GREMLIN Database
YXDJ - Transcriptional regulatory protein YxdJ
UniProt: P42421 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 229 (208)
Sequences: 77350 (54939)
Seq/√Len: 3809.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
14_R30_V3.7411.00
14_R32_A3.2991.00
18_Q30_V3.1781.00
7_V37_V2.7771.00
38_L66_Q2.6991.00
35_T57_A2.6101.00
34_F58_Y2.5201.00
29_V46_P2.5171.00
42_L70_H2.4301.00
33_D57_A2.4211.00
58_Y66_Q2.3631.00
3_K29_V2.2001.00
3_K27_Q2.1001.00
20_Y105_Y2.0591.00
31_A40_V2.0251.00
18_Q22_E2.0221.00
24_Y109_L1.9511.00
87_Q107_I1.9041.00
193_N196_N1.9041.00
32_A36_A1.9031.00
54_N81_R1.9011.00
51_L63_W1.8781.00
64_C75_I1.8431.00
158_K161_K1.8201.00
77_F90_A1.7731.00
33_D36_A1.7291.00
40_V44_E1.7281.00
29_V40_V1.7221.00
5_M31_A1.7191.00
66_Q70_H1.7111.00
84_E104_S1.7051.00
77_F95_G1.7041.00
68_R96_D1.6811.00
29_V44_E1.6461.00
58_Y62_Y1.6221.00
164_E168_E1.6081.00
59_D62_Y1.5721.00
34_F63_W1.5591.00
97_D111_K1.5451.00
136_G149_Q1.5111.00
66_Q69_Q1.4881.00
176_R196_N1.4871.00
40_V43_R1.4791.00
198_Y201_R1.4691.00
21_L112_I1.4671.00
65_R93_N1.4571.00
64_C77_F1.4551.00
165_V182_K1.4461.00
41_F67_I1.4451.00
81_R86_D1.4261.00
62_Y65_R1.4131.00
49_V73_S1.4061.00
38_L63_W1.3841.00
96_D118_R1.3791.00
35_T58_Y1.3771.00
48_V112_I1.3741.00
96_D115_Q1.3311.00
40_V46_P1.3211.00
8_E14_R1.3111.00
76_I115_Q1.3101.00
51_L64_C1.2931.00
165_V169_R1.2871.00
11_E32_A1.2831.00
53_I61_Y1.2651.00
53_I77_F1.2631.00
9_D52_D1.2601.00
39_D43_R1.2551.00
199_I203_R1.2491.00
38_L58_Y1.2431.00
3_K44_E1.2351.00
7_V55_L1.2291.00
31_A37_V1.2121.00
140_F143_R1.2051.00
36_A39_D1.2021.00
159_E205_K1.1941.00
41_F71_S1.1751.00
26_Y113_K1.1741.00
36_A40_V1.1701.00
61_Y90_A1.1671.00
5_M46_P1.1661.00
35_T39_D1.1621.00
61_Y89_M1.1531.00
178_R182_K1.1521.00
5_M37_V1.1421.00
83_G86_D1.1411.00
92_E113_K1.1331.00
133_E138_Q1.1261.00
138_Q147_R1.1191.00
131_V138_Q1.1091.00
109_L113_K1.1091.00
89_M93_N1.1071.00
175_S178_R1.1061.00
194_T198_Y1.1021.00
84_E88_V1.0831.00
65_R89_M1.0811.00
24_Y113_K1.0751.00
4_I26_Y1.0731.00
37_V63_W1.0671.00
48_V116_I1.0631.00
160_S164_E1.0521.00
170_G182_K1.0491.00
5_M40_V1.0421.00
197_V200_T1.0371.00
25_G113_K1.0361.00
38_L42_L1.0271.00
107_I110_A1.0241.00
110_A114_S1.0221.00
208_E217_A1.0151.00
170_G174_T1.0101.00
145_E152_K1.0031.00
15_G30_V0.9981.00
88_V92_E0.9971.00
85_M89_M0.9931.00
177_D192_D0.9881.00
61_Y93_N0.9871.00
5_M41_F0.9841.00
144_F221_E0.9771.00
141_V164_E0.9771.00
31_A36_A0.9761.00
37_V41_F0.9741.00
139_L167_L0.9741.00
193_N197_V0.9701.00
161_K164_E0.9691.00
12_D16_L0.9661.00
11_E15_G0.9641.00
49_V67_I0.9611.00
7_V49_V0.9571.00
51_L75_I0.9571.00
6_I17_L0.9541.00
45_K71_S0.9431.00
17_L78_I0.9421.00
18_Q28_T0.9371.00
39_D42_L0.9291.00
53_I59_D0.9251.00
64_C93_N0.9211.00
62_Y66_Q0.9191.00
7_V31_A0.9191.00
49_V75_I0.9171.00
87_Q100_E0.9151.00
51_L77_F0.9131.00
84_E87_Q0.9091.00
89_M92_E0.9041.00
6_I28_T0.8921.00
50_L108_V0.8891.00
76_I111_K0.8861.00
165_V179_L0.8831.00
157_K161_K0.8811.00
115_Q118_R0.8791.00
64_C95_G0.8771.00
11_E14_R0.8681.00
147_R152_K0.8591.00
174_T178_R0.8581.00
82_S100_E0.8581.00
165_V174_T0.8541.00
55_L63_W0.8531.00
15_G18_Q0.8521.00
208_E213_V0.8491.00
26_Y109_L0.8361.00
63_W67_I0.8321.00
131_V140_F0.8311.00
74_P96_D0.8281.00
88_V106_D0.8231.00
3_K46_P0.8221.00
53_I86_D0.8221.00
193_N200_T0.8201.00
