User:Adam Meade/Sandbox 1: Difference between revisions

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'''Background Information'''

----

Iron is potentially toxic to cells, as in the presence of oxygen, Fenton reactions can produce reactive oxygen species that can destroy essential biomolecules. Balancing the amount of iron in the cell is important and this importance is apparent from the elaborate mechanisms cells devote to iron homeostasis. Part of this iron balancing is achieved by regulation of iron import. The genes required for ferric citrate transport in ''Rhodobacter sphaeroides'' form a cluster in the order ''fecI-fecR-fecABCDE'', encoding a specialized sigma factor and a putative anti-sigma factor that together are responsible for regulated transcription of the ferric citrate transport operon, encoding an ABC-type ferric citrate transporter. In ''Escherichia coli'', ''fecI'' transcription is regulated by Fur in response to iron availability; in ''Bradyrhizobium japonicum'', as well as ''R. sphaeroides'', which both lack Fur, ''fecI'' transcription is thought to be regulated by another iron-responsive DNA binding protein, Irr, or the iron response regulator protein, which can also be considered to be a relative to the family of Fur proteins. <ref>1) Hamza I, S. Chauhan, R. Hassett, MR O'Brian, 1998. The bacterial irr protein is required for coordination of heme biosynthesis with iron availability.. Journal of Biological Chemistry 34:21669-74.</ref>

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'''Irr and Other Iron-Regulating Proteins'''

----

Since there are bacteria that have to have iron level-mediating proteins present but do not have the Fur (ferric uptake regulator) protein, there must be another protein that takes its place. In the case of ''B. japonicum'', which does not have the Fur protein, the Irr protein was found to be the regulator of iron levels within the cell.<ref>2) Small, S. K., S. Puri, and M. R. O’Brian. 2009. Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria. Biometals 22:89-97.</ref>

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'''Function of Irr'''

----

Irr behaves differently than other regulatory proteins. It functions as coordinating the heme biosynthetic pathway, which ends with the insertion of Fe2+ into a protoporphyrin ring to produce protoheme. It also controls the pathway by monitoring iron availability to prevent the accumulation of toxic porphyrin precursors under iron limitation, as when iron is limiting, heme cannot be produced. <ref>2) Small, S. K., S. Puri, and M. R. O’Brian. 2009. Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria. Biometals 22:89-97.</ref>

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'''Chemical and Physical Properties of Irr'''

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Molecular weight: 18338.8 Da

Theoretical pI: 6.03

{| border="1"

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~~Molecular weight~~: ~~18338~~.~~8 Da~~

'''Evolution of Irr/Fur'''

----

Amino Acid Conservation Scores

----

The following are scores on how well conserved the amino acids are in relation to proteins with a similar structure to Irr. This could potentially show us where Irr evolved from/what Irr will evolve into.

- 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.

~~Theoretical pI~~: 6.03

- 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 D ASP33: -1.189 9 -1.455,-0.986 9,8 10/29 D

