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
Q28DB5 UniProt NPD GO	ALAT2_XENTR	Alanine aminotransferase 2 (EC 2.6.1.2) (ALT2) (Glutamic--pyruvic transaminase 2) (GPT 2) (Glutamic- ...	0.19	-	cyt	0					524
P30840 UniProt NPD GO	ALDH1_ENTHI	Aldehyde dehydrogenase 1 (EC 1.2.1.3)	0.19	-	nuc	1 *					529
P43353 UniProt NPD GO	AL3B1_HUMAN	Aldehyde dehydrogenase 3B1 (EC 1.2.1.5) (Aldehyde dehydrogenase 7)	0.19	-	mit	0			600466		468
P52476 UniProt NPD GO	AL1B2_BOVIN	Aldehyde dehydrogenase X, mitochondrial (EC 1.2.1.3) (ALDHX) (ALDH class 2) (Fragment)	0.19	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				126
O54754 UniProt NPD GO	ADO_MOUSE	Aldehyde oxidase (EC 1.2.3.1) (Retinal oxidase)	0.19	-	cyt	0	Cytoplasm				1333
Q09923 UniProt NPD GO	YAKC_SCHPO	Aldo-keto reductase yakc [NADP+] (EC 1.1.1.-)	0.19	-	cyt	0					340
Q02896 UniProt NPD GO	YDC1_YEAST	Alkaline ceramidase YDC1 (EC 3.5.1.-)	0.19	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [IDA]			317
Q41233 UniProt NPD GO	ALLN2_ALLSA	Alliin lyase 2 precursor (EC 4.4.1.4) (Alliinase 2) (Cysteine sulphoxide lyase 2)	0.19	-	end	0	Vacuole				473
O12991 UniProt NPD GO	CRYAB_EUDEL	Alpha crystallin B chain (Alpha(B)-crystallin) (Fragment)	0.19	-	mit	0					52
Q99JB3 UniProt NPD GO	FUT9_RAT	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.19	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				359
Q6FWD1 UniProt NPD GO	ALG11_CANGA	Alpha-1,2-mannosyltransferase ALG11 (EC 2.4.1.-) (Asparagine-linked glycosylation protein 11)	0.19	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				505
Q8X092 UniProt NPD GO	ALG11_NEUCR	Alpha-1,2-mannosyltransferase alg-11 (EC 2.4.1.-) (Asparagine-linked glycosylation protein 11)	0.19	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				556
Q00897 UniProt NPD GO	A1AT4_MOUSE	Alpha-1-antitrypsin 1-4 precursor (Serine protease inhibitor 1-4) (Alpha-1 protease inhibitor 4)	0.19	-	end	0	Secreted protein				413
P61643 UniProt NPD GO	SIA8B_PANTR	Alpha-2,8-sialyltransferase 8B (EC 2.4.99.-) (ST8Sia II)	0.19	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				375
Q92186 UniProt NPD GO	SIA8B_HUMAN	Alpha-2,8-sialyltransferase 8B (EC 2.4.99.-) (ST8Sia II) (Sialyltransferase X) (STX)	0.19	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)		602546		375
Q9H4F1 UniProt NPD GO	SIA7D_HUMAN	Alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3-N-acetyl-galactosaminide alpha-2,6-sialyltransfera ...	0.19	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	soluble fraction [TAS]	606378		302
Q92442 UniProt NPD GO	AGLU_MUCJA	Alpha-glucosidase precursor (EC 3.2.1.20) (Maltase)	0.19	-	cyt	0					864
Q9UHK6 UniProt NPD GO	AMACR_HUMAN	Alpha-methylacyl-CoA racemase (EC 5.1.99.4) (2-methylacyl-CoA racemase)	0.19	-	nuc	0	Peroxisome. Mitochondrion	mitochondrion [TAS] peroxisome [TAS]	604489		382
P70473 UniProt NPD GO	AMACR_RAT	Alpha-methylacyl-CoA racemase (EC 5.1.99.4) (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimera ...	0.19	-	nuc	0	Peroxisome. Mitochondrion				381
P54920 UniProt NPD GO	SNAA_HUMAN	Alpha-soluble NSF attachment protein (SNAP-alpha) (N-ethylmaleimide-sensitive factor attachment prot ...	0.19	-	cyt	0	Membrane; peripheral membrane protein		603215		295
P41034 UniProt NPD GO	TTPA_RAT	Alpha-tocopherol transfer protein (Alpha-TTP)	0.19	-	cyt	0	Cytoplasm				278
P36633 UniProt NPD GO	ABP1_RAT	Amiloride-sensitive amine oxidase [copper-containing] precursor (EC 1.4.3.6) (Diamine oxidase) (DAO) ...	0.19	-	vac	0	Secreted protein; extracellular space				746
P49253 UniProt NPD GO	AOF_ONCMY	Amine oxidase [flavin-containing] (EC 1.4.3.4) (Monoamine oxidase) (MAO)	0.19	-	cyt	1	Mitochondrion; mitochondrial outer membrane				522