201_R204_K0.8201.00
65_R69_Q0.8131.00
58_Y63_W0.8131.00
105_Y109_L0.8071.00
17_L108_V0.7981.00
19_N23_K0.7901.00
107_I111_K0.7791.00
207_R213_V0.7781.00
177_D181_E0.7771.00
114_S117_R0.7711.00
41_F73_S0.7691.00
103_F108_V0.7681.00
50_L78_I0.7671.00
13_I103_F0.7651.00
139_L160_S0.7591.00
133_E136_G0.7591.00
144_F161_K0.7561.00
53_I81_R0.7541.00
34_F38_L0.7451.00
86_D89_M0.7441.00
162_L166_L0.7421.00
42_L71_S0.7401.00
41_F46_P0.7401.00
97_D114_S0.7391.00
178_R181_E0.7341.00
54_N80_A0.7321.00
166_L170_G0.7281.00
78_I103_F0.7261.00
74_P122_E0.7251.00
200_T204_K0.7231.00
7_V63_W0.7211.00
85_M106_D0.7201.00
3_K47_D0.7201.00
91_I111_K0.7191.00
209_L212_P0.7171.00
15_G19_N0.7151.00
167_L170_G0.7151.00
217_A221_E0.7151.00
76_I97_D0.7131.00
74_P118_R0.7121.00
195_L199_I0.7071.00
34_F57_A0.7071.00
104_S107_I0.7041.00
192_D196_N0.7021.00
50_L112_I0.7011.00
116_I119_A0.6971.00
42_L66_Q0.6951.00
67_I75_I0.6941.00
38_L41_F0.6911.00
156_S205_K0.6901.00
90_A95_G0.6881.00
6_I18_Q0.6851.00
119_A123_Y0.6811.00
147_R150_D0.6811.00
197_V201_R0.6751.00
6_I30_V0.6741.00
168_E182_K0.6721.00
72_T122_E0.6691.00
106_D110_A0.6661.00
111_K115_Q0.6581.00
8_E55_L0.6581.00
84_E106_D0.6571.00
176_R192_D0.6571.00
165_V168_E0.6571.00
92_E110_A0.6561.00
41_F49_V0.6531.00
191_D194_T0.6531.00
14_R18_Q0.6521.00
194_T199_I0.6501.00
68_R74_P0.6491.00
20_Y109_L0.6401.00
50_L76_I0.6341.00
210_N213_V0.6341.00
10_S13_I0.6321.00
61_Y86_D0.6311.00
114_S119_A0.6281.00
137_V148_F0.6271.00
144_F160_S0.6271.00
87_Q104_S0.6251.00
16_L20_Y0.6231.00
198_Y202_L0.6201.00
204_K207_R0.6171.00
212_P215_I0.6141.00
136_G140_F0.6091.00
74_P116_I0.6041.00
68_R73_S0.6031.00
38_L70_H0.6031.00
136_G148_F0.6021.00
51_L55_L0.6021.00
22_E28_T0.5971.00
34_F55_L0.5961.00
85_M88_V0.5941.00
113_K117_R0.5911.00
134_Y138_Q0.5891.00
79_S87_Q0.5871.00
190_I195_L0.5851.00
203_R208_E0.5831.00
41_F63_W0.5831.00
207_R212_P0.5821.00
64_C68_R0.5811.00
67_I73_S0.5811.00
72_T121_G0.5761.00
10_S80_A0.5751.00
4_I21_L0.5741.00
134_Y167_L0.5741.00
132_V141_V0.5721.00
52_D101_K0.5721.00
13_I16_L0.5711.00
110_A113_K0.5681.00
53_I90_A0.5641.00
133_E137_V0.5641.00
161_K165_V0.5601.00
67_I71_S0.5601.00
68_R71_S0.5591.00
103_F107_I0.5591.00
80_A102_P0.5581.00
21_L26_Y0.5571.00
152_K217_A0.5561.00
9_D79_S0.5521.00
22_E27_Q0.5501.00
88_V91_I0.5471.00
166_L199_I0.5461.00
199_I202_L0.5461.00
4_I48_V0.5431.00
135_A138_Q0.5431.00
74_P119_A0.5411.00
169_R182_K0.5391.00
207_R210_N0.5361.00
51_L67_I0.5361.00
139_L146_L0.5351.00
20_Y24_Y0.5311.00
139_L164_E0.5301.00
26_Y116_I0.5291.00
213_V216_E0.5271.00
33_D55_L0.5261.00
199_I211_A0.5251.00
196_N199_I0.5231.00
7_V34_F0.5201.00
176_R180_M0.5181.00
190_I194_T0.5171.00
36_A57_A0.5151.00
209_L213_V0.5121.00
6_I14_R0.5111.00
82_S102_P0.5101.00
112_I116_I0.5051.00
148_F151_E0.5001.00
134_Y137_V0.5001.00
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  
1ys7A 2 0.9825 100 0.188 Contact Map
2gwrA 1 0.9651 100 0.192 Contact Map
3r0jA 2 0.9563 100 0.195 Contact Map
2oqrA 2 0.9825 100 0.197 Contact Map
4kfcA 2 0.9738 100 0.199 Contact Map
4b09A 2 0.917 100 0.209 Contact Map
1kgsA 1 0.952 100 0.21 Contact Map
2hqrA 2 0.9432 100 0.239 Contact Map
1p2fA 1 0.9345 100 0.242 Contact Map
3q9sA 1 0.917 100 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.

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