2 V VAL34: 0.979 2* 0.016, 2.633 5,1 10/29 F,N,V,Y

3 N ASN35: -0.318 6 -0.859, 0.016 8,5 14/29 A,N,S,T

4 E GLU36: 0.737 3* 0.016, 1.214 5,1 19/29 E,G,K,Q,S,T

5 M MET37: 0.793 3* 0.016, 1.214 5,1 19/29 A,E,I,L,M,Q,T

6 L LEU38: -1.329 9 -1.588,-1.223 9,9 28/29 L

7 Q GLN39: -0.531 7 -0.859,-0.210 8,6 28/29 K,Q,R

8 S SER40: 2.423 1 2.633, 2.633 1,1 28/29 D,E,K,N,Q,R,S,T

9 A ALA41: 0.058 5 -0.403, 0.294 6,4 28/29 A,G,I,M,N,S,T,V

10 G GLY42: -1.069 8 -1.338,-0.859 9,8 28/29 D,G

11 L LEU43: -0.850 8 -1.223,-0.570 9,7 28/29 I,L,V

12 R ARG44: -0.998 8 -1.223,-0.859 9,8 28/29 K,R

13 P PRO45: 0.305 4 -0.210, 0.661 6,3 28/29 A,I,P,V,Y

14 T THR46: -1.473 9 -1.588,-1.455 9,9 28/29 T

15 R ARG47: 0.816 3* 0.016, 1.214 5,1 28/29 E,F,G,K,L,P,R,V

16 Q GLN48: -0.961 8 -1.223,-0.721 9,7 28/29 P,Q

17 R ARG49: -1.426 9 -1.588,-1.338 9,9 28/29 R

18 M MET50: 0.754 3* 0.016, 1.214 5,1 28/29 E,H,I,L,M,Q,V

19 A ALA51: -0.901 8 -1.223,-0.721 9,7 28/29 A,K,T,V

20 L LEU52: -0.710 7 -0.986,-0.403 8,6 28/29 I,L,V

21 G GLY53: -0.370 6 -0.859, 0.016 8,5 28/29 G,I,L,M

22 W TRP54: 1.698 1 1.214, 2.633 1,1 28/29 A,D,E,K,N,Q,R,W

23 L LEU55: 1.226 1 0.661, 2.633 3,1 28/29 A,F,I,L,M,T,V,Y

24 L LEU56: -0.594 7 -0.986,-0.210 8,6 28/29 F,L,M,V

25 F PHE57: 1.556 1 0.661, 2.633 3,1 28/29 D,E,F,I,K,N,Q,R,V,Y

26 G GLY58: 2.434 1 2.633, 2.633 1,1 28/29 A,E,G,H,K,N,Q,S,T

27 K LYS59: 0.609 3* 0.016, 1.214 5,1 28/29 A,E,H,K,P,S,T

28 G GLY60: 2.294 1 2.633, 2.633 1,1 29/29 A,D,E,G,H,K,M,P,R

29 A ALA61: 2.262 1 2.633, 2.633 1,1 27/29 A,C,E,G,L,M,N,Q,S,T

30 R ARG62: 1.468 1 0.661, 2.633 3,1 19/29 E,H,Q,R

31 H HIS63: -1.467 9 -1.588,-1.455 9,9 29/29 H

32 L LEU64: 0.771 3* 0.016, 1.214 5,1 29/29 A,F,I,L,M,P,V,Y

33 T THR65: -0.874 8 -1.107,-0.721 8,7 29/29 D,E,S,T

34 A ALA66: -1.188 9 -1.338,-0.986 9,8 29/29 A,P,T

35 E GLU67: -1.035 8 -1.338,-0.859 9,8 29/29 D,E

36 M MET68: 0.707 3* 0.016, 1.214 5,1 29/29 A,D,E,H,M,S,T

37 L LEU69: 0.078 5 -0.403, 0.294 6,4 29/29 C,I,L,V

38 Y TYR70: -0.574 7 -0.986,-0.210 8,6 29/29 F,I,Y

39 E GLU71: 0.157 5 -0.403, 0.661 6,3 29/29 E,G,K,M,N,Q,R

40 E GLU72: 1.498 1 0.661, 2.633 3,1 29/29 A,E,H,I,K,L,R

41 A ALA73: -0.319 6 -0.721, 0.016 7,5 29/29 A,F,I,L,V

42 T THR74: 1.036 2 0.294, 1.214 4,1 29/29 A,E,I,L,M,R,S,T

43 L LEU75: 1.694 1 0.661, 2.633 3,1 29/29 A,D,E,F,G,L,N,P,S,V

44 A ALA76: 2.302 1 2.633, 2.633 1,1 29/29 A,D,E,I,K,L,M,P,Q,R,S

45 K LYS77: 2.001 1 1.214, 2.633 1,1 29/29 D,F,G,H,K,L,N,S

46 V VAL78: 0.670 3* 0.016, 1.214 5,1 29/29 C,E,L,M,P,S,V

