GREMLIN Database
YCBG - Uncharacterized HTH-type transcriptional regulator YcbG
UniProt: P42239 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 233 (200)
Sequences: 24143 (17978)
Seq/√Len: 1271.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
132_Q204_A3.6911.00
117_T212_H3.3231.00
207_D210_K2.9291.00
36_R39_D2.8201.00
139_A197_K2.8071.00
29_L34_Q2.7421.00
29_L50_I2.4001.00
110_A114_G2.3061.00
44_E55_R2.2681.00
130_R156_I2.1451.00
23_I64_S2.1231.00
103_A164_P2.0911.00
27_V68_L2.0911.00
72_T82_N2.0641.00
109_M220_K2.0251.00
22_V53_V1.9571.00
121_E208_P1.9461.00
106_E118_I1.9281.00
73_R79_T1.8681.00
202_A210_K1.7911.00
22_V51_L1.7831.00
127_E162_N1.7461.00
159_L167_E1.7341.00
128_L204_A1.7311.00
156_I159_L1.7241.00
124_N127_E1.7121.00
25_R29_L1.6831.00
135_I200_Y1.6531.00
113_L216_Y1.6351.00
16_K24_E1.6321.00
195_Y221_F1.6121.00
107_A169_M1.5771.00
113_L212_H1.5741.00
28_H32_S1.5711.00
117_T208_P1.5701.00
212_H216_Y1.5641.00
114_G117_T1.5311.00
210_K214_H1.5291.00
154_H196_H1.5081.00
201_D205_K1.4601.00
23_I68_L1.4491.00
198_K214_H1.4471.00
155_R171_Q1.4091.00
165_V176_T1.4021.00
74_K77_G1.3921.00
116_V211_A1.3921.00
168_G172_S1.3681.00
127_E160_S1.3651.00
139_A193_V1.3521.00
109_M216_Y1.3431.00
137_D149_A1.3401.00
205_K210_K1.3321.00
134_T149_A1.3301.00
158_A170_I1.3261.00
132_Q136_D1.3251.00
45_M49_D1.3151.00
123_I128_L1.3061.00
132_Q200_Y1.2991.00
46_E50_I1.2921.00
208_P212_H1.2881.00
40_K80_Y1.2791.00
197_K201_D1.2691.00
133_K137_D1.2651.00
109_M223_R1.2641.00
103_A165_V1.2341.00
109_M113_L1.2151.00
43_T46_E1.2071.00
134_T156_I1.2021.00
137_D152_E1.1991.00
108_R112_E1.1911.00
74_K80_Y1.1911.00
21_Q25_R1.1841.00
213_Y217_E1.1781.00
25_R28_H1.1781.00
195_Y218_H1.1621.00
102_P227_L1.1611.00
135_I197_K1.1511.00
25_R51_L1.1471.00
47_L58_L1.1461.00
123_I206_R1.1371.00
155_R159_L1.1311.00
35_L81_F1.1231.00
66_E73_R1.1141.00
216_Y220_K1.1081.00
152_E156_I1.1081.00
150_D154_H1.1071.00
123_I160_S1.1051.00
117_T209_Y1.1051.00
157_I203_L1.0951.00
210_K213_Y1.0931.00
29_L51_L1.0921.00
223_R227_L1.0741.00
102_P223_R1.0741.00
135_I138_I1.0701.00
200_Y204_A1.0671.00
123_I127_E1.0661.00
128_L200_Y1.0661.00
113_L117_T1.0651.00
72_T80_Y1.0651.00
201_D204_A1.0611.00
116_V215_M1.0601.00
196_H218_H1.0561.00
66_E71_I1.0491.00
60_E63_S1.0461.00
97_A100_N1.0431.00
44_E59_R1.0431.00
115_L158_A1.0261.00
130_R159_L1.0221.00
116_V120_A1.0191.00
103_A163_N1.0171.00
156_I160_S1.0161.00
134_T152_E1.0021.00
130_R133_K1.0011.00
128_L206_R0.9991.00
149_A152_E0.9931.00
132_Q197_K0.9891.00
106_E163_N0.9851.00
16_K21_Q0.9751.00
19_A64_S0.9711.00
169_M172_S0.9681.00
135_I139_A0.9661.00
145_H148_E0.9631.00
120_A208_P0.9601.00
202_A207_D0.9561.00
114_G212_H0.9481.00
198_K217_E0.9481.00
29_L35_L0.9471.00
198_K210_K0.9371.00
154_H218_H0.9371.00
129_Q133_K0.9331.00
136_D139_A0.9331.00
194_E198_K0.9321.00
161_A167_E0.9241.00
130_R134_T0.9231.00
118_I122_K0.9231.00
30_L81_F0.9161.00
148_E152_E0.9101.00
40_K78_G0.9091.00
62_L79_T0.9071.00
209_Y213_Y0.9061.00
27_V70_V0.9021.00
128_L132_Q0.8941.00
114_G118_I0.8931.00
198_K201_D0.8891.00
71_I79_T0.8871.00
18_L21_Q0.8851.00
153_F200_Y0.8831.00
77_G80_Y0.8791.00
120_A203_L0.8771.00
74_K78_G0.8751.00
64_S67_T0.8691.00
48_M58_L0.8681.00
167_E171_Q0.8671.00
27_V31_S0.8631.00
112_E154_H0.8571.00
209_Y212_H0.8561.00
134_T137_D0.8471.00
