GREMLIN Database
LYSM - HTH-type transcriptional regulator LysM
UniProt: Q980W9 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 142 (133)
Sequences: 13503 (8671)
Seq/√Len: 751.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
16_I31_E2.9281.00
47_I55_F2.9181.00
94_V107_I2.6441.00
101_D133_N2.6191.00
72_Q131_G2.4281.00
25_Y43_I2.3711.00
111_T115_S2.2881.00
10_D42_R2.1781.00
16_I23_T2.0721.00
45_K49_Q2.0071.00
53_K60_E1.9961.00
74_T130_V1.9601.00
89_I122_E1.8841.00
78_P81_E1.8341.00
53_K58_E1.8201.00
89_I119_T1.7941.00
68_I96_Y1.7731.00
44_E48_R1.7551.00
9_S34_V1.7361.00
93_E109_R1.7241.00
66_R107_I1.6981.00
34_V38_A1.6821.00
16_I19_K1.6781.00
26_T30_K1.6321.00
23_T31_E1.5821.00
27_L30_K1.5791.00
115_S118_R1.5781.00
112_N115_S1.5341.00
13_I28_I1.5101.00
91_G115_S1.4851.00
25_Y40_R1.4811.00
85_K126_I1.4741.00
34_V39_I1.4601.00
70_M135_T1.4571.00
85_K88_K1.4531.00
117_N139_R1.4521.00
83_S87_A1.4361.00
82_I86_I1.4341.00
35_S38_A1.4171.00
26_T36_E1.4041.00
32_L39_I1.4041.00
22_R55_F1.3921.00
118_R121_D1.3501.00
80_P84_K1.3381.00
71_V106_V1.3251.00
72_Q101_D1.3041.00
83_S139_R1.2981.00
23_T28_I1.2581.00
17_L43_I1.2541.00
27_L31_E1.2521.00
70_M102_Y1.2521.00
8_E12_K1.2511.00
19_K31_E1.2481.00
9_S12_K1.2241.00
63_N111_T1.2041.00
91_G122_E1.2001.00
73_S82_I1.1901.00
72_Q130_V1.1811.00
24_P27_L1.1791.00
44_E47_I1.1761.00
7_D42_R1.1681.00
20_N31_E1.1581.00
69_V108_V1.1421.00
65_I113_I1.1411.00
70_M133_N1.1191.00
9_S32_L1.0671.00
98_T105_L1.0491.00
16_I28_I1.0491.00
54_R58_E1.0481.00
66_R109_R1.0411.00
25_Y29_A1.0271.00
15_E19_K1.0151.00
83_S104_I1.0091.00
95_V106_V0.9931.00
92_V108_V0.9931.00
12_K15_E0.9871.00
12_K16_I0.9771.00
23_T27_L0.9721.00
110_G115_S0.9701.00
29_A39_I0.9691.00
64_E112_N0.9661.00
81_E85_K0.9641.00
25_Y36_E0.9611.00
36_E40_R0.9561.00
84_K88_K0.9551.00
96_Y107_I0.9541.00
21_A55_F0.9491.00
68_I105_L0.9461.00
110_G119_T0.9391.00
108_V119_T0.9241.00
84_K87_A0.9131.00
29_A34_V0.9071.00
22_R47_I0.9041.00
40_R44_E0.9021.00
6_I11_L0.8991.00
110_G116_I0.8981.00
68_I107_I0.8691.00
46_L51_I0.8661.00
28_I43_I0.8361.00
26_T40_R0.8341.00
12_K32_L0.8331.00
92_V95_V0.8261.00
10_D45_K0.8051.00
11_L15_E0.8031.00
92_V106_V0.8021.00
68_I137_I0.7931.00
118_R122_E0.7801.00
79_T104_I0.7771.00
120_I134_S0.7731.00
28_I39_I0.7731.00
86_I95_V0.7681.00
82_I104_I0.7671.00
85_K89_I0.7611.00
80_P83_S0.7591.00
96_Y137_I0.7571.00
81_E84_K0.7561.00
101_D131_G0.7441.00
21_A27_L0.7431.00
114_T117_N0.7331.00
6_I51_I0.7311.00
71_V82_I0.7311.00
37_A41_K0.7261.00
74_T78_P0.7221.00
70_M105_L0.7141.00
7_D10_D0.7111.00
21_A57_I0.7081.00
13_I23_T0.7001.00
20_N23_T0.6901.00
99_T136_I0.6871.00
74_T128_G0.6851.00
13_I39_I0.6661.00
70_M101_D0.6541.00
91_G119_T0.6511.00
124_R132_T0.6491.00
115_S119_T0.6441.00
71_V129_V0.6421.00
72_Q102_Y0.6381.00
21_A54_R0.6371.00
16_I20_N0.6351.00
97_E104_I0.6351.00
8_E11_L0.6341.00
67_A116_I0.6321.00
41_K44_E0.6311.00
13_I16_I0.6311.00
13_I42_R0.6311.00
75_P78_P0.6261.00
13_I46_L0.6211.00
42_R46_L0.6161.00
66_R137_I0.6131.00
102_Y133_N0.6121.00
120_I132_T0.6111.00
86_I106_V0.6041.00
113_I136_I0.5981.00
41_K45_K0.5971.00
63_N109_R0.5871.00
25_Y39_I0.5841.00
10_D46_L0.5741.00
18_K56_T0.5721.00
67_A134_S0.5711.00
80_P125_S0.5681.00
14_L46_L0.5631.00
91_G111_T0.5631.00
114_T139_R0.5631.00
37_A40_R0.5601.00
52_I55_F0.5591.00
114_T118_R0.5571.00
50_G53_K0.5551.00
89_I126_I0.5521.00
81_E128_G0.5501.00
113_I138_L0.5491.00
9_S38_A0.5471.00
85_K128_G0.5461.00
29_A36_E0.5441.00
72_Q133_N0.5441.00
32_L38_A0.5421.00
69_V132_T0.5421.00
11_L18_K0.5371.00
89_I92_V0.5321.00
132_T138_L0.5321.00
69_V106_V0.5311.00
13_I43_I0.5291.00
78_P128_G0.5251.00
66_R96_Y0.5231.00
67_A136_I0.5221.00
98_T137_I0.5211.00
101_D135_T0.5141.00
85_K127_Q0.5141.00
97_E103_D0.5141.00
93_E107_I0.5131.00
70_M98_T0.5111.00
81_E127_Q0.5091.00
119_T122_E0.5091.00
24_P29_A0.5091.00
64_E109_R0.5081.00
20_N27_L0.5081.00
115_S122_E0.5071.00
120_I138_L0.5051.00
26_T29_A0.5011.00
124_R131_G0.5011.00
87_A95_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  
4ch7A 1 0.9648 100 0.179 Contact Map
4un1B 1 0.9789 100 0.213 Contact Map
4un1A 1 0.9507 100 0.222 Contact Map
2ia0A 2 0.9437 99.9 0.223 Contact Map
2p5vA 5 1 99.9 0.23 Contact Map
2e1cA 1 0.9648 99.9 0.235 Contact Map
4pcqA 2 0.993 99.9 0.235 Contact Map
2cg4A 6 0.9789 99.9 0.236 Contact Map
2pn6A 5 0.9577 99.9 0.279 Contact Map
3i4pA 5 0.9577 99.9 0.279 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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