47 P PRO79: 0.328 4 -0.210, 0.661 6,3 29/29 D,E,N,P

48 V VAL80: -0.744 7 -0.986,-0.570 8,7 29/29 I,M,V

49 S SER81: -1.279 9 -1.455,-1.107 9,8 29/29 G,S

50 L LEU82: -0.133 5 -0.570, 0.294 7,4 29/29 H,I,L,R,V

51 A ALA83: -1.171 9 -1.338,-0.986 9,8 29/29 A,Q,S

52 T THR84: -1.376 9 -1.588,-1.223 9,9 29/29 A,T

53 V VAL85: -1.007 8 -1.223,-0.859 9,8 29/29 I,V

54 Y TYR86: -1.335 9 -1.588,-1.223 9,9 29/29 Y

55 N ASN87: -1.123 8 -1.338,-0.986 9,8 29/29 D,N,R

56 T THR88: -0.956 8 -1.223,-0.721 9,7 29/29 N,T,V,X

57 L LEU89: -1.357 9 -1.588,-1.223 9,9 29/29 L

58 N ASN90: -0.647 7 -0.986,-0.403 8,6 29/29 H,K,N,R,T

59 Q GLN91: -0.558 7 -0.859,-0.210 8,6 29/29 A,L,Q,V

60 L LEU92: -0.570 7 -0.986,-0.210 8,6 29/29 F,L,M

61 T THR93: -0.099 5 -0.570, 0.294 7,4 29/29 A,D,E,K,R,T

62 D ASP94: 0.354 4 -0.210, 0.661 6,3 29/29 A,D,E,Q,R,S

63 A ALA95: -0.757 7 -1.107,-0.570 8,7 29/29 A,I,M,S,V

64 G GLY96: -0.841 8 -1.223,-0.570 9,7 29/29 E,G,H

65 L LEU97: -0.306 6 -0.721, 0.016 7,5 29/29 I,L,M

66 L LEU98: -0.712 7 -0.986,-0.403 8,6 29/29 L,V

67 R ARG99: 0.384 4 -0.210, 0.661 6,3 29/29 I,K,L,Q,R,S,T,V

68 Q GLN100: -0.238 6 -0.570, 0.016 7,5 29/29 E,K,Q,R,S

69 V VAL101: -0.147 5 -0.570, 0.294 7,4 29/29 H,I,L,N,S,V

70 S SER102: 0.078 5 -0.403, 0.294 6,4 29/29 D,H,N,P,Q,S,T

71 V VAL103: 0.145 5 -0.403, 0.661 6,3 29/29 F,L,P,V,Y

72 D ASP104: 0.881 2 0.294, 1.214 4,1 29/29 A,D,E,G,S,T

73 G GLY105: 0.110 5 -0.403, 0.661 6,3 29/29 D,E,G,S,T

74 T THR106: -0.006 5 -0.403, 0.294 6,4 29/29 A,D,G,N,S,T

75 K LYS107: 0.077 5 -0.403, 0.294 6,4 29/29 G,H,K,S,V

76 T THR108: -0.179 6 -0.570, 0.016 7,5 29/29 A,K,S,T

77 Y TYR109: -0.415 6 -0.721,-0.210 7,6 29/29 H,I,K,R,V,Y

78 F PHE110: -0.368 6 -0.721, 0.016 7,5 29/29 F,Y

79 D ASP111: -1.082 8 -1.338,-0.859 9,8 29/29 D,E

80 T THR112: -0.448 6 -0.859,-0.210 8,6 29/29 F,L,S,T

81 N ASN113: 0.772 3 0.294, 1.214 4,1 29/29 A,D,N,R,S,T,V

82 V VAL114: 0.383 4* -0.570, 1.214 7,1 2/29 Q,V

83 T THR115: 2.165 1 1.214, 2.633 1,1 23/29 D,E,K,N,P,Q,T,V

84 T THR116: 1.506 1 0.661, 2.633 3,1 29/29 D,G,K,L,N,Q,S,T

85 H HIS117: 1.472 1 0.661, 2.633 3,1 29/29 D,E,G,H,K,P,S

86 H HIS118: -0.825 8 -1.107,-0.570 8,7 29/29 D,E,H,N

87 H HIS119: -1.467 9 -1.588,-1.455 9,9 29/29 H

88 Y TYR120: -0.874 8 -1.107,-0.721 8,7 29/29 D,H,Y

89 Y TYR121: -1.329 9 -1.455,-1.223 9,9 29/29 H,Y

90 L LEU122: 1.136 2 0.294, 1.214 4,1 25/29 A,I,L,M,V

91 E GLU123: 1.417 1 0.661, 2.633 3,1 18/29 E,K,L,M,T,V

92 N ASN124: 0.930 2* 0.016, 1.214 5,1 18/29 D,E,K,N,Q,V

