User:Eric Martz/Cavities tests: Difference between revisions
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The template was <scene name='User:Eric_Martz/Sandbox_4/2qgz/3'>2qgz</scene>. The portion of the template used was Glu107-Arg300. Only the amino-terminal 6 residues were not used as template (translucent). Note that there are <scene name='User:Eric_Martz/Sandbox_4/2qgz/5'>three loops</scene> in this segment of the template that lack coordinates due to [[disorder]] in the crystal (marked with spacefilled alpha-carbon atoms). | The template was <scene name='User:Eric_Martz/Sandbox_4/2qgz/3'>2qgz</scene>. The portion of the template used was Glu107-Arg300. Only the amino-terminal 6 residues were not used as template (translucent). Note that there are <scene name='User:Eric_Martz/Sandbox_4/2qgz/5'>three loops</scene> in this segment of the template that lack coordinates due to [[disorder]] in the crystal (marked with spacefilled alpha-carbon atoms). | ||
The missing loops are 202-205 (NGSV), 226-231 (EQATSW), and 268-275 (TIKGSDET). | The missing loops are 202-205 (NGSV), 226-231 (EQATSW), and 268-275 (TIKGSDET). These gaps, which occur between the residues marked /\ below, were apparently ignored in making the model, which has a continuous main chain. | ||
Alignment produced by Swiss Model, used in making the 3D model: | Alignment produced by Swiss Model, used in making the 3D model: | ||
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TARGET 194 SKRPTGMLTN SNMEEMTKLL ---GERVMDR MRLGNSLWVI FNWDSYR | TARGET 194 SKRPTGMLTN SNMEEMTKLL ---GERVMDR MRLGNSLWVI FNWDSYR | ||
2qgzA 247 eelptfftsn ysfadlerkw awqakrvmer vr-ylarefh leganrr- | 2qgzA 247 eelptfftsn ysfadlerkw awqakrvmer vr-ylarefh leganrr- | ||
/\ | |||
TARGET h ssssss hhhhh hhhh hh ssssss s | TARGET h ssssss hhhhh hhhh hh ssssss s | ||
2qgzA h ssssss hhhh hhhh hh hh ssss s | 2qgzA h ssssss hhhh hhhh hh hh ssss s | ||
</pre> | </pre> | ||
Revision as of 03:01, 3 October 2008
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The following sequence was provided for DnaC from E. coli:
MKNVGDLMQR LQKMMPAHIK PAFKTGEELL AWQKEQGAIR SAALERENRA
MKMQRTFNRS GIRPLHQNCS FENYRVECEG QMNALSKARQ YVEEFDGNIA
SFIFSGKPGT GKNHLAAAIC NELLLRGKSV LIITVADIMS AMKDTFRNSG
TSEEQLLNDL SNVDLLVIDE IGVQTESKYE KVIINQIVDR RSSSKRPTGM
LTNSNMEEMT KLLGERVMDR MRLGNSLWVI FNWDSYRSRV TGKEY
This sequence was submitted to Swiss Model, which generated the homology model shown here () using 2qgz chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me. The homology model represents residues 55-237, shown in boldface in the above sequence.
In order to find specific residues, or see other aspects of this homology model, please use:
View DnaC Homology Model in FirstGlance in Jmol
The template was . The portion of the template used was Glu107-Arg300. Only the amino-terminal 6 residues were not used as template (translucent). Note that there are in this segment of the template that lack coordinates due to disorder in the crystal (marked with spacefilled alpha-carbon atoms).
The missing loops are 202-205 (NGSV), 226-231 (EQATSW), and 268-275 (TIKGSDET). These gaps, which occur between the residues marked /\ below, were apparently ignored in making the model, which has a continuous main chain.
Alignment produced by Swiss Model, used in making the 3D model:
TARGET 55 R TFNRSGIRPL HQNCSFENYR VECEGQMNAL SKARQYVEEF
2qgzA 100 qkqaais--e riqlvslpks yrhihlsdid vnnasrmeaf saildfveqy
TARGET sssss h h hhhhhhh hhhhhhhhh
2qgzA hhh h sss h h hhhhhhh hhhhhhhhh
TARGET 96 DGN-IASFIF SGKPGTGKNH LAAAICNELL L-RGKSVLII TVADIMSAMK
2qgzA 148 psaeqkglyl ygdmgigksy llaamahels ekkgvsttll hfpsfaidvk
TARGET ssss ss hhh hhhhhhhhhh h h ssss sshhhhhhh
2qgzA ssss ss hhh hhhhhhhhhh hh ssss sshhhhhhh
TARGET 144 DTFRNSGTSE EQLLNDLSNV DLLVIDEIGV QTESKYEKVI INQIVDRRSS
2qgzA 198 naiske---- --eidavknv pvlilddiga vrde-----v lqvilqyrml
/\ / \
TARGET hhh ssssss hhhhhhhhhh
2qgzA hh h ssssss hhhhhhhhhh
TARGET 194 SKRPTGMLTN SNMEEMTKLL ---GERVMDR MRLGNSLWVI FNWDSYR
2qgzA 247 eelptfftsn ysfadlerkw awqakrvmer vr-ylarefh leganrr-
/\
TARGET h ssssss hhhhh hhhh hh ssssss s
2qgzA h ssssss hhhh hhhh hh hh ssss s