GREMLIN Database
YRBF - UPF0092 membrane protein YrbF
UniProt: O32052 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 89 (79)
Sequences: 2316 (1545)
Seq/√Len: 173.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
36_Q40_E2.7001.00
69_T75_L2.3321.00
34_V38_Q2.1031.00
33_A36_Q2.1021.00
12_I16_F2.0681.00
54_H78_D2.0591.00
19_L23_L2.0421.00
29_K33_A1.9511.00
18_V22_L1.8371.00
9_L13_I1.7951.00
66_V74_R1.7421.00
41_L82_I1.7221.00
36_Q39_E1.6811.00
35_R39_E1.6731.00
53_L75_L1.6591.00
70_G73_T1.5261.00
31_Q35_R1.5171.00
47_V67_I1.4871.00
46_S56_T1.4841.00
41_L57_V1.4651.00
50_I81_A1.4591.00
30_Q33_A1.4491.00
28_Q31_Q1.4311.00
14_L17_A1.3561.00
8_T12_I1.3551.00
53_L69_T1.3331.00
10_V14_L1.3101.00
6_L11_P1.2771.00
54_H64_K1.2771.00
7_G11_P1.2701.00
28_Q32_K1.2591.00
15_M19_L1.1801.00
16_F24_I1.1771.00
12_I15_M1.1591.00
66_V76_T1.1561.00
13_I17_A1.1471.00
6_L10_V1.1341.00
25_R29_K1.1261.00
69_T73_T1.1021.00
53_L77_F1.0771.00
65_V82_I1.0400.99
58_D74_R1.0260.99
7_G10_V1.0100.99
11_P14_L0.9990.99
60_I79_R0.9830.99
16_F19_L0.9810.99
64_K76_T0.9560.99
68_K71_D0.9430.99
56_T68_K0.9420.99
54_H59_S0.9280.99
50_I83_R0.9270.99
11_P15_M0.9260.99
55_G67_I0.9200.99
24_I28_Q0.9080.99
30_Q34_V0.8970.98
78_D81_A0.8960.98
27_Q31_Q0.8890.98
68_K74_R0.8770.98
42_K45_D0.8740.98
68_K72_N0.8390.98
31_Q34_V0.8390.98
12_I19_L0.8380.98
8_T11_P0.8130.97
23_L28_Q0.8040.97
67_I77_F0.8030.97
41_L60_I0.7900.97
25_R28_Q0.7860.96
49_T67_I0.7840.96
9_L12_I0.7720.96
48_V54_H0.7590.96
61_D76_T0.7450.95
49_T77_F0.7430.95
78_D84_E0.7360.95
37_M40_E0.7350.95
48_V84_E0.7340.95
14_L18_V0.7240.94
25_R33_A0.7120.94
61_D64_K0.7020.93
37_M83_R0.6790.92
70_G75_L0.6620.91
64_K78_D0.6590.91
43_K58_D0.6560.91
43_K59_S0.6480.90
58_D68_K0.6460.90
65_V79_R0.6440.90
71_D74_R0.6430.90
37_M46_S0.6400.90
14_L23_L0.6340.89
17_A21_F0.6320.89
54_H76_T0.6270.89
47_V82_I0.6190.88
37_M45_D0.6120.88
68_K76_T0.6080.87
34_V37_M0.6050.87
21_F25_R0.5990.87
20_Y66_V0.5960.86
51_G77_F0.5930.86
69_T77_F0.5890.86
70_G74_R0.5870.86
34_V50_I0.5810.85
46_S54_H0.5790.85
46_S78_D0.5770.85
12_I17_A0.5750.84
66_V71_D0.5750.84
8_T16_F0.5700.84
46_S64_K0.5550.82
57_V60_I0.5530.82
77_F81_A0.5420.81
65_V77_F0.5400.80
7_G12_I0.5340.80
7_G14_L0.5340.80
50_I80_R0.5250.79
18_V23_L0.5090.76
10_V20_Y0.5040.76
49_T53_L0.5040.76
49_T82_I0.5020.76
15_M18_V0.5010.75
15_M71_D0.5000.75
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  
2rddB 1 0.4157 99.3 0.603 Contact Map
4hczA 1 0.5843 67.4 0.882 Contact Map
1zq1A 2 0.6404 60.4 0.888 Contact Map
4hw9A 3 0.764 46.8 0.896 Contact Map
1dbgA 1 0.7191 39.1 0.901 Contact Map
5ajiA 3 0.764 39.1 0.901 Contact Map
3udcA 3 0.764 31.9 0.906 Contact Map
3lrxA 3 0.427 30.9 0.906 Contact Map
4l5gA 1 0.5955 30.6 0.906 Contact Map
1u1sA 3 0.6404 27.6 0.908 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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