GREMLIN Database
RCDA - HTH-type transcriptional regulator RcdA
UniProt: P75811 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13680
Length: 178 (163)
Sequences: 35540 (28244)
Seq/√Len: 2212.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
32_R42_L4.1831.00
24_Y33_K4.1471.00
19_E37_L3.8711.00
50_S54_E2.8221.00
21_V29_V2.5511.00
9_R12_K2.2721.00
11_E62_S2.1821.00
23_L37_L2.1701.00
20_A29_V2.1641.00
35_A45_M2.0731.00
51_G54_E2.0531.00
41_P44_S2.0321.00
20_A37_L1.9281.00
11_E15_Q1.8521.00
80_D83_G1.8331.00
16_A37_L1.8271.00
18_L62_S1.7991.00
17_T21_V1.7981.00
32_R36_T1.7901.00
12_K16_A1.7691.00
31_H46_T1.7531.00
131_Q135_E1.7091.00
20_A33_K1.6941.00
14_I58_E1.6641.00
31_H42_L1.6341.00
10_R58_E1.6121.00
19_E23_L1.5951.00
58_E61_S1.5591.00
20_A24_Y1.5561.00
18_L59_A1.5221.00
15_Q62_S1.4781.00
61_S122_V1.4631.00
145_A149_F1.4621.00
31_H45_M1.4501.00
16_A19_E1.4411.00
8_Q12_K1.4211.00
25_G28_A1.3961.00
33_K36_T1.3941.00
33_K37_L1.3801.00
134_L137_W1.3721.00
62_S66_I1.3451.00
21_V26_I1.3351.00
54_E58_E1.3341.00
49_F58_E1.3321.00
17_T55_L1.3241.00
29_V34_I1.3221.00
18_L63_F1.3121.00
25_G29_V1.3081.00
57_L61_S1.3071.00
44_S47_Y1.2761.00
30_T33_K1.2661.00
40_V44_S1.2451.00
8_Q11_E1.2371.00
61_S65_E1.2231.00
42_L46_T1.2071.00
127_M131_Q1.1891.00
44_S48_Y1.1881.00
41_P47_Y1.1791.00
133_T137_W1.1791.00
70_Q91_M1.1681.00
14_I59_A1.1641.00
34_I55_L1.1611.00
46_T51_G1.1611.00
16_A38_A1.1581.00
134_L138_F1.1391.00
19_E101_D1.1281.00
26_I56_L1.1251.00
83_G87_A1.1211.00
24_Y28_A1.1201.00
6_D47_Y1.1161.00
104_E108_Q1.1121.00
148_A152_G1.1061.00
130_S137_W1.0991.00
54_E57_L1.0961.00
16_A20_A1.0931.00
17_T59_A1.0901.00
128_Q132_Q1.0651.00
14_I49_F1.0521.00
131_Q140_P1.0371.00
165_S168_E1.0321.00
7_P11_E1.0231.00
129_R132_Q1.0151.00
43_G47_Y1.0131.00
9_R48_Y1.0071.00
10_R48_Y1.0061.00
86_Q90_D1.0031.00
123_M127_M0.9981.00
87_A90_D0.9971.00
82_P86_Q0.9881.00
84_A136_Q0.9741.00
24_Y37_L0.9611.00
139_E142_T0.9611.00
164_L168_E0.9561.00
70_Q73_A0.9551.00
42_L47_Y0.9531.00
83_G86_Q0.9501.00
65_E69_R0.9421.00
95_S99_T0.9361.00
129_R133_T0.9341.00
18_L22_K0.9311.00
15_Q19_E0.9271.00
58_E62_S0.9221.00
57_L118_L0.9181.00
62_S65_E0.9171.00
121_T125_N0.9151.00
132_Q136_Q0.9111.00
63_F66_I0.9051.00
6_D9_R0.9051.00
133_T136_Q0.9011.00
104_E107_Y0.8971.00
31_H52_I0.8891.00
72_Q76_S0.8801.00
135_E140_P0.8791.00
36_T42_L0.8641.00
45_M55_L0.8631.00
9_R40_V0.8591.00
140_P144_R0.8551.00
68_S72_Q0.8491.00
74_F91_M0.8471.00
145_A148_A0.8391.00
99_T102_N0.8381.00
124_Q128_Q0.8351.00
26_I52_I0.8311.00
35_A42_L0.8291.00
13_I45_M0.8271.00
53_D57_L0.8251.00
122_V125_N0.8241.00
69_R73_A0.8191.00
74_F87_A0.8151.00
87_A91_M0.8151.00
