User:Eric Martz/Cavities tests

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).

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.)