User:Susana Retamal/Sandbox1

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*[[User:Susana Retamal/Sandbox1]]
 
- 
=Background Information=
=Background Information=
-
Rsp1275 is a member of the Fnr-Crp family of transcriptional regulators. Homologues of the Fnr protein from ''E. coli'' have been identified in a variety of taxonomically (1) diverse bacterial species. The bacterium ''Rhodobacter spheroides 2.4.1'' encodes 8 members of this family, however only 2 have known function. The modeling of 7 of them were successfully obtained using 3D-Jigsaw, all being very similar in structure to Crp (the only one with crystal structure solved). The DNA binding domain helix-turn-helix is located in the C-terminal, and the N-terminal part contains the allosteric effector domain. Rsp1275 has been linked with salt-tolerance in ''Rhodobacter spheroides''. Different genes coding for the Fnr-Crp proteins of unknown function have been cloned and a multicopy test was performed to evaluate these as potential regulators of NaCl-responsive genes.
+
Rsp1275 is a member of the Fnr-Crp family of transcriptional regulators. Homologues of the Fnr protein from ''E. coli'' have been identified in a variety of taxonomically diverse bacterial species.<ref>Spiro, S. 1994. The FNR family of transcriptional regulators. Antonie van Leeuwenhoek 66:23–36.</ref><ref>PredictProtein: B Rost, G Yachdav and J Liu (2004). The PredictProtein Server. Nucleic Acids Research 32(Web Server issue):W321-W326.</ref>The bacterium ''Rhodobacter sphaeroides" 2.4.1 encodes 8 members of this family, however only 2 have known function. Models of 7 of them, including RSP1275, were successfully obtained using 3D-Jigsaw, all being very similar in structure to Crp (the only one with crystal structure solved). The DNA binding domain helix-turn-helix is located in the C-terminal, and the N-terminal part contains the allosteric effector domain.
-
 
+
''
-
 
+
= Structure of the Proposed rsp1275 modeling obtained using 3D-Jigsaw =
-
# Jmol state version 11.5.35 2008-04-29 08:46;
+
''
-
# fullName = "jmolApplet0__null__";
+
-
# documentBase = "http://bip.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=/LIGIM/fgij/20090427/UPL_4ce0f944185ebb4f14fa229bc8fc7748.pdb";
+
-
# codeBase = "http://bip.weizmann.ac.il/oca-docs/fgij/";
+
-
 
