GREMLIN Database
YKOM - Uncharacterized HTH-type transcriptional regulator YkoM
UniProt: O34949 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 154 (133)
Sequences: 24153 (17854)
Seq/√Len: 1548.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
90_E102_H3.1131.00
133_E143_K2.9251.00
88_V102_H2.6611.00
59_K98_S2.5281.00
57_P102_H2.4951.00
92_D100_Y2.4641.00
130_S133_E2.3881.00
136_Q139_V2.1591.00
136_Q140_L2.0541.00
91_Q99_V2.0071.00
53_Y111_L1.9961.00
45_E84_N1.9741.00
59_K62_Q1.9011.00
92_D98_S1.8861.00
129_L140_L1.8471.00
133_E136_Q1.8061.00
53_Y103_L1.7771.00
128_G147_H1.7091.00
60_L78_I1.6441.00
82_E89_R1.6431.00
133_E139_V1.6311.00
106_K110_Y1.6071.00
20_V142_K1.5931.00
85_G106_K1.5931.00
45_E80_K1.5861.00
137_L140_L1.5701.00
78_I101_A1.5511.00
55_R66_R1.5351.00
42_N45_E1.4961.00
48_V77_V1.4751.00
110_Y113_K1.4601.00
79_D83_R1.4481.00
106_K109_E1.4461.00
140_L143_K1.4061.00
53_Y108_N1.3611.00
20_V145_G1.3131.00
70_V73_N1.2921.00
20_V138_I1.2831.00
62_Q65_S1.2831.00
51_L66_R1.2801.00
39_H117_I1.2751.00
60_L99_V1.2331.00
61_Q71_S1.2161.00
48_V74_V1.2111.00
139_V143_K1.2071.00
35_D117_I1.1911.00
109_E113_K1.1741.00
79_D96_K1.1551.00
24_A145_G1.1541.00
39_H113_K1.1491.00
61_Q65_S1.1431.00
69_L73_N1.1221.00
89_R99_V1.0971.00
38_E117_I1.0961.00
72_G75_T1.0901.00
132_D136_Q1.0861.00
33_I37_K1.0821.00
60_L74_V1.0701.00
133_E140_L1.0631.00
23_R145_G1.0381.00
134_Q138_I1.0381.00
86_F110_Y1.0271.00
60_L101_A1.0261.00
79_D82_E1.0241.00
60_L71_S1.0111.00
84_N106_K1.0061.00
105_D108_N1.0051.00
138_I142_K0.9961.00
57_P100_Y0.9831.00
75_T79_D0.9771.00
44_T77_V0.9671.00
58_Q62_Q0.9571.00
84_N110_Y0.9541.00
35_D124_R0.9531.00
117_I120_L0.9531.00
103_L107_G0.9521.00
62_Q66_R0.9461.00
105_D109_E0.9441.00
24_A141_L0.9421.00
88_V104_T0.9381.00
91_Q96_K0.9321.00
73_N76_Y0.9241.00
129_L144_A0.9241.00
78_I87_L0.9241.00
70_V76_Y0.9101.00
22_A25_F0.9101.00
69_L74_V0.8971.00
108_N112_D0.8961.00
58_Q66_R0.8941.00
56_G108_N0.8901.00
90_E100_Y0.8881.00
53_Y112_D0.8871.00
27_S145_G0.8741.00
17_L138_I0.8681.00
86_F106_K0.8631.00
33_I43_P0.8601.00
118_H122_I0.8591.00
55_R58_Q0.8561.00
82_E88_V0.8551.00
131_P135_D0.8521.00
35_D120_L0.8511.00
52_L87_L0.8491.00
116_P120_L0.8381.00
46_F114_I0.8371.00
122_I125_A0.8261.00
39_H114_I0.8251.00
40_G84_N0.8241.00
25_F29_S0.8201.00
113_K117_I0.8191.00
92_D95_D0.8081.00
47_A67_L0.7991.00
120_L124_R0.7961.00
76_Y80_K0.7921.00
93_P100_Y0.7871.00
95_D98_S0.7801.00
49_L111_L0.7791.00
136_Q143_K0.7771.00
56_G102_H0.7771.00
124_R127_S0.7771.00
76_Y79_D0.7761.00
22_A26_K0.7711.00
135_D139_V0.7681.00
121_R124_R0.7651.00
57_P90_E0.7641.00
53_Y115_Y0.7631.00
120_L123_A0.7601.00
48_V67_L0.7561.00
31_H121_R0.7441.00
35_D121_R0.7391.00
55_R62_Q0.7351.00
109_E112_D0.7351.00
51_L67_L0.7321.00
26_K30_E0.7321.00
82_E87_L0.7301.00
79_D89_R0.7261.00
116_P119_A0.7251.00
119_A123_A0.7241.00
78_I82_E0.7211.00
46_F118_H0.7211.00
130_S134_Q0.7161.00
103_L108_N0.7161.00
60_L75_T0.7161.00
48_V63_I0.7121.00
132_D135_D0.7111.00
142_K146_I0.7091.00
126_F134_Q0.7081.00
52_L58_Q0.7041.00
51_L58_Q0.7041.00
64_G71_S0.7021.00
51_L55_R0.6981.00
35_D38_E0.6981.00
135_D138_I0.6971.00
80_K83_R0.6971.00
44_T73_N0.6921.00
24_A144_A0.6911.00
80_K84_N0.6901.00
21_F25_F0.6831.00
51_L63_I0.6821.00
52_L103_L0.6761.00
29_S32_S0.6661.00
20_V23_R0.6511.00
64_G74_V0.6441.00
29_S33_I0.6391.00
31_H124_R0.6181.00
113_K116_P0.6181.00
31_H34_R0.6151.00
50_E54_T0.6131.00
46_F111_L0.6111.00
74_V78_I0.6001.00
45_E77_V0.5991.00
81_L86_F0.5951.00
143_K147_H0.5951.00
47_A51_L0.5891.00
104_T107_G0.5871.00
129_L134_Q0.5851.00
139_V142_K0.5851.00
21_F24_A0.5831.00
85_G88_V0.5781.00
140_L144_A0.5701.00
21_F141_L0.5661.00
140_L147_H0.5611.00
71_S75_T0.5541.00
50_E115_Y0.5501.00
32_S35_D0.5471.00
23_R27_S0.5451.00
112_D116_P0.5431.00
130_S143_K0.5421.00
49_L53_Y0.5411.00
111_L115_Y0.5371.00
59_K92_D0.5351.00
89_R101_A0.5341.00
34_R37_K0.5331.00
60_L98_S0.5291.00
32_S118_H0.5231.00
115_Y119_A0.5201.00
126_F130_S0.5181.00
129_L133_E0.5161.00
44_T69_L0.5081.00
59_K100_Y0.5061.00
123_A127_S0.5001.00
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 0.9351 99.9 0.271 Contact Map
2nyxA 2 0.961 99.9 0.271 Contact Map
2fbkA 2 0.9156 99.9 0.279 Contact Map
3cjnA 2 0.9351 99.9 0.28 Contact Map
3s2wA 3 0.9351 99.9 0.284 Contact Map
3e6mA 2 0.9545 99.9 0.287 Contact Map
3oopA 2 0.8896 99.9 0.288 Contact Map
3bj6A 2 0.9675 99.9 0.291 Contact Map
3u2rA 4 0.8571 99.9 0.294 Contact Map
3boqA 2 0.8831 99.9 0.296 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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