GREMLIN Database
YIHD - Protein YihD
UniProt: P0ADP9 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11830
Length: 89 (88)
Sequences: 118 (39)
Seq/√Len: 4.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
20_E31_K3.4320.74
29_L38_F2.7660.56
69_Q72_Y2.5040.48
16_A28_F2.4960.48
33_A48_D2.4440.46
57_R68_L2.1560.38
14_Q80_L2.1480.38
41_E44_D2.1290.37
64_V72_Y1.9560.33
16_A58_D1.9180.32
4_K46_T1.8770.31
4_K36_S1.8760.31
6_L9_V1.8700.31
61_K82_R1.7740.28
30_Q43_A1.5780.24
40_G53_H1.5690.24
6_L21_P1.4460.21
6_L36_S1.4160.20
6_L30_Q1.4010.20
24_N40_G1.3970.20
9_V50_L1.3970.20
9_V80_L1.3960.20
19_K86_V1.3460.19
46_T56_M1.3120.19
10_I18_Q1.3100.18
10_I14_Q1.2930.18
12_L79_A1.2850.18
26_L43_A1.2840.18
21_P73_E1.2590.18
73_E78_T1.2490.17
7_N10_I1.2390.17
27_Q72_Y1.2280.17
19_K58_D1.2210.17
60_A86_V1.2160.17
40_G50_L1.2160.17
6_L14_Q1.1830.16
16_A72_Y1.1550.16
46_T53_H1.1490.16
30_Q34_K1.1370.16
50_L57_R1.1270.15
64_V82_R1.1210.15
28_F57_R1.0890.15
15_P53_H1.0620.14
64_V69_Q1.0600.14
4_K56_M1.0490.14
24_N44_D1.0110.14
8_E65_I1.0030.14
57_R82_R0.9980.14
44_D59_S0.9540.13
3_C31_K0.9490.13
10_I49_I0.9220.13
28_F38_F0.9080.12
7_N61_K0.9070.12
63_A69_Q0.8960.12
22_D74_E0.8940.12
30_Q58_D0.8910.12
60_A74_E0.8910.12
11_E19_K0.8840.12
3_C86_V0.8530.12
21_P78_T0.8530.12
21_P53_H0.8460.12
59_S63_A0.8450.12
14_Q82_R0.8230.11
2_K6_L0.8120.11
15_P40_G0.8080.11
32_L53_H0.8040.11
10_I21_P0.8040.11
32_L40_G0.8030.11
18_Q21_P0.8020.11
60_A63_A0.7980.11
14_Q88_K0.7820.11
4_K9_V0.7800.11
63_A74_E0.7650.11
15_P24_N0.7630.11
2_K69_Q0.7550.11
30_Q72_Y0.7510.10
41_E64_V0.7430.10
59_S74_E0.7330.10
41_E60_A0.7250.10
19_K53_H0.7240.10
14_Q18_Q0.7230.10
32_L57_R0.7170.10
9_V36_S0.7170.10
50_L77_K0.7150.10
33_A63_A0.7140.10
32_L35_E0.7130.10
16_A38_F0.7070.10
7_N39_D0.7000.10
6_L73_E0.6950.10
16_A34_K0.6880.10
2_K57_R0.6870.10
21_P64_V0.6820.10
49_I74_E0.6670.10
7_N53_H0.6630.10
69_Q74_E0.6610.10
42_L46_T0.6520.09
24_N53_H0.6500.09
16_A64_V0.6420.09
34_K43_A0.6380.09
10_I33_A0.6370.09
49_I61_K0.6370.09
36_S86_V0.6310.09
31_K82_R0.6300.09
16_A50_L0.6290.09
3_C26_L0.6280.09
44_D56_M0.6200.09
33_A44_D0.6170.09
30_Q88_K0.6160.09
18_Q38_F0.6050.09
69_Q88_K0.6000.09
2_K72_Y0.5990.09
26_L34_K0.5950.09
29_L49_I0.5940.09
45_L61_K0.5840.09
40_G57_R0.5790.09
2_K78_T0.5710.09
2_K73_E0.5670.09
26_L46_T0.5640.09
45_L49_I0.5590.09
53_H87_I0.5560.08
2_K74_E0.5520.08
2_K88_K0.5460.08
6_L13_L0.5460.08
38_F41_E0.5440.08
62_D74_E0.5320.08
9_V19_K0.5290.08
41_E59_S0.5280.08
34_K62_D0.5220.08
32_L42_L0.5190.08
78_T87_I0.5120.08
4_K44_D0.5020.08
19_K68_L0.5000.08
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  
2ko6A 1 1 100 0.011 Contact Map
2wyhA 2 0.8202 11.5 0.944 Contact Map
4mijA 1 0.3933 10 0.946 Contact Map
3bvxA 1 0.8202 9.7 0.946 Contact Map
1b6cB 3 0.4157 9.1 0.947 Contact Map
4x0mA 1 0.427 7.9 0.948 Contact Map
2c5uA 1 0.618 7.9 0.948 Contact Map
2qk7A 1 0.4157 7.6 0.949 Contact Map
1o7dC 1 0.4831 6.5 0.95 Contact Map
3askA 1 0.7191 5.4 0.952 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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