93 S SER125: -0.572 7 -0.986,-0.210 8,6 18/29 C,S,T

94 H HIS126: -0.108 5 -0.721, 0.294 7,4 18/29 G,H,N,S

95 E GLU127: -0.355 6 -0.859, 0.016 8,5 18/29 E,K,T

96 L LEU128: -0.913 8 -1.223,-0.721 9,7 18/29 I,L,V

97 V VAL129: -0.280 6 -0.721, 0.016 7,5 18/29 F,I,T,V

98 D ASP130: -1.063 8 -1.338,-0.859 9,8 18/29 D,E

99 I ILE131: -0.905 8 -1.223,-0.721 9,7 18/29 F,I

100 E GLU132: 1.739 1 1.214, 2.633 1,1 18/29 E,H,K,M,Q,S,T

101 D ASP133: -0.254 6 -0.721, 0.016 7,5 18/29 D,N,S,Y

102 P PRO134: -0.193 6 -0.721, 0.294 7,4 18/29 A,E,N,P

103 H HIS135: 1.561 1 0.661, 2.633 3,1 16/29 D,E,G,H,I,Q,V

104 L LEU136: -1.023 8 -1.338,-0.859 9,8 16/29 I,L

105 A ALA137: 0.666 3* -0.210, 1.214 6,1 7/29 A,K,Q

106 L LEU138: 0.051 5* -0.721, 0.661 7,3 7/29 L,R

107 S SER139: -0.624 7 -1.107,-0.210 8,6 7/29 Q,S

108 K LYS140: 0.661 3* -0.210, 1.214 6,1 7/29 D,K,R

109 M MET141: 0.164 4* -0.570, 0.661 7,3 7/29 E,K,M

110 P PRO142: -0.492 7 -0.986,-0.210 8,6 7/29 I,P

111 E GLU143: 0.243 4* -0.570, 0.661 7,3 7/29 A,E,S,V

112 V VAL144: 0.835 2* 0.016, 1.214 5,1 7/29 A,E,R,V

113 P PRO145: 0.779 3* 0.016, 1.214 5,1 7/29 E,K,P,Q

114 E GLU146: 1.555 1 0.661, 2.633 3,1 7/29 E,H,N,R,Y

115 G GLY147: -0.540 7 -1.107,-0.210 8,6 7/29 G,N

116 Y TYR148: 1.072 2 0.294, 2.633 4,1 7/29 F,I,V,Y

117 E GLU149: -0.017 5* -0.859, 0.661 8,3 5/29 E,R

118 I ILE150: -0.332 6* -0.986, 0.016 8,5 5/29 I,L

119 A ALA151: -0.318 6* -0.986, 0.016 8,5 3/29 A,V

120 R ARG152: 0.307 4* -0.570, 1.214 7,1 3/29 D,R

121 I ILE153: 0.330 4* -0.570, 1.214 7,1 3/29 H,I

122 D ASP154: -0.429 6* -1.107, 0.016 8,5 3/29 D,N

123 M MET155: -0.296 6* -0.986, 0.016 8,5 3/29 L,M

124 V VAL156: -0.946 8* -1.455,-0.721 9,7 3/29 V

125 V VAL157: -0.137 5* -0.859, 0.294 8,4 3/29 L,V

126 R ARG158: 0.277 4* -0.570, 1.214 7,1 3/29 R,Y

127 L LEU159: -0.174 6* -0.859, 0.294 8,4 3/29 L,V

128 R ARG160: -0.959 8* -1.455,-0.721 9,7 3/29 R

129 K LYS161: -0.914 8* -1.455,-0.721 9,7 3/29 K

130 K LYS162: -0.914 8* -1.455,-0.721 9,7 3/29 K

131 R ARG163: -0.419 6* -1.107, 0.016 8,5 3/29 K,R

~~'''Evolution of Irr/Fur'''~~

Go to top 5 on Rasmol, put in amino acid sequence and find domain conservations, anything related to Irr/Fur in the past (conserf). Amino acid conservation scores tell you what aa are found in positions in related aa.

'''Structure of the Proposed Irr Protein'''<applet load='Irr.pdb' size='300' color='black' frame='true' align='right' caption='3D Image of proposed Irr protein'/>

