GREMLIN Database
RIBD - Riboflavin biosynthesis protein RibD
UniProt: P17618 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 361 (350)
Sequences: 3021 (2300)
Seq/√Len: 122.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
8_L39_M4.2171.00
98_A130_A3.8831.00
85_E113_M3.7331.00
67_I87_I3.4491.00
112_S116_E3.3961.00
97_V111_I3.1631.00
242_F275_V3.0351.00
66_D96_F2.9501.00
99_M138_L2.8741.00
261_N282_E2.8491.00
127_A131_E2.8241.00
149_T186_H2.7581.00
131_E142_R2.6691.00
85_E89_N2.5941.00
178_D311_Y2.5301.00
63_E91_G2.5201.00
139_H306_Q2.4111.00
289_V299_F2.3851.00
44_K47_E2.3121.00
75_S84_A2.3081.00
88_I113_M2.2531.00
28_A67_I2.2421.00
94_R120_E2.2321.00
200_N230_K2.2081.00
21_E187_Q2.2041.00
215_V240_W2.1681.00
278_I282_E2.1521.00
67_I92_I2.1491.00
139_H143_T2.1451.00
5_Y36_I2.0721.00
135_E307_E2.0711.00
122_R125_I2.0411.00
172_S350_R1.9991.00
139_H145_L1.9461.00
272_I304_C1.9301.00
315_K339_L1.9251.00
193_V197_K1.9191.00
75_S109_R1.9181.00
278_I281_E1.9151.00
148_V276_L1.8991.00
182_Y288_Y1.8851.00
100_R111_I1.8231.00
30_V67_I1.7891.00
190_L295_V1.7751.00
154_A312_F1.7631.00
9_A70_T1.7581.00
188_S217_V1.7491.00
88_I119_I1.7481.00
299_F304_C1.7411.00
191_V291_G1.7381.00
202_S230_K1.7281.00
43_L53_H1.7271.00
242_F278_I1.7141.00
45_Y79_K1.7011.00
86_L90_S1.6991.00
55_I62_A1.6921.00
197_K224_S1.6921.00
342_F356_A1.6811.00
77_Y85_E1.6721.00
35_Q61_H1.6531.00
193_V225_I1.6451.00
112_S115_K1.6391.00
309_I353_K1.6211.00
315_K337_V1.6151.00
145_L277_K1.6111.00
17_E185_T1.6071.00
172_S175_A1.6041.00
94_R122_R1.5961.00
87_I92_I1.5671.00
344_D355_T1.5271.00
15_Q41_A1.5231.00
150_L296_H1.5201.00
155_S317_I1.5171.00
135_E147_Y1.5171.00
7_K126_L1.5131.00
204_T237_A1.5061.00
219_L295_V1.4951.00
194_G198_A1.4911.00
155_S315_K1.4901.00
276_L299_F1.4881.00
103_N141_M1.4861.00
169_W176_R1.4771.00
196_V231_V1.4741.00
172_S351_D1.4571.00
84_A113_M1.4461.00
215_V284_I1.4441.00
311_Y353_K1.4381.00
182_Y309_I1.4371.00
75_S113_M1.4301.00
166_D334_M1.4291.00
160_I293_S1.4111.00
307_E355_T1.3951.00
252_K256_S1.3941.00
174_A349_G1.3701.00
84_A88_I1.3581.00
48_A56_H1.3541.00
100_R123_E1.3341.00
191_V196_V1.3331.00
243_T262_I1.3321.00
178_D353_K1.3321.00
126_L129_Q1.3251.00
218_I231_V1.3181.00
223_L243_T1.3171.00
132_R135_E1.3111.00
171_T175_A1.3061.00
55_I86_L1.2961.00
166_D333_S1.2921.00
20_T45_Y1.2921.00
7_K129_Q1.2861.00
147_Y307_E1.2811.00
221_T244_T1.2801.00
38_G57_M1.2781.00
154_A325_L1.2761.00
193_V224_S1.2711.00
219_L275_V1.2641.00
77_Y81_P1.2581.00
266_E274_D1.2581.00
238_P261_N1.2551.00
58_A62_A1.2501.00
5_Y31_V1.2320.99
225_I241_I1.2260.99
138_L142_R1.2250.99
218_I225_I1.2240.99
140_F280_A1.2190.99
317_I334_M1.2160.99
190_L299_F1.2140.99
197_K226_P1.2070.99
244_T270_I1.2030.99
184_K205_C1.1930.99
