GREMLIN Database
YDHB - UPF0721 transmembrane protein YdhB
UniProt: O05493 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 245 (234)
Sequences: 9701 (6664)
Seq/√Len: 435.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
12_I219_F3.6811.00
80_G140_I3.6701.00
87_L144_V3.1531.00
66_Q171_H2.9191.00
4_I208_G2.6961.00
226_V230_S2.5481.00
54_S210_M2.5281.00
60_Y67_M2.5171.00
6_V28_L2.4711.00
227_V230_S2.4521.00
74_G182_P2.4351.00
109_I113_I2.4171.00
50_F206_L2.3481.00
45_L187_G2.3371.00
76_F136_V2.2871.00
70_G178_L2.2251.00
218_K222_L2.2241.00
168_S171_H2.1891.00
54_S214_Y2.1821.00
108_A240_G2.0741.00
82_F190_G2.0371.00
39_T42_G1.9831.00
69_I167_L1.9571.00
43_T202_L1.9281.00
101_A240_G1.9161.00
46_A202_L1.8761.00
224_P227_V1.8281.00
66_Q69_I1.8241.00
108_A237_A1.8221.00
59_H64_N1.7911.00
58_S217_A1.7491.00
8_F211_C1.7481.00
7_M205_V1.7371.00
10_L24_F1.7231.00
29_L205_V1.7151.00
102_G106_L1.7111.00
68_K71_L1.6731.00
105_F240_G1.6661.00
138_L160_G1.6651.00
108_A233_F1.6351.00
112_L233_F1.6301.00
8_F212_G1.6271.00
140_I144_V1.5971.00
59_H220_T1.5771.00
71_L75_G1.5681.00
237_A241_L1.5621.00
86_K90_F1.5241.00
12_I215_V1.5201.00
198_D201_L1.5181.00
62_E221_N1.5111.00
68_K72_I1.5101.00
192_I199_Y1.4971.00
70_G175_T1.4921.00
5_L9_L1.4651.00
53_L181_I1.4381.00
116_F119_K1.4321.00
95_L99_L1.4161.00
83_F140_I1.4111.00
56_A178_L1.4091.00
78_A186_G1.4051.00
230_S234_L1.3881.00
71_L74_G1.3791.00
203_V207_V1.3681.00
189_I193_T1.3661.00
81_S187_G1.3651.00
80_G84_G1.3551.00
64_N221_N1.3391.00
30_T37_I1.3371.00
200_V204_K1.3361.00
4_I204_K1.3341.00
207_V211_C1.3321.00
214_Y218_K1.3271.00
103_M149_F1.3231.00
49_A185_V1.3151.00
35_I201_L1.3061.00
39_T198_D1.3001.00
57_Y61_R1.2991.00
67_M71_L1.2971.00
55_G177_M1.2861.00
133_T137_I1.2761.00
101_A105_F1.2701.00
77_A183_L1.2561.00
135_A165_L1.2391.00
82_F86_K1.2381.00
212_G216_G1.2191.00
36_P39_T1.2041.00
7_M208_G1.1991.00
159_I162_M1.1971.00
64_N174_G1.1951.00
91_I148_T1.1941.00
111_I232_I1.1721.00
234_L238_I1.1721.00
67_M70_G1.1711.00
116_F120_E1.1681.00
76_F80_G1.1671.00
56_A60_Y1.1671.00
41_L191_Y1.1651.00
196_F200_V1.1481.00
208_G212_G1.1471.00
113_I116_F1.1451.00
42_G197_V1.1431.00
212_G215_V1.1371.00
59_H217_A1.1291.00
55_G213_A1.1141.00
17_I231_A1.1021.00
4_I207_V1.1001.00
80_G144_V1.0971.00
85_A187_G1.0881.00
131_T134_R1.0801.00
85_A190_G1.0781.00
190_G194_E1.0751.00
56_A181_I1.0711.00
76_F139_G1.0681.00
53_L57_Y1.0601.00
180_I183_L1.0551.00
56_A67_M1.0321.00
44_S48_M1.0291.00
133_T136_V1.0271.00
