GREMLIN Database
YRDA - Protein YrdA
UniProt: P0A9W9 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12838
Length: 184 (159)
Sequences: 5116 (3254)
Seq/√Len: 258.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
57_R86_D3.3881.00
66_L81_L3.1251.00
56_A85_E2.7381.00
103_R121_D2.6141.00
36_D57_R2.5681.00
136_L142_Y2.5501.00
35_D56_A2.5331.00
16_G35_D2.4381.00
86_D103_R2.4021.00
117_I135_R2.3891.00
125_G143_L2.3871.00
34_A56_A2.3721.00
101_G120_D2.3581.00
120_D138_S2.2851.00
79_N115_G2.2551.00
121_D139_G2.1331.00
102_N120_D2.0011.00
85_E102_N1.9941.00
32_R53_Q1.9831.00
84_G102_N1.9091.00
131_P134_K1.8381.00
101_G117_I1.7451.00
41_P175_Y1.7421.00
37_V85_E1.7151.00
14_Q32_R1.6991.00
30_D51_Y1.6651.00
119_E138_S1.6591.00
95_L98_C1.6461.00
11_L30_D1.6421.00
82_T99_T1.5991.00
99_T117_I1.5861.00
18_R36_D1.5851.00
154_S157_E1.5581.00
122_V140_Y1.5501.00
43_V64_S1.5451.00
139_G158_K1.5251.00
119_E135_R1.5221.00
128_S147_V1.5131.00
65_M92_K1.5011.00
24_S42_L1.4991.00
112_L116_A1.4851.00
92_K109_G1.4781.00
57_R169_V1.4441.00
22_D41_P1.4321.00
63_G92_K1.3591.00
55_G85_E1.3301.00
137_E149_Q1.3301.00
143_L150_I1.3291.00
33_L39_I1.2811.00
60_I64_S1.2811.00
124_I130_V1.2681.00
140_Y152_P1.2681.00
142_Y149_Q1.2521.00
119_E137_E1.2511.00
149_Q152_P1.2471.00
64_S93_V1.2461.00
137_E140_Y1.2441.00
122_V138_S1.2291.00
140_Y149_Q1.2071.00
27_V31_V1.2051.00
104_V138_S1.2011.00
42_L63_G1.1921.00
34_A53_Q1.1871.00
167_N172_K1.1671.00
151_R157_E1.1601.00
18_R35_D1.1471.00
15_I19_V1.1351.00
33_L37_V1.1331.00
124_I136_L1.1271.00
53_Q82_T1.1091.00
114_D132_Q1.1051.00
32_R51_Y1.1051.00
115_G133_N1.0671.00
60_I89_V1.0541.00
58_T102_N1.0481.00
121_D158_K1.0451.00
50_H78_G1.0361.00
104_V122_V1.0351.00
88_T164_S1.0271.00
26_V42_L1.0141.00
116_A130_V1.0131.00
163_Y166_N1.0111.00
58_T87_V0.9891.00
100_I106_V0.9711.00
106_V112_L0.9581.00
94_M108_M0.9521.00
171_W174_E0.9511.00
45_I52_V0.9431.00
17_Q35_D0.9321.00
130_V147_V0.9321.00
27_V33_L0.9231.00
166_N170_K0.9201.00
159_A162_R0.9191.00
31_V45_I0.9141.00
54_I58_T0.9011.00
111_I127_G0.8991.00
34_A85_E0.8911.00
127_G145_S0.8891.00
39_I45_I0.8891.00
21_I25_S0.8881.00
155_D158_K0.8831.00
122_V142_Y0.8821.00
24_S41_P0.8811.00
94_M109_G0.8771.00
100_I104_V0.8701.00
50_H80_P0.8641.00
129_L145_S0.8571.00
36_D173_D0.8500.99
81_L95_L0.8460.99
142_Y147_V0.8450.99
141_L153_L0.8360.99
163_Y167_N0.8350.99
106_V124_I0.8320.99
161_L164_S0.8240.99
104_V120_D0.8230.99
122_V136_L0.8160.99
44_V63_G0.8060.99
69_T114_D0.8040.99
16_G19_V0.7950.99
55_G82_T0.7900.99
84_G101_G0.7860.99
139_G155_D0.7780.99
49_V68_V0.7770.99
124_I142_Y0.7700.99
105_L123_M0.7590.99
89_V95_L0.7530.99
164_S168_Y0.7530.99