32_R46_T0.8131.00
142_T148_A0.8131.00
142_T146_L0.8061.00
147_D151_E0.8031.00
53_D116_K0.7991.00
118_L121_T0.7991.00
91_M94_S0.7901.00
22_K101_D0.7821.00
103_M106_M0.7821.00
24_Y29_V0.7791.00
90_D94_S0.7741.00
14_I18_L0.7711.00
21_V56_L0.7711.00
139_E143_A0.7651.00
9_R44_S0.7631.00
126_W130_S0.7611.00
129_R137_W0.7601.00
132_Q135_E0.7541.00
12_K15_Q0.7471.00
14_I62_S0.7361.00
9_R41_P0.7321.00
32_R41_P0.7301.00
135_E138_F0.7291.00
13_I48_Y0.7261.00
13_I38_A0.7191.00
157_F160_D0.7161.00
120_K124_Q0.7141.00
69_R72_Q0.7121.00
122_V126_W0.7111.00
84_A137_W0.7071.00
128_Q131_Q0.7061.00
12_K38_A0.7041.00
125_N129_R0.7011.00
112_L116_K0.6991.00
100_P104_E0.6981.00
77_D87_A0.6971.00
105_L108_Q0.6951.00
118_L122_V0.6941.00
142_T147_D0.6941.00
94_S98_A0.6931.00
120_K123_M0.6911.00
78_V84_A0.6901.00
113_A116_K0.6851.00
80_D84_A0.6771.00
66_I69_R0.6761.00
151_E156_H0.6761.00
117_P120_K0.6751.00
133_T138_F0.6721.00
109_L112_L0.6721.00
73_A77_D0.6691.00
23_L33_K0.6661.00
68_S129_R0.6641.00
31_H35_A0.6621.00
20_A23_L0.6601.00
18_L66_I0.6581.00
144_R148_A0.6541.00
94_S166_R0.6521.00
131_Q144_R0.6471.00
148_A151_E0.6421.00
45_M50_S0.6371.00
141_G145_A0.6351.00
22_K104_E0.6351.00
103_M108_Q0.6351.00
74_F78_V0.6331.00
72_Q129_R0.6321.00
108_Q111_A0.6281.00
78_V87_A0.6231.00
42_L45_M0.6231.00
142_T145_A0.6201.00
117_P121_T0.6191.00
125_N128_Q0.6091.00
57_L122_V0.6031.00
26_I29_V0.5981.00
149_F152_G0.5941.00
53_D118_L0.5911.00
35_A41_P0.5841.00
81_A84_A0.5821.00
94_S97_V0.5811.00
15_Q18_L0.5791.00
38_A41_P0.5781.00
66_I99_T0.5751.00
105_L109_L0.5751.00
148_A156_H0.5701.00
89_T92_I0.5691.00
20_A30_T0.5671.00
123_M126_W0.5661.00
86_Q89_T0.5621.00
141_G168_E0.5581.00
121_T124_Q0.5531.00
113_A117_P0.5401.00
92_I96_Q0.5391.00
74_F77_D0.5361.00
6_D48_Y0.5361.00
26_I53_D0.5341.00
115_R118_L0.5311.00
127_M130_S0.5301.00
106_M109_L0.5301.00
17_T34_I0.5281.00
38_A42_L0.5271.00
47_Y50_S0.5251.00
41_P48_Y0.5211.00
70_Q74_F0.5211.00
27_H112_L0.5201.00
81_A137_W0.5191.00
126_W137_W0.5181.00
34_I38_A0.5141.00
135_E139_E0.5131.00
130_S138_F0.5101.00
127_M137_W0.5091.00
124_Q127_M0.5091.00
79_S87_A0.5071.00
66_I70_Q0.5061.00
111_A115_R0.5031.00
144_R147_D0.5001.00
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  
2dg8A 2 0.9719 100 0.189 Contact Map
3htaA 2 1 100 0.2 Contact Map
2np5A 3 0.9551 100 0.235 Contact Map
4kwaA 2 0.9775 100 0.238 Contact Map
3v6gA 2 0.9382 100 0.238 Contact Map
3he0A 2 0.9607 99.9 0.245 Contact Map
2gfnA 2 0.9888 99.9 0.245 Contact Map
3e7qA 2 1 99.9 0.245 Contact Map
2qkoA 2 0.9045 99.9 0.246 Contact Map
3g7rA 2 1 99.9 0.247 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.

Page generated in 0.0085 seconds.