59_H174_G1.0231.00
153_S157_I1.0221.00
227_V231_A1.0111.00
170_R220_T1.0101.00
83_F86_K0.9911.00
162_M172_S0.9861.00
137_I141_A0.9831.00
4_I8_F0.9821.00
94_D98_Y0.9771.00
51_T209_T0.9741.00
26_I44_S0.9651.00
25_V205_V0.9631.00
156_F159_I0.9631.00
160_G164_M0.9601.00
58_S62_E0.9551.00
65_I175_T0.9551.00
22_A147_G0.9551.00
77_A179_V0.9481.00
73_V179_V0.9461.00
34_H40_A0.9441.00
60_Y65_I0.9351.00
58_S214_Y0.9241.00
218_K221_N0.9161.00
98_Y102_G0.9151.00
75_G79_V0.9061.00
169_I173_V0.9051.00
84_G144_V0.9041.00
10_L25_V0.9031.00
43_T197_V0.9011.00
95_L98_Y0.8951.00
3_I204_K0.8911.00
54_S213_A0.8891.00
114_R229_K0.8781.00
211_C214_Y0.8781.00
156_F160_G0.8761.00
49_A188_G0.8731.00
8_F208_G0.8711.00
109_I237_A0.8711.00
238_I241_L0.8701.00
159_I163_I0.8641.00
83_F144_V0.8561.00
203_V206_L0.8561.00
150_G153_S0.8511.00
232_I236_P0.8491.00
105_F237_A0.8431.00
93_A97_H0.8431.00
204_K208_G0.8411.00
134_R137_I0.8411.00
58_S218_K0.8341.00
223_M227_V0.8271.00
3_I201_L0.8271.00
86_K89_S0.8251.00
83_F87_L0.8031.00
114_R117_I0.8001.00
76_F79_V0.7971.00
106_L110_L0.7961.00
11_G21_G0.7931.00
146_S153_S0.7921.00
15_G55_G0.7891.00
54_S58_S0.7881.00
92_P95_L0.7871.00
105_F109_I0.7831.00
39_T43_T0.7831.00
70_G179_V0.7821.00
88_T191_Y0.7811.00
213_A217_A0.7791.00
14_L22_A0.7791.00
30_T40_A0.7771.00
3_I205_V0.7741.00
162_M169_I0.7741.00
191_Y196_F0.7711.00
128_T131_T0.7701.00
10_L28_L0.7691.00
42_G188_G0.7691.00
146_S183_L0.7681.00
62_E218_K0.7671.00
87_L90_F0.7661.00
142_A153_S0.7661.00
94_D97_H0.7581.00
65_I70_G0.7561.00
139_G143_G0.7551.00
142_A157_I0.7531.00
52_S150_G0.7521.00
14_L24_F0.7501.00
50_F210_M0.7461.00
16_F216_G0.7461.00
108_A236_P0.7381.00
35_I39_T0.7371.00
177_M180_I0.7361.00
220_T228_L0.7341.00
178_L182_P0.7291.00
79_V83_F0.7271.00
52_S180_I0.7261.00
67_M178_L0.7261.00
7_M11_G0.7241.00
14_L146_S0.7241.00
60_Y63_G0.7231.00
22_A48_M0.7211.00
15_G217_A0.7191.00
169_I232_I0.7181.00
153_S159_I0.7171.00
8_F215_V0.7151.00
25_V29_L0.7151.00
99_L149_F0.7141.00
158_Q173_V0.7131.00
224_P228_L0.7121.00
47_G209_T0.7081.00
12_I212_G0.7041.00
57_Y60_Y0.7031.00
98_Y101_A0.7001.00
150_G176_T0.6981.00
81_S85_A0.6981.00
238_I242_L0.6961.00
85_A191_Y0.6931.00
45_L150_G0.6911.00
200_V203_V0.6911.00
158_Q172_S0.6901.00
16_F228_L0.6901.00
37_I41_L0.6821.00
137_I140_I0.6781.00
72_I132_Y0.6781.00
73_V139_G0.6771.00
46_A188_G0.6731.00
85_A186_G0.6701.00
58_S61_R0.6701.00
41_L45_L0.6691.00
89_S194_E0.6681.00
38_H96_L0.6661.00
202_L206_L0.6621.00
7_M25_V0.6621.00
215_V218_K0.6581.00
