GREMLIN Database
YDGJ - Uncharacterized HTH-type transcriptional regulator YdgJ
UniProt: P96708 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 164 (132)
Sequences: 21473 (15996)
Seq/√Len: 1392.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
101_R113_R3.1681.00
144_E154_R2.9121.00
70_S109_I2.6581.00
103_K111_L2.6451.00
99_S113_R2.5891.00
68_E113_R2.4921.00
141_S144_E2.4661.00
147_L151_V2.3021.00
147_L150_D2.2341.00
64_Y122_I2.0941.00
102_R110_T2.0651.00
56_R95_K2.0561.00
140_V151_V1.9671.00
70_S73_D1.9361.00
64_Y114_L1.8701.00
139_N158_N1.8551.00
103_K109_I1.8411.00
144_E147_L1.7591.00
93_E100_R1.7231.00
117_Q121_R1.6881.00
148_L151_V1.6781.00
59_L88_H1.6431.00
96_G117_Q1.6161.00
56_R91_Q1.5751.00
71_Q89_L1.5681.00
66_A77_K1.5621.00
53_S56_R1.5591.00
89_L112_V1.5301.00
144_E150_D1.5221.00
90_K94_S1.4791.00
121_R124_S1.4721.00
151_V154_R1.4641.00
62_L77_K1.4511.00
36_Q39_N1.4461.00
64_Y119_R1.4151.00
117_Q120_E1.3821.00
50_T128_E1.3711.00
45_K48_A1.2951.00
81_D84_A1.2881.00
144_E151_V1.2791.00
100_R110_T1.2501.00
90_K107_N1.2351.00
71_Q110_T1.2071.00
72_S82_S1.2061.00
73_D76_K1.1911.00
80_I84_A1.1861.00
68_E111_L1.1771.00
150_D154_R1.1711.00
49_C128_E1.1591.00
120_E124_S1.1581.00
72_S76_K1.1481.00
59_L85_V1.1411.00
71_Q82_S1.1161.00
149_I153_A1.0941.00
83_A86_T1.0931.00
71_Q112_V1.0861.00
97_M121_R1.0681.00
143_E147_L1.0651.00
66_A69_I1.0521.00
71_Q85_V1.0521.00
145_R149_I1.0411.00
84_A87_R1.0171.00
86_T90_K1.0101.00
69_I73_D1.0061.00
55_S88_H1.0051.00
50_T124_S0.9931.00
81_D87_R0.9881.00
99_S115_T0.9771.00
50_T125_S0.9591.00
90_K93_E0.9561.00
69_I77_K0.9491.00
114_L118_G0.9361.00
34_Q156_R0.9261.00
73_D77_K0.9241.00
95_K117_Q0.9231.00
95_K121_R0.9201.00
128_E131_R0.9141.00
119_R123_E0.9101.00
102_R107_N0.9091.00
63_L98_V0.9081.00
67_D119_R0.9011.00
40_K43_G0.8981.00
58_E78_V0.8981.00
106_D109_I0.8971.00
39_N43_G0.8911.00
133_M136_M0.8871.00
80_I85_V0.8771.00
142_A146_R0.8681.00
116_D120_E0.8651.00
30_E34_Q0.8621.00
103_K106_D0.8621.00
44_V47_E0.8521.00
116_D119_R0.8461.00
97_M117_Q0.8451.00
87_R90_K0.8401.00
71_Q86_T0.8381.00
64_Y126_K0.8361.00
51_G95_K0.8331.00
64_Y123_E0.8311.00
127_K131_R0.8311.00
34_Q153_A0.8231.00
89_L98_V0.8171.00
67_D113_R0.8141.00
101_R111_L0.8111.00
57_L125_S0.8091.00
140_V155_M0.8071.00
55_S84_A0.8031.00
124_S128_E0.8001.00
89_L93_E0.7971.00
129_K133_M0.7951.00
147_L154_R0.7941.00
68_E101_R0.7921.00
93_E98_V0.7861.00
87_R91_Q0.7841.00
131_R134_K0.7811.00
146_R149_I0.7791.00
60_L122_I0.7681.00
93_E99_S0.7651.00
57_L129_K0.7651.00
90_K100_R0.7641.00
91_Q94_S0.7631.00
104_P111_L0.7541.00
66_A73_D0.7521.00
59_L74_L0.7511.00
32_L35_L0.7491.00
59_L78_V0.7481.00
38_V156_R0.7471.00
75_Q85_V0.7461.00
62_L66_A0.7461.00
131_R135_E0.7351.00
35_L39_N0.7341.00
114_L119_R0.7221.00
75_Q82_S0.7211.00
141_S145_R0.7191.00
34_Q149_I0.7081.00
137_L145_R0.7051.00
36_Q40_K0.7051.00
153_A157_N0.7011.00
37_G41_V0.6991.00
62_L78_V0.6971.00
130_E134_K0.6891.00
43_G47_E0.6861.00
146_R150_D0.6801.00
85_V89_L0.6791.00
44_V48_A0.6721.00
127_K130_E0.6651.00
91_Q95_K0.6621.00
143_E146_R0.6611.00
62_L69_I0.6571.00
34_Q39_N0.6571.00
135_E138_A0.6561.00
154_R158_N0.6521.00
56_R88_H0.6401.00
124_S127_K0.6371.00
34_Q37_G0.6361.00
140_V145_R0.6341.00
132_F135_E0.6241.00
63_L114_L0.6231.00
35_L38_V0.6201.00
39_N42_I0.6181.00
33_Y37_G0.6161.00
96_G99_S0.6151.00
61_T65_H0.6141.00
63_L69_I0.6111.00
62_L74_L0.6091.00
32_L42_I0.6081.00
43_G46_F0.6061.00
61_T126_K0.6031.00
151_V155_M0.6001.00
28_E31_I0.5981.00
57_L122_I0.5981.00
38_V41_V0.5981.00
72_S75_Q0.5971.00
41_V45_K0.5961.00
120_E123_E0.5941.00
28_E32_L0.5851.00
58_E62_L0.5821.00
38_V43_G0.5691.00
126_K130_E0.5581.00
82_S86_T0.5551.00
55_S80_I0.5431.00
113_R119_R0.5401.00
72_S109_I0.5381.00
70_S103_K0.5301.00
151_V158_N0.5291.00
92_L97_M0.5271.00
32_L36_Q0.5261.00
102_R106_D0.5211.00
123_E126_K0.5211.00
30_E33_Y0.5211.00
36_Q43_G0.5201.00
141_S154_R0.5171.00
60_L64_Y0.5131.00
129_K132_F0.5111.00
29_A33_Y0.5091.00
33_Y36_Q0.5081.00
42_I46_F0.5041.00
138_A158_N0.5001.00
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  
4rguA 4 0.8537 99.9 0.34 Contact Map
3cjnA 2 0.872 99.9 0.344 Contact Map
3bj6A 2 0.9146 99.9 0.347 Contact Map
3e6mA 2 0.9024 99.9 0.348 Contact Map
3boqA 2 0.811 99.9 0.353 Contact Map
3deuA 2 0.7805 99.9 0.355 Contact Map
3u2rA 4 0.7927 99.9 0.357 Contact Map
3bddA 2 0.8476 99.9 0.359 Contact Map
2nyxA 2 0.878 99.9 0.361 Contact Map
3zplA 2 0.9207 99.9 0.361 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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