4DJIA

Structure of glutamate-gaba antiporter gadc
Warning
  • Chain breaks within knot 31 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
  • Chain breaks within knot 41 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 140
Slipknot S +31 41 +31

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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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+31 30-214 185 1-20, 390-500 21-29, 215-389 20 111 slipknot
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41 17-249 233 1-16 295-500 250-294 16 206 slipknot
Chain Sequence
AKQLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGA---IEMDSKTFFPDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHDANT----GVTLEPINSQNAPKGHFFLHPRARSPHYIVMNDK
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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3.2 10-240 231 1-9 248-493 241-247 9 246 slipknot
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4.1 6-248 243 1-5 256-493 249-255 5 238 slipknot
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4.1 8-267 260 1-7 284-493 268-283 7 210 slipknot
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4.1 10-281 272 1-9 292-493 282-291 9 202 slipknot
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3.2 10-291 282 1-9 294-493 292-293 9 200 slipknot
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3.2m 9-265 257 1-2, 271-493 3-8, 266-270 2 223 slipknot
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3.2 12-263 252 1-5, 272-493 6-11, 264-271 5 222 slipknot
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3.2 13-263 251 1-11, 272-493 12-12, 264-271 11 222 slipknot
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3.2 22-262 241 1-9, 283-493 10-21, 263-282 9 211 slipknot
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3.2 23-262 240 1-21, 283-493 22-22, 263-282 21 211 slipknot
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3.2 18-282 265 1-10, 290-493 11-17, 283-289 10 204 slipknot
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2.1 22-210 189 1-16, 229-493 17-21, 211-228 16 265 slipknot
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2.1 35-373 339 1-16, 423-493 17-34, 374-422 16 71 slipknot
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2.1 35-209 175 1-17, 230-493 18-34, 210-229 17 264 slipknot
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2.1 34-423 390 1-17, 474-493 18-33, 424-473 17 20 slipknot
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2.1 34-483 450 484-493 1-18 19-33 18 9 slipknot
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2.1 32-197 166 1-21, 209-493 22-31, 198-208 21 285 slipknot
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1.1 35-231 197 1-22, 247-493 23-34, 232-246 22 247 slipknot
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1.1 34-246 213 1-24, 248-493 25-33, 247-247 24 246 slipknot
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2.1 35-229 195 1-25, 232-493 26-34, 230-231 25 262 slipknot
sequence length 500
structure length 493
publication title Structure and mechanism of a glutamate-GABA antiporter
pubmed doi rcsb
molecule tags Transport protein
molecule keywords Probable glutamate/gamma-aminobutyrate antiporter
source organism Escherichia coli
missing residues 175-177, 460-463
total genus Genus: 140
ec nomenclature
pdb deposition date 2012-02-02
KnotProt deposition date 2014-09-29

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF13520 AA_permease_2 Amino acid permease
Image from the rcsb pdb (www.rcsb.org)
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similar chains in the KnotProt database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

  
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#similar chains, but unknotted
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How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling