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
Q59S72 UniProt NPD GO	ALG11_CANAL	Alpha-1,2-mannosyltransferase ALG11 (EC 2.4.1.-) (Asparagine-linked glycosylation protein 11)	0.34	-	nuc	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				609
Q9H553 UniProt NPD GO	ALG2_HUMAN	Alpha-1,3-mannosyltransferase ALG2 (EC 2.4.1.-) (GDP-Man:Man(1)GlcNAc(2)-PP-dolichol mannosyltransfe ...	0.34	-	cyt	0			607906		416
O19032 UniProt NPD GO	ADA2B_ORYAF	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.34	-	end	6 *	Membrane; multi-pass membrane protein				388
Q8JG69 UniProt NPD GO	AA2DB_BRARE	Alpha-2Db adrenergic receptor (Alpha-2Db adrenoceptor) (Alpha-2Db adrenoreceptor) (Alpha(2Db)AR)	0.34	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IC]			415
P39035 UniProt NPD GO	CAS1_PIG	Alpha-S1-casein precursor	0.34	-	exc	0	Secreted protein				206
Q9C206 UniProt NPD GO	AOX_PODAN	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.34	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				363
Q28989 UniProt NPD GO	AMBN_PIG	Ameloblastin precursor (Sheathlin)	0.34	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				421
Q28462 UniProt NPD GO	AMEL_MONDO	Amelogenin	0.34	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				202
P02817 UniProt NPD GO	AMELX_BOVIN	Amelogenin, X isoform precursor (Class I amelogenin)	0.34	-	exc	0	Secreted protein; extracellular space; extracellular matrix				213
P25285 UniProt NPD GO	GCST_BOVIN	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.34	-	mit	0	Mitochondrion	mitochondrial inner membrane [TAS] mitochondrion [IDA]			397
Q10737 UniProt NPD GO	AMPN_HAECO	Aminopeptidase N (EC 3.4.11.2) (Microsomal aminopeptidase) (Membrane glycoprotein H11)	0.34	-	mit	1 *	Membrane; single-pass type II membrane protein (By similarity)				971
P15541 UniProt NPD GO	AMPN_RABIT	Aminopeptidase N (EC 3.4.11.2) (rbAPN) (Alanyl aminopeptidase) (Microsomal aminopeptidase) (Aminopep ...	0.34	-	mit	1 *	Membrane; single-pass type II membrane protein				965
Q5IS80 UniProt NPD GO	A4_PANTR	Amyloid beta A4 protein precursor (APP) (ABPP) (Alzheimer disease amyloid protein homolog) [Contains ...	0.34	-	end	1	Membrane; single-pass type I membrane protein (By similarity). Cell surface protein that rapidly bec ...				770
P05067 UniProt NPD GO	A4_HUMAN	Amyloid beta A4 protein precursor (APP) (ABPP) (Alzheimer disease amyloid protein) (Cerebral vascula ...	0.34	-	end	1	Membrane; single-pass type I membrane protein. Cell surface protein that rapidly becomes internalize ...	cell surface [IDA] extracellular region [TAS] integral to plasma membrane [TAS]	104300	2BP4	770
Q12379 UniProt NPD GO	SWM1_YEAST	Anaphase-promoting complex subunit SWM1 (Spore wall maturation protein 1) (Anaphase-promoting comple ...	0.34	-	mit	0		anaphase-promoting complex [IDA] nucleus [IDA]			170
Q8I7X1 UniProt NPD GO	AGH_PORSC	Androgenic gland hormone precursor (Pos-AGH) [Contains: Androgenic gland hormone B chain; Androgenic ...	0.34	-	exc	0	Secreted protein				145
Q8NI99 UniProt NPD GO	ANGL6_HUMAN	Angiopoietin-related protein 6 precursor (Angiopoietin-like 6) (Angiopoietin-related growth factor) ...	0.34	-	mit	0	Secreted protein (Probable)		609336		470
Q3SX45 UniProt NPD GO	ASB2_BOVIN	Ankyrin repeat and SOCS box protein 2 (ASB-2)	0.34	-	nuc	0					633
Q9NU02 UniProt NPD GO	ANKR5_HUMAN	Ankyrin repeat domain-containing protein 5	0.34	-	cyt	0					776
Q3ZC08 UniProt NPD GO	ANXA9_BOVIN	Annexin A9	0.34	-	cyt	0					345
Q8R3W7 UniProt NPD GO	AGR3_MOUSE	Anterior gradient protein 3 homolog precursor	0.34	-	mit	0	Secreted protein (Probable)				165
P09809 UniProt NPD GO	APOA1_RABIT	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.34	-	exc	0	Secreted protein				266
P61801 UniProt NPD GO	APTX_XENTR	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.34	-	nuc	0	Nucleus (Probable)				347
