GREMLIN Database
YDDB - Uncharacterized protein YddB
UniProt: O31491 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 354 (293)
Sequences: 257 (199)
Seq/√Len: 11.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
272_F335_F3.5980.98
268_L272_F3.5520.98
320_V339_I3.5440.98
307_I314_F3.3000.97
176_Y333_E3.2460.97
276_A320_V3.1510.96
99_F241_K3.1260.96
285_Y345_Q3.0320.95
27_E30_E2.8840.94
271_F275_Y2.8730.94
278_E282_E2.8670.94
111_K264_I2.8560.94
276_A322_F2.7810.93
274_K282_E2.6800.91
265_E307_I2.6480.91
221_N224_D2.6070.90
287_M290_P2.3960.86
108_M215_L2.3450.84
272_F299_F2.3200.84
308_F347_Y2.2300.81
314_F339_I2.2210.81
109_N153_L2.2160.81
108_M151_R2.2060.81
305_V320_V2.1700.79
100_L170_F2.1610.79
323_K328_D2.1540.79
274_K287_M2.1420.78
172_Y235_T2.1420.78
54_S307_I2.1070.77
170_F219_V2.0830.76
302_V330_P2.0200.74
122_Q342_N1.9480.71
233_Y274_K1.9360.71
26_I33_K1.8940.69
264_I307_I1.8220.66
274_K333_E1.7890.64
73_L76_M1.7730.64
108_M339_I1.7550.63
127_Y264_I1.7000.60
45_A58_I1.6960.60
128_M244_I1.6950.60
233_Y283_M1.6590.58
99_F285_Y1.6210.57
274_K290_P1.6160.56
316_V337_L1.6040.56
272_F320_V1.5990.55
114_Q118_E1.5910.55
119_K351_L1.5850.55
100_L172_Y1.5840.55
30_E33_K1.5800.55
103_F107_Y1.5670.54
104_I172_Y1.5480.53
294_E349_N1.5300.52
280_K288_K1.5250.52
330_P339_I1.5220.52
111_K237_I1.5130.51
301_E321_R1.5060.51
47_T300_G1.4900.50
30_E34_Q1.4840.50
27_E33_K1.4800.50
283_M337_L1.4760.49
110_V151_R1.4630.49
41_S44_I1.4610.49
272_F322_F1.4560.48
58_I62_A1.4470.48
222_K299_F1.4430.48
231_V234_F1.4340.47
322_F335_F1.4300.47
264_I314_F1.4190.47
95_A335_F1.4160.46
97_E161_V1.4060.46
279_K300_G1.4010.46
156_Y320_V1.3790.45
109_N124_L1.3740.44
48_L66_S1.3660.44
110_V346_F1.3570.44
233_Y287_M1.3560.43
282_E290_P1.3540.43
161_V318_C1.3290.42
133_D351_L1.3270.42
82_K173_K1.3240.42
245_A269_Q1.3200.42
28_R31_K1.3110.41
110_V120_R1.2850.40
308_F343_S1.2750.40
98_N285_Y1.2730.40
27_E31_K1.2700.39
262_E329_I1.2620.39
216_N283_M1.2620.39
108_M331_V1.2590.39
45_A238_Y1.2490.38
122_Q175_T1.2470.38
159_Y285_Y1.2440.38
270_N285_Y1.2290.37
268_L299_F1.2220.37
251_E257_A1.2180.37
223_G299_F1.2100.37
107_Y320_V1.1990.36
100_L104_I1.1870.36
25_R30_E1.1820.35
274_K283_M1.1790.35
158_L172_Y1.1760.35
153_L156_Y1.1760.35
128_M333_E1.1720.35
26_I153_L1.1710.35
108_M139_E1.1650.35
217_I289_K1.1630.34
158_L283_M1.1580.34