+
-
function _setWindowState();
+
<applet load='Rsp1275.pdb' size='300' frame='true' align='right' caption='Insert caption here' />
-
# height 617;
+
-
# width 716;
+
-
stateVersion = 1105035;
+
-
backgroundColor = "[x000000]";
+
-
axis1Color = "[xff0000]";
+
-
axis2Color = "[x008000]";
+
-
axis3Color = "[x0000ff]";
+
-
ambientPercent = 45;
+
-
diffusePercent = 84;
+
-
specular = true;
+
-
specularPercent = 22;
+
-
specularPower = 40;
+
-
specularExponent = 6;
+
-
statusReporting = true;
+
-
end function;
+
-
function _setFileState();
+
The highlighted <scene name='User:Susana_Retamal/Sandbox1/Rsp1275/10'>alpha-helices</scene> of the protein.
-
set allowEmbeddedScripts false;
+
This is the <scene name='User:Susana_Retamal/Sandbox1/Rsp1275/12'>Amino to Carboxyl rainbow</scene> of the protein.
-
set autoBond true;
+
-
set appendNew true;
+
-
set appletProxy "";
+
-
set applySymmetryToBonds false;
+
-
set bondRadiusMilliAngstroms 150;
+
-
set bondTolerance 0.45;
+
-
set defaultDirectory "";
+
-
set defaultLattice {0.0 0.0 0.0};
+
-
set defaultLoadScript "";
+
-
set defaultVDW Jmol;
+
-
set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb";
+
-
set forceAutoBond false;
+
-
set minBondDistance 0.4;
+
-
set percentVdwAtom 20;
+
-
set smartAromatic true;
+
-
load /*file*/"http://bip.weizmann.ac.il/LIGIM/fgij/20090427/UPL_4ce0f944185ebb4f14fa229bc8fc7748.pdb";
+
-
end function;
+
=Protein Sequence=
-
function _setVariableState();
+
1 mfvpapdati tncrncplrr kplflpfsds elsfmeqfkv gelvvapgvt lleegqgsah
-
set defaultanglelabel "%VALUE %UNITS";
+
61 lftvlsglgi rstmlengrr qvinflfpgd figlqaglag emrhsvestt tmvlcvfnra
-
set defaultcolorscheme "Jmol";
+
-
set defaultdirectory "";
+
-
set defaultdistancelabel "%VALUE %UNITS";
+
-
set defaultdrawarrowscale 0.5;
+
-
set defaultlattice "{0 0 0}";
+
-
set defaultloadscript "";
+
-
set defaulttorsionlabel "%VALUE %UNITS";
+
-
set defaulttranslucent 0.5;
+
-
set defaultvdw "Jmol";
+
-
set allowembeddedscripts true;
+
-
set allowrotateselected false;
+
-
set appletproxy "";
+
-
set applysymmetrytobonds false;
+
-
set autobond true;
+
-
set autofps false;
+
-
set axes window;
+
-
set axesmode 0;
+
-
set axesscale 2.0;
+
-
set bondmodeor false;
+
-
set bondradiusmilliangstroms 150;
+
-
set bondtolerance 0.45;
+
-
set cartoonrockets false;
+
-
set chaincasesensitive false;
+
-
set dataseparator "[[User:Susana Retamal|Susana Retamal]]";
+
-
set delaymaximumms 0;
+
-
set dipolescale 1.0;
+
-
set disablepopupmenu false;
+
-
set displaycellparameters true;
+
-
set dotsselectedonly false;
+
-
set dotsurface true;
+
-
set drawpicking false;
+
-
set dynamicmeasurements false;
+
-
set ellipsoidarcs false;
+
-
set ellipsoidaxes false;
+
-
set ellipsoidaxisdiameter 0.02;
+
-
set ellipsoidball true;
+
-
set ellipsoiddotcount 200;
+
-
set ellipsoiddots false;
+
-
set ellipsoidfill false;
+
-
set forceautobond false;
+
-
set greyscalerendering false;
+
-
set hbondsbackbone false;
+
-
set hbondssolid false;
+
-
set helppath "http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm";
+
-
set hermitelevel 0;
+
-
set hidenameinpopup false;
+
-
set hidenavigationpoint false;
+
-
set highresolution false;
+
-
set historylevel 0;
+
-
set hoverdelay 0.5;
+
-
set isosurfacepropertysmoothing true;
+
-
set justifymeasurements false;
+
-
set loadformat "http://www.rcsb.org/pdb/files/%FILE.pdb";
+
-
set measureallmodels false;
+
-
set measurementlabels true;
+
-
set minbonddistance 0.4;
+
-
set navigationperiodic false;
+
-
set navigationspeed 5.0;
+
-
set percentvdwatom 20;
+
-
set pickingspinrate 10;
+
-
set propertyatomnumberfield 0;
+
-
set propertycolorscheme "roygb";
+
-
set propertydatafield 0;
+
-
set rangeselected false;
+
-
set ribbonaspectratio 16;
+
-
set ribbonborder false;
+
-
set rocketbarrels false;
+
-
set selecthetero true;
+
-
set selecthydrogen true;
+
-
set sheetsmoothing 1.0;
+
-
set showhiddenselectionhalos false;
+
-
set showhydrogens true;
+
-
set showmeasurements true;
+
-
set showmultiplebonds true;
+
-
set shownavigationpointalways false;
+
-
set smartaromatic true;
+
-
set solventprobe false;
+
-
set solventproberadius 1.2;
+
-
set ssbondsbackbone true;
+
-
set stereodegrees 5;
+
-
set strandcountformeshribbon 7;
+
-
set strandcountforstrands 5;
+
-
set testflag1 false;
+
-
set testflag2 false;
+
-
set testflag3 false;
+
-
set testflag4 false;
+
-
set tracealpha true;
+
-
set usenumberlocalization true;
+
-
set vectorscale 1.0;
+
-
set vibrationperiod 1.0;
+
-
set vibrationscale 1.0;
+
-
set wireframerotation false;
+
-
set zoomlarge true;
+
-
set zshade false;
+
-
#user-defined variables;
+
121 dlwdlfreep eraydltwia aveehflget iaslgqrdat erlawallri herlsaigla
-
@isd ({0:6 25:32 41:58 76:81 116:122 130:137 156:159 208:216 275:282 294:301 355:371 426:435 478:492 586:593 602:632 658:668 674:685 702:722 736:740 766:786 879:885 1017:1021 1034:1041 1056:1081 1089:1095 1270:1277 1339:1425});
+
-
@~anomalous_atoms ({});
+
-
@~backbone_invisible ({});
+
-
@~hidden_jdef ({});
+
-
@~hydroxy_unchained_nucs ({});
+
-
@~incomplete_aa_sidechains ({});
+
-
@~incomplete_nuc_sidechains ({});
+
-
@~incomplete_sidechains ({});
+
-
@~nobackbone_aas ({});
+
-
@~nophosphorus_nucs ({});
+
-
@~nucleic ({});
+
-
@~protein ({0:1425});
+
-
@~unbondable_aas ({});
+
-
@~unchained_aas ({});
+
-
@~unchained_nucs ({});
+
-
# label defaults;
+
181 ergrvpmpwr qqdladalgl slvhtnktir rlretghalw eggtlfvdre rlatlaladp
-
select none;
+
-
color label none;
+
-
background label none;
+
-
set labelOffset 4 4;
+
-
set labelAlignment left;
+
-
set labelPointer off;
+
-
font label 13.0 SansSerif Plain;
+
-
end function;
+
241 drprrrpli
-
function _setModelState();
 
-
select ({105:115 148:155 168:178 332:342 407:414 633:641 669:673 686:693 723:730 828:833 954:964 973:982 1308:1318});
+
=Physico - Chemical parameters for Rsp1275=
-
color atoms opaque [xeaffff];
+
From http://ca.expasy.org/tools/protparam.html
-
select ({18:24 72:75 82:86 97:104 381:406 514:520 532:539 551:563 572:585 741:747 946:953 983:991 1003:1016 1022:1029 1047:1055 1328:1334});
+
-
color atoms opaque [x10c8d1];
+
-
select ({0:1425});
+
-
Spacefill 0.0;
+
-
select ({0:6 25:32 41:58 76:81 116:122 130:137 156:159 208:216 275:282 294:301 355:371 426:435 478:492 586:593 602:632 658:668 674:685 702:722 736:740 766:786 879:885 1017:1021 1034:1041 1056:1081 1089:1095 1270:1277 1339:1425});
+
-
color atoms opaque [xffff96];
+
-
select ({33:40 138:143 185:191 200:207 217:224 343:350 377:380 464:470 493:507 649:657 808:814 823:827 855:865 1183:1187 1319:1327});
+
-
color atoms opaque [xffffff];
+
-
select ({59:62 87:96 160:167 179:184 192:199 267:274 302:312 372:376 540:550 564:571 594:601 694:701 757:765 795:798 866:873 906:913 919:937 965:972 1030:1033 1082:1088 1145:1153 1214:1221 1278:1299});
+
-
color atoms opaque [xfcedf4];
+
-
select ({11:17 415:425});
+
-
color atoms opaque [x8cffff];
+
-
select ({7:10 123:129 240:250 320:323 442:448 458:463 748:756 834:841 992:1002 1096:1124 1136:1144 1154:1169 1200:1207 1239:1245});
+
-
color atoms opaque [xf07dab];
+
-
select ({144:147 225:228 251:259 324:331 351:354 642:648 842:845 874:878 886:894 914:918 1170:1182 1188:1199 1208:1213 1222:1238 1246:1262 1335:1338});
+
-
color atoms opaque [xa02560];
+
-
select ({63:71 229:239 260:266 283:293 313:319 436:441 449:457 471:477 508:513 521:531 731:735 787:794 799:807 815:822 846:854 895:905 938:945 1042:1046 1125:1135 1263:1269 1300:1307});
+
-
color atoms opaque [xfac9de];
+
-
select BONDS ({0:1453});
+
-
wireframe 0.0;
+
-
measures delete;
 
