALDH2_LEITA	Aldehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.3) (ALDH class 2) (P51)	0.08	-	mit	0	Mitochondrion				498
O96759 UniProt NPD GO	ADAS_DICDI	Alkyldihydroxyacetonephosphate synthase (EC 2.5.1.26) (Alkyl-DHAP synthase) (Alkylglycerone-phosphat ...	0.08	-	cyt	0	Peroxisome				611
P54962 UniProt NPD GO	BLG4_BLAGE	Allergen Bla g 4 precursor (Bla g IV) (Fragment)	0.08	-	cyt	0					182
Q92410 UniProt NPD GO	TPS1_CANAL	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] (EC 2.4.1.15) (Trehalose-6-phosphate synthase ...	0.08	-	mit	0					478
Q9H6U8 UniProt NPD GO	ALG9_HUMAN	Alpha-1,2-mannosyltransferase ALG9 (EC 2.4.1.-) (Asparagine-linked glycosylation protein 9 homolog) ...	0.08	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)		608776		611
Q6BVA4 UniProt NPD GO	ALG2_DEBHA	Alpha-1,3-mannosyltransferase ALG2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransfe ...	0.08	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				476
Q9EPH1 UniProt NPD GO	A1BG_RAT	Alpha-1B-glycoprotein precursor (Liver regeneration-related protein 1) (C44)	0.08	-	vac	0	Secreted protein (By similarity)	extracellular region [ISS]			513
P61647 UniProt NPD GO	SIA8F_HUMAN	Alpha-2,8-sialyltransferase 8F (EC 2.4.99.-) (ST8Sia VI)	0.08	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				398
P58783 UniProt NPD GO	CXVB_CONER	Alpha-A-conotoxin EIVB	0.08	-	nuc	0	Secreted protein				30
P83127 UniProt NPD GO	NAGAB_BOSIN	Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) (Alpha-galactosidase B) (Fragment)	0.08	-		0	Lysosome (By similarity)				12
P91778 UniProt NPD GO	AMY_PECMA	Alpha-amylase precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.08	-	exc	0					508
P17314 UniProt NPD GO	IAAC3_WHEAT	Alpha-amylase/trypsin inhibitor CM3 precursor (Chloroform/methanol-soluble protein CM3)	0.08	-	mit	1 *	Secreted protein				168
P69657 UniProt NPD GO	CXA1_CONBU	Alpha-conotoxin BuIA precursor	0.08	-	end	0	Secreted protein				60
P56973 UniProt NPD GO	CXA1_CONCN	Alpha-conotoxin CnIA [Contains: Alpha-conotoxin CnIB]	0.08	-		0	Secreted protein			1B45	14
P01521 UniProt NPD GO	CXA1_CONMA	Alpha-conotoxin MI (Alpha-MI) (M1)	0.08	-		0	Secreted protein				14
P28879 UniProt NPD GO	CXAS2_CONST	Alpha-conotoxin SII precursor (S2)	0.08	-	exc	1 *	Secreted protein				72
P69747 UniProt NPD GO	CXA1A_CONVC	Alpha-conotoxin Vc1A precursor (Alpha-Vc1A) (Vc1.1) (ACV1)	0.08	-	vac	1 *	Secreted protein			2H8S	66
Q03647 UniProt NPD GO	MEL_SACPS	Alpha-galactosidase precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrolase) (MELx ...	0.08	-	exc	0					471
P28546 UniProt NPD GO	LALBA_EQUAS	Alpha-lactalbumin (Lactose synthase B protein)	0.08	-	nuc	0	Secreted protein				123
P93798 UniProt NPD GO	SNAA_VITVI	Alpha-soluble NSF attachment protein (Alpha-SNAP) (N-ethylmaleimide-sensitive factor attachment prot ...	0.08	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				289
O23913 UniProt NPD GO	AOX1B_ARATH	Alternative oxidase 1b, mitochondrial precursor (EC 1.-.-.-)	0.08	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable). Mitochondrial, ...				325
O74180 UniProt NPD GO	AOX_ASPNG	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.08	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				351
Q92367 UniProt NPD GO	AAP1_SCHPO	Amino-acid permease 1	0.08	-	end	12	Membrane; multi-pass membrane protein (Probable)				594
Q99JB7 UniProt NPD GO	AMNLS_MOUSE	Amnionless protein precursor	0.08	-	end	1	Membrane; single-pass type I membrane protein (Potential)	apical part of cell [IDA]			458
P29259 UniProt NPD GO	AH1_PRUSE	Amygdalin beta-glucosidase 1 (EC 3.2.1.117) (Amygdalin beta-glucosidase I) (Amygdalin hydrolase isoz ...	0.08	-		0					16
O74358 UniProt NPD GO	APC13_SCHPO	Anaphase-promoting complex subunit 13 (20S cyclosome/APC complex protein apc13)	0.08	-	cyt	0		anaphase-promoting complex [IDA]			135

You are viewing entries 67551 to 67600 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.