Secondary Structure Prediction BCKDHA
Contents
1. Secondary structure prediction
PSIPRED
Basic information
author: David Jones (University College London)
year:1998
version: 2
References
[PSIPRED Server]
[Overview of prediction methods]
[History of the PSIPRED]
Theory
PSIPRED uses neuronal networks which has a single hidden layer and a feed-forward back-propagation architecture. FOr the online prediction on the server it is enough to enter a amino acid sequence. Since PSIPRED uses a very stringent cross validation method to evaluate the performance it reaches an average Q3 score of 80.7%.
Algorithm
The predicition is splitted into three different steps. In the first step sequence profiles are generated by using a position specific scoring matrix from PSI-BLAST as input for the neuronal network. In the next step the secondary structure is predicted. In the last step the output of the secundary structure prediction is filtered.
What is predicted
PSIPRED predicts the secondary structure
Features
There are three different options:
- Mask low complexity regions
- Mask transmembrane helices
- Mask coiled-coil regions
It is also possible to get an email with the results of PSIPRED.
Required information
PSIPRED requires the output of PSI-BLAST (Position Specific Iterated - BLAST) as input data.
Prediction
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
1. line: Sequence
2. line: structral elements
3. line: if a residue is involved in symmetrie contacts it is labeled with a star
4. line: if a residue is solvent accessible it is labeled with an "A"
Letter code for the secundary structure elements:
- H (blue): alpha
- 3 (yellow): residue in isolated beta-bridge
- T (red): hydrogen bonded turn
- S (green): bend
File:Output.pdf
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
The probability can reach from 0 to 1. Where 0 means there is no disordered region and 1 that there is a disordered region.
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
The probability can reach from 0 to 1. Where 0 means there is no disordered region and 1 that there is a disordered region.
POODLE-W
The regions which could be disordered regions but poodle is not sure are bordered by blue squares and the disordered regions are bordered by red squares.
Detailed sequence with disordered region:
File:PoodleWDOSeq.pdf
0=ordered regions
5=perhaps disordered regions
9=disordered regions
IUPred
Prediction type: long disorder
Detailed sequence with disordered region probability: File:LongSeqOut.pdf
Prediction type: short disorder
Detailed sequence with disordered region probability: File:ShortSeqOut.pdf
Prediction type: structured regions
With the option "structured regions" there was no prediction of disordered regions.
Only the command "Unkown globular domains: 1-445" appeared.
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) |