----

Go to polyview 3d, select "secondary structures" for coloring mode and re-upload

@@ Line 2: / Line 2: @@
 ----
 '''Background Information'''
+----
 Iron is potentially toxic to cells, as in the presence of oxygen, Fenton reactions can produce reactive oxygen species that can destroy essential biomolecules.  Balancing the amount of iron in the cell is important and this importance is apparent from the elaborate mechanisms cells devote to iron homeostasis.  Part of this iron balancing is achieved by regulation of iron import. The genes required for ferric citrate transport in ''Rhodobacter sphaeroides'' form a cluster in the order ''fecI-fecR-fecABCDE'', encoding a specialized sigma factor and a putative anti-sigma factor that together are responsible for regulated transcription of the ferric citrate transport operon, encoding an ABC-type ferric citrate transporter.  In ''Escherichia coli'', ''fecI'' transcription is regulated by Fur in response to iron availability; in ''Bradyrhizobium japonicum'', as well as ''R. sphaeroides'', which both lack Fur, ''fecI'' transcription is thought to be regulated by another iron-responsive DNA binding protein, Irr, or the iron response regulator protein, which can also be considered to be a relative to the family of Fur proteins.  <ref>1) Hamza I, S. Chauhan, R. Hassett, MR O'Brian, 1998.  <u>The bacterial irr protein is required for coordination of heme biosynthesis with iron availability.</u>.  Journal of Biological Chemistry 34:21669-74.</ref>
@@ Line 8: / Line 8: @@
 '''Irr and Other Iron-Regulating Proteins'''
+----
 Since there are bacteria that have to have iron level-mediating proteins present but do not have the Fur (ferric uptake regulator) protein, there must be another protein that takes its place.  In the case of ''B. japonicum'', which does not have the Fur protein, the Irr protein was found to be the regulator of iron levels within the cell.<ref>2) Small, S. K., S. Puri, and M. R. O’Brian. 2009. <u>Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria</u>.  Biometals 22:89-97.</ref>
@@ Line 14: / Line 14: @@
 '''Function of Irr'''
+----
 Irr behaves differently than other regulatory proteins.  It functions as coordinating the heme biosynthetic pathway, which ends with the insertion of Fe<sup>2+</sup> into a protoporphyrin ring to produce protoheme.  It also controls the pathway by monitoring iron availability to prevent the accumulation of toxic porphyrin precursors under iron limitation, as when iron is limiting, heme cannot be produced.  <ref>2) Small, S. K., S. Puri, and M. R. O’Brian. 2009. <u>Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other alpha-proteobacteria</u>.  Biometals 22:89-97.</ref>
@@ Line 22: / Line 22: @@
 '''Chemical and Physical Properties of Irr'''
+----
+Molecular weight: 18338.8 Da
+Theoretical pI: 6.03
 {| border="1"
@@ Line 96: / Line 103: @@
-Molecular weight: 18338.8 Da
+'''Evolution of Irr/Fur'''
+----
+Amino Acid Conservation Scores
+----
+The following are scores on how well conserved the amino acids are in relation to proteins with a similar structure to Irr.  This could potentially show us where Irr evolved from/what Irr will evolve into.
+- 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.
-Theoretical pI: 6.03
+- 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)
+	   D	    ASP33:	-1.189		  9	-1.455,-0.986			    9,8			   10/29	D