340_L356_A1.1920.99
152_A310_F1.1860.99
99_M131_E1.1820.99
190_L219_L1.1800.99
220_D224_S1.1750.99
140_F285_M1.1740.99
124_G127_A1.1690.99
111_I123_E1.1640.99
252_K264_T1.1600.99
17_E25_L1.1580.99
178_D346_T1.1510.99
16_G19_Q1.1510.99
8_L36_I1.1400.99
37_V61_H1.1390.99
28_A87_I1.1340.99
37_V62_A1.1330.99
19_Q184_K1.1330.99
32_K61_H1.1280.99
150_L300_V1.1280.99
227_E254_R1.1100.99
149_T309_I1.1100.99
152_A296_H1.1100.99
242_F263_F1.1050.99
31_V68_Y1.1010.99
52_V56_H1.1000.99
166_D335_K1.0950.99
109_R113_M1.0930.99
48_A53_H1.0890.99
48_A52_V1.0880.99
197_K220_D1.0790.99
150_L305_F1.0780.99
157_D318_G1.0760.98
345_I352_I1.0530.98
16_G41_A1.0490.98
8_L11_D1.0490.98
342_F354_L1.0450.98
53_H56_H1.0450.98
57_M62_A1.0410.98
47_E53_H1.0350.98
14_K17_E1.0330.98
229_A232_I1.0330.98
32_K37_V1.0310.98
219_L270_I1.0300.98
76_H106_V1.0120.98
289_V295_V1.0090.98
196_V225_I1.0020.98
8_L12_L0.9980.98
42_H47_E0.9950.97
134_N138_L0.9940.97
97_V123_E0.9920.97
312_F354_L0.9890.97
39_M57_M0.9880.97
263_F278_I0.9880.97
66_D94_R0.9880.97
43_L47_E0.9870.97
52_V86_L0.9780.97
217_V279_L0.9660.97
59_G62_A0.9660.97
16_G20_T0.9640.97
25_L134_N0.9630.97
193_V232_I0.9630.97
113_M117_A0.9630.97
109_R112_S0.9600.97
186_H286_S0.9600.97
277_K281_E0.9570.97
284_I287_V0.9540.97
240_W282_E0.9530.97
154_A310_F0.9480.97
191_V218_I0.9470.97
55_I90_S0.9460.97
152_A325_L0.9430.97
136_K140_F0.9420.96
225_I232_I0.9410.96
216_R239_T0.9400.96
144_G280_A0.9360.96
12_L39_M0.9340.96
167_S176_R0.9320.96
150_L289_V0.9300.96
193_V220_D0.9260.96
10_L130_A0.9220.96
96_F125_I0.9220.96
96_F122_R0.9170.96
300_V326_I0.9160.96
25_L42_H0.9150.96
230_K233_C0.9150.96
231_V239_T0.9120.96
270_I275_V0.9100.96
30_V54_A0.9070.96
178_D182_Y0.9060.96
170_I334_M0.9050.96
143_T280_A0.9030.96
187_Q285_M0.9030.96
226_P229_A0.8980.95
3_E126_L0.8970.95
190_L287_V0.8960.95
14_K133_L0.8950.95
53_H57_M0.8890.95
99_M133_L0.8880.95
75_S88_I0.8830.95
232_I260_V0.8760.95
145_L273_P0.8730.95
190_L289_V0.8710.95
92_I95_V0.8610.94
161_A169_W0.8580.94
200_N228_D0.8570.94
196_V229_A0.8560.94
7_K11_D0.8560.94
156_L356_A0.8530.94
148_V289_V0.8520.94
30_V86_L0.8500.94
16_G42_H0.8490.94
347_Q352_I0.8490.94
38_G58_A0.8440.94
274_D278_I0.8430.94
178_D181_Q0.8400.93
38_G52_V0.8360.93
253_K257_A0.8350.93
244_T247_A0.8340.93
37_V57_M0.8340.93
193_V221_T0.8300.93
221_T270_I0.8290.93
321_H324_S0.8240.93
271_Q274_D0.8230.93
13_A133_L0.8210.93
84_A87_I0.8200.93
149_T286_S0.8180.93
13_A134_N0.8160.92
340_L354_L0.8150.92
246_R264_T0.8120.92
193_V226_P0.8120.92
297_G301_K0.8090.92
131_E138_L0.8060.92
12_L38_G0.8060.92
240_W263_F0.8020.92
178_D309_I0.7960.92
225_I255_L0.7960.92
225_I229_A0.7950.91
88_I117_A0.7940.91
115_K121_V0.7930.91
30_V92_I0.7900.91
310_F325_L0.7890.91
253_K256_S0.7880.91