-
select *; set measures angstroms;
 
-
font measures 15.0 SansSerif Plain;
 
-
select measures ({null});
 
-
select ({0:1425});
+
'''Number of amino acids: 249'''
-
Cartoon on;
+
-
boundBox off;
+
'''Molecular weight: 28014.2'''
-
set echo off;
+
'''Theoretical pI: 6.10'''
-
set echo top left; echo " (Uploaded data)";
+
-
font echo 15.0 SansSerif Bold;
+
-
color echo [xffffff];
+
-
hover "%n %r, Chain=%c, Element=%e";
+
'''Atomic composition:'''
-
frank on;
+
Carbon C 1249
-
font frank 16.0 SansSerif Bold;
+
Hydrogen H 1986
-
set fontScaling false;
+
Nitrogen N 360
 +
Oxygen O 355
 +
Sulfur S 9
-
end function;
+
Formula: C1249H1986N360O355S9
 +
Total number of atoms: 3959
-
function _setPerspectiveState();
+
'''Extinction coefficients:'''
-
set perspectiveModel 11;
+
-
set scaleAngstromsPerInch 0.0;
+
-
set perspectiveDepth true;
+
-
set visualRange 5.0;
+
-
set cameraDepth 3.0;
+
-
boundbox corners {-39.613 2.3779984 -30.096} {-6.684002 52.818996 31.98} # volume = 103106.46;
+
-
center {-23.255371 31.41681 2.846095};
+
-
moveto 0.0 { -417 -265 870 177.93} 100.0 0.0 0.08 {-23.255371 31.41681 2.846095} 35.494194 {0.0 0.0 0.0} -26.387678 -54.92651 50.0;;
+
-
slab 100;depth 0;
+
-
set spinX 0; set spinY 5; set spinZ 0; set spinFps 30;
+
-
end function;
+
-
function _setSelectionState();
+
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
-
set hideNotSelected false;
+
-
end function;
+
-
function _setState();
+
*Ext. coefficient 29115
-
initialize;
+
Abs 0.1% (=1 g/l) 1.039, assuming ALL Cys residues appear as half cystines
-
set refreshing false;
+
-
_setWindowState;
+
-
_setFileState;
+
-
_setVariableState;
+
-
_setModelState;
+
-
_setPerspectiveState;
+
-
_setSelectionState;
+
-
set refreshing true;
+
-
set antialiasDisplay false;
+
-
set antialiasTranslucent true;
+
-
set antialiasImages true;
+
-
end function;
+
-
_setState;
+
*Ext. coefficient 28990
 +
Abs 0.1% (=1 g/l) 1.035, assuming NO Cys residues appear as half cystines
 +
'''Estimated half-life:'''
 +
The N-terminal of the sequence considered is M (Met).
-
=Evidence of Fnr-Crp protein Involvement in Transcriptional Response to NaCl=
+
'''The estimated half-life is''':
 +
 +
*30 hours (mammalian reticulocytes, in vitro).
 +
* >20 hours (yeast, in vivo).
 +
* >10 hours (Escherichia coli, in vivo).
-
=Physico - Chemical parameters for Rsp1275=
+
'''Instability index:'''
 +
The instability index (II) is computed to be 41.06
 +
This classifies the protein as unstable.
-
Number of amino acids: 249
+
'''Aliphatic index:''' 97.19
-
Molecular weight: 28014.2
+
'''Grand average of hydropathicity (GRAVY):''' -0.097
-
Theoretical pI: 6.10
+
'''Globe Predictio'''n: it appears as compact, as a globular domain.
 +
'''Secondary Structure:'''
 +
Helix 34.94%
 +
Extended (sheet) 17.67%
 +
Loop 47.39%
{| border="1"
{| border="1"
Line 348: Line 157:
- POS: The position of the AA in the SEQRES derived sequence.
- POS: The position of the AA in the SEQRES derived sequence.
 +
- SEQ: The SEQRES derived sequence in one letter code.
- SEQ: The SEQRES derived sequence in one letter code.
 +
- 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier.
- 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier.
 +
- SCORE: The normalized conservation scores.
- SCORE: The normalized conservation scores.
 +
- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).
- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).
 +
- CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores.
- CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores.
 +
- CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval.
- CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval.
 +
- MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position.
- MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position.
 +
- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.
- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.
Line 379: Line 196:
19 L LEU65: 0.975 2* 0.108, 1.367 5,1 18/19 A,I,L,M,R,S,V
19 L LEU65: 0.975 2* 0.108, 1.367 5,1 18/19 A,I,L,M,R,S,V
20 S SER66: -0.045 5 -0.697, 0.404 7,4 18/19 E,H,R,S,T
20 S SER66: -0.045 5 -0.697, 0.404 7,4 18/19 E,H,R,S,T
-
21 G GLY67: -1.418 9 -1.755,-1.277 9,9 18/19 G
+
21 G GLY67: -1.418 9 -1.755,-1.277 9,9 18/19 G
22 L LEU68: 0.334 4 -0.344, 0.790 6,3 18/19 A,I,K,L,T,V
22 L LEU68: 0.334 4 -0.344, 0.790 6,3 18/19 A,I,K,L,T,V
23 G GLY69: 0.572 3* -0.136, 1.367 5,1 18/19 A,G,I,L,M,V
23 G GLY69: 0.572 3* -0.136, 1.367 5,1 18/19 A,G,I,L,M,V
Line 542: Line 359:
 +
 +
== Phylogenetic Tree of rsp1275 ==
 +
http://consurf.tau.ac.il/results/1240240806/treeView.html
 +
 +
 +
 +
''
 +
== Reference ==
 +
''
 +
<references/>
 +
 +
 +
''
 +
== Animated Image Construction ==
 +
''
 +
 +
1. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html
 +
 +
2. On the submission form, first select 'animation' in the "type of request" section, select the size of the animation to be generated in pixels(here the size is 600), then upload the PDB format protein structure file in the "source of structural data" section.
 +
 +
3. On the "chain color and rendering section" select 'cartoon' and 'secondary structure'.
 +
 +
4. On "advanced structural annotation" section select 'docking models in Capri format'.
 +
 +
5. Any other forms for the animation may be selected by referring to the "Samples" according to the protein structure to be animated.
 +
 +
''
 +
== JMol Image Construction ==
 +
''
 +
 +
1. First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/.
 +
 +
2. Go to 3D-JIGSAW page http://bmm.cancerresearchuk.org/~3djigsaw/ and paste the sequence on the submission page. A .pdb format image of your protein will be sent to you on your email which can be opened by RASMOL.
 +
 +
3. Upload this file on Proteopedia and then load the JMol applet for the protein following instructions on the Help:Editing page http://www.proteopedia.org/wiki/index.php/Help:Editing.
 +
 +
4. You can edit your protein by using the scene authoring tools after loading the applet.
 +
Page Created by Susana Retamal, email:susana.retamal@gmail.com
-
''Structure of the Proposed rsp1275'''<applet load='rsp1275.pdb' size='300' color='black' frame='true' align='right' caption='3D Image of proposed rsp1275 protein'/>
+
Acknownledment: Jill Zeilstra Ryalls, Adam Meade and Yana Fedotova.