P55249 UniProt NPD GO	LX12E_MOUSE	Arachidonate 12-lipoxygenase, epidermal-type (EC 1.13.11.31) (12-LOX)	0.34	-	nuc	0	Cytoplasm (Potential)				662
P51399 UniProt NPD GO	LOX5_MESAU	Arachidonate 5-lipoxygenase (EC 1.13.11.34) (5-lipoxygenase) (5-LO)	0.34	-	cyt	0	Cytoplasm				672
Q400C8 UniProt NPD GO	AMZ2_MOUSE	Archaemetzincin-2 (EC 3.-.-.-) (Archeobacterial metalloproteinase-like protein 2)	0.34	-	cyt	0					359
Q6A058 UniProt NPD GO	ARMX2_MOUSE	Armadillo repeat-containing X-linked protein 2	0.34	-	mit	1 *					784
Q497K5 UniProt NPD GO	ARRD5_MOUSE	Arrestin domain-containing protein 5	0.34	-	cyt	0					325
P18440 UniProt NPD GO	ARY1_HUMAN	Arylamine N-acetyltransferase 1 (EC 2.3.1.5) (Arylamide acetylase 1) (Arylamine N-acetyltransferase, ...	0.34	-	cyt	0	Cytoplasm		108345		290
P50292 UniProt NPD GO	ARY1_MESAU	Arylamine N-acetyltransferase 1 (EC 2.3.1.5) (Arylamide acetylase 1) (Arylamine N-acetyltransferase, ...	0.34	-	cyt	0	Cytoplasm				290
P07306 UniProt NPD GO	ASGR1_HUMAN	Asialoglycoprotein receptor 1 (ASGPR 1) (ASGP-R 1) (Hepatic lectin H1)	0.34	-	cyt	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	108360	1DV8	290
P27104 UniProt NPD GO	ANF_HORSE	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin)	0.34	-	exc	0	Secreted protein				153
Q5AKU4 UniProt NPD GO	ATG12_CANAL	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier ATG12)	0.34	-	nuc	0	Cytoplasm (Probable)				164
Q6C6M0 UniProt NPD GO	ATG2_YARLI	Autophagy-related protein 2	0.34	-	end	0	Perivacuolar compartment (By similarity)				1520
Q51IZ9 UniProt NPD GO	ATG22_MAGGR	Autophagy-related protein 22	0.34	-	end	11	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				679
O43069 UniProt NPD GO	ATG7_SCHPO	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme atg7)	0.34	-	nuc	0	Cytoplasm (By similarity)				649
Q8H715 UniProt NPD GO	ATG8_PHYIN	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8)	0.34	-	nuc	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				116
P49680 UniProt NPD GO	IAA6_PEA	Auxin-induced protein IAA6	0.34	-	cyt	0	Nucleus				179
Q7Y1H8 UniProt NPD GO	IAA14_ORYSA	Auxin-responsive protein IAA14 (Indoleacetic acid-induced protein 14)	0.34	-	cyt	0	Nucleus (By similarity)				195
Q09114 UniProt NPD GO	AVEE_AVESA	Avenin-E (Alpha-2 avenin) (Avenin N9) (Prolamin) (Celiac immunoreactive protein 3) (CIP-3)	0.34	-	nuc	0	Protein body (By similarity). Protein bodies inside vacuoles (By similarity)				182
Q6PNM1 UniProt NPD GO	BTLA_RAT	B- and T-lymphocyte attenuator precursor (B- and T-lymphocyte-associated protein) (CD272 antigen)	0.34	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				308
P46663 UniProt NPD GO	BKRB1_HUMAN	B1 bradykinin receptor (BK-1 receptor) (B1R)	0.34	-	end	7 *	Membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	600337		353
Q8HZN9 UniProt NPD GO	BKRB1_PIG	B1 bradykinin receptor (BK-1 receptor) (B1R)	0.34	+	end	7 *	Membrane; multi-pass membrane protein				353
P34568 UniProt NPD GO	BAT43_CAEEL	BTB and MATH domain-containing protein 43	0.34	-	nuc	0					451
Q8C726 UniProt NPD GO	BTBD9_MOUSE	BTB/POZ domain-containing protein 9	0.34	-	cyt	0					612
P34743 UniProt NPD GO	BTG1_CHICK	BTG1 protein (B-cell translocation gene 1 protein)	0.34	-	nuc	0		cytoplasm [ISS] nucleus [ISS]			170
P62324 UniProt NPD GO	BTG1_HUMAN	BTG1 protein (B-cell translocation gene 1 protein)	0.34	-	nuc	0		cytoplasm [IMP] nucleus [IMP]	109580		171
P62325 UniProt NPD GO	BTG1_MOUSE	BTG1 protein (B-cell translocation gene 1 protein)	0.34	-	nuc	0		cytoplasm [ISS] nucleus [ISS]			171
P53348 UniProt NPD GO	BTG1_BOVIN	BTG1 protein (B-cell translocation gene 1 protein) (Myocardial vascular inhibition factor) (VIF)	0.34	-	nuc	0		cytoplasm [ISS] nucleus [ISS]			171
Q06342 UniProt NPD GO	BJSB1_TRINI	Basic juvenile hormone-suppressible protein 1 precursor (BJHSP1)	0.34	-	exc	0					748

You are viewing entries 36451 to 36500 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.