194_G224_S0.7880.91
343_T355_T0.7840.91
32_K64_G0.7820.91
291_G296_H0.7810.91
76_H82_P0.7790.91
179_A334_M0.7780.91
42_H133_L0.7750.90
243_T247_A0.7750.90
159_K324_S0.7740.90
148_V287_V0.7720.90
106_V110_G0.7710.90
178_D348_I0.7690.90
52_V89_N0.7690.90
193_V255_L0.7680.90
233_C236_I0.7670.90
100_R127_A0.7640.90
346_T355_T0.7610.90
238_P282_E0.7610.90
295_V299_F0.7610.90
155_S162_T0.7570.89
145_L306_Q0.7560.89
102_P138_L0.7560.89
32_K65_A0.7540.89
161_A167_S0.7540.89
219_L242_F0.7530.89
162_T166_D0.7510.89
174_A350_R0.7500.89
136_K286_S0.7500.89
31_V65_A0.7480.89
37_V59_G0.7470.89
6_M124_G0.7470.89
255_L259_G0.7390.88
189_I213_Q0.7380.88
93_K120_E0.7380.88
12_L41_A0.7380.88
84_A109_R0.7380.88
99_M127_A0.7360.88
174_A177_Q0.7320.88
3_E7_K0.7300.88
333_S336_D0.7290.88
234_D237_A0.7290.88
324_S328_G0.7290.88
105_L141_M0.7280.87
225_I231_V0.7260.87
347_Q350_R0.7260.87
265_L274_D0.7250.87
348_I353_K0.7240.87
115_K123_E0.7230.87
319_G328_G0.7230.87
75_S85_E0.7200.87
188_S287_V0.7200.87
52_V81_P0.7190.87
123_E126_L0.7170.87
168_K334_M0.7170.87
11_D14_K0.7160.87
232_I239_T0.7140.86
30_V38_G0.7100.86
10_L98_A0.7090.86
176_R311_Y0.7010.85
97_V121_V0.6930.85
251_K255_L0.6920.85
105_L109_R0.6880.84
319_G330_G0.6850.84
149_T182_Y0.6820.84
225_I251_K0.6810.84
14_K129_Q0.6800.84
188_S284_I0.6800.84
345_I354_L0.6790.84
64_G93_K0.6790.84
316_L340_L0.6770.83
324_S327_S0.6760.83
240_W261_N0.6750.83
111_I115_K0.6740.83
172_S349_G0.6710.83
309_I355_T0.6700.83
195_T201_P0.6700.83
294_A298_S0.6680.83
60_A63_E0.6680.83
233_C237_A0.6670.82
173_E177_Q0.6640.82
10_L14_K0.6640.82
55_I87_I0.6620.82
233_C258_F0.6600.82
241_I255_L0.6600.82
42_H45_Y0.6590.82
296_H305_F0.6590.82
30_V62_A0.6580.82
104_P141_M0.6550.81
221_T269_R0.6540.81
272_I302_E0.6510.81
97_V115_K0.6500.81
67_I91_G0.6490.81
219_L299_F0.6490.81
162_T317_I0.6480.81
102_P142_R0.6470.81
175_A351_D0.6470.81
22_S45_Y0.6440.80
149_T307_E0.6440.80
12_L15_Q0.6430.80
75_S106_V0.6420.80
191_V203_L0.6410.80
59_G90_S0.6410.80
172_S348_I0.6410.80
136_K186_H0.6400.80
232_I255_L0.6400.80
25_L286_S0.6390.80
99_M123_E0.6390.80
66_D93_K0.6370.79
42_H53_H0.6360.79
339_L350_R0.6360.79
136_K285_M0.6350.79
21_E285_M0.6350.79
25_L133_L0.6340.79
159_K320_T0.6340.79
205_C213_Q0.6330.79
343_T356_A0.6330.79
67_I70_T0.6320.79
100_R115_K0.6310.79
186_H288_Y0.6290.79
200_N229_A0.6290.79
216_R237_A0.6270.78
182_Y186_H0.6230.78
272_I276_L0.6180.77
274_D277_K0.6180.77
289_V305_F0.6170.77
223_L247_A0.6160.77
97_V124_G0.6160.77
232_I258_F0.6140.77
99_M130_A0.6110.77
99_M134_N0.6110.77
269_R294_A0.6090.76
42_H134_N0.6080.76
180_Q205_C0.6060.76
111_I121_V0.6060.76
273_P302_E0.6060.76
234_D239_T0.6050.76
342_F352_I0.6030.76
6_M9_A0.6030.76
215_V238_P0.6030.76
175_A311_Y0.6020.76
346_T353_K0.5980.75