+	   V	    VAL34:	 0.979		  2*	 0.016, 2.633			    5,1			   10/29	F,N,V,Y
+	   N	    ASN35:	-0.318		  6	-0.859, 0.016			    8,5			   14/29	A,N,S,T
+	   E	    GLU36:	 0.737		  3*	 0.016, 1.214			    5,1			   19/29	E,G,K,Q,S,T
+	   M	    MET37:	 0.793		  3*	 0.016, 1.214			    5,1			   19/29	A,E,I,L,M,Q,T
+	   L	    LEU38:	-1.329		  9	-1.588,-1.223			    9,9			   28/29	L
+	   Q	    GLN39:	-0.531		  7	-0.859,-0.210			    8,6			   28/29	K,Q,R
+	   S	    SER40:	 2.423		  1	 2.633, 2.633			    1,1			   28/29	D,E,K,N,Q,R,S,T
+	   A	    ALA41:	 0.058		  5	-0.403, 0.294			    6,4			   28/29	A,G,I,M,N,S,T,V
+	   G	    GLY42:	-1.069		  8	-1.338,-0.859			    9,8			   28/29	D,G
+	   L	    LEU43:	-0.850		  8	-1.223,-0.570			    9,7			   28/29	I,L,V
+	   R	    ARG44:	-0.998		  8	-1.223,-0.859			    9,8			   28/29	K,R
+	   P	    PRO45:	 0.305		  4	-0.210, 0.661			    6,3			   28/29	A,I,P,V,Y
+	   T	    THR46:	-1.473		  9	-1.588,-1.455			    9,9			   28/29	T
+	   R	    ARG47:	 0.816		  3*	 0.016, 1.214			    5,1			   28/29	E,F,G,K,L,P,R,V
+	   Q	    GLN48:	-0.961		  8	-1.223,-0.721			    9,7			   28/29	P,Q
+	   R	    ARG49:	-1.426		  9	-1.588,-1.338			    9,9			   28/29	R
+	   M	    MET50:	 0.754		  3*	 0.016, 1.214			    5,1			   28/29	E,H,I,L,M,Q,V
+	   A	    ALA51:	-0.901		  8	-1.223,-0.721			    9,7			   28/29	A,K,T,V
+	   L	    LEU52:	-0.710		  7	-0.986,-0.403			    8,6			   28/29	I,L,V
+	   G	    GLY53:	-0.370		  6	-0.859, 0.016			    8,5			   28/29	G,I,L,M
+	   W	    TRP54:	 1.698		  1	 1.214, 2.633			    1,1			   28/29	A,D,E,K,N,Q,R,W
+	   L	    LEU55:	 1.226		  1	 0.661, 2.633			    3,1			   28/29	A,F,I,L,M,T,V,Y
+	   L	    LEU56:	-0.594		  7	-0.986,-0.210			    8,6			   28/29	F,L,M,V
+	   F	    PHE57:	 1.556		  1	 0.661, 2.633			    3,1			   28/29	D,E,F,I,K,N,Q,R,V,Y
+	   G	    GLY58:	 2.434		  1	 2.633, 2.633			    1,1			   28/29	A,E,G,H,K,N,Q,S,T
+	   K	    LYS59:	 0.609		  3*	 0.016, 1.214			    5,1			   28/29	A,E,H,K,P,S,T
+	   G	    GLY60:	 2.294		  1	 2.633, 2.633			    1,1			   29/29	A,D,E,G,H,K,M,P,R
+	   A	    ALA61:	 2.262		  1	 2.633, 2.633			    1,1			   27/29	A,C,E,G,L,M,N,Q,S,T
+	   R	    ARG62:	 1.468		  1	 0.661, 2.633			    3,1			   19/29	E,H,Q,R
+	   H	    HIS63:	-1.467		  9	-1.588,-1.455			    9,9			   29/29	H
+	   L	    LEU64:	 0.771		  3*	 0.016, 1.214			    5,1			   29/29	A,F,I,L,M,P,V,Y
+	   T	    THR65:	-0.874		  8	-1.107,-0.721			    8,7			   29/29	D,E,S,T
+	   A	    ALA66:	-1.188		  9	-1.338,-0.986			    9,8			   29/29	A,P,T
+	   E	    GLU67:	-1.035		  8	-1.338,-0.859			    9,8			   29/29	D,E
+	   M	    MET68:	 0.707		  3*	 0.016, 1.214			    5,1			   29/29	A,D,E,H,M,S,T
+	   L	    LEU69:	 0.078		  5	-0.403, 0.294			    6,4			   29/29	C,I,L,V
+	   Y	    TYR70:	-0.574		  7	-0.986,-0.210			    8,6			   29/29	F,I,Y
+	   E	    GLU71:	 0.157		  5	-0.403, 0.661			    6,3			   29/29	E,G,K,M,N,Q,R
+	   E	    GLU72:	 1.498		  1	 0.661, 2.633			    3,1			   29/29	A,E,H,I,K,L,R
+	   A	    ALA73:	-0.319		  6	-0.721, 0.016			    7,5			   29/29	A,F,I,L,V
+	   T	    THR74:	 1.036		  2	 0.294, 1.214			    4,1			   29/29	A,E,I,L,M,R,S,T
+	   L	    LEU75:	 1.694		  1	 0.661, 2.633			    3,1			   29/29	A,D,E,F,G,L,N,P,S,V
+	   A	    ALA76:	 2.302		  1	 2.633, 2.633			    1,1			   29/29	A,D,E,I,K,L,M,P,Q,R,S
+	   K	    LYS77:	 2.001		  1	 1.214, 2.633			    1,1			   29/29	D,F,G,H,K,L,N,S
