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
Q71UN7 UniProt NPD GO	B2MG_SAIUS	Beta-2-microglobulin precursor	0.02	-	exc	0	Secreted protein				119
Q95252 UniProt NPD GO	ADRB3_PIG	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor) (Fragment)	0.02	-	end	2 *	Membrane; multi-pass membrane protein				101
Q30KP8 UniProt NPD GO	DB136_HUMAN	Beta-defensin 136 precursor (Defensin, beta 136)	0.02	-	vac	0	Secreted protein (Potential)				78
Q30KJ3 UniProt NPD GO	DB136_PANTR	Beta-defensin 136 precursor (Defensin, beta 136)	0.02	-	vac	0	Secreted protein (Potential)				78
Q8R2I5 UniProt NPD GO	BD15_MOUSE	Beta-defensin 15 precursor (Defensin, beta 15) (BD-15) (mBD-15)	0.02	-	end	0	Secreted protein (By similarity)				79
Q9TT12 UniProt NPD GO	BD02_PANTR	Beta-defensin 2 precursor (BD-2) (Defensin, beta 2)	0.02	-	end	1 *	Secreted protein (By similarity)				64
Q7TNV8 UniProt NPD GO	BD34_MOUSE	Beta-defensin 34 precursor (Defensin, beta 34) (BD-34) (mBD-34)	0.02	-	exc	0	Secreted protein (By similarity)				81
P01203 UniProt NPD GO	COLI_CAMDR	Beta-endorphin [Contains: Met-enkephalin]	0.02	-	nuc	0					31
P07583 UniProt NPD GO	LEG4_CHICK	Beta-galactoside-binding lectin (14 kDa lectin) (C-14)	0.02	-	cyt	0					134
P08520 UniProt NPD GO	LEG_ELEEL	Beta-galactoside-binding lectin (14 kDa lectin) (Electrolectin)	0.02	-	cyt	0					129
P48825 UniProt NPD GO	BGL1_ASPAC	Beta-glucosidase 1 precursor (EC 3.2.1.21) (Gentiobiase) (Cellobiase) (Beta-D-glucoside glucohydrola ...	0.02	-	exc	0					860
Q9SE50 UniProt NPD GO	BGL1_ARATH	Beta-glucosidase homolog precursor (EC 3.2.1.-)	0.02	+	mit	1 *	Endoplasmic reticulum				528
P21742 UniProt NPD GO	THNB_HORVU	Beta-hordothionin precursor [Contains: Beta-hordothionin; Acidic protein]	0.02	-	nuc	0	Secreted protein (Potential)			1WUW	136
O97935 UniProt NPD GO	MSPE_SAGOE	Beta-microseminoprotein E1 precursor (msp-E1)	0.02	-	exc	1 *	Secreted protein. Sperm surface (By similarity)	extracellular region [TAS]			114
Q93088 UniProt NPD GO	BHMT_HUMAN	Betaine--homocysteine S-methyltransferase (EC 2.1.1.5)	0.02	-	cyt	0	Cytoplasm		602888	1LT8	406
P17202 UniProt NPD GO	BADH_SPIOL	Betaine-aldehyde dehydrogenase, chloroplast precursor (EC 1.2.1.8) (BADH)	0.02	-	cyt	0	Plastid; chloroplast				497
Q91X34 UniProt NPD GO	BAAT_MOUSE	Bile acid CoA:amino acid N-acyltransferase (EC 2.3.1.65) (BAT) (BACAT) (Glycine N-choloyltransferase ...	0.02	-	nuc	0	Cytoplasm (By similarity). Peroxisome (By similarity). Cytoplasmic or/and peroxisomal (By similarity ...				420
P50236 UniProt NPD GO	ST2A2_MOUSE	Bile salt sulfotransferase 2 (EC 2.8.2.14) (Hydroxysteroid sulfotransferase) (ST)	0.02	-	cyt	0	Cytoplasm				285
Q9U2M7 UniProt NPD GO	AP4A_CAEEL	Bis(5'-nucleosyl)-tetraphosphatase [Asymmetrical] (EC 3.6.1.-) (Diadenosine 5',5'''-P1,P4-tetraphosp ...	0.02	-	cyt	0				1KTG	138
P62954 UniProt NPD GO	BC10_BOVIN	Bladder cancer-associated protein	0.02	-	vac	2 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			87
P62953 UniProt NPD GO	BC10_FELCA	Bladder cancer-associated protein (Bladder cancer 10 kDa protein) (Bc10)	0.02	-	vac	2 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			87
P62952 UniProt NPD GO	BC10_HUMAN	Bladder cancer-associated protein (Bladder cancer 10 kDa protein) (Bc10)	0.02	-	vac	2 *	Membrane; multi-pass membrane protein (Potential)				87
P62951 UniProt NPD GO	BC10_MOUSE	Bladder cancer-associated protein (Bladder cancer 10 kDa protein) (Bc10)	0.02	-	vac	2 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			87
P62950 UniProt NPD GO	BC10_RAT	Bladder cancer-associated protein (Bladder cancer 10 kDa protein) (Bc10)	0.02	-	vac	2 *	Membrane; multi-pass membrane protein (Potential)				87
Q5R692 UniProt NPD GO	BC10_PONPY	Bladder cancer-associated protein homolog (Bladder cancer 10 kDa protein homolog) (Bc10)	0.02	-	vac	2 *	Membrane; multi-pass membrane protein (Potential)				87
P12865 UniProt NPD GO	BS2_TRYBB	Bloodstream-specific protein 2 precursor	0.02	-	mit	0					497
