GREMLIN Database
CODY - GTP-sensing transcriptional pleiotropic repressor CodY
UniProt: P39779 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 259 (254)
Sequences: 421 (197)
Seq/√Len: 12.4

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
96_T104_D4.6911.00
76_T80_F4.6401.00
59_N96_T3.8540.99
59_N104_D3.5200.99
10_I149_V3.2240.97
32_R52_S2.9360.95
193_E209_R2.8500.95
23_N27_M2.3420.86
35_I146_G2.2860.85
43_S47_K2.2290.83
189_H210_V2.2100.83
215_S237_M2.1820.82
13_M27_M2.1600.81
178_S224_L2.1080.80
251_I254_E2.0920.79
59_N131_L2.0760.79
120_G149_V2.0620.78
168_S178_S2.0380.77
148_T155_L2.0300.77
252_E255_N1.9950.76
190_I203_A1.9860.75
75_Y111_T1.9680.75
10_I244_V1.9570.74
28_A154_I1.9420.74
57_I96_T1.9380.73
171_V233_R1.9370.73
168_S247_N1.9340.73
114_V143_A1.9080.72
96_T109_G1.8980.72
151_G243_K1.8840.71
13_M174_M1.8810.71
67_E108_A1.8790.71
190_I222_R1.8560.70
130_R233_R1.8260.69
24_F191_F1.8220.69
40_F109_G1.7900.67
146_G241_Y1.7870.67
38_N150_V1.7820.67
166_A170_A1.7710.66
22_V126_L1.7660.66
119_G150_V1.7340.65
98_F150_V1.7180.64
189_H209_R1.7100.63
48_L79_L1.7100.63
6_K31_L1.6910.63
185_E193_E1.6810.62
185_E205_K1.6630.61
201_L208_D1.6420.60
125_T199_G1.6400.60
48_L103_R1.5840.57
72_P98_F1.5830.57
37_S135_F1.5250.54
216_V222_R1.5190.54
208_D211_G1.5170.54
181_Y232_S1.5130.54
185_E189_H1.5010.53
244_V249_F1.4870.52
57_I104_D1.4830.52
43_S161_E1.4460.50
59_N109_G1.4170.49
41_V72_P1.3990.48
43_S243_K1.3860.47
17_A32_R1.3820.47
42_V48_L1.3690.46
109_G131_L1.3660.46
122_R125_T1.3490.45
33_D128_L1.3430.45
59_N129_S1.3310.44
23_N26_E1.3270.44
61_R109_G1.3180.44
73_E256_L1.3060.43
24_F153_E1.2980.43
109_G129_S1.2960.43
177_S187_I1.2950.43
119_G154_I1.2950.43
175_A226_S1.2900.42
24_F157_E1.2850.42
91_I97_A1.2830.42
143_A154_I1.2750.42
119_G160_E1.2700.41
76_T157_E1.2620.41
106_F209_R1.2560.41
22_V247_N1.2500.40
106_F111_T1.2490.40
186_A212_I1.2460.40
189_H229_V1.2160.39
182_S203_A1.1970.38
119_G158_K1.1900.38
61_R96_T1.1850.37
231_E243_K1.1810.37
221_L242_I1.1770.37
201_L212_I1.1730.37
130_R243_K1.1700.37
20_K32_R1.1650.36
27_M174_M1.1590.36
188_E244_V1.1580.36
12_S224_L1.1560.36
181_Y190_I1.1410.35
190_I232_S1.1410.35
202_V229_V1.1380.35
19_G209_R1.1340.35
210_V224_L1.1300.35
165_E246_N1.1260.35
169_K229_V1.1170.34
149_V244_V1.1080.34
24_F170_A1.1040.34
197_N254_E1.1030.33
6_K33_D1.1030.33
48_L174_M1.1000.33
15_Q135_F1.0980.33
21_P44_R1.0900.33
201_L224_L1.0700.32
186_A201_L1.0650.32
5_Q87_S1.0640.32
157_E178_S1.0580.31
168_S224_L1.0570.31
64_K106_F1.0530.31
26_E156_R1.0470.31
107_Q130_R1.0430.31
96_T131_L1.0320.30
5_Q127_I1.0300.30
61_R99_P1.0300.30
154_I250_L1.0270.30
121_E158_K1.0270.30
122_R230_I1.0250.30
53_I178_S1.0240.30