+	   V	    VAL78:	 0.670		  3*	 0.016, 1.214			    5,1			   29/29	C,E,L,M,P,S,V
+	   P	    PRO79:	 0.328		  4	-0.210, 0.661			    6,3			   29/29	D,E,N,P
+	   V	    VAL80:	-0.744		  7	-0.986,-0.570			    8,7			   29/29	I,M,V
+	   S	    SER81:	-1.279		  9	-1.455,-1.107			    9,8			   29/29	G,S
+	   L	    LEU82:	-0.133		  5	-0.570, 0.294			    7,4			   29/29	H,I,L,R,V
+	   A	    ALA83:	-1.171		  9	-1.338,-0.986			    9,8			   29/29	A,Q,S
+	   T	    THR84:	-1.376		  9	-1.588,-1.223			    9,9			   29/29	A,T
+	   V	    VAL85:	-1.007		  8	-1.223,-0.859			    9,8			   29/29	I,V
+	   Y	    TYR86:	-1.335		  9	-1.588,-1.223			    9,9			   29/29	Y
+	   N	    ASN87:	-1.123		  8	-1.338,-0.986			    9,8			   29/29	D,N,R
+	   T	    THR88:	-0.956		  8	-1.223,-0.721			    9,7			   29/29	N,T,V,X
+	   L	    LEU89:	-1.357		  9	-1.588,-1.223			    9,9			   29/29	L
+	   N	    ASN90:	-0.647		  7	-0.986,-0.403			    8,6			   29/29	H,K,N,R,T
+	   Q	    GLN91:	-0.558		  7	-0.859,-0.210			    8,6			   29/29	A,L,Q,V
+	   L	    LEU92:	-0.570		  7	-0.986,-0.210			    8,6			   29/29	F,L,M
+	   T	    THR93:	-0.099		  5	-0.570, 0.294			    7,4			   29/29	A,D,E,K,R,T
+	   D	    ASP94:	 0.354		  4	-0.210, 0.661			    6,3			   29/29	A,D,E,Q,R,S
+	   A	    ALA95:	-0.757		  7	-1.107,-0.570			    8,7			   29/29	A,I,M,S,V
+	   G	    GLY96:	-0.841		  8	-1.223,-0.570			    9,7			   29/29	E,G,H
+	   L	    LEU97:	-0.306		  6	-0.721, 0.016			    7,5			   29/29	I,L,M
+	   L	    LEU98:	-0.712		  7	-0.986,-0.403			    8,6			   29/29	L,V
+	   R	    ARG99:	 0.384		  4	-0.210, 0.661			    6,3			   29/29	I,K,L,Q,R,S,T,V
+	   Q	   GLN100:	-0.238		  6	-0.570, 0.016			    7,5			   29/29	E,K,Q,R,S
+	   V	   VAL101:	-0.147		  5	-0.570, 0.294			    7,4			   29/29	H,I,L,N,S,V
+	   S	   SER102:	 0.078		  5	-0.403, 0.294			    6,4			   29/29	D,H,N,P,Q,S,T
+	   V	   VAL103:	 0.145		  5	-0.403, 0.661			    6,3			   29/29	F,L,P,V,Y
+	   D	   ASP104:	 0.881		  2	 0.294, 1.214			    4,1			   29/29	A,D,E,G,S,T
+	   G	   GLY105:	 0.110		  5	-0.403, 0.661			    6,3			   29/29	D,E,G,S,T
+	   T	   THR106:	-0.006		  5	-0.403, 0.294			    6,4			   29/29	A,D,G,N,S,T
+	   K	   LYS107:	 0.077		  5	-0.403, 0.294			    6,4			   29/29	G,H,K,S,V
+	   T	   THR108:	-0.179		  6	-0.570, 0.016			    7,5			   29/29	A,K,S,T
+	   Y	   TYR109:	-0.415		  6	-0.721,-0.210			    7,6			   29/29	H,I,K,R,V,Y
+	   F	   PHE110:	-0.368		  6	-0.721, 0.016			    7,5			   29/29	F,Y
+	   D	   ASP111:	-1.082		  8	-1.338,-0.859			    9,8			   29/29	D,E
+	   T	   THR112:	-0.448		  6	-0.859,-0.210			    8,6			   29/29	F,L,S,T
+	   N	   ASN113:	 0.772		  3	 0.294, 1.214			    4,1			   29/29	A,D,N,R,S,T,V
+	   V	   VAL114:	 0.383		  4*	-0.570, 1.214			    7,1			    2/29	Q,V
+	   T	   THR115:	 2.165		  1	 1.214, 2.633			    1,1			   23/29	D,E,K,N,P,Q,T,V
+	   T	   THR116:	 1.506		  1	 0.661, 2.633			    3,1			   29/29	D,G,K,L,N,Q,S,T
+	   H	   HIS117:	 1.472		  1	 0.661, 2.633			    3,1			   29/29	D,E,G,H,K,P,S
+	   H	   HIS118:	-0.825		  8	-1.107,-0.570			    8,7			   29/29	D,E,H,N
+	   H	   HIS119:	-1.467		  9	-1.588,-1.455			    9,9			   29/29	H
+	   Y	   TYR120:	-0.874		  8	-1.107,-0.721			    8,7			   29/29	D,H,Y
+	   Y	   TYR121:	-1.329		  9	-1.455,-1.223			    9,9			   29/29	H,Y
+	   L	   LEU122:	 1.136		  2	 0.294, 1.214			    4,1			   25/29	A,I,L,M,V
+	   E	   GLU123:	 1.417		  1	 0.661, 2.633			    3,1			   18/29	E,K,L,M,T,V
