GREMLIN Database
PADR - Negative transcription regulator PadR
UniProt: P94443 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 182 (168)
Sequences: 3470 (2378)
Seq/√Len: 183.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
121_L173_E4.1401.00
125_Q173_E3.6371.00
166_K170_S2.8571.00
79_E82_D2.8191.00
55_T71_T2.7701.00
132_Q166_K2.7651.00
114_S176_L2.6771.00
132_Q162_L2.5441.00
56_F68_K2.3331.00
121_L169_V2.2881.00
159_T174_S2.2061.00
118_K176_L2.1581.00
163_E170_S2.1461.00
128_L166_K2.1231.00
13_R80_L2.0901.00
105_I113_A2.0541.00
121_L176_L2.0321.00
57_R71_T2.0291.00
156_L175_I2.0211.00
10_G104_F1.9891.00
49_T56_F1.9191.00
19_G45_L1.8941.00
124_R165_E1.8911.00
163_E167_N1.8871.00
128_L162_L1.8561.00
121_L125_Q1.7881.00
14_K29_E1.7631.00
19_G42_Y1.7461.00
125_Q169_V1.7401.00
61_Q65_L1.7331.00
9_L72_L1.6701.00
163_E174_S1.6361.00
85_I112_E1.6331.00
121_L172_L1.5951.00
6_Y83_W1.5741.00
16_E57_R1.5721.00
6_Y79_E1.5211.00
23_T27_K1.5061.00
12_L54_I1.5041.00
48_L53_F1.5021.00
5_K51_E1.4901.00
13_R77_K1.4691.00
120_Q168_Y1.4621.00
114_S118_K1.4571.00
129_S132_Q1.4311.00
122_Q125_Q1.4311.00
74_D77_K1.4211.00
16_E71_T1.4001.00
152_F178_M1.3891.00
74_D78_Q1.3691.00
75_S78_Q1.3341.00
39_S44_E1.3161.00
109_S112_E1.3141.00
135_Y159_T1.3061.00
118_K122_Q1.3051.00
53_F75_S1.2781.00
59_T67_K1.2761.00
13_R72_L1.2731.00
169_V173_E1.2391.00
117_F172_L1.2361.00
4_L36_A1.2071.00
49_T54_I1.1991.00
99_M160_K1.1991.00
133_G136_E1.1901.00
61_Q66_E1.1771.00
17_L25_Y1.1661.00
125_Q129_S1.1631.00
40_Q44_E1.1421.00
128_L169_V1.1351.00
82_D86_R1.1081.00
124_R172_L1.1051.00
163_E166_K1.0771.00
98_F120_Q1.0761.00
117_F175_I1.0661.00
130_D133_G1.0631.00
173_E177_A1.0591.00
122_Q126_A1.0331.00
159_T163_E1.0241.00
116_L119_D1.0231.00
53_F79_E1.0170.99
164_R167_N1.0130.99
8_I41_I1.0090.99
39_S43_P1.0000.99
25_Y29_E0.9920.99
5_K79_E0.9910.99
37_K43_P0.9780.99
162_L166_K0.9720.99
110_R114_S0.9680.99
18_S67_K0.9640.99
78_Q82_D0.9460.99
24_S27_K0.9330.99
61_Q64_K0.9280.99
89_P119_D0.9260.99
128_L132_Q0.9250.99
72_L77_K0.9240.99
87_H101_K0.9220.99
10_G80_L0.9090.99
15_G21_D0.9070.99
112_E115_D0.9000.99
80_L107_C0.8980.99
62_G65_L0.8900.99
135_Y162_L0.8900.99
84_L104_F0.8800.99
127_K130_D0.8770.98
23_T39_S0.8740.98
123_K126_A0.8740.98
19_G41_I0.8640.98
21_D67_K0.8590.98
30_L33_F0.8540.98
119_D122_Q0.8500.98
117_F176_L0.8450.98
81_H112_E0.8340.98
23_T38_H0.8330.98
40_Q83_W0.8170.98
88_Q101_K0.8150.98
4_L44_E0.8120.98
115_D119_D0.8110.97
46_K49_T0.8030.97
124_R169_V0.8010.97
124_R168_Y0.7980.97
23_T37_K0.7970.97
80_L104_F0.7970.97
165_E168_Y0.7970.97
12_L17_L0.7940.97
131_L158_L0.7910.97
120_Q172_L0.7790.97
83_W101_K0.7790.97
43_P46_K0.7740.97
133_G137_K0.7710.97
132_Q135_Y0.7650.96
160_K164_R0.7640.96
21_D24_S0.7610.96
160_K167_N0.7610.96
