Alpha galactosidase A

Alpha-galactosidase is a glycoside hydrolase enzyme that hydrolyses the terminal alphagalactosyl moieties from glycolipids and glycoproteins. It is encoded by the GLA gene.[1]
PSG: a new signal peptide prediction method N-region: length 7; pos.chg 1; neg.chg 1 H-region: length 9; peak value 6.06 PSG score: 1.66 von Heijne's method for signal seq. recognition GvH score (threshold: -2.1): -0.06 possible cleavage site: between 31 and 32

GvH:

>>> Seems to have a cleavable signal peptide (1 to 31) ALOM: Klein et al's method for TM region allocation Init position for calculation: 32 Tentative number of TMS(s) for the threshold 0.5: number of TMS(s) .. fixed PERIPHERAL Likelihood = 1.27 (at 281) ALOM score: 1.27 (number of TMSs: 0) MTOP: Prediction of membrane topology (Hartmann et al.) Center position for calculation: 15 Charge difference: -0.5 C( 1.0) - N( 1.5) N >= C: N-terminal side will be inside MITDISC: discrimination of mitochondrial targeting seq R content: 2 Hyd Moment(75): 2.26 Hyd Moment(95): 3.97 G content: 1 D/E content: 2 S/T content: 1 Score: -6.18 Gavel: prediction of cleavage sites for mitochondrial preseq R-2 motif at 27 LRF|LA NUCDISC: discrimination of nuclear localization signals pat4: none pat7: PVKRKLG (5) at 389 bipartite: none content of basic residues: 9.1% NLS Score: -0.04 KDEL: ER retention motif in the C-terminus: none ER Membrane Retention Signals: XXRR-like motif in the N-terminus: QLRN KKXX-like motif in the C-terminus: LKDL SKL: peroxisomal targeting signal in the C-terminus: none SKL2: 2nd peroxisomal targeting signal: none

VAC: possible vacuolar targeting motif: none RNA-binding motif: none Actinin-type actin-binding motif:

type 1: none type 2: none NMYR: N-myristoylation pattern : none Prenylation motif: none memYQRL: transport motif from cell surface to Golgi: none Tyrosines in the tail: none Dileucine motif in the tail: none checking 63 PROSITE DNA binding motifs: none none none

checking 71 PROSITE ribosomal protein motifs:

checking 33 PROSITE prokaryotic DNA binding motifs:

NNCN: Reinhardt's method for Cytplasmic/Nuclear discrimination Prediction: cytoplasmic Reliability: 94.1 COIL: Lupas's algorithm to detect coiled-coil regions total: 0 residues

Results of the k-NN Prediction

k = 9/23
34.8 21.7 17.4 13.0 8.7 4.3 %: %: %: %: %: %: cytoplasmic mitochondrial extracellular, including cell wall endoplasmic reticulum vacuolar nuclear

>> prediction for QUERY is cyt (k=23) SeqName Potential Jury N-Glyc agreement result ---------------------------------------------------------------------Sequence 139 NKTC 0.6557 (9/9) ++ Sequence 192 NRTG 0.7524 (9/9) +++ Sequence 215 NYTE 0.7338 (9/9) ++ Sequence 408 NPTG 0.6258 (7/9) + WARNING: PRO-X1. Position

Acyl CoA oxidase

In enzymology, an acyl-CoA oxidase (EC 1.3.3.6) is an enzyme that catalyzes the chemical reaction acyl-CoA + O2 trans-2,3-dehydroacyl-CoA + H2O2 Thus, the two substrates of this enzyme are acyl-CoA and O2, whereas its two products are trans-2,3-dehydroacyl-CoA and H2O2. This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-CH group of donor with oxygen as acceptor.
PSG: a new signal peptide prediction method N-region: length 10; pos.chg 3; neg.chg 3 H-region: length 6; peak value -2.04 PSG score: -6.44 von Heijne's method for signal seq. recognition GvH score (threshold: -2.1): -10.95 possible cleavage site: between 25 and 26

GvH:

>>> Seems to have no N-terminal signal peptide ALOM: Klein et al's method for TM region allocation Init position for calculation: 1 Tentative number of TMS(s) for the threshold 0.5: number of TMS(s) .. fixed PERIPHERAL Likelihood = 1.59 (at 551) ALOM score: 1.59 (number of TMSs: 0) MITDISC: discrimination of mitochondrial targeting seq R content: 2 Hyd Moment(75): 10.10 Hyd Moment(95): 8.81 G content: 0 D/E content: 2 S/T content: 0 Score: -4.35 Gavel: prediction of cleavage sites for mitochondrial preseq cleavage site motif not found NUCDISC: discrimination of nuclear localization signals pat4: RRRR (5) at 31 pat7: PDLRRER (3) at 3 pat7: PEKTRRR (4) at 27 bipartite: none content of basic residues: 11.1% NLS Score: 0.44 KDEL: ER retention motif in the C-terminus: none ER Membrane Retention Signals: KKXX-like motif in the C-terminus: LQSK SKL: peroxisomal targeting signal in the C-terminus: SKL SKL2: 2nd peroxisomal targeting signal: none