+	   N	   ASN124:	 0.930		  2*	 0.016, 1.214			    5,1			   18/29	D,E,K,N,Q,V
+	   S	   SER125:	-0.572		  7	-0.986,-0.210			    8,6			   18/29	C,S,T
+	   H	   HIS126:	-0.108		  5	-0.721, 0.294			    7,4			   18/29	G,H,N,S
+	   E	   GLU127:	-0.355		  6	-0.859, 0.016			    8,5			   18/29	E,K,T
+	   L	   LEU128:	-0.913		  8	-1.223,-0.721			    9,7			   18/29	I,L,V
+	   V	   VAL129:	-0.280		  6	-0.721, 0.016			    7,5			   18/29	F,I,T,V
+	   D	   ASP130:	-1.063		  8	-1.338,-0.859			    9,8			   18/29	D,E
+	   I	   ILE131:	-0.905		  8	-1.223,-0.721			    9,7			   18/29	F,I
+	   E	   GLU132:	 1.739		  1	 1.214, 2.633			    1,1			   18/29	E,H,K,M,Q,S,T
+	   D	   ASP133:	-0.254		  6	-0.721, 0.016			    7,5			   18/29	D,N,S,Y
+	   P	   PRO134:	-0.193		  6	-0.721, 0.294			    7,4			   18/29	A,E,N,P
+	   H	   HIS135:	 1.561		  1	 0.661, 2.633			    3,1			   16/29	D,E,G,H,I,Q,V
+	   L	   LEU136:	-1.023		  8	-1.338,-0.859			    9,8			   16/29	I,L
+	   A	   ALA137:	 0.666		  3*	-0.210, 1.214			    6,1			    7/29	A,K,Q
+	   L	   LEU138:	 0.051		  5*	-0.721, 0.661			    7,3			    7/29	L,R
+	   S	   SER139:	-0.624		  7	-1.107,-0.210			    8,6			    7/29	Q,S
+	   K	   LYS140:	 0.661		  3*	-0.210, 1.214			    6,1			    7/29	D,K,R
+	   M	   MET141:	 0.164		  4*	-0.570, 0.661			    7,3			    7/29	E,K,M
+	   P	   PRO142:	-0.492		  7	-0.986,-0.210			    8,6			    7/29	I,P
+	   E	   GLU143:	 0.243		  4*	-0.570, 0.661			    7,3			    7/29	A,E,S,V
+	   V	   VAL144:	 0.835		  2*	 0.016, 1.214			    5,1			    7/29	A,E,R,V
+	   P	   PRO145:	 0.779		  3*	 0.016, 1.214			    5,1			    7/29	E,K,P,Q
+	   E	   GLU146:	 1.555		  1	 0.661, 2.633			    3,1			    7/29	E,H,N,R,Y
+	   G	   GLY147:	-0.540		  7	-1.107,-0.210			    8,6			    7/29	G,N
+	   Y	   TYR148:	 1.072		  2	 0.294, 2.633			    4,1			    7/29	F,I,V,Y
+	   E	   GLU149:	-0.017		  5*	-0.859, 0.661			    8,3			    5/29	E,R
+	   I	   ILE150:	-0.332		  6*	-0.986, 0.016			    8,5			    5/29	I,L
+	   A	   ALA151:	-0.318		  6*	-0.986, 0.016			    8,5			    3/29	A,V
+	   R	   ARG152:	 0.307		  4*	-0.570, 1.214			    7,1			    3/29	D,R
+	   I	   ILE153:	 0.330		  4*	-0.570, 1.214			    7,1			    3/29	H,I
+	   D	   ASP154:	-0.429		  6*	-1.107, 0.016			    8,5			    3/29	D,N
+	   M	   MET155:	-0.296		  6*	-0.986, 0.016			    8,5			    3/29	L,M
+	   V	   VAL156:	-0.946		  8*	-1.455,-0.721			    9,7			    3/29	V
+	   V	   VAL157:	-0.137		  5*	-0.859, 0.294			    8,4			    3/29	L,V
+	   R	   ARG158:	 0.277		  4*	-0.570, 1.214			    7,1			    3/29	R,Y
+	   L	   LEU159:	-0.174		  6*	-0.859, 0.294			    8,4			    3/29	L,V
+	   R	   ARG160:	-0.959		  8*	-1.455,-0.721			    9,7			    3/29	R
+	   K	   LYS161:	-0.914		  8*	-1.455,-0.721			    9,7			    3/29	K
+	   K	   LYS162:	-0.914		  8*	-1.455,-0.721			    9,7			    3/29	K
+	   R	   ARG163:	-0.419		  6*	-1.107, 0.016			    8,5			    3/29	K,R
-'''Evolution of Irr/Fur'''
-Go to top 5 on Rasmol, put in amino acid sequence and find domain conservations, anything related to Irr/Fur in the past (conserf).  Amino acid conservation scores tell you what aa are found in positions in related aa.
 '''Structure of the Proposed Irr Protein'''<applet load='Irr.pdb' size='300' color='black' frame='true' align='right' caption='3D Image of proposed Irr protein'/>
+----
 Go to polyview 3d, select "secondary structures" for coloring mode and re-upload