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
Q9CR42 UniProt NPD GO	ANKR1_MOUSE	Ankyrin repeat domain-containing protein 1 (Cardiac ankyrin repeat protein)	0.39	+	cyt	0	Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA] transcription factor complex [IDA]			319
P10107 UniProt NPD GO	ANXA1_MOUSE	Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) (Chromobindin-9) (p35) (Phospholipase A2 inhibi ...	0.39	-	nuc	0		sarcolemma [IDA]			345
Q4R5L5 UniProt NPD GO	ANXA7_MACFA	Annexin A7 (Annexin VII)	0.39	-	nuc	0					488
P20073 UniProt NPD GO	ANXA7_HUMAN	Annexin A7 (Annexin VII) (Synexin)	0.39	-	nuc	0			186360		488
Q9JHQ0 UniProt NPD GO	ANXA9_MOUSE	Annexin A9 (Annexin-31) (Annexin XXXI)	0.39	-	cyt	0		cell surface [ISS] cytosol [ISS]			345
Q23971 UniProt NPD GO	OSC_DROME	Antennal-specific protein OS-C precursor	0.39	-	end	0					131
P23126 UniProt NPD GO	SM25_SCHMA	Antigenic integral membrane glycoprotein precursor (Antigen Sm25)	0.39	-	mit	3 *					182
Q91488 UniProt NPD GO	APOA1_SALTR	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.39	-	exc	0	Secreted protein (By similarity)				262
Q5ZMW3 UniProt NPD GO	API5_CHICK	Apoptosis inhibitor 5 (API-5)	0.39	-	cyt	0	Nucleus (By similarity). Mainly. Cytoplasm (By similarity)	cytoplasm [ISS] nucleus [ISS]			523
Q3ZCL5 UniProt NPD GO	ARFP2_BOVIN	Arfaptin-2 (ADP-ribosylation factor-interacting protein 2)	0.39	-	cyt	0					341
Q02453 UniProt NPD GO	ARM_MUSDO	Armadillo segment polarity protein	0.39	-	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein; cytoplasmic side (By similari ...				813
Q922B2 UniProt NPD GO	SYD_MOUSE	Aspartyl-tRNA synthetase (EC 6.1.1.12) (Aspartate--tRNA ligase) (AspRS)	0.39	-	nuc	0	Cytoplasm				501
P42662 UniProt NPD GO	ASTL_COTJA	Astacin-like metalloendopeptidase (EC 3.4.24.-)	0.39	-	nuc	0					310
P31178 UniProt NPD GO	GLE_CHLRE	Autolysin precursor (EC 3.4.24.38) (Gametolysin) (Gamete lytic enzyme) (GLE)	0.39	-	exc	1 *	Stored in the periplasm of gametes until its release. Secreted concurrently with release of the cell ...				638
Q6C0L6 UniProt NPD GO	ATG17_YARLI	Autophagy-related protein 17	0.39	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasmic and pu ...				408
Q6BT31 UniProt NPD GO	ATG8_DEBHA	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8)	0.39	-	cyt	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				136
Q6CMF8 UniProt NPD GO	ATG8_KLULA	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8)	0.39	-	nuc	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				124
O94272 UniProt NPD GO	ATG8_SCHPO	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier atg8)	0.39	-	cyt	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				121
Q5RCS0 UniProt NPD GO	ATG9A_PONPY	Autophagy-related protein 9A (APG9-like 1)	0.39	-	end	5	Membrane; multi-pass membrane protein (Potential)				839
Q5FWU3 UniProt NPD GO	ATG9A_RAT	Autophagy-related protein 9A (APG9-like 1)	0.39	-	end	5	Membrane; multi-pass membrane protein (Potential)				839
Q84WU6 UniProt NPD GO	ARFQ_ARATH	Auxin response factor 17	0.39	-	nuc	0	Nucleus				585
Q59AA1 UniProt NPD GO	IAA10_ORYSA	Auxin-responsive protein IAA10 (Indoleacetic acid-induced protein 10)	0.39	-	nuc	0	Nucleus (By similarity)				281
Q59AF3 UniProt NPD GO	IAA5_ORYSA	Auxin-responsive protein IAA5 (Indoleacetic acid-induced protein 5)	0.39	-	nuc	0	Nucleus (By similarity)				271
O08664 UniProt NPD GO	BCL7C_MOUSE	B-cell CLL/lymphoma 7 protein family member C (B-cell chronic lymphocytic leukemia/lymphoma 7C prote ...	0.39	-	nuc	0					217
Q9BDQ5 UniProt NPD GO	BKRB1_CANFA	B1 bradykinin receptor (BK-1 receptor) (B1R)	0.39	+	end	7 *	Membrane; multi-pass membrane protein				350
P06470 UniProt NPD GO	HOR1_HORVU	B1-hordein precursor	0.39	-	nuc	0					293
Q91XN4 UniProt NPD GO	BAMBI_RAT	BMP and activin membrane-bound inhibitor homolog precursor (Kinase-deficient TGFbeta superfamily rec ...	0.39	-	mit	1	Membrane; single-pass type I membrane protein (Potential)				260