Current revision

Contents

Background Information

Rsp1275 is a member of the Fnr-Crp family of transcriptional regulators. Homologues of the Fnr protein from E. coli have been identified in a variety of taxonomically diverse bacterial species.[1][2]The bacterium Rhodobacter sphaeroides" 2.4.1 encodes 8 members of this family, however only 2 have known function. Models of 7 of them, including RSP1275, were successfully obtained using 3D-Jigsaw, all being very similar in structure to Crp (the only one with crystal structure solved). The DNA binding domain helix-turn-helix is located in the C-terminal, and the N-terminal part contains the allosteric effector domain.

Structure of the Proposed rsp1275 modeling obtained using 3D-Jigsaw

Insert caption here

Drag the structure with the mouse to rotate

The highlighted of the protein.

This is the of the protein.

Protein Sequence

1 mfvpapdati tncrncplrr kplflpfsds elsfmeqfkv gelvvapgvt lleegqgsah

61 lftvlsglgi rstmlengrr qvinflfpgd figlqaglag emrhsvestt tmvlcvfnra

121 dlwdlfreep eraydltwia aveehflget iaslgqrdat erlawallri herlsaigla

181 ergrvpmpwr qqdladalgl slvhtnktir rlretghalw eggtlfvdre rlatlaladp

241 drprrrpli


Physico - Chemical parameters for Rsp1275

From http://ca.expasy.org/tools/protparam.html


Number of amino acids: 249

Molecular weight: 28014.2

Theoretical pI: 6.10

Atomic composition:

Carbon C 1249 Hydrogen H 1986 Nitrogen N 360 Oxygen O 355 Sulfur S 9

Formula: C1249H1986N360O355S9 Total number of atoms: 3959

Extinction coefficients:

Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.

  • Ext. coefficient 29115

Abs 0.1% (=1 g/l) 1.039, assuming ALL Cys residues appear as half cystines

  • Ext. coefficient 28990

Abs 0.1% (=1 g/l) 1.035, assuming NO Cys residues appear as half cystines

Estimated half-life:

The N-terminal of the sequence considered is M (Met).

The estimated half-life is:

  • 30 hours (mammalian reticulocytes, in vitro).
  • >20 hours (yeast, in vivo).
  • >10 hours (Escherichia coli, in vivo).

Instability index:

The instability index (II) is computed to be 41.06 This classifies the protein as unstable.

Aliphatic index: 97.19

Grand average of hydropathicity (GRAVY): -0.097

Globe Prediction: it appears as compact, as a globular domain.

Secondary Structure: Helix 34.94% Extended (sheet) 17.67% Loop 47.39%

Amino Acid Composition
Amino Acid Number present Percentage of total present
Ala (A) 15 8.8%
Arg (R) 10 10.4%
Asn (N) 6 2.4%
Asp (D) 10 4.8%
Cys (C) 1 1.2%
Gln (Q) 5 2.8%
Glu (E) 11 8.0%
Gly (G) 9 7.6%
His (H) 10 2.4%
Ile (I) 3 4.0%
Leu (L) 21 14.5%
Lys (K) 6 1.2%
Met (M) 6 2.4%
Phe (F) 2 4.0%
Pro (P) 8 5.2%
Ser (S) 7 4.4%
Thr (T) 13 6.4%
Trp (W) 2 2.0%
Tyr (Y) 6 0.4%
Val (V) 12 5.6%
Pyl (O) 0 0.%
Sec (U) 0 0.0%

Amino Acid Conservation Scores

- POS: The position of the AA in the SEQRES derived sequence.

- SEQ: The SEQRES derived sequence in one letter code.

- 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier.

- SCORE: The normalized conservation scores.

- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).

- CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores.

- CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval.

- MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position.

- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment. 