O65396 UniProt NPD GO	GCST_ARATH	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.19	-	cyt	0	Mitochondrion (By similarity)				408
O23936 UniProt NPD GO	GCST_FLATR	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.19	-	cyt	0	Mitochondrion				407
P15145 UniProt NPD GO	AMPN_PIG	Aminopeptidase N (EC 3.4.11.2) (pAPN) (Alanyl aminopeptidase) (Microsomal aminopeptidase) (Aminopept ...	0.19	-	exc	1 *	Membrane; single-pass type II membrane protein				962
Q9WV72 UniProt NPD GO	ASB3_MOUSE	Ankyrin repeat and SOCS box protein 3 (ASB-3)	0.19	-	cyt	0					525
Q8WWX0 UniProt NPD GO	ASB5_HUMAN	Ankyrin repeat and SOCS box protein 5 (ASB-5)	0.19	-	nuc	1 *					329
Q5F478 UniProt NPD GO	ANR44_CHICK	Ankyrin repeat domain-containing protein 44	0.19	-	cyt	0					990
Q2QLB5 UniProt NPD GO	ASZ1_CALMO	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.19	-	cyt	0	Cytoplasm (By similarity)				476
Q8HZM6 UniProt NPD GO	ANXA1_HORSE	Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II)	0.19	-	cyt	0					345
Q5R1W0 UniProt NPD GO	ANXA5_PANTR	Annexin A5 (Annexin V)	0.19	-	cyt	0					319
P08758 UniProt NPD GO	ANXA5_HUMAN	Annexin A5 (Annexin V) (Lipocortin V) (Endonexin II) (Calphobindin I) (CBP-I) (Placental anticoagula ...	0.19	-	cyt	0		cytoplasm [TAS]	131230	1SAV	319
O95994 UniProt NPD GO	AGR2_HUMAN	Anterior gradient protein 2 homolog precursor (Secreted cement gland protein XAG-2 homolog) (AG-2 pr ...	0.19	-	exc	0	Secreted protein (Probable)		606358		175
P00908 UniProt NPD GO	TRPG_NEUCR	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.19	-	cyt	0					762
P32068 UniProt NPD GO	TRPE_ARATH	Anthranilate synthase component I-1, chloroplast precursor (EC 4.1.3.27)	0.19	-	mit	0	Plastid; chloroplast (Probable)				595
P84884 UniProt NPD GO	AFP1_PASED	Antifungal protein 1 (Pf-AFP1) (Fragment)	0.19	-	nuc	0					25
O47042 UniProt NPD GO	CYF_PICAB	Apocytochrome f precursor	0.19	-	cyt	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				319
Q13790 UniProt NPD GO	APOF_HUMAN	Apolipoprotein F precursor (Apo-F) (Lipid transfer inhibitor protein) (LTIP)	0.19	-	mit	0	Secreted protein	extracellular region [NAS]	107760		308
Q9BWW9 UniProt NPD GO	APOL5_HUMAN	Apolipoprotein-L5 (Apolipoprotein L-V) (ApoL-V)	0.19	-	nuc	0	Cytoplasm (Probable)		607255		433
P29975 UniProt NPD GO	AQP1_RAT	Aquaporin-1 (AQP-1) (Aquaporin-CHIP) (Water channel protein for red blood cells and kidney proximal ...	0.19	+	end	6 *	Membrane; multi-pass membrane protein	basolateral plasma membrane [IDA]			268
Q02013 UniProt NPD GO	AQP1_MOUSE	Aquaporin-1 (AQP-1) (Aquaporin-CHIP) (Water channel protein for red blood cells and kidney proximal ...	0.19	+	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			268
P51541 UniProt NPD GO	KARG_LIMPO	Arginine kinase (EC 2.7.3.3) (AK)	0.19	-	cyt	0	Cytoplasm			1SD0	357
P20673 UniProt NPD GO	ARLY_RAT	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL)	0.19	-	cyt	0					461
Q5XID7 UniProt NPD GO	ARMX3_RAT	Armadillo repeat-containing X-linked protein 3	0.19	+	mit	1 *					379
P27718 UniProt NPD GO	DDC_BOVIN	Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC)	0.19	-	cyt	0					487
Q7TP90 UniProt NPD GO	ARRD4_RAT	Arrestin domain-containing protein 4 (Liver regeneration-related protein LRRGT00117)	0.19	-	nuc	0					300
O62696 UniProt NPD GO	ARYL_FELCA	Arylamine N-acetyltransferase (EC 2.3.1.5) (Arylamine acetylase) (Fragment)	0.19	-	cyt	0	Cytoplasm				258
Q19722 UniProt NPD GO	SYNC_CAEEL	Asparaginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.22) (Asparagine--tRNA ligase) (AsnRS)	0.19	-	cyt	0	Cytoplasm (Probable)				545
P46446 UniProt NPD GO	ACY2_BOVIN	Aspartoacylase (EC 3.5.1.15) (Aminoacylase-2) (ACY-2)	0.19	-	cyt	0					313

You are viewing entries 51551 to 51600 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.