GREMLIN Database
BACH - Halorhodopsin
UniProt: P0DMH7 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 274 (225)
Sequences: 691 (493)
Seq/√Len: 32.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
72_V114_L6.7521.00
116_T141_D3.7901.00
39_L239_V3.7031.00
44_I70_P3.5671.00
41_G74_I3.5651.00
106_W110_L3.5621.00
79_G164_F3.3461.00
111_T115_S3.3201.00
111_T242_K3.2421.00
34_W81_L3.1711.00
165_Y169_C2.8641.00
147_T168_S2.7661.00
206_L240_F2.6471.00
143_G171_F2.5321.00
48_V67_L2.4410.99
97_L100_E2.4160.99
47_F246_A2.3150.99
43_A243_Y2.2490.99
144_M148_G2.1400.99
25_E227_V2.0540.98
70_P246_A2.0000.98
66_T246_A1.9700.98
140_A174_V1.8980.97
209_G213_V1.8810.97
116_T242_K1.8800.97
213_V233_A1.8550.96
151_A214_W1.8250.96
66_T122_A1.8180.96
41_G71_L1.7820.96
115_S242_K1.7390.95
73_S80_L1.7310.95
76_S80_L1.7170.95
128_D162_W1.7130.94
43_A47_F1.7070.94
116_T144_M1.7050.94
87_G153_M1.6740.94
33_L231_S1.6590.93
111_T116_T1.6330.93
147_T241_A1.6290.93
207_W242_K1.6290.93
65_A118_M1.6010.92
141_D144_M1.6010.92
26_N228_G1.5610.91
165_Y208_L1.5570.91
40_A73_S1.5530.91
148_G242_K1.4940.89
24_R103_R1.4590.88
78_L154_T1.4580.88
120_L141_D1.4390.87
44_I71_L1.4270.87
109_Y112_W1.4210.87
232_W236_V1.3720.85
215_A221_L1.3670.84
214_W220_G1.3600.84
113_A142_I1.3500.84
121_L138_I1.3340.83
162_W215_A1.3310.83
214_W230_T1.3260.83
147_T164_F1.3250.83
216_V233_A1.3190.82
219_E230_T1.3140.82
161_R166_A1.3130.82
73_S115_S1.2920.81
112_W148_G1.2780.80
115_S118_M1.2580.79
144_M175_V1.2460.78
107_G150_A1.2440.78
47_F70_P1.2380.78
46_V50_M1.2340.78
164_F226_S1.2070.76
167_I216_V1.2060.76
73_S242_K1.2010.76
66_T138_I1.1910.75
73_S211_P1.1820.75
86_V105_Q1.1770.74
172_F176_L1.1700.74
40_A148_G1.1650.74
41_G239_V1.1490.72
120_L148_G1.1390.72
37_V74_I1.1290.71
73_S111_T1.1280.71
202_L206_L1.1260.71
166_A228_G1.1250.71
116_T207_W1.1230.71
33_L173_V1.1160.70
39_L243_Y1.1150.70
42_I239_V1.0770.67
32_S36_N1.0740.67
215_A233_A1.0600.66
44_I74_I1.0590.66
115_S141_D1.0570.66
110_L180_V1.0520.66
115_S148_G1.0450.65
177_S181_T1.0400.65
153_M219_E1.0330.64
73_S144_M1.0260.64
36_N235_S1.0180.63
118_M151_A1.0080.62
164_F236_V0.9970.61
73_S122_A0.9910.61
209_G233_A0.9830.60
41_G196_F0.9800.60
71_L240_F0.9760.60
245_F250_L0.9760.60
108_R242_K0.9700.59
83_G105_Q0.9670.59
47_F66_T0.9550.58
154_T160_F0.9530.58
42_I173_V0.9530.58
116_T148_G0.9520.58
149_L156_S0.9500.58
66_T70_P0.9500.58
148_G245_F0.9450.57
145_C242_K0.9380.57
112_W211_P0.9380.57