POS	 SEQ	    3LATOM	SCORE		COLOR	CONFIDENCE INTERVAL	CONFIDENCE INTERVAL COLORS	MSA DATA	RESIDUE VARIETY
   	    	        	(normalized)	        	               
  1	   P	    PRO47:	-1.063		  8*	-1.567,-0.697			    9,7			    3/19	P                 
  2	   G	    GLY48:	-0.916		  8	-1.417,-0.529			    9,7			   13/19	G,K               
  3	   V	    VAL49:	 1.226		  2	 0.404, 2.816			    4,1			   13/19	C,E,Q,R,V         
  4	   T	    THR50:	 1.816		  1	 0.790, 2.816			    3,1			   14/19	A,E,Q,T           
  5	   L	    LEU51:	 0.649		  3*	-0.136, 1.367			    5,1			   18/19	I,L,V             
  6	   L	    LEU52:	-0.142		  5	-0.697, 0.404			    7,4			   18/19	F,I,L,Y           
  7	   E	    GLU53:	 1.061		  2*	 0.108, 1.367			    5,1			   18/19	A,E,I,K,Q,S,W     
  8	   E	    GLU54:	 0.909		  2*	 0.108, 1.367			    5,1			   18/19	A,E,Q,S           
  9	   G	    GLY55:	-0.349		  6	-0.852, 0.108			    7,5			   18/19	D,E,G,P           
 10	   Q	    GLN56:	-0.600		  7	-0.998,-0.344			    8,6			   18/19	D,E,Q,S           
 11	   G	    GLY57:	 2.391		  1	 2.816, 2.816			    1,1			   18/19	E,G,I,K,L,P,S,T,V 
 12	   S	    SER58:	 0.521		  4*	-0.136, 1.367			    5,1			   18/19	A,L,M,N,S,T       
 13	   A	    ALA59:	 2.175		  1	 1.367, 2.816			    1,1			   18/19	A,D,K,N,R,S,T     
 14	   H	    HIS60:	-0.278		  6	-0.852, 0.108			    7,5			   18/19	F,H,K,S           
 15	   L	    LEU61:	 1.898		  1	 0.790, 2.816			    3,1			   18/19	C,F,I,L,V,Y       
 16	   F	    PHE62:	 0.468		  4	-0.136, 0.790			    5,3			   18/19	A,F,L,S,Y         
 17	   T	    THR63:	 0.156		  5*	-0.529, 0.790			    7,3			   18/19	A,N,Q,S,T,V       
 18	   V	    VAL64:	-0.901		  8	-1.277,-0.697			    9,7			   18/19	I,L,V             
 19	   L	    LEU65:	 0.975		  2*	 0.108, 1.367			    5,1			   18/19	A,I,L,M,R,S,V     
 20	   S	    SER66:	-0.045		  5	-0.697, 0.404			    7,4			   18/19	E,H,R,S,T         
 21	   G	    GLY67:	-1.418		  9	-1.755,-1.277			    9,9			   18/19	G              
 22	   L	    LEU68:	 0.334		  4	-0.344, 0.790			    6,3			   18/19	A,I,K,L,T,V       
 23	   G	    GLY69:	 0.572		  3*	-0.136, 1.367			    5,1			   18/19	A,G,I,L,M,V       
 24	   I	    ILE70:	-0.318		  6	-0.852, 0.108			    7,5			   18/19	I,K,R,T           
 25	   R	    ARG71:	 0.405		  4	-0.344, 0.790			    6,3			   18/19	I,L,R,S,T         
 26	   S	    SER72:	-0.248		  6	-0.852, 0.108			    7,5			   18/19	C,S,T,Y           
 27	   T	    THR73:	-0.039		  5	-0.529, 0.404			    7,4			   18/19	K,Q,R,T           
 28	   M	    MET74:	-0.296		  6	-0.852, 0.108			    7,5			   19/19	I,L,M,T,V         
 29	   L	    LEU75:	-0.075		  5	-0.529, 0.404			    7,4			   19/19	A,L,M,S,T         
 30	   E	    GLU76:	 0.959		  2*	 0.108, 1.367			    5,1			   19/19	E,G,P,S,T         
 31	   N	    ASN77:	 0.131		  5	-0.344, 0.404			    6,4			   19/19	D,E,N,Q,S,T       
 32	   G	    GLY78:	-1.441		  9	-1.755,-1.277			    9,9			   19/19	G                 
 33	   R	    ARG79:	-0.815		  7	-1.139,-0.529			    8,7			   19/19	D,E,K,R           
 34	   R	    ARG80:	-0.887		  8	-1.277,-0.529			    9,7			   19/19	E,Q,R             
 35	   Q	    GLN81:	-1.577		  9	-1.755,-1.417			    9,9			   19/19	Q                 
 36	   V	    VAL82:	-0.767		  7	-1.139,-0.529			    8,7			   19/19	I,L,M,V           
 37	   I	    ILE83:	-0.369		  6	-0.852, 0.108			    7,5			   19/19	E,I,L,T,V         
 38	   N	    ASN84:	 0.834		  3*	 0.108, 1.367			    5,1			   19/19	A,G,N,R,S         
 39	   F	    PHE85:	-0.749		  7	-1.139,-0.344			    8,6			   19/19	F,L,V             
 40	   L	    LEU86:	 0.791		  3*	 0.108, 1.367			    5,1			   19/19	A,C,D,H,L,Q       
 41	   F	    PHE87:	-0.246		  6	-0.852, 0.108			    7,5			   19/19	F,G,L             
 42	   P	    PRO88:	-0.534		  7	-0.998,-0.136			    8,5			   19/19	A,P,V             
 43	   G	    GLY89:	-0.907		  8	-1.277,-0.697			    9,7			   19/19	G,P,S             
 44	   D	    ASP90:	-1.388		  9	-1.567,-1.277			    9,9			   19/19	D,E               
 45	   F	    PHE91:	 0.303		  4	-0.344, 0.790			    6,3			   19/19	A,F,L,M,V,Y       
 46	   I	    ILE92:	-0.023		  5	-0.697, 0.404			    7,4			   19/19	E,F,I,L,V         
 47	   G	    GLY93:	-1.441		  9	-1.755,-1.277			    9,9			   19/19	G                 
 48	   L	    LEU94:	 0.935		  2*	 0.108, 1.367			    5,1			   19/19	E,F,L,M,R,W       
 49	   Q	    GLN95:	 0.552		  3*	-0.136, 1.367			    5,1			   19/19	A,D,E,N,P,Q       
 50	   A	    ALA96:	-0.391		  6	-1.139, 0.108			    8,5			   13/19	A,G               
 51	   G	    GLY97:	 0.022		  5	-0.697, 0.404			    7,4			   13/19	G,I,L             
 52	   L	    LEU98:	 2.561		  1	 2.816, 2.816			    1,1			   19/19	A,F,G,H,L,M,P,S,T 
 53	   A	    ALA99:	 2.362		  1	 1.367, 2.816			    1,1			   19/19	A,G,N,Q,R,S,T,V   
 54	   G	   GLY100:	 2.565		  1	 2.816, 2.816			    1,1			   19/19	D,E,G,I,L,M,N,Q,R,S
 55	   E	   GLU101:	 1.976		  1	 1.367, 2.816			    1,1			   19/19	A,E,H,K,N,Q,R,S,T 
 56	   M	   MET102:	 0.254		  4	-0.344, 0.790			    6,3			   19/19	H,M,N,S,V,Y       
 57	   R	   ARG103:	 1.111		  2	 0.404, 1.367			    4,1			   19/19	A,N,P,Q,R,S,T,V   
 58	   H	   HIS104:	 0.562		  3*	-0.136, 1.367			    5,1			   19/19	F,G,H,L,N,S,Y     
 59	   S	   SER105:	-0.561		  7	-0.998,-0.136			    8,5			   19/19	D,F,S,Y           