Q96CX2 UniProt NPD GO	KCD12_HUMAN	BTB/POZ domain-containing protein KCTD12 (Pfetin) (Predominantly fetal expressed T1 domain)	0.39	-	nuc	0					325
Q13829 UniProt NPD GO	TNAP1_HUMAN	BTB/POZ domain-containing protein TNFAIP1 (Tumor necrosis factor, alpha-induced protein 1, endotheli ...	0.39	-	nuc	0			191161		316
Q96RK4 UniProt NPD GO	BBS4_HUMAN	Bardet-Biedl syndrome 4 protein	0.39	-	cyt	0			600374		519
Q06343 UniProt NPD GO	BJSB2_TRINI	Basic juvenile hormone-suppressible protein 2 precursor (BJHSP2)	0.39	-	mit	0					749
P34971 UniProt NPD GO	ADRB1_MOUSE	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor)	0.39	-	end	7	Cell membrane; multi-pass membrane protein (By similarity). Localized at the plasma membrane. Found ...	membrane fraction [IMP]			466
P18090 UniProt NPD GO	ADRB1_RAT	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor)	0.39	-	end	7	Cell membrane; multi-pass membrane protein (By similarity). Localized at the plasma membrane. Found ...				466
Q09327 UniProt NPD GO	MGAT3_HUMAN	Beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase (EC 2.4.1.144) (N-glycosyl-oli ...	0.39	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	integral to membrane [TAS]	604621		533
P35222 UniProt NPD GO	CTNB1_HUMAN	Beta-catenin	0.39	-	cyt	0	Cytoplasm. Cytoplasmic when it is unstabilized (high level of phosphorylation) or bound to CDH1. Nuc ...	cytoskeleton [TAS] lateral plasma membrane [IDA] nucleus [TAS] plasma membrane [TAS]	116806	2G57	781
Q9WU82 UniProt NPD GO	CTNB1_RAT	Beta-catenin	0.39	-	cyt	0	Cytoplasm. Cytoplasmic when it is unstabilized (high level of phosphorylation) or bound to CDH1. Nuc ...	cytoplasm [TAS] dendritic shaft [IDA] synapse [IDA]			781
P26233 UniProt NPD GO	CTNB_XENLA	Beta-catenin	0.39	-	cyt	0					781
P52850 UniProt NPD GO	NDST2_MOUSE	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 2 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.39	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				883
P13497 UniProt NPD GO	BMP1_HUMAN	Bone morphogenetic protein 1 precursor (EC 3.4.24.19) (BMP-1) (Procollagen C-proteinase) (PCP) (Mamm ...	0.39	-	exc	0		extracellular region [NAS]	112264		986
Q6PX77 UniProt NPD GO	BMP15_BOVIN	Bone morphogenetic protein 15 precursor (BMP-15)	0.39	-	nuc	0	Secreted protein (By similarity)				394
P56158 UniProt NPD GO	BRAC_HALRO	Brachyury protein homolog (T protein) (AS-T)	0.39	-	nuc	0	Nucleus (Potential)				471
Q09948 UniProt NPD GO	BRD1_SCHPO	Bromodomain protein brd1	0.39	-	nuc	0					542
Q9BWV1 UniProt NPD GO	BOC_HUMAN	Brother of CDO precursor (Protein BOC)	0.39	-	nuc	1	Cell membrane; single-pass type I membrane protein. Enriched at sites of cell-cell contact		608708		1114
P53226 UniProt NPD GO	BUD9_YEAST	Bud site selection protein BUD9	0.39	-	end	2	Cell membrane; multi-pass membrane protein. Found at the necks of large-budded cells and the proxima ...	bud neck [IDA]			547
Q86T13 UniProt NPD GO	CLC14_HUMAN	C-type lectin domain family 14 member A precursor (Epidermal growth factor receptor 5) (EGFR-5)	0.39	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				490
Q8N1N0 UniProt NPD GO	CLC4F_HUMAN	C-type lectin domain family 4 member F (C-type lectin superfamily member 13) (C-type lectin 13)	0.39	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)				539
P34122 UniProt NPD GO	CAP2_DICDI	CABP1-related protein p31/p34	0.39	-	nuc	0	Nucleus. Mainly				287
P21272 UniProt NPD GO	CEBPB_RAT	CCAAT/enhancer-binding protein beta (C/EBP beta) (Interleukin-6-dependent-binding protein) (IL-6DBP) ...	0.39	+	nuc	0	Nucleus	nucleus [IDA]			297
Q99467 UniProt NPD GO	CD180_HUMAN	CD180 antigen precursor (Lymphocyte antigen 64) (Radioprotective 105 kDa protein)	0.39	-	end	1	Cell membrane; single-pass type I membrane protein		602226		661
Q8MIS5 UniProt NPD GO	209L2_MACMU	CD209 antigen-like protein 2	0.39	-	nuc	1 *	Membrane; single-pass type II membrane protein (By similarity)				256

You are viewing entries 32401 to 32450 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.