O13092 UniProt NPD GO	OPSB_SAIBB	Blue-sensitive opsin (BOP) (Blue cone photoreceptor pigment)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				349
P87365 UniProt NPD GO	OPSB_ORYLA	Blue-sensitive opsin (Blue cone photoreceptor pigment) (KFH-B)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				352
P51471 UniProt NPD GO	OPSB_ANOCA	Blue-sensitive opsin (Blue photoreceptor pigment) (RH2 opsin)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				355
P84212 UniProt NPD GO	BOML1_BOMVA	Bombesin-like peptide 1	0.02	-		0	Secreted protein	extracellular region [IDA]			13
P33721 UniProt NPD GO	BXB1_SAMCY	Bombyxin B-1 homolog precursor [Contains: Bombyxin B-1 homolog B chain; Bombyxin B-1 homolog A chain ...	0.02	-	exc	0	Secreted protein				91
P29519 UniProt NPD GO	BXB12_BOMMO	Bombyxin B-12 precursor (BBX-B12) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-12 ...	0.02	-	exc	0	Secreted protein				90
P33722 UniProt NPD GO	BXB2_SAMCY	Bombyxin B-2 homolog precursor [Contains: Bombyxin B-2 homolog B chain; Bombyxin B-2 homolog A chain ...	0.02	-	exc	0	Secreted protein				91
P26737 UniProt NPD GO	BXB3_BOMMO	Bombyxin B-3 precursor (BBX-B3) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-3 B ...	0.02	-	exc	0	Secreted protein				90
P26738 UniProt NPD GO	BXB4_BOMMO	Bombyxin B-4 precursor (BBX-B4) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-4 B ...	0.02	-	mit	0	Secreted protein				90
P26740 UniProt NPD GO	BXB6_BOMMO	Bombyxin B-6 precursor (BBX-B6) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin B-6 B ...	0.02	-	vac	0	Secreted protein				90
O09209 UniProt NPD GO	BXRA_AGRCO	Bombyxin-related peptide A precursor (ABRP) [Contains: Bombyxin-related peptide A chain B; Bombyxin- ...	0.02	-	end	0	Secreted protein (By similarity)	extracellular region [IC]			103
Q9LPM9 UniProt NPD GO	BCAT6_ARATH	Branched-chain-amino-acid aminotransferase 6 (EC 2.6.1.42) (Atbcat-6)	0.02	-	nuc	0	Cytoplasm				356
P54687 UniProt NPD GO	BCAT1_HUMAN	Branched-chain-amino-acid aminotransferase, cytosolic (EC 2.6.1.42) (BCAT(c)) (ECA39 protein)	0.02	-	cyt	0	Cytoplasm		113520	2COJ	386
P38891 UniProt NPD GO	BCA1_YEAST	Branched-chain-amino-acid aminotransferase, mitochondrial precursor (EC 2.6.1.42) (BCAT) (TWT1 prote ...	0.02	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			393
P41725 UniProt NPD GO	PGCB_FELCA	Brevican core protein precursor (Brain-enriched hyaluronan-binding protein) (Protein BEHAB) (Fragmen ...	0.02	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				417
P40836 UniProt NPD GO	BR1EB_RANES	Brevinin-1Eb	0.02	-	cyt	0	Secreted protein				23
P40840 UniProt NPD GO	BR2ED_RANES	Brevinin-2Ed	0.02	-	nuc	0	Secreted protein				29
P81782 UniProt NPD GO	BUCA_BUNCA	Bucandin	0.02	-	nuc	0	Secreted protein			1IJC	63
P39988 UniProt NPD GO	BUD16_YEAST	Bud site selection protein BUD16	0.02	-	nuc	0	Cytoplasm. Nucleus				312
O96553 UniProt NPD GO	C1TC_DROME	C-1-tetrahydrofolate synthase, cytoplasmic (C1-THF synthase) [Includes: Methylenetetrahydrofolate de ...	0.02	-	cyt	0	Cytoplasm	cytoplasm [IDA]			968
Q9CRA4 UniProt NPD GO	ERG25_MOUSE	C-4 methylsterol oxidase (EC 1.14.13.72) (Methylsterol monooxygenase)	0.02	-	nuc	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				293
O93875 UniProt NPD GO	ERG3_CANAL	C-5 sterol desaturase (EC 1.3.3.-) (Sterol-C5-desaturase) (Ergosterol delta 5,6 desaturase)	0.02	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				386
P50860 UniProt NPD GO	ERG3_CANGA	C-5 sterol desaturase (EC 1.3.3.-) (Sterol-C5-desaturase) (Ergosterol delta 5,6 desaturase)	0.02	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				364
P32353 UniProt NPD GO	ERG3_YEAST	C-5 sterol desaturase (EC 1.3.3.-) (Sterol-C5-desaturase) (Ergosterol delta 5,6 desaturase)	0.02	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				365

You are viewing entries 82601 to 82650 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.