172_Y176_Y1.1530.34
226_F316_V1.1450.34
170_F282_E1.1450.34
57_F62_A1.1290.33
91_I109_N1.1260.33
120_R316_V1.1230.33
322_F333_E1.1200.33
134_N217_I1.1200.33
281_E293_L1.1180.32
278_E281_E1.1170.32
25_R28_R1.1140.32
288_K347_Y1.1120.32
176_Y322_F1.1090.32
180_Y318_C1.1090.32
57_F162_K1.1080.32
106_E235_T1.1070.32
126_S177_E1.1040.32
104_I123_S1.0950.31
40_R43_L1.0820.31
48_L52_V1.0770.31
215_L348_V1.0760.31
60_L279_K1.0740.31
48_L150_D1.0730.31
151_R176_Y1.0630.30
38_R179_L1.0630.30
295_G324_E1.0630.30
162_K260_K1.0520.30
56_L217_I1.0500.30
272_F275_Y1.0480.30
151_R287_M1.0470.29
66_S99_F1.0420.29
108_M287_M1.0390.29
271_F348_V1.0370.29
174_V305_V1.0360.29
151_R171_Q1.0330.29
266_S269_Q1.0310.29
54_S346_F1.0240.29
150_D328_D1.0240.29
151_R290_P1.0230.28
304_S319_A1.0200.28
321_R330_P1.0140.28
122_Q312_K1.0090.28
92_S345_Q1.0050.28
92_S228_V1.0040.28
38_R42_K1.0040.28
268_L302_V1.0000.28
104_I160_N0.9980.27
270_N333_E0.9940.27
267_F283_M0.9910.27
176_Y267_F0.9910.27
82_K312_K0.9900.27
215_L308_F0.9860.27
133_D348_V0.9850.27
214_L235_T0.9760.27
64_L99_F0.9720.26
45_A102_G0.9600.26
146_G330_P0.9550.26
100_L297_L0.9550.26
122_Q269_Q0.9480.26
259_E343_S0.9450.25
107_Y232_P0.9420.25
239_D343_S0.9400.25
159_Y238_Y0.9330.25
285_Y324_E0.9310.25
101_S111_K0.9290.25
54_S125_E0.9260.25
59_C64_L0.9230.25
78_D99_F0.9220.25
148_K346_F0.9210.25
171_Q215_L0.9190.24
98_N278_E0.9180.24
114_Q313_G0.9180.24
309_E341_E0.9180.24
172_Y182_V0.9170.24
98_N241_K0.9170.24
233_Y290_P0.9150.24
182_V207_E0.9120.24
65_L335_F0.9100.24
179_L252_T0.9080.24
277_S294_E0.9070.24
234_F331_V0.8920.24
155_G217_I0.8880.23
111_K132_E0.8850.23
34_Q54_S0.8790.23
55_L251_E0.8690.23
183_E312_K0.8660.23
61_L300_G0.8620.22
281_E347_Y0.8580.22
100_L219_V0.8580.22
124_L262_E0.8570.22
36_V215_L0.8520.22
108_M231_V0.8510.22
169_L219_V0.8470.22
295_G313_G0.8420.22
172_Y333_E0.8360.22
123_S126_S0.8330.21
46_V113_D0.8330.21
238_Y345_Q0.8320.21
49_W285_Y0.8310.21
60_L318_C0.8300.21
45_A285_Y0.8290.21
222_K229_S0.8260.21
120_R124_L0.8250.21
72_Q262_E0.8230.21
127_Y278_E0.8220.21
241_K298_L0.8190.21
23_L27_E0.8180.21
303_Q321_R0.8160.21
67_I110_V0.8110.21
42_K46_V0.8080.21
44_I347_Y0.8070.21
267_F282_E0.8050.21
129_V228_V0.8050.21
95_A272_F0.8040.21
224_D311_K0.7980.20
106_E111_K0.7970.20
161_V302_V0.7960.20
268_L283_M0.7960.20
270_N282_E0.7930.20
