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
Q9D2X0 UniProt NPD GO	ANR39_MOUSE	Ankyrin repeat domain-containing protein 39	0.18	+	nuc	0					183
Q2QLA4 UniProt NPD GO	ASZ1_HORSE	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.18	-	cyt	0	Cytoplasm (By similarity)				475
P14668 UniProt NPD GO	ANXA5_RAT	Annexin A5 (Annexin V) (Lipocortin V) (Endonexin II) (Calphobindin I) (CBP-I) (Placental anticoagula ...	0.18	-	cyt	0				2RAN	318
P10290 UniProt NPD GO	MYBC_MAIZE	Anthocyanin regulatory C1 protein	0.18	-	mit	0	Nucleus (Probable)				273
P06531 UniProt NPD GO	TRPG_EMENI	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.18	-	nuc	0					768
P09575 UniProt NPD GO	TRPG_PICAN	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.18	-	cyt	0					367
P17165 UniProt NPD GO	APOB_RABIT	Apolipoprotein B (Fragment)	0.18	-	nuc	0					144
Q5R894 UniProt NPD GO	APOM_PONPY	Apolipoprotein M (Apo-M) (ApoM)	0.18	-	cyt	0	Secreted protein (By similarity). Present in high density lipoprotein (HDL) and to a lesser extent i ...				188
O54926 UniProt NPD GO	SIVA_MOUSE	Apoptosis regulatory protein Siva (CD27-binding protein) (CD27BP)	0.18	-	nuc	0	Cytoplasm				175
Q9ULZ3 UniProt NPD GO	ASC_HUMAN	Apoptosis-associated speck-like protein containing a CARD (hASC) (PYD and CARD domain-containing pro ...	0.18	-	mit	0	Cytoplasm. Upstream of caspase activation, a redistribution from the cytoplasm to the aggregates occ ...	cytoplasm [NAS]	606838	1UCP	195
Q9BDJ6 UniProt NPD GO	GHRL_BOVIN	Appetite-regulating hormone precursor (Growth hormone secretagogue) (Growth hormone-releasing peptid ...	0.18	-	exc	0	Secreted protein (By similarity)				116
Q9N2J4 UniProt NPD GO	AQP1_CANFA	Aquaporin-1 (AQP-1) (Aquaporin-CHIP) (Water channel protein for red blood cells and kidney proximal ...	0.18	+	end	6 *	Membrane; multi-pass membrane protein				270
Q6PQZ1 UniProt NPD GO	AQP1_PIG	Aquaporin-1 (AQP-1) (Aquaporin-CHIP) (Water channel protein for red blood cells and kidney proximal ...	0.18	+	end	6 *	Membrane; multi-pass membrane protein				270
P49900 UniProt NPD GO	ARGI_RANCA	Arginase, hepatic (EC 3.5.3.1)	0.18	-	cyt	0					323
Q6CBX2 UniProt NPD GO	RMT2_YARLI	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				475
P40369 UniProt NPD GO	ARLY_SCHPO	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL)	0.18	-	cyt	0					461
P22781 UniProt NPD GO	DDC_CAVPO	Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC)	0.18	-	nuc	0					480
Q99KN1 UniProt NPD GO	ARRD1_MOUSE	Arrestin domain-containing protein 1	0.18	-	cyt	0					434
Q7TPQ9 UniProt NPD GO	ARRD3_MOUSE	Arrestin domain-containing protein 3	0.18	-	nuc	0					414
P55274 UniProt NPD GO	ARRH_HELVI	Arrestin homolog	0.18	-	cyt	0					381
P50429 UniProt NPD GO	ARSB_MOUSE	Arylsulfatase B precursor (EC 3.1.6.12) (ASB) (N-acetylgalactosamine-4-sulfatase) (G4S) (Fragment)	0.18	-	cyt	0	Lysosome				388
Q43064 UniProt NPD GO	PYRB3_PEA	Aspartate carbamoyltransferase 3, chloroplast precursor (EC 2.1.3.2) (Aspartate transcarbamylase 3) ...	0.18	-	cyt	0	Plastid; chloroplast				391
P13825 UniProt NPD GO	ASP_PLAFS	Aspartic acid-rich protein precursor	0.18	-	cyt	1 *					253
P69477 UniProt NPD GO	NEP2_NEPDI	Aspartic proteinase nepenthesin-2 (EC 3.4.23.-) (Nepenthesin-II) (Fragments)	0.18	-	nuc	0	Secreted protein				178
P24665 UniProt NPD GO	PRTA_ASPNG	Aspergillopepsin-2 precursor (EC 3.4.23.19) (Aspergillopepsin II) (Acid protease A) (Proctase A) [Co ...	0.18	-	vac	0				1Y43	282
Q9JJ43 UniProt NPD GO	A2BP1_MOUSE	Ataxin-2-binding protein 1	0.18	-	nuc	0					396
Q7M461 UniProt NPD GO	ATT_APLVA	Attractin	0.18	-	nuc	0	Secreted protein (By similarity)				56