23_G104_L0.6581.00
100_T149_F0.6571.00
86_K190_G0.6520.99
45_L146_S0.6500.99
72_I75_G0.6500.99
43_T198_D0.6490.99
77_A157_I0.6470.99
35_I198_D0.6430.99
146_S151_I0.6420.99
48_M153_S0.6420.99
45_L48_M0.6410.99
188_G202_L0.6380.99
38_H42_G0.6360.99
64_N171_H0.6340.99
127_S131_T0.6320.99
188_G192_I0.6310.99
166_N172_S0.6220.99
153_S180_I0.6190.99
197_V202_L0.6180.99
210_M214_Y0.6160.99
7_M201_L0.6130.99
48_M52_S0.6130.99
91_I95_L0.6130.99
154_A213_A0.6130.99
108_A112_L0.6120.99
171_H174_G0.6110.99
66_Q71_L0.6110.99
4_I7_M0.6110.99
172_S176_T0.6100.99
48_M146_S0.6100.99
52_S181_I0.6100.99
16_F219_F0.6080.99
8_F12_I0.6040.99
159_I172_S0.5990.99
176_T180_I0.5970.99
68_K132_Y0.5950.99
53_L56_A0.5930.99
154_A176_T0.5910.99
41_L88_T0.5910.99
158_Q179_V0.5860.99
38_H88_T0.5830.99
129_L132_Y0.5800.99
31_L242_L0.5780.99
106_L109_I0.5780.99
16_F223_M0.5720.99
14_L51_T0.5720.99
25_V44_S0.5720.99
233_F237_A0.5710.99
37_I97_H0.5710.99
100_T243_L0.5710.99
105_F241_L0.5700.99
86_K194_E0.5670.99
13_I24_F0.5660.99
142_A156_F0.5660.99
48_M184_A0.5600.98
112_L230_S0.5570.98
93_A148_T0.5550.98
26_I100_T0.5550.98
4_I211_C0.5540.98
192_I197_V0.5520.98
82_F193_T0.5510.98
12_I16_F0.5490.98
132_Y136_V0.5490.98
21_G151_I0.5480.98
219_F223_M0.5450.98
79_V140_I0.5430.98
87_L91_I0.5430.98
129_L133_T0.5430.98
17_I235_T0.5430.98
81_S186_G0.5410.98
41_L96_L0.5410.98
48_M180_I0.5360.98
153_S176_T0.5350.98
219_F222_L0.5350.98
139_G157_I0.5340.98
8_F11_G0.5330.98
11_G209_T0.5330.98
170_R225_K0.5320.98
226_V229_K0.5280.98
17_I213_A0.5270.98
111_I233_F0.5230.98
14_L180_I0.5210.98
230_S233_F0.5200.97
46_A206_L0.5200.97
11_G15_G0.5190.97
157_I179_V0.5190.97
24_F27_A0.5190.97
38_H41_L0.5180.97
23_G149_F0.5160.97
126_Q131_T0.5130.97
37_I96_L0.5130.97
211_C215_V0.5130.97
74_G77_A0.5120.97
46_A199_Y0.5090.97
26_I40_A0.5070.97
52_S184_A0.5060.97
23_G156_F0.5040.97
35_I43_T0.5040.97
73_V161_L0.5040.97
156_F161_L0.5020.97
66_Q175_T0.5010.97
69_I171_H0.5000.97
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  
3o7qA 1 0.8653 85.3 0.895 Contact Map
2gfpA 2 0.8449 82.7 0.899 Contact Map
1pw4A 1 0.8408 80.5 0.901 Contact Map
3wdoA 1 0.8531 75 0.906 Contact Map
2cfqA 1 0.8531 74.7 0.906 Contact Map
4j05A 3 0.8408 61.6 0.914 Contact Map
4pypA 1 0.7837 53.8 0.918 Contact Map
4m64A 1 0.8612 44.5 0.922 Contact Map
4zw9A 1 0.8449 40.5 0.924 Contact Map
4xnjA 1 0.9633 38.7 0.925 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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