User:Eric Martz/Cavities tests
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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.
Swiss Model has apparently used the temperature value field in the PDB file to indicate regions that are highly unreliable, namely the regions that are red when the model is . These regions are shown as translucent white in the initial scene (using the Jmol command select temperature >50).
The evolutionary conservation pattern, revealed by ConSurf, is quite interesting, showing .[1]
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.
Below is the alignment produced by Swiss Model, used in making the 3D model. Vertical bars for identity were inserted by hand.
| | | | || 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
Below is the sequence with ATOM records (coordinates) from 2QGZ, numbered 100-300, showing the gaps as "...". This sequence listing was used to locate the positions marked /\ above.
1 .......... .......... .......... .......... .......... 51 .......... .......... .......... .......... .........Q 101 KQAAISERIQ LVSLPKSYRH IHLSDIDVNN ASRMEAFSAI LDFVEQYPSA 151 EQKGLYLYGD MGIGKSYLLA AMAHELSEKK GVSTTLLHFP SFAIDVKNAI 201 S....KEEID AVKNVPVLIL DDIGA..... .VRDEVLQVI LQYRMLEELP 251 TFFTSNYSFA DLERKWA... .....WQAKR VMERVRYLAR EFHLEGANRR
(Copied from Protein Explorer's sequence display.)