Difference between revisions of "Secondary Structure Prediction BCKDHA"
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Detailed sequence with disordered region probability: |
Detailed sequence with disordered region probability: |
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[[File:PoodleSFactorBOut.pdf]] |
[[File:PoodleSFactorBOut.pdf]] |
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+ | ===IUPred=== |
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== 3. Prediction of transmembrane alpha-helices and signal peptides == |
== 3. Prediction of transmembrane alpha-helices and signal peptides == |
Revision as of 00:46, 25 May 2011
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
1u5b (e-value:0) | 1umd (e-value:6e-58) | 1qs0 (e-value:1e-57) | 3dv0 (e-value:2e-51) | |||||||
---|---|---|---|---|---|---|---|---|---|---|
EMBL-EBI | EMBL-EBI | EMBL-EBI | EMBL-EBI | |||||||
UniProt | UniProt | UniProt | UniProt | |||||||
position | structural element | position | structural element | position | structural element | position | structural element | |||
10–19 | alpha helix | |||||||||
24-26 | alpha helix | |||||||||
35-60 | alpha helix | 36–38 | alpha helix | |||||||
61-64 | beta strand | 44–47 | alpha helix | 44–69 | alpha helix | |||||
48–51 | alpha helix | |||||||||
67–69 | alpha helix | |||||||||
74-83 | alpha helix | 74–99 | alpha helix | |||||||
83–91 | alpha helix | |||||||||
91-93 | alpha helix | 89-92 | beta strand | |||||||
99-124 | alpha helix | 98-104 | alpha helix | 102–104 | beta strand | 98–100 | beta strand | |||
108-116 | alpha helix | 110–112 | turn | 106–111 | alpha helix | |||||
122-125 | turn | 113–122 | alpha helix | 116–124 | alpha helix | |||||
127-129 | beta strand | 127–130 | beta strand | 127–130 | alpha helix | |||||
135-138 | turn | |||||||||
138-146 | alpha helix | 144-147 | beta strand | 136–141 | alpha helix | |||||
152-154 | beta strand | 150-162 | alpha helix | 146–154 | alpha helix | 147 – 161 | alpha helix | |||
161-166 | alpha helix | 160–163 | turn | |||||||
171-179 | alpha helix | 169-173 | beta strand | 173–175 | alpha helix | 168–173 | beta strand | |||
176-179 | alpha helix | 175–178 | alpha helix | |||||||
185-188 | turn | 181-193 | alpha helix | 182–185 | beta strand | 180–191 | alpha helix | |||
198-201 | turn | 196-204 | beta strand | 186–200 | alpha helix | 196–202 | beta strand | |||
207–212 | beta strand | 204–206 | beta strand | |||||||
209-211 | turn | 211–213 | alpha helix | |||||||
212-226 | alpha helix | 222-227 | alpha helix | 214–217 | alpha helix | 221–226 | alpha helix | |||
232-237 | beta strand | 232-236 | beta strand | 219–231 | alpha helix | 231–235 | beta strand | |||
240-242 | alpha helix | 240-255 | alpha helix | 235–241 | beta strand | 239–254 | alpha helix | |||
244-255 | alpha helix | 243–245 | beta strand | |||||||
250–253 | alpha helix | |||||||||
254–257 | turn | |||||||||
260-266 | beta strand | 261-267 | beta strand | 262–266 | alpha helix | 260–265 | beta strand | |||
268-270 | beta strand | |||||||||
270–275 | beta strand | |||||||||
275-277 | alpha helix | |||||||||
280-282 | beta strand | 279 – 294 | alpha helix | |||||||
285-287 | alpha helix | 285–292 | alpha helix | |||||||
289-291 | alpha helix | |||||||||
294-299 | beta strand | 296-305 | alpha helix | 300–305 | beta strand | 296–306 | alpha helix | |||
303-320 | beta strand | 306-308 | turn | 318–320 | alpha helix | |||||
324-329 | beta strand | 312-334 | alpha helix | 326–329 | alpha helix | 312–334 | alpha helix | |||
341-345 | alpha helix | 335–345 | alpha helix | 341–346 | alpha helix | |||||
348-351 | beta strand | |||||||||
360-368 | alpha helix | 354-366 | alpha helix | 351–373 | alpha helix | 354–366 | alpha helix | |||
369-372 | turn | |||||||||
376-399 | alpha helix | 378–380 | beta strand | |||||||
388–390 | alpha helix | |||||||||
391–396 | beta strand | |||||||||
405-408 | alpha helix | 399–406 | alpha helix | |||||||
412-415 | beta strand | |||||||||
418-434 | alpha helix | |||||||||
435-437 | alpha helix | |||||||||
440-442 | alpha helix |
1u5b | 1umd | 1qs0 | 3dv0 |
---|---|---|---|
e-value:0 | e-value:6e-58 | e-value:1e-57 | e-value:2e-51 |
|
DSSP
2. Prediction of disordered regions
DISOPRED
The disordered regions in BCKDHA are predicted by DISOPRED in the beginning and in the end of the protein.
POODLE
POODLE-S (Missing residues)
POODLE-S (which predicts short disordered regions) with the option "Missing residues" predicted the disordered regions between the positions 1-56, 341-345 and 420-423. This is also shown in the plot above.
Detailed sequence with disordered region probability: File:PoodleSMissingResiduesOut.pdf
POODLE-S (High B-Factor residues)
POODLE-S (which predicts short disordered regions) with the option "High B-Factor residues" predicted the disordered regions between the positions 6-9, 15-57, 93, 95-96, 340-354 and 379-402. This is also shown in the plot above.
Detailed sequence with disordered region probability: File:PoodleSFactorBOut.pdf
IUPred
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) |