Secondary Structure Prediction BCKDHA

1. Secondary structure prediction

PSIPRED

Secundary Structure

start	end	structural element
1	1	C
2	16	A
17	17	C
18	25	A
26	77	C
78	82	E
83	98	C
99	124	H
125	136	C
137	146	H
147	152	C
153	155	E
156	159	C
160	166	H
167	170	C
171	178	H
179	212	C
213	125	H
126	130	C
231	236	E
237	242	C
243	256	H
257	259	C
260	265	E
266	276	C
277	278	H
279	282	C
283	287	H
288	296	C
297	298	E
299	300	C
301	318	H
319	323	C
324	329	E
330	347	C
348	356	H
357	360	C
361	370	H
371	375	C
377	399	H
400	404	C
405	413	H
414	417	C
418	434	H
435	445	C

legend: A=alpha helix, E=beta strand, C=coil

Jpred3

PDB-ID	Score	Identity	Evalue

3. Prediction of transmembrane alpha-helices and signal peptides

Transmembrane topology and signal peptides are features that are likely to be conserved during evolution.

Phobius

Phobius predicted a signal peptide with about 90% probability at the beginning of the sequence. The predicted signal peptide is 34 amino acids long. The rest of the amino acid is a non cytoplasmic protein sequence. No part of the protein is predicted to be transmembrane spanning.

sp|P12694|ODBA_HUMAN (BCKDHA)
Signal	1	34
Region	1	16	N-Region
Region	17	25	H-Region
Region	26	34	C-Region
TOPO_DOM	35	445	non cytoplasmic

sp|P02945|BACR_HALSA
TOPO_DOM	1	22	NON CYTOPLASMIC.
TRANSMEM	23	42
TOPO_DOM	43	53	CYTOPLASMIC.
TRANSMEM	54	76
TOPO_DOM	77	95	NON CYTOPLASMIC.
TRANSMEM	96	114
TOPO_DOM	115	120	CYTOPLASMIC.
TRANSMEM	121	142
TOPO_DOM	143	147	NON CYTOPLASMIC.
TRANSMEM	148	169
TOPO_DOM	170	189	CYTOPLASMIC.
TRANSMEM	190	212
TOPO_DOM	213	217	NON CYTOPLASMIC.
TRANSMEM	218	237
TOPO_DOM	238	262	CYTOPLASMIC.

sp|Q9Y5Q6|INSL5_HUMAN
SIGNAL	1	22
REGION	1	5	N-REGION
REGION	6	17	H-REGION
REGION	18	22	C-REGION
TOPO_DOM	23	135	NON CYTOPLASMIC

sp|P11279|LAMP1_HUMAN
SIGNAL	1	28
REGION	1	10	N-REGION
REGION	11	22	H-REGION
REGION	23	28	C-REGION
TOPO_DOM	29	381	NON CYTOPLASMIC
TRANSMEM	382	405
TOPO_DOM	405	417	CYTOPLASMIC

sp|P05067|A4_HUMAN
SIGNAL	1	17
REGION	1	1	N-REGION
REGION	2	12	H-REGION
REGION	13	17	C-REGION
TOPO_DOM	18	700	NON CYTOPLASMIC
TRANSMEM	701	723
TOPO_DOM	724	770	CYTOPLASMIC

sp|P02753|RET4_HUMAN
SIGNAL	1	18
REGION	1	2	N-REGION
REGION	3	13	H-REGION
REGION	14	18	C-REGION
TOPO_DOM	19	201	NON CYTOPLASMIC

Polyphobius

OBDA_HUMAN (BCKDHA)
TOPO_DOM	1	445	Non cytoplasmic

sp|P02945|BACR_HALSA
TOPO_DOM	1	21	NON CYTOPLASMIC.
TRANSMEM	22	43
TOPO_DOM	44	54	CYTOPLASMIC.
TRANSMEM	55	77
TOPO_DOM	78	94	NON CYTOPLASMIC.
TRANSMEM	95	114
TOPO_DOM	115	120	CYTOPLASMIC.
TRANSMEM	121	141
TOPO_DOM	142	147	NON CYTOPLASMIC.
TRANSMEM	148	166
TOPO_DOM	167	186	CYTOPLASMIC.
TRANSMEM	187	205
TOPO_DOM	206	215	NON CYTOPLASMIC.
TRANSMEM	216	237
TOPO_DOM	238	262	CYTOPLASMIC.

sp|Q9Y5Q6|INSL5_HUMAN
SIGNAL	1	22
REGION	1	4	N-REGION
REGION	5	16	H-REGION
REGION	17	22	C-REGION
TOPO_DOM	23	135	NON CYTOPLASMIC

sp|P11279|LAMP1_HUMAN
SIGNAL	1	28
REGION	1	9	N-REGION
REGION	10	22	H-REGION
REGION	23	28	C-REGION
TOPO_DOM	29	381	NON CYTOPLASMIC
TRANSMEM	382	405
TOPO_DOM	405	417	CYTOPLASMIC

sp|P05067|A4_HUMAN
SIGNAL	1	17
REGION	1	3	N-REGION
REGION	4	12	H-REGION
REGION	13	17	C-REGION
TOPO_DOM	18	700	NON CYTOPLASMIC
TRANSMEM	701	723
TOPO_DOM	724	770	CYTOPLASMIC

sp|P02753|RET4_HUMAN
SIGNAL	1	18
REGION	1	3	N-REGION
REGION	4	13	H-REGION
REGION	14	18	C-REGION
TOPO_DOM	19	201	NON CYTOPLASMIC