204_S237_M1.0230.30
181_Y224_L1.0220.30
57_I111_T1.0160.30
59_N65_M1.0140.30
196_G209_R1.0130.30
32_R35_I1.0100.29
91_I96_T0.9990.29
61_R65_M0.9860.28
42_V121_E0.9830.28
28_A32_R0.9780.28
19_G28_A0.9780.28
73_E77_K0.9730.28
30_T78_N0.9700.28
28_A174_M0.9660.28
76_T79_L0.9600.27
181_Y253_L0.9560.27
116_I151_G0.9500.27
6_K128_L0.9420.27
81_N256_L0.9400.27
47_K161_E0.9400.27
169_K205_K0.9380.26
45_R161_E0.9360.26
207_A216_V0.9350.26
204_S215_S0.9320.26
58_E243_K0.9310.26
24_F56_Q0.9290.26
185_E210_V0.9260.26
37_S40_F0.9230.26
130_R133_D0.9220.26
185_E200_L0.9190.26
65_M104_D0.9190.26
52_S62_M0.9180.26
40_F129_S0.9170.26
9_I41_V0.9160.26
77_K116_I0.9140.25
123_L253_L0.9090.25
75_Y140_L0.9040.25
139_D148_T0.9030.25
12_S177_S0.8970.25
37_S60_D0.8880.24
232_S253_L0.8850.24
140_L250_L0.8830.24
28_A152_M0.8800.24
230_I252_E0.8790.24
128_L173_Q0.8790.24
42_V151_G0.8750.24
73_E197_N0.8700.24
24_F47_K0.8690.24
224_L249_F0.8640.24
56_Q90_D0.8630.24
11_N15_Q0.8610.23
6_K48_L0.8580.23
65_M96_T0.8560.23
38_N98_F0.8510.23
27_M32_R0.8410.23
225_E230_I0.8410.23
157_E224_L0.8370.23
28_A35_I0.8360.23
162_I166_A0.8320.22
91_I94_E0.8320.22
98_F159_A0.8280.22
190_I220_A0.8270.22
27_M119_G0.8270.22
130_R248_K0.8210.22
192_E197_N0.8200.22
186_A206_I0.8140.22
91_I141_I0.8140.22
47_K160_E0.8140.22
126_L149_V0.8120.22
77_K82_V0.8090.22
222_R232_S0.8050.21
173_Q177_S0.7940.21
58_E141_I0.7930.21
138_D141_I0.7930.21
50_G124_G0.7880.21
165_E170_A0.7870.21
24_F76_T0.7860.21
161_E243_K0.7800.21
229_V256_L0.7790.21
32_R101_E0.7790.21
75_Y96_T0.7740.20
146_G246_N0.7740.20
108_A132_Q0.7700.20
15_Q200_L0.7650.20
121_E256_L0.7640.20
168_S246_N0.7610.20
61_R89_L0.7590.20
172_V196_G0.7560.20
20_K149_V0.7510.20
37_S55_Q0.7490.20
42_V250_L0.7450.20
10_I19_G0.7450.20
48_L61_R0.7430.19
100_V103_R0.7400.19
8_R221_L0.7380.19
15_Q118_G0.7350.19
166_A210_V0.7340.19
191_F253_L0.7330.19
11_N113_I0.7330.19
78_N95_Y0.7310.19
18_A146_G0.7300.19
189_H245_L0.7290.19
13_M149_V0.7290.19
130_R174_M0.7280.19
30_T146_G0.7250.19
49_L123_L0.7220.19
2_A108_A0.7180.19
71_F77_K0.7180.19
193_E225_E0.7150.19
85_T212_I0.7140.19
141_I165_E0.7130.19
153_E242_I0.7120.18
198_E243_K0.7100.18
210_V230_I0.7100.18
153_E205_K0.7070.18
56_Q128_L0.7060.18
168_S206_I0.7050.18
9_I152_M0.7040.18
9_I94_E0.6970.18
51_Y111_T0.6950.18
48_L105_L0.6930.18
87_S110_L0.6930.18
89_L93_S0.6930.18
38_N130_R0.6900.18
12_S48_L0.6880.18
209_R222_R0.6860.18
13_M145_Y0.6850.18
30_T165_E0.6850.18
39_I48_L0.6810.18
59_N111_T0.6790.17
24_F45_R0.6790.17
35_I56_Q0.6780.17
170_A210_V0.6770.17
175_A213_T0.6770.17
10_I16_A0.6760.17
48_L177_S0.6760.17
50_G123_L0.6750.17
37_S120_G0.6730.17
33_D185_E0.6700.17
216_V226_S0.6660.17
179_L226_S0.6660.17
35_I87_S0.6630.17