175_A178_D0.5960.75
16_G45_Y0.5950.75
272_I299_F0.5950.75
325_L328_G0.5940.75
182_Y311_Y0.5930.75
317_I331_F0.5920.74
193_V229_A0.5920.74
152_A308_I0.5900.74
175_A349_G0.5900.74
334_M337_V0.5890.74
216_R238_P0.5890.74
332_Q336_D0.5880.74
261_N264_T0.5860.74
202_S233_C0.5830.73
25_L136_K0.5800.73
293_S327_S0.5790.73
233_C239_T0.5780.73
21_E212_K0.5780.73
162_T331_F0.5780.73
23_N26_V0.5760.72
301_K329_E0.5720.72
243_T264_T0.5710.72
6_M125_I0.5700.72
266_E271_Q0.5690.71
244_T267_T0.5670.71
159_K319_G0.5660.71
205_C208_P0.5660.71
40_G53_H0.5650.71
256_S262_I0.5650.71
37_V58_A0.5640.71
98_A124_G0.5640.71
144_G277_K0.5640.71
137_F141_M0.5630.71
327_S330_G0.5610.70
95_V119_I0.5590.70
187_Q212_K0.5560.70
191_V201_P0.5550.70
245_A264_T0.5540.69
156_L312_F0.5530.69
317_I337_V0.5530.69
65_A92_I0.5520.69
166_D317_I0.5520.69
184_K213_Q0.5520.69
19_Q41_A0.5510.69
204_T216_R0.5500.69
244_T264_T0.5470.68
189_I208_P0.5470.68
175_A348_I0.5450.68
181_Q185_T0.5450.68
103_N107_A0.5440.68
77_Y82_P0.5430.68
171_T313_A0.5430.68
217_V275_V0.5430.68
162_T169_W0.5420.68
30_V52_V0.5410.68
344_D353_K0.5400.68
155_S170_I0.5390.67
162_T167_S0.5370.67
313_A351_D0.5370.67
220_D223_L0.5370.67
103_N106_V0.5350.67
196_V220_D0.5340.67
305_F308_I0.5320.66
128_D132_R0.5320.66
223_L251_K0.5310.66
187_Q286_S0.5300.66
190_L284_I0.5300.66
289_V296_H0.5290.66
195_T203_L0.5290.66
6_M70_T0.5290.66
9_A28_A0.5290.66
288_Y299_F0.5270.66
251_K254_R0.5270.66
190_L217_V0.5270.66
74_C83_C0.5250.65
170_I313_A0.5240.65
247_A255_L0.5240.65
86_L89_N0.5230.65
3_E125_I0.5230.65
272_I289_V0.5210.65
11_D36_I0.5200.65
272_I298_S0.5190.64
308_I356_A0.5190.64
310_F356_A0.5180.64
221_T267_T0.5170.64
16_G25_L0.5170.64
149_T288_Y0.5160.64
197_K225_I0.5160.64
342_F345_I0.5150.64
161_A168_K0.5150.64
217_V240_W0.5140.64
171_T179_A0.5140.64
204_T234_D0.5140.64
55_I92_I0.5130.64
156_L165_G0.5130.64
166_D170_I0.5120.63
92_I119_I0.5120.63
192_G299_F0.5110.63
192_G291_G0.5110.63
159_K317_I0.5110.63
242_F270_I0.5100.63
30_V55_I0.5100.63
84_A117_A0.5100.63
187_Q284_I0.5090.63
45_Y48_A0.5090.63
311_Y348_I0.5080.63
115_K122_R0.5070.63
188_S215_V0.5050.62
10_L70_T0.5030.62
317_I321_H0.5030.62
45_Y283_G0.5010.62
140_F283_G0.5010.62
252_K262_I0.5000.62
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  
2b3zA 3 0.9917 100 0.227 Contact Map
2g6vA 2 0.9584 100 0.24 Contact Map
3zpgA 2 0.9529 100 0.274 Contact Map
2hxvA 2 0.9446 100 0.279 Contact Map
2p4gA 2 0.6399 100 0.632 Contact Map
2aznA 2 0.5983 100 0.639 Contact Map
3g8qA 2 0.7673 100 0.643 Contact Map
4ha7A 2 0.5706 100 0.651 Contact Map
1z3aA 2 0.3823 100 0.717 Contact Map
2nx8A 2 0.4044 100 0.718 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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