36_A41_I0.7570.96
77_K81_H0.7530.96
99_M157_V0.7510.96
129_S133_G0.7490.96
15_G25_Y0.7470.96
119_D123_K0.7390.96
88_Q113_A0.7390.96
38_H43_P0.7340.96
130_D134_S0.7320.95
55_T73_T0.7320.95
170_S174_S0.7300.95
158_L161_A0.7260.95
24_S28_E0.7210.95
84_L108_L0.7210.95
79_E83_W0.7200.95
156_L159_T0.7170.95
126_A130_D0.7150.95
10_G39_S0.7140.95
13_R107_C0.7090.95
5_K44_E0.7040.94
59_T66_E0.7030.94
26_F36_A0.6990.94
19_G68_K0.6880.94
150_P154_H0.6860.94
66_E100_L0.6780.93
159_T178_M0.6730.93
43_P47_K0.6720.93
11_L22_I0.6710.93
164_R168_Y0.6570.92
137_K140_A0.6550.92
57_R69_M0.6550.92
8_I44_E0.6540.92
126_A129_S0.6540.92
135_Y155_Y0.6530.92
4_L26_F0.6530.92
8_I171_W0.6520.92
60_I66_E0.6520.92
119_D137_K0.6520.92
174_S177_A0.6510.92
80_L84_L0.6490.92
136_E139_M0.6470.91
20_Y24_S0.6460.91
34_W40_Q0.6460.91
52_G55_T0.6450.91
128_L165_E0.6420.91
152_F156_L0.6410.91
156_L160_K0.6400.91
19_G43_P0.6380.91
73_T76_G0.6350.91
18_S36_A0.6330.91
49_T55_T0.6300.90
111_Q115_D0.6200.90
46_K50_D0.6180.90
61_Q67_K0.6170.89
169_V176_L0.6160.89
55_T75_S0.6150.89
132_Q136_E0.6140.89
22_I45_L0.6120.89
105_I153_G0.6090.89
5_K53_F0.5980.88
52_G75_S0.5920.87
91_P96_D0.5880.87
127_K165_E0.5870.87
135_Y140_A0.5860.87
7_A100_L0.5850.87
59_T65_L0.5840.87
86_R91_P0.5820.87
174_S178_M0.5810.86
102_A156_L0.5810.86
36_A95_K0.5800.86
140_A177_A0.5770.86
115_D118_K0.5770.86
18_S21_D0.5750.86
131_L161_A0.5750.86
40_Q101_K0.5740.86
6_Y26_F0.5730.86
20_Y67_K0.5730.86
108_L112_E0.5690.85
112_E170_S0.5680.85
33_F103_Y0.5670.85
48_L54_I0.5670.85
110_R113_A0.5650.85
7_A26_F0.5650.85
6_Y80_L0.5640.85
14_K25_Y0.5620.85
47_K51_E0.5600.84
81_H85_I0.5590.84
7_A11_L0.5540.84
157_V160_K0.5530.84
55_T60_I0.5510.83
30_L38_H0.5510.83
10_G84_L0.5490.83
19_G31_G0.5480.83
160_K168_Y0.5460.83
59_T69_M0.5450.83
138_L155_Y0.5430.83
39_S104_F0.5400.82
7_A22_I0.5400.82
155_Y159_T0.5370.82
29_E32_Q0.5370.82
7_A83_W0.5350.82
98_F116_L0.5350.82
8_I45_L0.5340.82
131_L162_L0.5320.81
5_K47_K0.5310.81
22_I35_S0.5310.81
161_A164_R0.5270.81
60_I69_M0.5250.80
85_I115_D0.5230.80
106_S153_G0.5210.80
108_L113_A0.5210.80
23_T44_E0.5140.79
97_E156_L0.5100.79
47_K50_D0.5080.78
34_W38_H0.5050.78
20_Y42_Y0.5040.78
85_I109_S0.5030.78
33_F95_K0.5020.77
33_F161_A0.5000.77
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  
3l9fA 2 0.9286 100 0.269 Contact Map
1yg2A 2 0.9231 100 0.275 Contact Map
2rkhA 2 0.8297 100 0.295 Contact Map
2zfwA 2 0.5055 99.6 0.623 Contact Map
2dqlA 2 0.522 99.6 0.628 Contact Map
1bm9A 2 0.5659 99.6 0.632 Contact Map
2e1nA 2 0.5055 99.6 0.633 Contact Map
1xmaA 2 0.533 99.6 0.633 Contact Map
2co5A 2 0.4835 99.5 0.646 Contact Map
2eshA 2 0.5824 99.5 0.651 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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