121_D162_R0.7520.99
37_V58_T0.7450.99
84_G99_T0.7420.99
128_S145_S0.7400.99
45_I54_I0.7350.98
58_T83_I0.7330.98
111_I129_L0.7210.98
51_Y80_P0.7170.98
137_E142_Y0.7150.98
139_G152_P0.7050.98
60_I66_L0.7030.98
153_L157_E0.7020.98
42_L92_K0.7010.98
51_Y82_T0.6980.98
19_V37_V0.6970.98
16_G34_A0.6910.98
15_I33_L0.6870.98
110_S128_S0.6860.98
170_K174_E0.6840.98
155_D159_A0.6800.97
11_L14_Q0.6790.97
170_K173_D0.6750.97
103_R162_R0.6730.97
50_H79_N0.6730.97
36_D56_A0.6720.97
113_L126_A0.6720.97
109_G127_G0.6710.97
55_G58_T0.6690.97
87_V100_I0.6680.97
58_T85_E0.6680.97
106_V110_S0.6670.97
18_R176_L0.6660.97
101_G122_V0.6640.97
101_G104_V0.6630.97
169_V172_K0.6630.97
101_G119_E0.6620.97
98_C116_A0.6600.97
162_R166_N0.6580.97
87_V102_N0.6560.97
166_N169_V0.6540.97
97_G114_D0.6540.97
172_K176_L0.6520.97
61_Q91_H0.6500.97
86_D162_R0.6490.97
68_V77_D0.6480.97
37_V56_A0.6480.97
113_L129_L0.6470.97
87_V104_V0.6430.96
113_L116_A0.6400.96
167_N170_K0.6360.96
173_D176_L0.6360.96
14_Q30_D0.6330.96
103_R120_D0.6330.96
167_N171_W0.6310.96
124_I147_V0.6230.96
57_R85_E0.6230.96
83_I87_V0.6220.96
159_A163_Y0.6210.96
136_L149_Q0.6150.95
37_V54_I0.6140.95
26_V44_V0.6130.95
101_G138_S0.6130.95
91_H108_M0.6050.95
68_V79_N0.6050.95
87_V120_D0.5890.94
31_V47_G0.5870.94
79_N97_G0.5850.94
86_D169_V0.5850.94
30_D53_Q0.5820.94
15_I27_V0.5780.94
20_M41_P0.5680.93
93_V110_S0.5670.93
34_A55_G0.5670.93
39_I43_V0.5670.93
119_E122_V0.5630.93
141_L151_R0.5620.93
137_E152_P0.5600.93
83_I95_L0.5600.93
169_V173_D0.5580.93
86_D166_N0.5570.92
136_L140_Y0.5510.92
110_S124_I0.5510.92
116_A134_K0.5500.92
64_S92_K0.5490.92
59_N88_T0.5410.91
98_C114_D0.5410.91
96_H114_D0.5390.91
66_L83_I0.5380.91
95_L100_I0.5360.91
160_G163_Y0.5340.91
153_L158_K0.5330.91
89_V106_V0.5280.90
144_G147_V0.5270.90
69_T77_D0.5270.90
45_I66_L0.5240.90
50_H69_T0.5230.90
49_V167_N0.5210.90
171_W175_Y0.5190.90
49_V69_T0.5190.90
67_H96_H0.5180.90
33_L54_I0.5170.89
36_D172_K0.5160.89
94_M111_I0.5140.89
19_V33_L0.5090.89
121_D138_S0.5060.88
164_S167_N0.5060.88
38_G172_K0.5060.88
83_I89_V0.5030.88
131_P147_V0.5020.88
116_A135_R0.5020.88
55_G102_N0.5000.88
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  
3r3rA 3 0.9783 100 0.296 Contact Map
1xhdA 3 0.9348 100 0.328 Contact Map
3r1wA 3 0.9837 100 0.333 Contact Map
3ixcA 3 0.8967 100 0.334 Contact Map
1v3wA 3 0.9402 100 0.348 Contact Map
4n27A 3 0.9348 100 0.36 Contact Map
4mfgA 3 0.913 100 0.365 Contact Map
3c8vA 3 0.8804 100 0.393 Contact Map
3tv0A 3 0.7609 100 0.397 Contact Map
4r36A 3 0.9891 100 0.404 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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