GREMLIN Database
YFMP - HTH-type transcriptional regulator YfmP
UniProt: O06474 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 140 (111)
Sequences: 12610 (8677)
Seq/√Len: 823.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
91_K101_Q3.7431.00
43_S46_D3.5641.00
94_K98_E3.1561.00
22_F26_I2.9101.00
18_R25_E2.7591.00
87_S105_N2.4401.00
17_K21_R2.2481.00
86_L89_D2.0481.00
57_K64_L2.0201.00
35_T41_L1.8811.00
7_D11_K1.8751.00
87_S91_K1.8331.00
101_Q105_N1.8321.00
93_R96_K1.7681.00
9_V47_M1.7241.00
54_I57_K1.6961.00
9_V50_L1.6511.00
98_E101_Q1.6261.00
4_M41_L1.6261.00
63_S66_E1.5531.00
26_I68_Q1.5461.00
94_K97_L1.4951.00
8_Q11_K1.4861.00
5_K41_L1.4781.00
49_E71_M1.4661.00
91_K105_N1.4231.00
81_K84_Y1.3861.00
6_I21_R1.3761.00
5_K8_Q1.3521.00
97_L101_Q1.3341.00
87_S108_L1.3201.00
9_V46_D1.3151.00
49_E75_R1.3071.00
28_L53_V1.2481.00
88_L92_E1.2311.00
95_E98_E1.2131.00
16_T19_T1.1971.00
23_Y50_L1.1811.00
87_S101_Q1.1801.00
94_K101_Q1.1791.00
92_E96_K1.1751.00
19_T22_F1.1581.00
26_I65_Q1.0891.00
13_S50_L1.0771.00
100_I103_T1.0701.00
5_K39_V1.0661.00
86_L93_R1.0331.00
93_R97_L1.0161.00
89_D93_R1.0141.00
108_L112_D1.0121.00
24_E30_P1.0091.00
98_E102_E1.0001.00
66_E86_L1.0001.00
96_K100_I0.9991.00
53_V67_L0.9931.00
94_K112_D0.9861.00
10_A17_K0.9861.00
91_K94_K0.9801.00
85_L88_L0.9761.00
86_L100_I0.9761.00
93_R100_I0.9641.00
24_E29_I0.9601.00
12_R47_M0.9591.00
33_K41_L0.9521.00
66_E69_H0.9461.00
90_P97_L0.9431.00
33_K43_S0.9371.00
32_P46_D0.9311.00
89_D92_E0.9271.00
61_G93_R0.9061.00
68_Q72_E0.9011.00
62_F70_F0.8991.00
13_S47_M0.8981.00
91_K95_E0.8961.00
65_Q68_Q0.8951.00
8_Q12_R0.8881.00
4_M12_R0.8881.00
20_I50_L0.8841.00
95_E99_E0.8831.00
54_I58_E0.8811.00
80_N84_Y0.8691.00
29_I53_V0.8631.00
105_N109_D0.8541.00
92_E95_E0.8471.00
20_I42_Y0.8471.00
79_L83_G0.8441.00
106_H110_L0.8321.00
102_E106_H0.8311.00
7_D17_K0.8311.00
50_L57_K0.8231.00
88_L91_K0.8051.00
4_M44_E0.7991.00
66_E85_L0.7891.00
52_K56_T0.7841.00
22_F64_L0.7811.00
58_E96_K0.7771.00
12_R44_E0.7741.00
111_I114_K0.7731.00
105_N108_L0.7681.00
77_L80_N0.7671.00
44_E48_E0.7651.00
29_I46_D0.7581.00
13_S20_I0.7471.00
47_M51_E0.7471.00
10_A20_I0.7361.00
20_I24_E0.7251.00
90_P100_I0.7191.00
99_E102_E0.7161.00
35_T39_V0.7111.00
12_R51_E0.7111.00
56_T62_F0.7091.00
80_N83_G0.7041.00
48_E51_E0.7021.00
30_P34_R0.7001.00
15_L54_I0.6801.00
76_Q79_L0.6571.00
99_E103_T0.6491.00
98_E108_L0.6471.00
6_I10_A0.6461.00
90_P94_K0.6391.00
33_K46_D0.6361.00
100_I111_I0.6311.00
69_H72_E0.6291.00
15_L50_L0.6241.00
24_E32_P0.6211.00
49_E72_E0.6171.00
45_D48_E0.6151.00
15_L19_T0.6151.00
103_T106_H0.6091.00
76_Q80_N0.6081.00
102_E105_N0.6061.00
106_H109_D0.6031.00
104_L108_L0.6031.00
76_Q81_K0.5971.00
96_K99_E0.5901.00
4_M47_M0.5851.00
51_E55_S0.5851.00
16_T22_F0.5821.00
37_G41_L0.5761.00
62_F66_E0.5751.00
26_I64_L0.5681.00
58_E103_T0.5671.00
22_F25_E0.5651.00
78_E81_K0.5631.00
64_L67_L0.5621.00
24_E42_Y0.5571.00
51_E54_I0.5541.00
34_R37_G0.5541.00
101_Q104_L0.5491.00
19_T57_K0.5461.00
104_L111_I0.5461.00
109_D113_E0.5401.00
46_D49_E0.5401.00
91_K98_E0.5381.00
90_P104_L0.5341.00
77_L84_Y0.5311.00
77_L82_E0.5281.00
18_R52_K0.5271.00
13_S23_Y0.5211.00
7_D10_A0.5161.00
90_P101_Q0.5161.00
104_L107_Q0.5111.00
60_L107_Q0.5061.00
9_V13_S0.5041.00
101_Q108_L0.5041.00
103_T107_Q0.5001.00
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  
3qaoA 2 0.95 99.9 0.229 Contact Map
3gp4A 4 0.9429 99.9 0.238 Contact Map
3gpvA 2 0.8286 99.9 0.256 Contact Map
3hh0A 4 0.9357 99.9 0.266 Contact Map
1q06A 2 0.8643 99.9 0.283 Contact Map
2dg6A 2 0.9071 99.9 0.289 Contact Map
2vz4A 2 0.7143 99.9 0.29 Contact Map
1r8dA 2 0.7786 99.9 0.29 Contact Map
4ua1A 2 0.8429 99.9 0.297 Contact Map
2zhgA 2 0.8286 99.9 0.302 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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