Difference between revisions of "Secondary Structure Prediction BCKDHA"

From Bioinformatikpedia
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!colspan="3" |[http://www.ebi.ac.uk/pdbsum/1u5b]
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!colspan="3" |[http://www.ebi.ac.uk/pdbsum/1u5b EMBL-EBI]
 
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!colspan="3"|[http://www.ebi.ac.uk/pdbsum/1umd]
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!colspan="3"|[http://www.ebi.ac.uk/pdbsum/1umd EMBL-EBI]
 
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!colspan="3"|[http://www.ebi.ac.uk/pdbsum/1qs0]
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!colspan="3"|[http://www.ebi.ac.uk/pdbsum/1qs0 EMBL-EBI]
 
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!colspan="3"|[http://www.ebi.ac.uk/pdbsum/3dv0]
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!colspan="3"|[http://www.ebi.ac.uk/pdbsum/3dv0 EMBL-EBI]
 
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!colspan="3" |[http://www.uniprot.org/uniprot/P12694]
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!colspan="3" |[http://www.uniprot.org/uniprot/P12694 UniProt]
 
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!colspan="3"|[http://www.uniprot.org/uniprot/Q5SLR4]
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!colspan="3"|[http://www.uniprot.org/uniprot/Q5SLR4 UniProt]
 
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!colspan="3"|[http://www.uniprot.org/uniprot/P09060]
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!colspan="3"|[http://www.uniprot.org/uniprot/P09060 UniProt]
 
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!colspan="3"|[http://www.uniprot.org/uniprot/P21873]
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!colspan="3"|[http://www.uniprot.org/uniprot/P21873 UniProt]
 
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Revision as of 18:25, 24 May 2011

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

1u5b (e-value:0) 1umd (e-value:6e-58) 1qs0 (e-value:1e-57) PDB-ID PDB-ID
EMBL-EBI EMBL-EBI EMBL-EBI EMBL-EBI
UniProt UniProt UniProt UniProt
start end structural element start end structural element start end structural element start end structural element
35 60 alpha helix
61 64 beta strand
74 83 alpha helix
91 93 alpha helix 89 92 beta strand
99 124 alpha helix 98 104 alpha helix
108 116 alpha helix
122 125 turn
127 129 beta strand
135 138 turn
138 146 alpha helix 144 147 beta strand
152 154 beta strand 150 162 alpha helix
161 166 alpha helix
171 179 alpha helix 169 173 beta strand
176 179 alpha helix
185 188 turn 181 193 alpha helix
198 201 turn 196 204 beta strand
209 211 turn
212 226 alpha helix 222 227 alpha helix
232 237 beta strand 232 236 beta strand
240 242 alpha helix 240 255 alpha helix
244 255 alpha helix
260 266 beta strand 261 267 beta strand
268 270 beta strand
275 277 alpha helix
280 282 beta strand
285 287 alpha helix
289 291 alpha helix
294 299 beta strand 296 305 alpha helix
303 320 beta strand 306 308 turn
324 329 beta strand 312 334 alpha helix
341 345 alpha helix
348 351 beta strand
360 368 alpha helix 354 366 alpha helix
369 372 turn
376 399 alpha helix
405 408 alpha helix
412 415 beta strand
418 434 alpha helix
435 437 alpha helix
440 442 alpha helix

DSSP

2. Prediction of disordered regions

DISOPRED

Disopredplot.png

The disordered regions in BCKDHA are predicted by DISOPRED in the beginning and in the end of the protein.

POODLE

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)
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