 60	   V	   VAL106:	-1.054		  8	-1.417,-0.852			    9,7			   19/19	A,T,V             
 61	   E	   GLU107:	-0.753		  7	-1.139,-0.529			    8,7			   19/19	D,E,Q,T           
 62	   S	   SER108:	-1.062		  8	-1.417,-0.852			    9,7			   19/19	A,S,T             
 63	   T	   THR109:	-0.040		  5	-0.529, 0.404			    7,4			   19/19	A,I,L,T,V         
 64	   T	   THR110:	-0.845		  7	-1.277,-0.529			    9,7			   19/19	E,G,S,T           
 65	   T	   THR111:	 0.081		  5*	-0.529, 0.790			    7,3			   19/19	A,D,E,G,T         
 66	   M	   MET112:	 0.816		  3*	 0.108, 1.367			    5,1			   19/19	A,C,L,M,S,T,V     
 67	   V	   VAL113:	 0.008		  5	-0.529, 0.404			    7,4			   19/19	E,L,M,R,T,V       
 68	   L	   LEU114:	-0.103		  5	-0.697, 0.404			    7,4			   19/19	I,L,M,V           
 69	   C	   CYS115:	-0.836		  7	-1.277,-0.529			    9,7			   19/19	A,C,V             
 70	   V	   VAL116:	 2.036		  1	 1.367, 2.816			    1,1			   19/19	C,E,I,K,Q,R,T,V   
 71	   F	   PHE117:	-0.769		  7	-1.277,-0.344			    9,6			   19/19	F,I,V             
 72	   N	   ASN118:	 1.494		  1	 0.790, 2.816			    3,1			   19/19	A,F,G,K,N,P,R,S   
 73	   R	   ARG119:	-0.223		  6	-0.697, 0.108			    7,5			   19/19	A,F,K,R,Y         
 74	   A	   ALA120:	 1.689		  1	 0.790, 2.816			    3,1			   18/19	A,D,E,G,K,N,S,T   
 75	   D	   ASP121:	 1.492		  1	 0.790, 2.816			    3,1			   18/19	D,I,L,P,T,V       
 76	   L	   LEU122:	-0.309		  6	-0.852, 0.108			    7,5			   18/19	F,L               
 77	   W	   TRP123:	 1.635		  1	 0.790, 2.816			    3,1			   18/19	D,E,F,G,L,Q,W     
 78	   D	   ASP124:	 0.991		  2*	 0.108, 1.367			    5,1			   18/19	A,D,E,Q,R         
 79	   L	   LEU125:	-0.503		  6	-0.998,-0.136			    8,5			   18/19	F,L,M,R           
 80	   F	   PHE126:	 0.962		  2*	 0.108, 1.367			    5,1			   18/19	A,F,I,L,M,S       
 81	   R	   ARG127:	 1.061		  2*	 0.108, 1.367			    5,1			   19/19	E,G,L,Q,R,S       
 82	   E	   GLU128:	 0.612		  3*	-0.136, 1.367			    5,1			   19/19	E,K,N,S,T         
 83	   E	   GLU129:	 0.413		  4	-0.344, 0.790			    6,3			   19/19	D,E,M,Q,R,T       
 84	   P	   PRO130:	-1.243		  9	-1.567,-0.998			    9,8			   19/19	P,Q               
 85	   E	   GLU131:	-0.080		  5	-0.697, 0.404			    7,4			   19/19	E,H,K,N,Q         
 86	   R	   ARG132:	 0.801		  3*	 0.108, 1.367			    5,1			   19/19	I,L,M,R,V         
 87	   A	   ALA133:	 0.460		  4	-0.344, 0.790			    6,3			   19/19	A,G,L,Q,R,S       
 88	   Y	   TYR134:	 0.879		  2*	 0.108, 1.367			    5,1			   19/19	C,H,L,Q,R,Y       
 89	   D	   ASP135:	 0.376		  4	-0.344, 0.790			    6,3			   19/19	A,D,E,Q,R,S       
 90	   L	   LEU136:	-0.372		  6	-0.852, 0.108			    7,5			   19/19	I,L,M             
 91	   T	   THR137:	 0.789		  3*	 0.108, 1.367			    5,1			   19/19	H,L,M,N,T,W       
 92	   W	   TRP138:	 0.918		  2*	 0.108, 1.367			    5,1			   19/19	A,D,E,R,T,W       
 93	   I	   ILE139:	 0.435		  4	-0.344, 0.790			    6,3			   19/19	E,F,I,L,M,Q       
 94	   A	   ALA140:	-0.562		  7	-0.998,-0.136			    8,5			   19/19	A,M,N,S,T         
 95	   A	   ALA141:	 0.604		  3*	-0.136, 1.367			    5,1			   19/19	A,F,I,L,S,T       
 96	   V	   VAL142:	 1.537		  1	 0.790, 2.816			    3,1			   19/19	A,D,G,K,N,R,S,T,V 
 97	   E	   GLU143:	-1.054		  8	-1.417,-0.852			    9,7			   19/19	E,G,K             
 98	   E	   GLU144:	-0.200		  6	-0.697, 0.108			    7,5			   19/19	E,I,L,M           
 99	   H	   HIS145:	 0.536		  3*	-0.136, 1.367			    5,1			   19/19	A,D,H,K,M,Q,S     
100	   F	   PHE146:	 1.103		  2*	 0.108, 2.816			    5,1			   19/19	A,F,G,L,N,Q,R,S   
101	   L	   LEU147:	-0.661		  7	-1.139,-0.344			    8,6			   19/19	A,D,L             
102	   G	   GLY148:	-0.441		  6	-0.852,-0.136			    7,5			   19/19	E,G,Q,R           
103	   E	   GLU149:	-0.539		  7	-0.998,-0.136			    8,5			   19/19	D,E,K,Q           
104	   T	   THR150:	 0.063		  5	-0.529, 0.404			    7,4			   19/19	H,M,Q,T,W         
105	   I	   ILE151:	-0.555		  7	-0.998,-0.136			    8,5			   19/19	A,I,L,M           
106	   A	   ALA152:	-0.041		  5	-0.697, 0.404			    7,4			   19/19	A,G,L,V           
107	   S	   SER153:	 0.364		  4	-0.344, 0.790			    6,3			   19/19	L,S,T,V,Y         
108	   L	   LEU154:	-1.173		  8	-1.567,-0.998			    9,8			   19/19	I,L               
109	   G	   GLY155:	-1.243		  9	-1.567,-0.998			    9,8			   19/19	G,S               
110	   Q	   GLN156:	-0.805		  7	-1.139,-0.529			    8,7			   19/19	K,N,Q,R           
111	   R	   ARG157:	 0.138		  5	-0.344, 0.404			    6,4			   19/19	D,K,M,Q,R         
112	   D	   ASP158:	-0.224		  6	-0.697, 0.108			    7,5			   19/19	C,D,N,S,T         
113	   A	   ALA159:	-1.362		  9	-1.567,-1.139			    9,8			   19/19	A,I               
114	   T	   THR160:	 0.916		  2*	 0.108, 1.367			    5,1			   19/19	D,E,N,Q,R,T,V     
115	   E	   GLU161:	-1.294		  9	-1.567,-1.139			    9,8			   19/19	E,V               
116	   R	   ARG162:	-0.855		  7	-1.277,-0.529			    9,7			   19/19	K,R               
117	   L	   LEU163:	-0.418		  6	-0.852,-0.136			    7,5			   19/19	I,L,V             
118	   A	   ALA164:	-1.261		  9	-1.567,-1.139			    9,8			   19/19	A,G,T             
119	   W	   TRP165:	-0.387		  6	-0.852,-0.136			    7,5			   19/19	A,H,S,W           
120	   A	   ALA166:	-0.327		  6	-0.852, 0.108			    7,5			   19/19	A,F,L,Y           
