GREMLIN Database
YSMB - Uncharacterized HTH-type transcriptional regulator YsmB
UniProt: P97247 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 146 (131)
Sequences: 24429 (17908)
Seq/√Len: 1564.6

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_V97_H3.1391.00
128_E138_K2.8751.00
83_E97_H2.6231.00
54_T93_V2.5391.00
87_D95_R2.4901.00
52_D97_H2.4701.00
125_T128_E2.3801.00
131_I134_K2.1991.00
131_I135_S2.0781.00
86_K94_V2.0491.00
48_Y106_I2.0191.00
40_Q79_N1.9911.00
124_F135_S1.9271.00
54_T57_E1.8951.00
87_D93_V1.8831.00
48_Y98_L1.8231.00
128_E131_I1.7571.00
77_Q84_R1.6521.00
15_S137_M1.6371.00
80_E101_E1.6271.00
55_I73_I1.6071.00
132_F135_S1.6011.00
101_E105_I1.5731.00
40_Q75_R1.5631.00
128_E134_K1.5581.00
50_L61_K1.5151.00
73_I96_I1.5131.00
43_G72_L1.5011.00
37_T40_Q1.4531.00
74_D78_K1.4431.00
101_E104_R1.4261.00
48_Y103_E1.4021.00
105_I108_E1.4001.00
135_S138_K1.3961.00
46_W61_K1.2931.00
57_E60_G1.2791.00
34_Y112_K1.2731.00
15_S140_Q1.2681.00
65_A68_T1.2451.00
15_S133_E1.2431.00
56_G66_C1.2231.00
134_K138_K1.2201.00
19_I140_Q1.2141.00
74_D91_R1.2091.00
43_G69_T1.2051.00
84_R94_V1.1951.00
55_I94_V1.1791.00
104_R108_E1.1551.00
56_G60_G1.1501.00
30_I112_K1.1441.00
34_Y108_E1.1431.00
64_L68_T1.1301.00
18_H140_Q1.0951.00
129_I133_E1.0591.00
55_I69_T1.0551.00
52_D95_R1.0501.00
133_E137_M1.0461.00
127_E131_I1.0301.00
28_R32_N1.0291.00
112_K115_E1.0241.00
33_Q112_K1.0241.00
67_S70_T1.0231.00
128_E135_S1.0151.00
55_I96_I1.0031.00
53_M57_E0.9981.00
57_E61_K0.9951.00
98_L102_G0.9901.00
55_I66_C0.9891.00
81_L105_I0.9881.00
74_D77_Q0.9831.00
70_T74_D0.9761.00
51_G103_E0.9751.00
83_E99_L0.9711.00
68_T71_D0.9631.00
100_P103_E0.9561.00
30_I115_E0.9501.00
39_P72_L0.9401.00
79_N101_E0.9381.00
117_L120_M0.9331.00
64_L69_T0.9321.00
53_M61_K0.9271.00
50_L53_M0.9241.00
65_A71_D0.9161.00
85_V95_R0.9151.00
86_K91_R0.9131.00
100_P104_R0.9101.00
22_I140_Q0.9101.00
34_Y109_V0.9071.00
124_F139_L0.9041.00
30_I119_D0.8961.00
47_L82_V0.8961.00
79_N105_I0.8931.00
19_I136_L0.8801.00
103_E107_Q0.8781.00
73_I82_V0.8751.00
41_F109_V0.8681.00
48_Y107_Q0.8641.00
17_R20_A0.8581.00
90_D93_V0.8561.00
35_A79_N0.8531.00
87_D90_D0.8381.00
81_L101_E0.8361.00
20_A24_K0.8351.00
126_D130_A0.8341.00
77_Q83_E0.8281.00
108_E112_K0.8221.00
48_Y110_I0.8171.00
17_R21_A0.8161.00
113_R117_L0.8141.00
115_E118_R0.8111.00
131_I138_K0.8051.00
71_D75_R0.7991.00
111_T115_E0.7981.00
28_R38_P0.7941.00
50_L57_E0.7921.00
52_D85_V0.7921.00
26_K116_Y0.7861.00
12_I133_E0.7811.00
46_W62_M0.7671.00
125_T129_I0.7651.00
71_D74_D0.7621.00
119_D122_E0.7481.00
42_V62_M0.7471.00
130_A133_E0.7461.00
121_F129_I0.7451.00
130_A134_K0.7441.00
43_G62_M0.7371.00
77_Q82_V0.7371.00
127_E130_A0.7341.00
43_G58_L0.7291.00
44_L106_I0.7291.00
88_P95_R0.7291.00
16_L20_A0.7281.00
74_D84_R0.7231.00
46_W53_M0.7221.00
46_W50_L0.7221.00
104_R107_Q0.7191.00
55_I70_T0.7161.00
39_P68_T0.7141.00
75_R78_K0.7121.00
30_I116_Y0.7081.00
73_I77_Q0.7061.00
59_S66_C0.7041.00
30_I33_Q0.7031.00
46_W58_L0.7021.00
111_T114_Q0.6981.00
21_A25_Q0.6941.00
116_Y119_D0.6941.00
51_G97_H0.6821.00
98_L103_E0.6771.00
24_K28_R0.6691.00
59_S69_T0.6681.00
75_R79_N0.6681.00
47_L53_M0.6661.00
115_E119_D0.6651.00
137_M141_H0.6631.00
26_K119_D0.6591.00
19_I139_L0.6591.00
124_F129_I0.6561.00
41_F113_R0.6541.00
69_T73_I0.6491.00
114_Q118_R0.6301.00
47_L98_L0.6251.00
24_K27_G0.6241.00
108_E111_T0.6231.00
45_Q49_E0.6091.00
26_K29_E0.6061.00
134_K137_M0.5871.00
76_M81_L0.5841.00
15_S18_H0.5831.00
44_L48_Y0.5791.00
42_V46_W0.5751.00
29_E32_N0.5681.00
40_Q72_L0.5671.00
99_L102_G0.5601.00
41_F106_I0.5591.00
135_S139_L0.5551.00
45_Q110_I0.5511.00
80_E83_E0.5501.00
27_G30_I0.5471.00
11_D14_K0.5441.00
16_L19_I0.5381.00
16_L136_L0.5371.00
110_I114_Q0.5351.00
121_F125_T0.5301.00
23_I26_K0.5291.00
27_G113_R0.5261.00
106_I110_I0.5241.00
107_Q111_T0.5191.00
125_T138_K0.5191.00
85_V88_P0.5171.00
54_T87_D0.5131.00
39_P64_L0.5101.00
56_G59_S0.5091.00
124_F138_K0.5081.00
18_H22_I0.5001.00
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  
3cjnA 2 0.9589 99.9 0.235 Contact Map
3cdhA 4 0.9178 99.9 0.238 Contact Map
1z91A 2 0.9315 99.9 0.251 Contact Map
3deuA 2 0.8973 99.9 0.253 Contact Map
3jw4A 2 0.8904 99.9 0.253 Contact Map
3bj6A 2 0.9932 99.9 0.255 Contact Map
4rguA 4 0.9658 99.9 0.256 Contact Map
4yifA 2 0.9589 99.9 0.257 Contact Map
3e6mA 2 0.9863 99.9 0.258 Contact Map
3zplA 2 1 99.9 0.262 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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