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=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 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.  
Rsp1275 is a member of the Fnr-Crp family of [[Regulation of Gene Expression|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.  
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= Structure of the Proposed rsp1275 modeling obtained using 3D-Jigsaw =
= Structure of the Proposed rsp1275 modeling obtained using 3D-Jigsaw =
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=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
==Additional Resources==
For additional information, see: [[Transcription and RNA Processing]]
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== Animated Image Construction ==
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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.
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== 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.




Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Susana Retamal, Eran Hodis, David Canner
Retrieved from "https://proteopedia.openfox.io/w/RSP1275"