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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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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"