GREMLIN Database
YXAD - Uncharacterized HTH-type transcriptional regulator YxaD
UniProt: P42103 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 143 (130)
Sequences: 22489 (16782)
Seq/√Len: 1471.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
83_F95_T3.1621.00
50_P95_T3.0821.00
126_E136_R2.8951.00
81_Y95_T2.6171.00
52_R91_V2.5961.00
85_D93_L2.4981.00
123_S126_E2.3731.00
129_M133_L2.1401.00
129_M132_E2.1301.00
46_D104_L2.0601.00
84_S92_S2.0161.00
52_R55_E1.9531.00
38_S77_K1.9391.00
50_P93_L1.9001.00
122_W133_L1.8531.00
126_E129_M1.8071.00
46_D96_I1.7971.00
85_D91_V1.7271.00
99_L103_L1.5951.00
53_V71_A1.5931.00
50_P83_F1.5881.00
38_S73_A1.5821.00
126_E132_E1.5431.00
78_E99_L1.5421.00
75_E82_R1.5191.00
71_A94_F1.5081.00
13_E135_Q1.4601.00
35_E38_S1.4581.00
99_L102_Q1.4571.00
41_L70_Q1.4531.00
133_L136_R1.4501.00
48_F59_S1.4281.00
72_A76_A1.4221.00
130_F133_L1.4161.00
103_L106_A1.4121.00
32_G110_K1.3741.00
46_D101_K1.3391.00
44_Q59_S1.3051.00
55_E58_E1.2411.00
13_E131_G1.2371.00
13_E138_N1.2281.00
54_K64_I1.2081.00
53_V92_S1.1981.00
132_E136_R1.1931.00
63_D66_T1.1851.00
102_Q106_A1.1761.00
54_K58_E1.1631.00
62_L66_T1.1571.00
32_G106_A1.1341.00
72_A89_G1.1261.00
53_V67_L1.1241.00
41_L67_L1.1031.00
17_F138_N1.0991.00
127_K131_G1.0881.00
126_E133_L1.0831.00
79_L103_L1.0821.00
15_T18_I1.0731.00
53_V64_I1.0711.00
53_V94_F1.0711.00
125_Q129_M1.0671.00
51_A55_E1.0551.00
65_S68_S1.0511.00
82_R92_S1.0221.00
26_Q30_R1.0181.00
31_T110_K1.0171.00
28_E110_K0.9981.00
110_K113_E0.9901.00
131_G135_Q0.9891.00
48_F51_A0.9731.00
115_Y118_M0.9611.00
51_A59_S0.9601.00
16_T138_N0.9531.00
66_T69_R0.9501.00
55_E59_S0.9461.00
32_G107_D0.9431.00
77_K103_L0.9421.00
37_S70_Q0.9251.00
98_K102_Q0.9191.00
72_A75_E0.9161.00
96_I100_G0.9101.00
81_Y97_T0.9101.00
98_K101_K0.9081.00
49_G101_K0.9061.00
77_K99_L0.9051.00
79_L99_L0.8961.00
28_E31_T0.8921.00
62_L67_L0.8911.00
68_S72_A0.8891.00
46_D108_Q0.8851.00
83_F93_L0.8841.00
17_F134_L0.8781.00
111_R115_Y0.8771.00
96_I101_K0.8691.00
39_Y107_D0.8651.00
84_S89_G0.8631.00
101_K105_K0.8621.00
63_D69_R0.8601.00
45_L80_I0.8581.00
124_T128_E0.8511.00
46_D105_K0.8491.00
122_W137_M0.8491.00
69_R73_A0.8471.00
113_E116_E0.8431.00
106_A110_K0.8381.00
88_D91_V0.8371.00
69_R72_A0.8211.00
18_I22_V0.8161.00
42_L104_L0.8091.00
109_Q113_E0.8081.00
41_L56_L0.7961.00
71_A80_I0.7941.00
15_T19_R0.7891.00
33_N77_K0.7871.00
20_R138_N0.7771.00
10_I131_G0.7761.00
44_Q60_F0.7681.00
75_E80_I0.7641.00
26_Q36_R0.7611.00
71_A75_E0.7591.00
40_L60_F0.7591.00
73_A76_A0.7471.00
129_M136_R0.7421.00
75_E81_Y0.7381.00
113_E117_Q0.7311.00
44_Q48_F0.7291.00
114_R117_Q0.7251.00
28_E113_E0.7211.00
125_Q128_E0.7201.00
53_V68_S0.7181.00
48_F55_E0.7181.00
14_L18_I0.7161.00
86_P93_L0.7131.00
135_Q139_K0.7111.00
28_E117_Q0.7091.00
39_Y111_R0.7081.00
123_S127_K0.7071.00
19_R23_Y0.7061.00
109_Q112_L0.7051.00
24_L114_R0.6931.00
37_S66_T0.6911.00
22_V25_D0.6841.00
119_L127_K0.6831.00
17_F137_M0.6811.00
102_Q105_K0.6741.00
128_E132_E0.6731.00
49_G95_T0.6711.00
44_Q51_A0.6711.00
57_A67_L0.6701.00
117_Q120_K0.6681.00
128_E131_G0.6621.00
85_D88_D0.6591.00
38_S70_Q0.6581.00
28_E114_R0.6581.00
72_A82_R0.6471.00
41_L60_F0.6451.00
43_R47_E0.6381.00
39_Y104_L0.6351.00
112_L116_E0.6351.00
57_A64_I0.6321.00
22_V26_Q0.6211.00
14_L17_F0.6101.00
73_A77_K0.6061.00
74_L79_L0.6031.00
45_L96_I0.6011.00
13_E16_T0.6001.00
106_A109_Q0.5991.00
44_Q56_L0.5991.00
45_L51_A0.5961.00
67_L71_A0.5841.00
43_R104_L0.5791.00
24_L117_Q0.5771.00
108_Q112_L0.5701.00
122_W127_K0.5651.00
78_E81_Y0.5631.00
16_T20_R0.5621.00
97_T100_G0.5611.00
40_L44_Q0.5571.00
132_E135_Q0.5501.00
105_K108_Q0.5481.00
54_K91_V0.5451.00
52_R93_L0.5371.00
123_S136_R0.5321.00
42_L46_D0.5291.00
37_S62_L0.5291.00
54_K57_A0.5281.00
43_R108_Q0.5241.00
56_L94_F0.5201.00
122_W136_R0.5201.00
24_L27_S0.5191.00
25_D111_R0.5151.00
122_W126_E0.5141.00
21_A24_L0.5081.00
52_R85_D0.5071.00
10_I130_F0.5041.00
83_F86_P0.5001.00
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  
3e6mA 2 1 99.9 0.249 Contact Map
3cjnA 2 0.986 99.9 0.25 Contact Map
3cdhA 4 0.9231 99.9 0.25 Contact Map
2fbkA 2 0.9371 99.9 0.25 Contact Map
3bj6A 2 1 99.9 0.252 Contact Map
4rguA 4 0.979 99.9 0.257 Contact Map
1s3jA 2 1 99.9 0.258 Contact Map
4yifA 2 0.972 99.9 0.259 Contact Map
3deuA 2 0.9091 99.9 0.262 Contact Map
4mnuA 2 0.965 99.9 0.264 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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