121	   L	   LEU167:	-0.623		  7	-1.139,-0.344			    8,6			   19/19	I,L               
122	   L	   LEU168:	 2.061		  1	 1.367, 2.816			    1,1			   19/19	A,H,L,S,V,Y       
123	   R	   ARG169:	 0.245		  4	-0.344, 0.790			    6,3			   19/19	D,G,I,L,N,R       
124	   I	   ILE170:	-0.525		  6	-0.998,-0.136			    8,5			   19/19	I,L,W             
125	   H	   HIS171:	 0.296		  4	-0.344, 0.790			    6,3			   19/19	A,C,H,R,S         
126	   E	   GLU172:	 2.674		  1	 2.816, 2.816			    1,1			   19/19	C,D,E,H,K,N,Q,R,T 
127	   R	   ARG173:	-1.085		  8	-1.417,-0.852			    9,7			   19/19	A,H,R             
128	   L	   LEU174:	 1.821		  1	 0.790, 2.816			    3,1			   19/19	A,D,F,L,Q,S,Y     
129	   S	   SER175:	 1.545		  1	 0.790, 2.816			    3,1			   19/19	A,E,G,L,S         
130	   A	   ALA176:	 0.878		  2*	-0.136, 1.367			    5,1			   19/19	A,G,N,P,Q,R,T     
131	   I	   ILE177:	 1.408		  1	 0.404, 2.816			    4,1			   17/19	E,I,K,P,Q,R,T     
132	   G	   GLY178:	-0.288		  6	-0.852, 0.108			    7,5			   17/19	G,N,S,T           
133	   L	   LEU179:	 0.548		  3*	-0.344, 1.367			    6,1			   17/19	A,F,L,N,V         
134	   A	   ALA180:	-0.547		  7	-0.998,-0.136			    8,5			   17/19	A,G,S,T           
135	   E	   GLU181:	 1.841		  1	 0.790, 2.816			    3,1			   18/19	A,D,E,G,H,K,P,S   
136	   R	   ARG182:	 0.783		  3*	-0.136, 1.367			    5,1			   17/19	D,K,M,R,T,V       
137	   G	   GLY183:	 0.172		  5*	-0.697, 0.790			    7,3			    2/19	G,T               
138	   R	   ARG184:	 0.226		  4*	-0.529, 0.790			    7,3			   19/19	A,E,Q,R,T         
139	   V	   VAL185:	-0.496		  6	-1.139,-0.136			    8,5			   19/19	F,L,V             
140	   P	   PRO186:	 0.687		  3*	-0.136, 1.367			    5,1			   19/19	D,P,R,S,T         
141	   M	   MET187:	-0.889		  8	-1.277,-0.529			    9,7			   19/19	L,M,V             
142	   P	   PRO188:	-0.993		  8	-1.417,-0.697			    9,7			   19/19	A,P,T             
143	   W	   TRP189:	-1.104		  8	-1.417,-0.852			    9,7			   19/19	L,M,W             
144	   R	   ARG190:	-0.591		  7	-0.998,-0.344			    8,6			   19/19	A,G,R,S,T         
145	   Q	   GLN191:	-1.107		  8	-1.417,-0.852			    9,7			   19/19	Q,R,W             
146	   Q	   GLN192:	-0.300		  6	-0.852, 0.108			    7,5			   19/19	A,E,G,Q,T         
147	   D	   ASP193:	-0.990		  8	-1.277,-0.697			    9,7			   19/19	D,E,Q             
148	   L	   LEU194:	-0.925		  8	-1.277,-0.697			    9,7			   19/19	I,L,M             
149	   A	   ALA195:	-1.427		  9	-1.755,-1.277			    9,9			   19/19	A,G               
150	   D	   ASP196:	-1.403		  9	-1.567,-1.277			    9,9			   19/19	D,N               
151	   A	   ALA197:	 0.072		  5	-0.529, 0.404			    7,4			   19/19	A,F,Y             
152	   L	   LEU198:	-1.443		  9	-1.755,-1.277			    9,9			   19/19	L                 
153	   G	   GLY199:	-1.441		  9	-1.755,-1.277			    9,9			   19/19	G                 
154	   L	   LEU200:	-1.044		  8	-1.417,-0.697			    9,7			   19/19	L,T               
155	   S	   SER201:	-1.493		  9	-1.755,-1.417			    9,9			   19/19	S,T               
156	   L	   LEU202:	-0.226		  6	-0.697, 0.108			    7,5			   19/19	I,L,P,V           
157	   V	   VAL203:	-1.296		  9	-1.567,-1.139			    9,8			   19/19	E,V               
158	   H	   HIS204:	-1.435		  9	-1.755,-1.277			    9,9			   19/19	H,T               
159	   T	   THR205:	-1.190		  8	-1.417,-0.998			    9,8			   19/19	I,T,V             
160	   N	   ASN206:	-1.519		  9	-1.755,-1.417			    9,9			   19/19	N,S               
161	   K	   LYS207:	-1.390		  9	-1.567,-1.277			    9,9			   19/19	K,R               
162	   T	   THR208:	-0.802		  7	-1.277,-0.529			    9,7			   19/19	L,Q,T,V           
163	   I	   ILE209:	 0.127		  5*	-0.529, 0.790			    7,3			   19/19	F,I,L,M,V         
164	   R	   ARG210:	-0.459		  6	-0.852,-0.136			    7,5			   19/19	G,K,R,S,T         
165	   R	   ARG211:	-0.501		  6	-0.998,-0.136			    8,5			   19/19	A,K,R,Y           
166	   L	   LEU212:	-0.866		  7	-1.277,-0.529			    9,7			   19/19	F,L               
167	   R	   ARG213:	 0.305		  4	-0.344, 0.790			    6,3			   18/19	A,E,K,Q,R         
168	   E	   GLU214:	-0.134		  5	-0.697, 0.404			    7,4			   18/19	E,K,R             
169	   T	   THR215:	 1.641		  1	 0.790, 2.816			    3,1			   16/19	D,H,I,L,M,Q,S,T   
170	   G	   GLY216:	-1.323		  9	-1.755,-1.139			    9,8			   14/19	G                 
171	   H	   HIS217:	 0.687		  3*	-0.136, 1.367			    5,1			    4/19	A,H,M,V           
172	   A	   ALA218:	-0.749		  7*	-1.277,-0.344			    9,6			    4/19	A,I               
173	   L	   LEU219:	-0.200		  6*	-0.852, 0.404			    7,4			    4/19	A,L,T             
174	   W	   TRP220:	 0.478		  4*	-0.344, 1.367			    6,1			    4/19	I,L,V,W           
175	   E	   GLU221:	 0.163		  5*	-0.697, 0.790			    7,3			    4/19	E,I,Q             
176	   G	   GLY222:	-0.526		  7*	-1.139,-0.136			    8,5			    4/19	G,H               
177	   G	   GLY223:	-0.842		  7*	-1.417,-0.529			    9,7			    2/19	G                 
178	   T	   THR224:	 0.181		  4*	-0.697, 0.790			    7,3			    2/19	G,T               
179	   L	   LEU225:	-0.327		  6*	-1.139, 0.404			    8,4			    1/19	L                 
180	   F	   PHE226:	-0.327		  6*	-1.139, 0.404			    8,4			    1/19	F                 
181	   V	   VAL227:	-0.327		  6*	-1.139, 0.404			    8,4			    1/19	V


