GREMLIN Database
YDGG - Uncharacterized HTH-type transcriptional regulator YdgG
UniProt: P96705 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 152 (131)
Sequences: 24328 (17931)
Seq/√Len: 1566.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
85_D99_N3.0121.00
87_C91_S2.7801.00
130_H140_I2.7761.00
52_P99_N2.7021.00
87_C97_L2.5711.00
54_S95_S2.5641.00
83_Q99_N2.5471.00
127_D130_H2.3401.00
133_S136_E2.1711.00
133_S137_I2.1371.00
48_K108_L2.0111.00
86_D96_K2.0031.00
54_S57_S1.9671.00
40_Q79_K1.9011.00
48_K100_I1.8891.00
87_C95_S1.8571.00
125_D144_K1.8571.00
126_I137_I1.8461.00
130_H133_S1.6691.00
77_L84_W1.6571.00
80_G103_S1.6171.00
134_I137_I1.5641.00
103_S107_I1.5601.00
87_C90_K1.5341.00
55_P73_L1.5271.00
16_V139_T1.5051.00
50_K61_Y1.4741.00
43_L72_R1.4661.00
40_Q75_K1.4551.00
130_H136_E1.4181.00
103_S106_H1.4181.00
73_L98_I1.4131.00
74_K78_E1.4041.00
48_K105_E1.3991.00
37_S40_Q1.3791.00
52_P97_L1.3681.00
107_I110_E1.3671.00
16_V142_K1.3341.00
84_W96_K1.3211.00
46_I61_Y1.3151.00
137_I140_I1.2551.00
34_K114_A1.2471.00
16_V135_I1.2371.00
74_K93_R1.2171.00
136_E140_I1.1661.00
57_S60_M1.1571.00
43_L69_I1.1501.00
31_D114_A1.1431.00
56_G66_K1.1311.00
50_K53_T1.1281.00
65_H68_A1.1241.00
34_K110_E1.1051.00
130_H137_I1.0871.00
56_G60_M1.0871.00
19_E142_K1.0821.00
135_I139_T1.0731.00
106_H110_E1.0661.00
55_P96_K1.0581.00
131_L135_I1.0491.00
67_S70_S1.0431.00
52_P85_D1.0361.00
18_L21_T1.0291.00
20_G142_K1.0261.00
64_V68_A1.0211.00
55_P66_K1.0151.00
129_E133_S1.0101.00
53_T57_S0.9971.00
34_K111_L0.9891.00
55_P69_I0.9811.00
29_N33_F0.9771.00
81_L107_I0.9741.00
51_G105_E0.9681.00
39_E72_R0.9601.00
55_P98_I0.9541.00
70_S74_K0.9511.00
57_S61_Y0.9411.00
64_V69_I0.9391.00
68_A71_N0.9351.00
102_P105_E0.9331.00
53_T61_Y0.9231.00
85_D97_L0.9221.00
47_L82_V0.9151.00
83_Q101_T0.9101.00
133_S140_I0.9051.00
65_H71_N0.9051.00
100_I104_G0.8991.00
23_F142_K0.8961.00
102_P106_H0.8911.00
27_E118_A0.8911.00
114_A117_N0.8821.00
74_K77_L0.8811.00
79_K103_S0.8731.00
21_T25_H0.8701.00
35_H79_K0.8681.00
119_L122_L0.8671.00
105_E109_E0.8671.00
20_G138_F0.8621.00
128_E132_H0.8591.00
115_I119_L0.8551.00
48_K112_D0.8291.00
86_D93_R0.8251.00
51_G99_N0.8191.00
43_L58_L0.8091.00
81_L103_S0.8021.00
87_C92_D0.7981.00
13_F135_I0.7961.00
117_N120_K0.7941.00
100_I105_E0.7921.00
79_K107_I0.7921.00
113_S117_N0.7891.00
44_L108_L0.7881.00
42_D62_Q0.7821.00
90_K97_L0.7761.00
31_D117_N0.7741.00
73_L82_V0.7721.00
46_I62_Q0.7701.00
71_N74_K0.7601.00
92_D95_S0.7571.00
126_I141_L0.7571.00
50_K57_S0.7521.00
127_D131_L0.7511.00
75_K78_E0.7441.00
31_D121_P0.7361.00
59_A69_I0.7291.00
48_K109_E0.7281.00
77_L83_Q0.7281.00
46_I50_K0.7221.00
39_E68_A0.7201.00
41_A111_L0.7171.00
123_I131_L0.7131.00
121_P124_D0.7121.00
75_K79_K0.7121.00
55_P70_S0.7121.00
74_K84_W0.7081.00
18_L22_E0.7061.00
132_H135_I0.7021.00
139_T143_S0.7011.00
86_D90_K0.6941.00
71_N75_K0.6941.00
77_L82_V0.6921.00
113_S116_F0.6901.00
106_H109_E0.6771.00
73_L77_L0.6761.00
132_H136_E0.6761.00
25_H29_N0.6671.00
59_A66_K0.6631.00
69_I73_L0.6581.00
46_I58_L0.6581.00
22_E26_R0.6531.00
46_I53_T0.6531.00
110_E114_A0.6511.00
126_I131_L0.6511.00
129_E132_H0.6501.00
31_D118_A0.6471.00
17_L21_T0.6461.00
84_W98_I0.6441.00
117_N121_P0.6381.00
27_E30_Q0.6291.00
29_N38_R0.6281.00
17_L20_G0.6261.00
43_L62_Q0.6241.00
28_I31_D0.6221.00
20_G141_L0.6221.00
140_I144_K0.6131.00
45_K49_V0.6091.00
137_I144_K0.6051.00
47_L100_I0.6001.00
118_A121_P0.5881.00
112_D116_F0.5831.00
116_F120_K0.5811.00
16_V19_E0.5801.00
12_L135_I0.5781.00
47_L53_T0.5761.00
27_E121_P0.5741.00
41_A115_I0.5631.00
56_G59_A0.5541.00
108_L112_D0.5531.00
76_L81_L0.5531.00
42_D46_I0.5491.00
80_G83_Q0.5441.00
110_E113_S0.5421.00
45_K112_D0.5391.00
24_V27_E0.5391.00
25_H28_I0.5361.00
41_A108_L0.5271.00
139_T142_K0.5241.00
17_L138_F0.5221.00
123_I127_D0.5181.00
127_D140_I0.5171.00
58_L98_I0.5131.00
39_E64_V0.5121.00
28_I115_I0.5121.00
86_D92_D0.5091.00
115_I118_A0.5021.00
26_R30_Q0.5011.00
27_E31_D0.5001.00
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  
3cdhA 4 0.8816 99.9 0.29 Contact Map
3bj6A 2 0.9737 99.9 0.292 Contact Map
2rdpA 2 0.9145 99.9 0.292 Contact Map
2nnnA 2 0.8816 99.9 0.293 Contact Map
3boqA 2 0.8618 99.9 0.294 Contact Map
3cjnA 2 0.9211 99.9 0.297 Contact Map
3e6mA 2 0.9474 99.9 0.299 Contact Map
4yifA 2 0.9276 99.9 0.3 Contact Map
1s3jA 2 0.9408 99.9 0.3 Contact Map
3deuA 2 0.8553 99.9 0.3 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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