Secondary Structure Prediction BCKDHA
From Bioinformatikpedia
Contents
1. Secondary structure prediction
PSIPRED
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
1umd | PDB-ID | PDB-ID | PDB-ID | PDB-ID | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
http://www.ebi.ac.uk/pdbsum/1umd | ||||||||||||||||||
http://www.uniprot.org/uniprot/Q5SLR4 | ||||||||||||||||||
start | end | structural element | start | end | structural element | start | end | structural element | start | end | structural element | start | end | structural element | ||||
35 | 60 | alpha helix | ||||||||||||||||
74 | 83 | alpha helix | ||||||||||||||||
89 | 92 | beta strand | ||||||||||||||||
98 | 104 | alpha helix | ||||||||||||||||
108 | 116 | alpha helix | ||||||||||||||||
122 | 125 | turn | ||||||||||||||||
135 | 138 | turn | ||||||||||||||||
144 | 147 | beta strand | ||||||||||||||||
150 | 162 | alpha helix | ||||||||||||||||
169 | 173 | beta strand | ||||||||||||||||
176 | 179 | alpha helix | ||||||||||||||||
181 | 193 | alpha helix | ||||||||||||||||
196 | 204 | beta strand | ||||||||||||||||
222 | 227 | alpha helix | ||||||||||||||||
232 | 236 | beta strand | ||||||||||||||||
240 | 255 | alpha helix | ||||||||||||||||
261 | 267 | beta strand | ||||||||||||||||
296 | 305 | alpha helix | ||||||||||||||||
306 | 308 | turn | ||||||||||||||||
312 | 334 | alpha helix | ||||||||||||||||
341 | 345 | alpha helix | ||||||||||||||||
348 | 351 | beta strand | ||||||||||||||||
354 | 366 | alpha helix |
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 |
GOPET results for BACR_HALSA:
GOid | Aspect | Confidence | GOterm |
---|---|---|---|
GO:0005216 | F | 77% | ion channel activiy |
GO:0008020 | F | 75% | G-protein coupled photoreceptor activity |
GO:0015078 | F | 60% | hydrogen ion transmembrane transporter activity |
GOPET results for INSL5_HUMAN:
GOid | Aspect | Confidence | GOterm |
---|---|---|---|
GO:0005179 | F | 80% | hormone activity |
GOPET results for LAMP1_HUMAN:
GOid | Aspect | Confidence | GOterm |
---|---|---|---|
GO:0004812 | F | 60% | aminoacyl-tRNA ligase activity |
GO:0005524 | F | 60% | ATP binding |
GOPET results for RET4_HUMAN:
GOid | Aspect | Confidence | GOterm |
---|---|---|---|
GO:0005488 | F | 90% | binding |
GO:0005501 | F | 81% | retinoid binding |
GO:0008289 | F | 80% | lipid binding |
GO:0019841 | F | 78% | retinol binding |
GO:0005215 | F | 78% | transporter activity |
GO:0016918 | F | 78% | retinal binding |
GO:0005319 | F | 69% | lipid transporter activity |
GO:0008035 | F | 60% | high-density lipoprotein particle 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) |