GREMLIN Database
YVDR - Uncharacterized membrane protein YvdR
UniProt: O06999 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 106 (102)
Sequences: 4275 (2968)
Seq/√Len: 293.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
89_S99_G2.9101.00
12_E41_L2.6841.00
48_Q51_I2.6341.00
5_L48_Q2.4071.00
75_L82_F2.3911.00
19_A34_V2.3121.00
2_A52_V2.2241.00
15_I38_G2.1191.00
71_S90_L2.0241.00
10_G65_I1.9461.00
73_V77_W1.9451.00
50_M58_A1.8131.00
53_L58_A1.8031.00
92_L96_G1.7921.00
30_W34_V1.7421.00
16_A38_G1.6031.00
91_C95_A1.5471.00
92_L95_A1.5231.00
36_T40_G1.5011.00
44_Y48_Q1.4971.00
15_I34_V1.4961.00
39_F43_F1.4871.00
84_L88_I1.4651.00
18_I22_Y1.4451.00
50_M55_A1.3771.00
26_T32_I1.3751.00
23_I32_I1.3621.00
23_I26_T1.3591.00
16_A39_F1.3561.00
89_S103_T1.3341.00
12_E38_G1.3341.00
14_I69_G1.2871.00
5_L45_C1.2821.00
20_M35_M1.2631.00
49_A58_A1.2591.00
18_I73_V1.2591.00
29_K32_I1.2551.00
89_S96_G1.2461.00
98_I102_L1.2401.00
93_I96_G1.2301.00
22_Y78_F1.2221.00
83_Q86_Q1.2161.00
90_L100_L1.1851.00
87_V91_C1.1781.00
3_W61_V1.1591.00
85_S103_T1.1441.00
15_I19_A1.1391.00
46_L58_A1.1381.00
67_S71_S1.1211.00
28_K31_P1.1071.00
81_R86_Q1.0991.00
30_W33_I1.0761.00
89_S93_I1.0701.00
85_S88_I1.0621.00
7_V65_I1.0511.00
86_Q100_L1.0481.00
82_F87_V1.0441.00
40_G44_Y1.0181.00
93_I97_V0.9771.00
57_V86_Q0.9621.00
29_K33_I0.9431.00
61_V65_I0.9431.00
21_K25_G0.9411.00
82_F86_Q0.9321.00
68_I90_L0.9181.00
72_A76_I0.9151.00
95_A99_G0.9151.00
24_D28_K0.8961.00
4_F8_I0.8941.00
55_A70_V0.8741.00
8_I45_C0.8681.00
68_I94_L0.8641.00
19_A22_Y0.8571.00
84_L87_V0.8451.00
27_R32_I0.8441.00
89_S92_L0.8431.00
56_G60_A0.8341.00
2_A53_L0.8261.00
7_V10_G0.8241.00
74_G80_E0.8241.00
73_V78_F0.8171.00
80_E86_Q0.8141.00
81_R84_L0.8121.00
17_A70_V0.7890.99
60_A63_T0.7870.99
10_G42_S0.7830.99
94_L98_I0.7810.99
74_G78_F0.7730.99
27_R51_I0.7560.99
33_I37_V0.7530.99
67_S94_L0.7510.99
64_G97_V0.7500.99
14_I73_V0.7480.99
18_I78_F0.7320.99
24_D27_R0.7280.99
92_L99_G0.7100.99
19_A38_G0.7080.99
19_A35_M0.6990.99
99_G103_T0.6980.99
55_A78_F0.6970.99
27_R31_P0.6930.99
63_T74_G0.6860.98
9_A45_C0.6850.98
88_I92_L0.6850.98
71_S100_L0.6830.98
85_S89_S0.6750.98
54_P57_V0.6710.98
2_A5_L0.6670.98
16_A35_M0.6620.98
76_I79_K0.6600.98
11_I69_G0.6550.98
25_G31_P0.6520.98
13_E42_S0.6490.98
75_L81_R0.6370.97
37_V41_L0.6340.97
33_I36_T0.6280.97
65_I69_G0.6260.97
75_L87_V0.6120.97
57_V60_A0.6030.97
21_K24_D0.6000.96
74_G86_Q0.5980.96
10_G97_V0.5900.96
39_F63_T0.5880.96
26_T31_P0.5860.96
19_A23_I0.5850.96
23_I27_R0.5830.96
48_Q52_V0.5810.96
39_F55_A0.5810.96
60_A90_L0.5800.96
11_I15_I0.5790.96
43_F50_M0.5760.96
18_I55_A0.5730.95
18_I74_G0.5690.95
9_A46_L0.5640.95
32_I35_M0.5630.95
20_M62_W0.5510.94
34_V38_G0.5490.94
6_L58_A0.5490.94
43_F47_S0.5430.94
5_L49_A0.5430.94
16_A63_T0.5300.93
80_E83_Q0.5250.93
19_A36_T0.5240.93
41_L45_C0.5200.92
32_I47_S0.5180.92
38_G42_S0.5170.92
20_M42_S0.5130.92
26_T35_M0.5120.92
88_I91_C0.5090.92
63_T101_R0.5050.91
2_A49_A0.5040.91
26_T29_K0.5020.91
37_V40_G0.5000.91
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  
3b5dA 2 0.9623 99.9 0.317 Contact Map
2i68A 2 0.7358 99.9 0.358 Contact Map
4pypA 1 1 3.3 0.94 Contact Map
4gx0A 3 0.7547 2.4 0.944 Contact Map
2ls4A 1 0.2264 1.9 0.947 Contact Map
3rqwA 4 0.4717 1.9 0.947 Contact Map
3effK 4 0.7736 1.9 0.947 Contact Map
4uisB 1 0.3868 1.8 0.948 Contact Map
4o9uB 2 0.6981 1.8 0.948 Contact Map
4j05A 3 0.9811 1.7 0.949 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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