Q6FIW0 UniProt NPD GO	ATG27_CANGA	Autophagy-related protein 27 precursor	0.18	-	end	1	Intracytoplasmic membrane; single-pass type I membrane protein (By similarity). Perivacuolar punctat ...				276
Q6CL19 UniProt NPD GO	ATG3_KLULA	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme ATG3)	0.18	-	mit	0	Cytoplasm (By similarity)				302
Q9N1E6 UniProt NPD GO	CD22_PANTR	B-cell receptor CD22 precursor (Siglec-2) (Fragment)	0.18	-	exc	0	Membrane; single-pass type I membrane protein				332
P17243 UniProt NPD GO	PHEB_GUITH	B-phycoerythrin beta chain	0.18	-	nuc	0	Within the thylakoid lumen. Periphery of the rods of the phycobilisome				177
Q9D7X1 UniProt NPD GO	KCTD4_MOUSE	BTB/POZ domain-containing protein KCTD4	0.18	-	nuc	0					259
Q04211 UniProt NPD GO	BTG2_MOUSE	BTG2 protein (NGF-inducible protein TIS21)	0.18	-	nuc	0					158
Q8C186 UniProt NPD GO	BPIL2_MOUSE	Bactericidal/permeability-increasing protein-like 2 precursor	0.18	-	end	1 *	Secreted protein (By similarity)	extracellular region [ISS]			509
Q96CA5 UniProt NPD GO	BIRC7_HUMAN	Baculoviral IAP repeat-containing protein 7 (Kidney inhibitor of apoptosis protein) (KIAP) (Melanoma ...	0.18	-	mit	0	Nucleus. Cytoplasm. When in the nucleus Nuclear, and in a filamentous pattern throughout the cytopla ...		605737	1TW6	298
P15575 UniProt NPD GO	B3AT_CHICK	Band 3 anion transport protein (Solute carrier family 4 member 1)	0.18	-	end	10	Membrane; multi-pass membrane protein				922
Q66IS6 UniProt NPD GO	BBS5_XENLA	Bardet-Biedl syndrome 5 protein homolog	0.18	-	cyt	0					365
P12630 UniProt NPD GO	BAR1_YEAST	Barrierpepsin precursor (EC 3.4.23.35) (Extracellular 'barrier' protein) (BAR proteinase)	0.18	-	nuc	1 *	Secreted protein	periplasmic space (sensu Fungi) [TAS]			587
P22914 UniProt NPD GO	CRBS_HUMAN	Beta crystallin S (Gamma crystallin S)	0.18	-	nuc	0			123730	1HA4	177
Q9LDH0 UniProt NPD GO	XYLT_ARATH	Beta-(1,2)-xylosyltransferase (EC 2.4.2.38)	0.18	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				534
Q924T4 UniProt NPD GO	LFNG_RAT	Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-ac ...	0.18	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				378
P15291 UniProt NPD GO	B4GT1_HUMAN	Beta-1,4-galactosyltransferase 1 (EC 2.4.1.-) (Beta-1,4-GalTase 1) (Beta4Gal-T1) (b4Gal-T1) (UDP-gal ...	0.18	-	mit	1 *	Isoform Long, isoform Short: Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II ...	Golgi apparatus [TAS]	137060	2FYB	397
P25962 UniProt NPD GO	ADRB3_MOUSE	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor)	0.18	-	end	7 *	Membrane; multi-pass membrane protein	membrane fraction [IDA]			400
Q9TSI0 UniProt NPD GO	CASB_BUBBU	Beta-casein precursor	0.18	-	exc	0	Secreted protein				224
P33048 UniProt NPD GO	CASB_CAPHI	Beta-casein precursor	0.18	-	exc	0	Secreted protein				222
O19038 UniProt NPD GO	BD01_SHEEP	Beta-defensin 1 precursor (BD-1) (sBD1)	0.18	-	mit	1 *	Secreted protein (By similarity)				64
Q30KK2 UniProt NPD GO	DB126_PANTR	Beta-defensin 126 precursor (Defensin, beta 126)	0.18	-	nuc	1 *	Secreted protein (Potential)				108
P81126 UniProt NPD GO	SNAB_BOVIN	Beta-soluble NSF attachment protein (SNAP-beta) (N-ethylmaleimide-sensitive factor attachment protei ...	0.18	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				298
Q9H115 UniProt NPD GO	SNAB_HUMAN	Beta-soluble NSF attachment protein (SNAP-beta) (N-ethylmaleimide-sensitive factor attachment protei ...	0.18	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				298
P28663 UniProt NPD GO	SNAB_MOUSE	Beta-soluble NSF attachment protein (SNAP-beta) (N-ethylmaleimide-sensitive factor attachment protei ...	0.18	-	cyt	0	Membrane; peripheral membrane protein				298

You are viewing entries 52751 to 52800 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.