69_I118_M0.9330.56
120_L129_V0.9250.56
120_L241_A0.9210.55
221_L229_V0.9200.55
76_S152_A0.9190.55
166_A170_A0.9180.55
109_Y117_P0.9170.55
149_L234_Y0.9140.55
188_S193_A0.9090.54
100_E205_V0.9080.54
43_A247_F0.9030.54
149_L153_M0.8950.53
137_V178_A0.8910.53
173_V180_V0.8830.52
213_V237_L0.8820.52
143_G167_I0.8810.52
128_D166_A0.8790.52
73_S119_I0.8770.52
36_N40_A0.8750.51
74_I78_L0.8730.51
194_E197_D0.8700.51
82_S219_E0.8640.50
37_V41_G0.8610.50
174_V178_A0.8610.50
180_V204_V0.8610.50
75_S143_G0.8600.50
172_F204_V0.8590.50
40_A177_S0.8580.50
129_V133_S0.8570.50
38_A75_S0.8560.50
176_L180_V0.8520.49
119_I122_A0.8360.48
166_A221_L0.8310.48
104_S152_A0.8310.48
167_I184_A0.8310.48
175_V178_A0.8300.48
89_I205_V0.8280.48
128_D204_V0.8280.48
48_V176_L0.8270.47
40_A243_Y0.8250.47
64_G130_D0.8180.47
84_L154_T0.8160.47
112_W117_P0.8140.46
34_W149_L0.8110.46
160_F163_A0.8110.46
144_M169_C0.8080.46
116_T145_C0.7980.45
78_L82_S0.7980.45
45_L71_L0.7960.45
47_F249_L0.7960.45
226_S229_V0.7950.45
170_A244_V0.7940.45
151_A165_Y0.7820.44
76_S127_A0.7790.43
69_I122_A0.7750.43
84_L160_F0.7720.43
242_K246_A0.7720.43
28_L229_V0.7720.43
62_I134_L0.7690.43
109_Y245_F0.7680.43
162_W165_Y0.7660.42
46_V137_V0.7630.42
156_S222_A0.7630.42
89_I96_A0.7620.42
214_W237_L0.7600.42
130_D151_A0.7550.42
147_T167_I0.7550.42
53_T56_P0.7530.41
174_V179_L0.7520.41
144_M207_W0.7500.41
137_V183_W0.7490.41
78_L162_W0.7470.41
127_A151_A0.7450.41
107_G114_L0.7440.41
145_C243_Y0.7420.40
78_L163_A0.7410.40
138_I236_V0.7400.40
156_S220_G0.7370.40
153_M161_R0.7280.39
112_W210_Y0.7270.39
73_S108_R0.7220.39
229_V233_A0.7200.39
202_L248_I0.7190.39
84_L102_V0.7180.39
172_F208_L0.7170.38
49_Y135_F0.7150.38
27_A95_H0.7070.38
252_W255_N0.7040.37
79_G256_N0.7040.37
76_S79_G0.7030.37
206_L241_A0.7030.37
127_A184_A0.7020.37
36_N75_S0.7020.37
78_L221_L0.7010.37
224_V229_V0.6980.37
156_S164_F0.6960.37
185_A244_V0.6940.37
185_A191_G0.6930.37
126_L253_V0.6910.36
175_V245_F0.6890.36
60_R86_V0.6870.36
61_L75_S0.6860.36
69_I119_I0.6850.36
203_T241_A0.6820.36
50_M135_F0.6820.36
138_I142_I0.6790.36
40_A111_T0.6790.36
36_N142_I0.6770.35
161_R219_E0.6740.35
201_V205_V0.6740.35
51_G71_L0.6720.35
165_Y168_S0.6710.35
153_M157_A0.6700.35
148_G211_P0.6700.35
124_G134_L0.6690.35
125_L128_D0.6660.35
115_S151_A0.6560.34
29_L227_V0.6530.34
224_V232_W0.6530.34
77_Y80_L0.6500.33
170_A229_V0.6500.33
87_G151_A0.6490.33
112_W145_C0.6490.33
85_T102_V0.6480.33
38_A74_I0.6440.33
