GREMLIN Database
YMDE - Putative uncharacterized protein YmdE
UniProt: Q7DFV4 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG14357
Length: 107 (94)
Sequences: 5366 (4393)
Seq/√Len: 453.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
52_K55_E3.2561.00
45_L49_H2.8351.00
54_T58_D2.6351.00
9_R41_E2.3741.00
24_V38_I2.3731.00
27_N56_S2.3411.00
7_A11_Y2.2881.00
2_E48_T2.2711.00
12_L17_I2.1831.00
5_V44_S2.0141.00
4_G47_L1.9981.00
25_L32_S1.9441.00
57_L82_L1.9181.00
61_L86_A1.7911.00
5_V9_R1.6551.00
86_A93_V1.6091.00
28_V49_H1.5891.00
2_E44_S1.5771.00
9_R44_S1.5291.00
33_E38_I1.4831.00
27_N46_H1.4771.00
54_T85_F1.4641.00
41_E45_L1.4581.00
34_V37_S1.4061.00
25_L59_T1.3921.00
7_A10_D1.3781.00
93_V96_C1.3661.00
59_T63_M1.3541.00
37_S40_K1.3421.00
31_K59_T1.2831.00
33_E37_S1.2831.00
9_R13_A1.2811.00
25_L63_M1.2471.00
5_V41_E1.2421.00
25_L56_S1.2061.00
92_R95_H1.1931.00
57_L85_F1.1891.00
19_S35_A1.1841.00
29_T45_L1.1641.00
59_T62_N1.1631.00
53_W82_L1.1261.00
61_L69_F1.1231.00
8_M47_L1.1231.00
20_P35_A1.1111.00
10_D13_A1.0801.00
61_L87_G1.0601.00
19_S36_P1.0591.00
60_F66_P1.0531.00
4_G8_M1.0341.00
23_Q32_S1.0231.00
28_V46_H0.9921.00
6_Q44_S0.9491.00
6_Q9_R0.9361.00
69_F82_L0.9301.00
24_V33_E0.9201.00
32_S59_T0.9131.00
66_P69_F0.9081.00
6_Q10_D0.9021.00
31_K37_S0.8961.00
26_M29_T0.8961.00
11_Y14_G0.8781.00
32_S56_S0.8721.00
30_A56_S0.8611.00
2_E5_V0.8561.00
63_M66_P0.8531.00
5_V48_T0.8451.00
58_D85_F0.8371.00
92_R96_C0.8361.00
58_D61_L0.8361.00
71_E78_L0.8261.00
44_S47_L0.8201.00
62_N89_D0.8101.00
83_N87_G0.8051.00
58_D89_D0.8041.00
18_A21_E0.7961.00
80_N83_N0.7881.00
32_S63_M0.7821.00
76_P80_N0.7651.00
25_L60_F0.7611.00
61_L89_D0.7571.00
28_V45_L0.7461.00
50_T54_T0.7441.00
61_L88_V0.7401.00
61_L85_F0.7341.00
17_I39_I0.7331.00
8_M12_L0.7261.00
67_V91_Q0.7071.00
20_P38_I0.7001.00
58_D62_N0.7001.00
56_S59_T0.6861.00
19_S39_I0.6811.00
56_S60_F0.6801.00
82_L85_F0.6791.00
13_A41_E0.6781.00
87_G90_Q0.6751.00
4_G7_A0.6701.00
77_Y81_M0.6701.00
3_D6_Q0.6641.00
58_D88_V0.6601.00
64_P67_V0.6541.00
24_V42_N0.6511.00
24_V27_N0.6410.99
55_E58_D0.6350.99
12_L15_L0.6350.99
89_D93_V0.6350.99
8_M46_H0.6090.99
20_P36_P0.6080.99
87_G93_V0.6070.99
82_L86_A0.6060.99
28_V42_N0.5890.99
79_G95_H0.5840.99
27_N51_V0.5770.99
90_Q93_V0.5760.99
35_A38_I0.5710.99
37_S45_L0.5700.99
66_P75_K0.5680.99
29_T37_S0.5660.99
88_V92_R0.5640.99
57_L69_F0.5610.99
13_A17_I0.5580.99
10_D14_G0.5540.99
82_L93_V0.5450.98
50_T55_E0.5430.98
90_Q95_H0.5420.98
5_V45_L0.5370.98
43_L71_E0.5340.98
30_A55_E0.5340.98
27_N42_N0.5340.98
24_V37_S0.5300.98
12_L44_S0.5270.98
26_M42_N0.5230.98
79_G82_L0.5220.98
25_L66_P0.5200.98
91_Q94_M0.5200.98
61_L91_Q0.5180.98
60_F69_F0.5100.97
3_D74_N0.5050.97
61_L67_V0.5030.97
43_L53_W0.5020.97
51_V71_E0.5020.97
76_P79_G0.5000.97
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  
2qo3A 2 0.9907 99.9 0.242 Contact Map
4mz0A 2 0.9907 99.9 0.25 Contact Map
4rl1A 1 0.9626 99.9 0.254 Contact Map
2hg4A 2 0.9907 99.9 0.254 Contact Map
4qbuA 1 0.9907 99.9 0.28 Contact Map
3tzyA 1 0.9907 99.9 0.3 Contact Map
3sbmA 1 0.8131 99.9 0.301 Contact Map
4rr5A 1 0.9533 99.9 0.304 Contact Map
3ptwA 1 0.972 99.9 0.307 Contact Map
3g87A 1 0.8318 99.9 0.307 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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