Phylogenetic Tree of rsp1275

http://consurf.tau.ac.il/results/1240240806/treeView.html


Reference

  1. ↑ Spiro, S. 1994. The FNR family of transcriptional regulators. Antonie van Leeuwenhoek 66:23–36.
  2. ↑ PredictProtein: B Rost, G Yachdav and J Liu (2004). The PredictProtein Server. Nucleic Acids Research 32(Web Server issue):W321-W326.


Animated Image Construction

1. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html

2. On the submission form, first select 'animation' in the "type of request" section, select the size of the animation to be generated in pixels(here the size is 600), then upload the PDB format protein structure file in the "source of structural data" section.

3. On the "chain color and rendering section" select 'cartoon' and 'secondary structure'.

4. On "advanced structural annotation" section select 'docking models in Capri format'.

5. Any other forms for the animation may be selected by referring to the "Samples" according to the protein structure to be animated.

JMol Image Construction

1. First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/.

2. Go to 3D-JIGSAW page http://bmm.cancerresearchuk.org/~3djigsaw/ and paste the sequence on the submission page. A .pdb format image of your protein will be sent to you on your email which can be opened by RASMOL.

3. Upload this file on Proteopedia and then load the JMol applet for the protein following instructions on the Help:Editing page http://www.proteopedia.org/wiki/index.php/Help:Editing.

4. You can edit your protein by using the scene authoring tools after loading the applet.


Page Created by Susana Retamal, email:susana.retamal@gmail.com

Acknownledment: Jill Zeilstra Ryalls, Adam Meade and Yana Fedotova.

Proteopedia Page Contributors and Editors (what is this?)

Susana Retamal, Eran Hodis

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