123_L184_A0.6430.33
136_T178_A0.6430.33
221_L224_V0.6420.33
29_L153_M0.6420.33
81_L166_A0.6350.32
63_W250_L0.6320.32
60_R135_F0.6310.32
176_L199_L0.6280.32
219_E229_V0.6280.32
141_D241_A0.6280.32
144_M211_P0.6270.32
41_G203_T0.6270.32
45_L48_V0.6240.31
39_L145_C0.6240.31
134_L196_F0.6210.31
248_I251_R0.6200.31
114_L174_V0.6180.31
163_A215_A0.6110.31
42_I58_R0.6100.30
219_E222_A0.6100.30
195_I202_L0.6070.30
104_S224_V0.6030.30
152_A214_W0.6020.30
189_S192_T0.5950.29
86_V89_I0.5870.29
189_S193_A0.5840.29
108_R148_G0.5830.29
114_L236_V0.5820.29
122_A249_L0.5820.29
85_T230_T0.5800.28
138_I255_N0.5770.28
173_V208_L0.5770.28
69_I245_F0.5770.28
44_I169_C0.5750.28
103_R217_G0.5750.28
37_V78_L0.5730.28
216_V221_L0.5710.28
45_L133_S0.5710.28
102_V105_Q0.5660.27
153_M166_A0.5650.27
77_Y210_Y0.5650.27
135_F186_S0.5640.27
168_S199_L0.5640.27
32_S235_S0.5590.27
116_T206_L0.5580.27
135_F177_S0.5580.27
196_F200_R0.5570.27
123_L203_T0.5570.27
44_I66_T0.5560.27
27_A212_I0.5550.27
51_G179_L0.5550.27
131_L139_A0.5540.27
128_D183_W0.5530.27
73_S116_T0.5520.27
81_L237_L0.5500.26
139_A143_G0.5500.26
132_G136_T0.5490.26
83_G154_T0.5470.26
49_Y53_T0.5430.26
50_M181_T0.5430.26
48_V69_I0.5410.26
147_T171_F0.5400.26
65_A115_S0.5390.26
165_Y170_A0.5370.26
142_I215_A0.5370.26
41_G247_F0.5360.26
29_L103_R0.5360.26
71_L174_V0.5340.25
166_A169_C0.5320.25
47_F68_M0.5300.25
120_L134_L0.5280.25
226_S259_T0.5260.25
141_D242_K0.5250.25
31_S34_W0.5230.25
101_M255_N0.5200.25
87_G106_W0.5190.24
32_S221_L0.5170.24
53_T129_V0.5170.24
38_A113_A0.5130.24
40_A144_M0.5120.24
164_F168_S0.5120.24
96_A100_E0.5100.24
73_S241_A0.5090.24
175_V241_A0.5090.24
206_L212_I0.5080.24
114_L234_Y0.5070.24
151_A174_V0.5070.24
208_L212_I0.5060.24
116_T241_A0.5060.24
73_S207_W0.5050.24
195_I213_V0.5050.24
96_A204_V0.5050.24
148_G241_A0.5050.24
45_L63_W0.5020.23
146_V150_A0.5010.23
222_A230_T0.5000.23
144_M242_K0.5000.23
252_W256_N0.5000.23
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  
3wqjA 3 0.8467 100 0.259 Contact Map
2jafA 3 0.8759 100 0.265 Contact Map
1m0kA 3 0.8029 100 0.271 Contact Map
3qbgA 3 0.9124 100 0.273 Contact Map
4l35A 3 0.8577 100 0.278 Contact Map
3wt9A 1 0.8467 100 0.278 Contact Map
4fbzA 3 0.854 100 0.281 Contact Map
4qi1A 3 0.8212 100 0.282 Contact Map
3am6A 3 0.8102 100 0.291 Contact Map
3qapA 1 0.792 100 0.298 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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