53_G236_Q0.7860.20
63_V113_D0.7850.20
161_V320_V0.7840.20
229_S304_S0.7760.20
55_L149_G0.7740.20
100_L335_F0.7730.20
348_V351_L0.7730.20
340_T349_N0.7690.19
328_D348_V0.7670.19
37_P40_R0.7660.19
37_P110_V0.7660.19
260_K289_K0.7650.19
56_L94_T0.7650.19
270_N283_M0.7640.19
47_T114_Q0.7630.19
59_C100_L0.7620.19
181_P292_A0.7620.19
300_G323_K0.7570.19
47_T297_L0.7530.19
268_L322_F0.7510.19
56_L302_V0.7490.19
109_N281_E0.7480.19
67_I346_F0.7470.19
159_Y276_A0.7460.19
182_V228_V0.7430.19
273_E336_S0.7420.19
56_L104_I0.7420.19
100_L331_V0.7420.19
154_K177_E0.7410.19
124_L155_G0.7400.19
263_S341_E0.7330.18
66_S149_G0.7310.18
339_I344_G0.7300.18
70_R76_M0.7270.18
233_Y333_E0.7270.18
163_E234_F0.7260.18
53_G259_E0.7230.18
113_D208_K0.7230.18
170_F299_F0.7210.18
91_I154_K0.7210.18
96_A99_F0.7200.18
55_L238_Y0.7190.18
230_A286_M0.7190.18
35_K73_L0.7190.18
129_V227_A0.7120.18
151_R335_F0.7120.18
265_E305_V0.7090.18
108_M276_A0.7090.18
43_L174_V0.7090.18
82_K116_S0.7050.18
82_K257_A0.7040.17
111_K243_D0.7030.17
49_W307_I0.7020.17
125_E149_G0.6990.17
282_E333_E0.6920.17
55_L283_M0.6900.17
48_L62_A0.6890.17
62_A66_S0.6890.17
122_Q262_E0.6890.17
62_A272_F0.6860.17
48_L339_I0.6820.17
99_F226_F0.6820.17
171_Q214_L0.6750.17
60_L339_I0.6750.17
231_V323_K0.6720.17
269_Q309_E0.6710.17
164_G174_V0.6700.17
310_T340_T0.6680.16
82_K297_L0.6670.16
342_N347_Y0.6670.16
122_Q246_F0.6660.16
42_K234_F0.6660.16
102_G239_D0.6650.16
94_T121_M0.6650.16
151_R286_M0.6650.16
108_M283_M0.6620.16
74_N93_V0.6600.16
233_Y282_E0.6590.16
246_F302_V0.6590.16
333_E336_S0.6590.16
158_L286_M0.6540.16
221_N282_E0.6530.16
151_R234_F0.6520.16
100_L333_E0.6510.16
109_N157_S0.6500.16
36_V236_Q0.6490.16
278_E295_G0.6480.16
155_G230_A0.6470.16
60_L302_V0.6460.16
119_K217_I0.6460.16
37_P228_V0.6450.16
212_Q322_F0.6440.16
119_K169_L0.6440.16
314_F330_P0.6410.16
100_L217_I0.6390.16
103_F131_Q0.6390.16
92_S288_K0.6380.16
150_D327_N0.6380.16
120_R320_V0.6370.16
80_T156_Y0.6370.16
122_Q163_E0.6360.16
166_K207_E0.6350.16
119_K212_Q0.6340.16
118_E208_K0.6310.16
89_Q157_S0.6290.15
69_T73_L0.6290.15
304_S316_V0.6280.15
63_V73_L0.6270.15
287_M333_E0.6260.15
168_S228_V0.6260.15
23_L30_E0.6230.15
171_Q265_E0.6220.15
153_L233_Y0.6190.15
25_R40_R0.6180.15
127_Y305_V0.6180.15
224_D294_E0.6140.15
49_W219_V0.6120.15
90_K113_D0.6120.15
114_Q335_F0.6110.15
302_V316_V0.6110.15
