User:Eric Martz/Cavities tests: Difference between revisions
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This sequence was submitted to Swiss Model, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/6'>restore initial scene</scene>) 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. | This sequence was submitted to Swiss Model, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/6'>restore initial scene</scene>) 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 <font color="red"><b>red</b></font> when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent white''' in the initial scene (using the Jmol command <i>select temperature >50</i>). | 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 <font color="red"><b>red</b></font> when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent white''' in the initial scene (using the Jmol command <i>select temperature >50</i>). Three of these regions are explained by gaps in the template model (see below). | ||
The [[Conservation, Evolutionary|evolutionary conservation]] pattern, revealed by ConSurf, is quite interesting, showing <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/7'>two conserved patches</scene>.<ref>ConSurf found only 10 sequences in SwissProt, with an Average Pairwise Distance of 1.6. The [http://consurf.tau.ac.il/results/1222995227/output.html run shown here] used 100 sequences from Uniprot, with an APD of 1.4.</ref> | The [[Conservation, Evolutionary|evolutionary conservation]] pattern, revealed by ConSurf, is quite interesting, showing <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/7'>two conserved patches</scene>.<ref>ConSurf found only 10 sequences in SwissProt, with an Average Pairwise Distance of 1.6. The [http://consurf.tau.ac.il/results/1222995227/output.html run shown here] used 100 sequences from Uniprot, with an APD of 1.4.</ref> | ||
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[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=http%3A//proteopedia.org/wiki/images/3/3e/Dnac_from_2ggz_a.pdb View DnaC Homology Model in FirstGlance in Jmol] | [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=http%3A//proteopedia.org/wiki/images/3/3e/Dnac_from_2ggz_a.pdb View DnaC Homology Model in FirstGlance in Jmol] | ||
==Gaps in the Template Model== | |||
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). | ||
Revision as of 15:46, 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.
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). Three of these regions are explained by gaps in the template model (see below).
The evolutionary conservation pattern, revealed by ConSurf, is quite interesting, showing .[1]
In order to find specific residues, or see charge distribution or other aspects of this homology model, please use:
View DnaC Homology Model in FirstGlance in Jmol
Gaps in the Template ModelGaps in the Template Model
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.)
NotesNotes
- ↑ ConSurf found only 10 sequences in SwissProt, with an Average Pairwise Distance of 1.6. The run shown here used 100 sequences from Uniprot, with an APD of 1.4.