62_L71_I0.8451.00
107_A165_V0.8441.00
46_E49_D0.8391.00
137_D140_N0.8371.00
199_I215_M0.8361.00
63_S66_E0.8341.00
23_I27_V0.8341.00
54_S57_V0.8301.00
108_R219_L0.8261.00
100_N165_V0.8221.00
136_D140_N0.8221.00
122_K162_N0.8221.00
125_E129_Q0.8171.00
40_K43_T0.8161.00
123_I203_L0.8141.00
17_T20_K0.8121.00
20_K64_S0.8071.00
53_V58_L0.8031.00
141_S145_H0.8031.00
99_D162_N0.7961.00
47_L62_L0.7961.00
199_I214_H0.7901.00
193_V197_K0.7861.00
99_D103_A0.7831.00
132_Q201_D0.7771.00
120_A211_A0.7711.00
120_A206_R0.7691.00
127_E130_R0.7691.00
63_S73_R0.7661.00
106_E223_R0.7651.00
18_L57_V0.7641.00
220_K224_D0.7641.00
165_V169_M0.7631.00
190_D194_E0.7621.00
19_A23_I0.7551.00
138_I146_Y0.7531.00
165_V168_G0.7511.00
150_D196_H0.7501.00
119_A160_S0.7441.00
125_E206_R0.7411.00
131_L156_I0.7391.00
136_D197_K0.7341.00
118_I121_E0.7291.00
202_A214_H0.7261.00
106_E122_K0.7201.00
198_K202_A0.7181.00
117_T121_E0.7161.00
145_H149_A0.7101.00
16_K20_K0.7101.00
105_I222_V0.7071.00
64_S68_L0.7061.00
118_I163_N0.7051.00
140_N144_N0.6981.00
131_L200_Y0.6961.00
155_R174_L0.6961.00
214_H217_E0.6951.00
34_Q50_I0.6941.00
137_D145_H0.6911.00
130_R152_E0.6851.00
129_Q132_Q0.6821.00
217_E221_F0.6681.00
133_K136_D0.6671.00
213_Y216_Y0.6651.00
129_Q204_A0.6631.00
155_R167_E0.6621.00
139_A143_D0.6621.00
199_I211_A0.6611.00
107_A166_V0.6591.00
137_D141_S0.6581.00
221_F225_K0.6561.00
119_A123_I0.6481.00
199_I218_H0.6351.00
127_E159_L0.6351.00
135_I193_V0.6331.00
116_V208_P0.6331.00
151_K178_A0.6291.00
76_R79_T0.6281.00
127_E156_I0.6211.00
57_V61_A0.6161.00
151_K174_L0.6161.00
152_E155_R0.6151.00
107_A111_L0.6141.00
128_L203_L0.6131.00
109_M219_L0.6091.00
141_S149_A0.6081.00
220_K223_R0.6021.00
195_Y198_K0.5941.00
106_E114_G0.5941.00
35_L39_D0.5931.00
29_L33_G0.5901.00
100_N164_P0.5901.00
19_A60_E0.5881.00
146_Y192_T0.5801.00
125_E204_A0.5801.00
37_A83_D0.5791.00
115_L161_A0.5781.00
51_L58_L0.5771.00
63_S67_T0.5721.00
110_A166_V0.5681.00
224_D227_L0.5671.00
98_T102_P0.5631.00
138_I193_V0.5621.00
82_N179_K0.5551.00
15_R21_Q0.5551.00
107_A115_L0.5551.00
113_L208_P0.5541.00
131_L160_S0.5531.00
119_A161_A0.5531.00
112_E196_H0.5521.00
41_L71_I0.5511.00
113_L215_M0.5481.00
126_E130_R0.5471.00
111_L170_I0.5441.00
202_A208_P0.5431.00
38_G83_D0.5411.00
45_M48_M0.5411.00
168_G176_T0.5401.00
75_T78_G0.5381.00
187_R190_D0.5371.00
151_K155_R0.5351.00
117_T216_Y0.5331.00
115_L166_V0.5311.00
188_E225_K0.5301.00
188_E191_V0.5301.00
35_L41_L0.5281.00
141_S144_N0.5271.00
96_L179_K0.5271.00
150_D192_T0.5211.00
110_A113_L0.5181.00
49_D52_H0.5181.00
158_A174_L0.5171.00
217_E220_K0.5131.00
119_A157_I0.5111.00
140_N143_D0.5101.00
146_Y189_R0.5101.00
44_E79_T0.5091.00
26_I47_L0.5071.00
29_L32_S0.5071.00
107_A110_A0.5051.00
31_S70_V0.5051.00
211_A215_M0.5031.00
112_E219_L0.5021.00
99_D164_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  
3sxyA 2 0.8541 100 0.188 Contact Map
4p96A 2 0.9528 100 0.202 Contact Map
3c7jA 4 0.9442 100 0.207 Contact Map
3ihuA 1 0.8584 100 0.207 Contact Map
4p9fA 1 0.8712 100 0.213 Contact Map
2hs5A 1 0.8627 100 0.217 Contact Map
2di3A 2 0.927 100 0.218 Contact Map
1hw1A 2 0.9313 100 0.235 Contact Map
3ic7A 2 0.4764 99.9 0.524 Contact Map
3by6A 2 0.5322 99.9 0.528 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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