49_W94_T0.6100.15
120_R267_F0.6100.15
304_S346_F0.6090.15
42_K64_L0.6070.15
124_L315_E0.6060.15
34_Q89_Q0.6020.15
221_N226_F0.5980.15
259_E269_Q0.5970.15
176_Y286_M0.5970.15
152_E291_E0.5970.15
75_D159_Y0.5960.15
112_N117_I0.5930.15
183_E256_Y0.5920.15
122_Q125_E0.5910.15
320_V348_V0.5910.15
104_I226_F0.5900.14
23_L34_Q0.5900.14
103_F232_P0.5870.14
101_S156_Y0.5860.14
122_Q165_D0.5840.14
243_D350_K0.5830.14
70_R110_V0.5830.14
151_R278_E0.5820.14
127_Y315_E0.5800.14
162_K261_K0.5790.14
97_E339_I0.5780.14
89_Q248_G0.5780.14
217_I227_A0.5750.14
124_L271_F0.5750.14
127_Y220_T0.5750.14
288_K301_E0.5700.14
172_Y347_Y0.5690.14
63_V152_E0.5670.14
50_S349_N0.5670.14
206_N337_L0.5670.14
151_R214_L0.5650.14
66_S110_V0.5650.14
108_M159_Y0.5640.14
46_V228_V0.5640.14
219_V331_V0.5630.14
263_S320_V0.5630.14
216_N343_S0.5620.14
99_F107_Y0.5600.14
177_E288_K0.5600.14
58_I69_T0.5580.14
41_S178_N0.5580.14
209_Y248_G0.5570.14
172_Y267_F0.5570.14
181_P257_A0.5570.14
169_L289_K0.5560.14
106_E123_S0.5540.14
162_K236_Q0.5500.14
233_Y348_V0.5490.14
99_F266_S0.5490.14
182_V298_L0.5470.13
75_D256_Y0.5460.13
285_Y347_Y0.5460.13
96_A129_V0.5450.13
96_A316_V0.5440.13
116_S303_Q0.5430.13
61_L81_N0.5420.13
273_E351_L0.5400.13
112_N150_D0.5370.13
107_Y158_L0.5370.13
131_Q265_E0.5360.13
182_V311_K0.5350.13
122_Q309_E0.5340.13
313_G339_I0.5300.13
241_K342_N0.5280.13
146_G178_N0.5260.13
47_T206_N0.5250.13
302_V339_I0.5220.13
35_K350_K0.5220.13
228_V239_D0.5210.13
58_I61_L0.5210.13
33_K121_M0.5200.13
98_N237_I0.5200.13
234_F333_E0.5200.13
175_T324_E0.5180.13
35_K266_S0.5180.13
66_S333_E0.5140.13
158_L227_A0.5110.13
164_G227_A0.5080.13
45_A335_F0.5070.13
280_K309_E0.5050.13
115_E312_K0.5040.12
34_Q247_K0.5030.12
58_I67_I0.5030.12
329_I346_F0.5020.12
142_F146_G0.5010.12
154_K237_I0.5010.12
163_E248_G0.5000.12
124_L336_S0.5000.12
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  
3ub1A 3 0.6667 100 0.487 Contact Map
4ec6A 3 0.3079 99.6 0.792 Contact Map
3k7cA 2 0.2401 75 0.947 Contact Map
1vqqA 1 0.2486 46.4 0.956 Contact Map
3kztA 2 0.2938 42.1 0.957 Contact Map
3b7cA 2 0.2599 39.9 0.957 Contact Map
3bb9A 2 0.2768 39.7 0.957 Contact Map
3f7sA 2 0.2797 35.5 0.958 Contact Map
4ovmA 2 0.2712 19 0.964 Contact Map
2rgqA 3 0.2853 16.8 0.965 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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