VAC: possible vacuolar targeting motif: none RNA-binding motif: none

Actinin-type actin-binding motif: type 1: none type 2: none NMYR: N-myristoylation pattern : none Prenylation motif: none memYQRL: transport motif from cell surface to Golgi: none Tyrosines in the tail: none Dileucine motif in the tail: none checking 63 PROSITE DNA binding motifs: none none none

checking 71 PROSITE ribosomal protein motifs:

checking 33 PROSITE prokaryotic DNA binding motifs:

NNCN: Reinhardt's method for Cytplasmic/Nuclear discrimination Prediction: cytoplasmic Reliability: 89 COIL: Lupas's algorithm to detect coiled-coil regions total: 0 residues

Results of the k-NN Prediction

k = 9/23
77.8 %: peroxisomal 11.1 %: cytoplasmic 11.1 %: mitochondrial >> prediction for QUERY is pox (k=9) Potential Jury N-Glyc agreement result ---------------------------------------------------------------------Sequence 103 NYSM 0.7141 (9/9) ++ Sequence 413 NFTP 0.2318 (9/9) --Sequence 517 NLTS 0.7623 (9/9) +++ SeqName Position

Thyroid stimulating hormone receptor

The thyrotropin receptor (or TSH receptor) is a receptor (and associated protein) that responds to thyroid-stimulating hormone (also known as "thyrotropin") and stimulates the production of thyroxine (T4) and triiodothyronine (T3). The TSH receptor is a member of the G protein-coupled

receptor superfamily of integral membrane proteins and is coupled to the Gs protein.

PSG: a new signal peptide prediction method N-region: length 5; pos.chg 1; neg.chg 1 H-region: length 8; peak value 7.99 PSG score: 3.59 von Heijne's method for signal seq. recognition GvH score (threshold: -2.1): -2.34 possible cleavage site: between 21 and 22

GvH:

>>> Seems to have no N-terminal signal peptide ALOM: Klein et al's method for TM region allocation Init position for calculation: 1 Tentative number of TMS(s) for the threshold 0.5: INTEGRAL Likelihood =-10.88 Transmembrane 424 INTEGRAL Likelihood = -2.39 Transmembrane 457 INTEGRAL Likelihood = 0.26 Transmembrane 499 INTEGRAL Likelihood = -8.12 Transmembrane 539 INTEGRAL Likelihood =-12.42 Transmembrane 583 INTEGRAL Likelihood = -3.35 Transmembrane 626 INTEGRAL Likelihood = 0.16 Transmembrane 653 PERIPHERAL Likelihood = 3.66 (at 556) ALOM score: -12.42 (number of TMSs: 7) MTOP: Prediction of membrane topology (Hartmann et al.) Center position for calculation: 431 Charge difference: 3.5 C( 2.5) - N(-1.0) C > N: C-terminal side will be inside >>>Caution: Inconsistent mtop result with signal peptide >>> membrane topology: type 3b MITDISC: discrimination of mitochondrial targeting seq R content: 1 Hyd Moment(75): 1.57 Hyd Moment(95): 8.19 G content: 0 D/E content: 2 S/T content: 0 Score: -6.52 Gavel: prediction of cleavage sites for mitochondrial preseq R-2 motif at 12 MRP|AD NUCDISC: discrimination of nuclear localization signals pat4: none pat7: none bipartite: none content of basic residues: 9.0% NLS Score: -0.47 KDEL: ER retention motif in the C-terminus: none ER Membrane Retention Signals: XXRR-like motif in the N-terminus: RPAD none SKL: peroxisomal targeting signal in the C-terminus: none SKL2: 2nd peroxisomal targeting signal: none

440 473 515 555 599 642 669

VAC: possible vacuolar targeting motif: none RNA-binding motif: none Actinin-type actin-binding motif: type 1: none type 2: none NMYR: N-myristoylation pattern : none Prenylation motif: none memYQRL: transport motif from cell surface to Golgi: none Tyrosines in the tail: none Dileucine motif in the tail: none checking 63 PROSITE DNA binding motifs: none none none

checking 71 PROSITE ribosomal protein motifs:

checking 33 PROSITE prokaryotic DNA binding motifs:

NNCN: Reinhardt's method for Cytplasmic/Nuclear discrimination Prediction: cytoplasmic Reliability: 89 COIL: Lupas's algorithm to detect coiled-coil regions total: 0 residues

Results of the k-NN Prediction k = 9/23

56.5 21.7 8.7 4.3 4.3 4.3 >> prediction SeqName %: plasma membrane %: endoplasmic reticulum %: vacuolar %: cytoplasmic %: Golgi %: nuclear for QUERY is pla (k=23) Position

Potential Jury N-Glyc agreement result ---------------------------------------------------------------------Sequence 77 NISR 0.6659 (8/9) + Sequence 99 NLSK 0.7387 (9/9) ++ Sequence 113 NLTY 0.6722 (7/9) + Sequence 177 NETL 0.7619 (9/9) +++ Sequence 198 NGTK 0.6811 (9/9) ++ Sequence 302 NESS 0.5574 (7/9) + Sequence 715 NSTD 0.5137 (4/9) +

Thyroid hormone receptor alpha

Thyroid hormone receptor alpha (TR-alpha) also known as nuclear receptor subfamily 1, group A, member 1 (NR1A1), is a nuclear receptor protein that in humans is encoded by the THRA gene. The protein encoded by this gene is a nuclear hormone receptor for triiodothyronine. It is one of the several receptors for thyroid hormone, and has been shown to mediate the biological activities of

thyroid hormone. Knockout studies in mice suggest that the different receptors, while having certain extent of redundancy, may mediate different functions of thyroid hormone. Alternatively spliced transcript variants encoding distinct isoforms have been reported.
PSG: a new signal peptide prediction method N-region: length 9; pos.chg 2; neg.chg 2 H-region: length 3; peak value -14.11 PSG score: -18.51 von Heijne's method for signal seq. recognition GvH score (threshold: -2.1): -13.71 possible cleavage site: between 44 and 45

GvH:

>>> Seems to have no N-terminal signal peptide ALOM: Klein et al's method for TM region allocation Init position for calculation: 1 Tentative number of TMS(s) for the threshold 0.5: number of TMS(s) .. fixed PERIPHERAL Likelihood = 1.43 (at 248) ALOM score: 1.43 (number of TMSs: 0) MITDISC: discrimination of mitochondrial targeting seq R content: 0 Hyd Moment(75): 7.67 Hyd Moment(95): 7.87 G content: 0 D/E content: 2 S/T content: 1 Score: -6.32 Gavel: prediction of cleavage sites for mitochondrial preseq cleavage site motif not found NUCDISC: discrimination of nuclear localization signals pat4: KRKR (5) at 25 pat4: RKRK (5) at 26 pat4: RRRK (5) at 144 pat7: PDGKRKR (5) at 22 bipartite: KRVAKRKLIEQNRERRR at 130 content of basic residues: 13.5% NLS Score: 1.56 KDEL: ER retention motif in the C-terminus: none ER Membrane Retention Signals: none SKL: peroxisomal targeting signal in the C-terminus: none SKL2: 2nd peroxisomal targeting signal: KITRNQCQL at 101 found

VAC: possible vacuolar targeting motif: none RNA-binding motif: none Actinin-type actin-binding motif: type 1: none type 2: none NMYR: N-myristoylation pattern : none Prenylation motif: none

memYQRL: transport motif from cell surface to Golgi: none Tyrosines in the tail: none Dileucine motif in the tail: none checking 63 PROSITE DNA binding motifs: Nuclear hormones receptors DNA-binding region signature (PS00031): *** found *** CVVCGDKATGYHYRCITCEGCKGFFRR at 53 checking 71 PROSITE ribosomal protein motifs: none none

checking 33 PROSITE prokaryotic DNA binding motifs:

NNCN: Reinhardt's method for Cytplasmic/Nuclear discrimination Prediction: nuclear Reliability: 89 COIL: Lupas's algorithm to detect coiled-coil regions 127 D 0.52 128 S 0.52 129 K 0.75 130 R 0.75 131 V 0.75 132 A 0.75 133 K 0.75 134 R 0.75 135 K 0.75 136 L 0.75 137 I 0.75 138 E 0.75 139 Q 0.75 140 N 0.75 141 R 0.75 142 E 0.75 143 R 0.75 144 R 0.75 145 R 0.75 146 K 0.75 147 E 0.75 148 E 0.75 149 M 0.75 150 I 0.75 151 R 0.75 152 S 0.75 153 L 0.75 154 Q 0.75 155 Q 0.75 156 R 0.75 total: 30 residues

Results of the k-NN Prediction

k = 9/23
65.2 %: nuclear 26.1 %: cytoplasmic

4.3 %: endoplasmic reticulum 4.3 %: mitochondrial >> prediction for QUERY is nuc (k=23)