Secondary Structure Prediction BCKDHA

From Bioinformatikpedia
Revision as of 15:27, 24 May 2011 by Demel (talk | contribs) (GOPET)

1. Secondary structure prediction

PSIPRED

PSIPREDbild.png

Secundary Structure

start end structural element
1 1 C
2 16 H
17 17 C
18 25 H
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

PSIPRED has predicted 23 coils, 16 alpha helices and 6 beta sheets.

Jpred3

PDB-ID Score Identity Evalue

DSSP

2. Prediction of disordered regions

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

OCTOPUS

SPOCTOPUS

4. Prediction of GO terms

GOPET

GOPET results fot BCKDHA:

GOid Aspect Confidence GOTerm
GO:0003824 F 97% catalytic activity
Go:0016491 F 96% oxidoreductase activity
GO:0016624 F 95% oxidoredusctase activity acting on the aldehyde or oxo group of donors disulfide as acceptor
GO:0003863 F 90% 3-methyl-2-oxobutanoate dehydrogenase 2-methylpropanoyl-transferring activity
GO:0004739 F 89% pyruvate dehydrogenase acetyl-transferring activity
GO:0004738 F 78% pyruvat dehydrogenase activity
GO:0003826 F 77% alpha-ketoacid dehydrogenase activity
GO:0047101 F 75% 2-oxoisovalerate dehydrogenase acylting activity
GO:0008677 F 65% 2-dehydropantoate 2-reductase activity
GO:0019152 F 63% acetoin dehydrogenase activity
GO:0030955 F 63% potassium ion binding
GO:0016616 F 62% oxidoreductase activity acting on the CH-OH group of donors NAD or NADP as acceptor
GO:0046872 F 62% metal ion binding

GOPET results for A4_HUMAN

GOid Aspect Confidence GOTerm
GO:0004866 F 87% endopeptidase inhibitor activity
GO:0004867 F 86% serine-type endopeptidase inhibitor activity
GO:0030568 F 83% plasmin inhibitor activity
GO:0030304 F 83% trypsin inhibitor activity
GO:0030414 F 82% peptidase inhibitor activity
GO:0005488 F 79% binding
GO:0005515 F 74% protein binding
GO:0046872 F 73% metal ion binding
GO:0003677 F 71% DNA binding
GO:0008201 F 70% heparin binding
GO:0008270 F 69% zinc ion binding
GO:0005507 F 69% copper ion binding
GO:0005506 F 67% iron ion binding

Pfam

Query Cellular Component Molecular function Biological Process
BCKDHA GO:0016624 (oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor) GO:0008152 (metabolic process)
A4_HUMAN GO:0016021 (integral to membrane) GO:0005488 (bindung)
BACR_HALSA GO:0016020 (membrane) GO:0005216 (ion channel activity) GO: 0006811 (ion transport)
INSL5_HUMAN GO:0005576 (extracellular region) GO:0005179 (hormone activity)
LAMP1_HUMAN GO:0016020 (membrane)
RET4_HUMAN GO:0005488 (binding)