10_I91_I0.6630.17
247_N255_N0.6600.17
24_F161_E0.6600.17
130_R224_L0.6560.17
7_T10_I0.6550.17
72_P129_S0.6550.17
172_V201_L0.6530.17
149_V160_E0.6510.17
222_R233_R0.6440.16
138_D161_E0.6430.16
116_I177_S0.6430.16
153_E156_R0.6420.16
163_E235_L0.6370.16
76_T97_A0.6370.16
48_L106_F0.6350.16
10_I21_P0.6350.16
172_V190_I0.6340.16
42_V125_T0.6310.16
184_L252_E0.6300.16
5_Q244_V0.6270.16
172_V182_S0.6230.16
181_Y203_A0.6220.16
27_M59_N0.6200.16
86_S251_I0.6190.16
105_L152_M0.6160.16
82_V168_S0.6150.16
37_S152_M0.6140.16
87_S158_K0.6110.16
89_L127_I0.6060.15
56_Q168_S0.6040.15
114_V250_L0.6030.15
113_I157_E0.6010.15
41_V80_F0.6010.15
174_M233_R0.5990.15
2_A137_D0.5980.15
146_G174_M0.5970.15
176_I191_F0.5960.15
97_A132_Q0.5920.15
86_S89_L0.5900.15
55_Q80_F0.5890.15
41_V47_K0.5890.15
123_L182_S0.5870.15
200_L229_V0.5860.15
51_Y98_F0.5850.15
37_S108_A0.5830.15
156_R160_E0.5830.15
113_I132_Q0.5790.15
174_M209_R0.5780.15
38_N193_E0.5760.15
19_G95_Y0.5750.15
204_S207_A0.5740.15
204_S213_T0.5710.15
176_I210_V0.5700.15
4_L8_R0.5690.14
17_A26_E0.5680.14
19_G106_F0.5670.14
107_Q134_Q0.5670.14
120_G241_Y0.5650.14
64_K188_E0.5640.14
203_A233_R0.5620.14
61_R100_V0.5610.14
113_I133_D0.5580.14
63_K70_Q0.5570.14
36_D116_I0.5560.14
63_K131_L0.5540.14
42_V142_L0.5490.14
53_I185_E0.5480.14
82_V195_D0.5480.14
116_I198_E0.5480.14
61_R69_R0.5470.14
9_I27_M0.5450.14
40_F59_N0.5450.14
38_N55_Q0.5430.14
26_E76_T0.5420.14
59_N101_E0.5400.14
194_L215_S0.5390.14
158_K249_F0.5380.14
179_L213_T0.5380.14
52_S134_Q0.5370.14
41_V176_I0.5350.14
59_N174_M0.5340.14
14_L137_D0.5340.14
44_R47_K0.5330.14
171_V206_I0.5310.14
146_G244_V0.5300.14
91_I174_M0.5290.13
59_N94_E0.5270.13
82_V247_N0.5270.13
84_E137_D0.5260.13
167_R181_Y0.5260.13
30_T158_K0.5260.13
29_E74_E0.5240.13
210_V245_L0.5240.13
179_L216_V0.5230.13
128_L154_I0.5210.13
6_K28_A0.5210.13
174_M243_K0.5200.13
36_D133_D0.5190.13
207_A226_S0.5180.13
13_M192_E0.5170.13
83_P157_E0.5170.13
62_M65_M0.5160.13
54_N59_N0.5150.13
87_S112_T0.5130.13
116_I256_L0.5110.13
174_M248_K0.5100.13
29_E149_V0.5100.13
152_M241_Y0.5070.13
110_L138_D0.5070.13
64_K247_N0.5050.13
130_R188_E0.5040.13
113_I254_E0.5010.13
18_A152_M0.5000.13
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
2gx5A 2 0.6178 100 0.485 Contact Map
2w1rA 2 0.444 99 0.895 Contact Map
2b0lA 4 0.3784 98.2 0.919 Contact Map
3vv4A 2 0.5714 97.4 0.931 Contact Map
3e0yA 2 0.5676 97.4 0.932 Contact Map
2vxzA 1 0.3012 97.4 0.932 Contact Map
3trcA 2 0.6139 97.2 0.934 Contact Map
4g3vA 2 0.5598 97.1 0.935 Contact Map
2zmfA 2 0.6293 97.1 0.935 Contact Map
3k2nA 2 0.6293 96.8 0.938 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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