GREMLIN Database
YGAE - UPF0421 protein YgaE
UniProt: P71083 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 353 (293)
Sequences: 5726 (4607)
Seq/√Len: 269.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
17_A134_S3.1641.00
9_K139_N2.8521.00
262_Y266_W2.6931.00
13_A138_V2.6051.00
57_A61_G2.5291.00
28_A31_F2.4551.00
295_L299_F2.3871.00
13_A36_A2.2821.00
176_H179_L2.2761.00
267_H271_L2.2541.00
9_K138_V2.2161.00
12_I138_V2.1911.00
296_T299_F2.1591.00
54_Q124_R2.1301.00
17_A36_A2.1121.00
58_N124_R2.1041.00
14_I37_I2.0581.00
293_Q297_K2.0401.00
98_T103_L1.9641.00
9_K142_F1.9481.00
289_I295_L1.9141.00
183_I187_K1.9131.00
43_S46_R1.8621.00
16_L134_S1.8441.00
101_I104_V1.8311.00
298_S302_N1.8311.00
85_I89_I1.8281.00
86_V90_M1.8021.00
76_P79_I1.7971.00
35_A128_V1.7891.00
87_I91_L1.7201.00
81_L85_I1.6991.00
290_R294_L1.6961.00
58_N128_V1.6671.00
105_T110_L1.6621.00
20_L24_I1.6611.00
275_V279_K1.6591.00
173_S176_H1.6551.00
203_E207_F1.6531.00
31_F124_R1.6461.00
103_L106_V1.6311.00
229_N236_K1.6211.00
296_T300_L1.6181.00
257_T261_D1.6131.00
101_I109_I1.5921.00
264_L268_E1.5821.00
89_I93_L1.5681.00
102_A106_V1.5671.00
31_F58_N1.5601.00
101_I107_I1.5591.00
289_I293_Q1.5541.00
288_G295_L1.5531.00
137_I141_V1.5481.00
264_L271_L1.5471.00
20_L134_S1.5381.00
288_G291_Y1.5381.00
77_I81_L1.5221.00
139_N145_P1.5211.00
232_L236_K1.5131.00
124_R127_T1.5071.00
263_L271_L1.5041.00
18_L33_G1.5031.00
67_V71_I1.5031.00
122_L126_S1.4971.00
294_L298_S1.4911.00
268_E271_L1.4831.00
161_E189_K1.4781.00
295_L298_S1.4711.00
107_I111_E1.4631.00
11_G15_T1.4571.00
180_K183_I1.4541.00
105_T124_R1.4541.00
204_R207_F1.4491.00
233_D237_K1.4441.00
291_Y296_T1.4401.00
179_L183_I1.4381.00
121_A124_R1.4361.00
287_E295_L1.4311.00
50_I97_H1.4261.00
35_A39_A1.4191.00
291_Y295_L1.3981.00
100_S111_E1.3941.00
105_T109_I1.3681.00
54_Q57_A1.3601.00
88_T92_K1.3551.00
100_S103_L1.3431.00
108_A111_E1.3431.00
101_I105_T1.3391.00
295_L302_N1.3351.00
285_V288_G1.3341.00
98_T105_T1.3331.00
250_E254_E1.3291.00
255_T259_E1.3281.00
104_V110_L1.3221.00
86_V106_V1.3201.00
156_V163_M1.3191.00
31_F54_Q1.3181.00
61_G65_A1.3111.00
288_G296_T1.3091.00
257_T260_L1.3021.00
129_I133_L1.3011.00
253_Q256_L1.2921.00
99_I111_E1.2891.00
277_K284_A1.2881.00
123_I126_S1.2881.00
74_P78_M1.2871.00
35_A38_F1.2761.00
54_Q58_N1.2711.00
102_A109_I1.2711.00
104_V107_I1.2601.00
260_L264_L1.2351.00
32_A36_A1.2311.00
106_V109_I1.2291.00
65_A69_G1.2271.00
269_R273_R1.2261.00
217_K221_F1.2211.00
194_D229_N1.2071.00
260_L263_L1.2061.00
52_I56_Q1.2041.00
101_I110_L1.2001.00
101_I108_A1.1911.00
187_K190_M1.1901.00
291_Y294_L1.1841.00
286_E289_I1.1841.00
233_D236_K1.1821.00
185_K189_K1.1821.00
225_I229_N1.1791.00
66_T70_L1.1791.00
7_I11_G1.1761.00
75_S78_M1.1761.00
292_K295_L1.1711.00
253_Q257_T1.1691.00
60_I63_V1.1601.00
258_E262_Y1.1551.00
188_E192_K1.1551.00
49_L53_D1.1541.00
295_L300_L1.1521.00
40_I135_S1.1501.00
296_T302_N1.1411.00
187_K193_L1.1391.00
106_V110_L1.1381.00
193_L197_Y1.1291.00
105_T108_A1.1271.00
55_V132_V1.1261.00
226_I233_D1.1231.00
199_L203_E1.1211.00
167_R268_E1.1141.00
164_K168_L1.1121.00
156_V160_E1.1111.00
99_I105_T1.1061.00
254_E258_E1.0971.00
55_V129_I1.0911.00
14_I18_L1.0791.00
16_L138_V1.0781.00
221_F224_A1.0781.00
17_A32_A1.0771.00
51_I136_F1.0771.00
297_K300_L1.0771.00
100_S104_V1.0681.00
35_A54_Q1.0681.00
164_K167_R1.0681.00
147_Y199_L1.0671.00
17_A21_A1.0671.00
270_I278_I1.0651.00
129_I132_V1.0571.00
54_Q97_H1.0511.00
44_I47_S1.0421.00
126_S130_L1.0411.00
292_K296_T1.0251.00
231_A236_K1.0221.00
186_L189_K1.0191.00
197_Y200_Y1.0191.00
19_Y23_W1.0181.00
119_M123_I1.0041.00
98_T102_A1.0001.00
122_L125_T1.0001.00
288_G300_L0.9921.00
180_K184_E0.9911.00
21_A29_P0.9841.00
32_A127_T0.9761.00
287_E291_Y0.9751.00
294_L302_N0.9701.00
131_G135_S0.9671.00
242_E245_I0.9551.00
70_L74_P0.9541.00
31_F127_T0.9531.00
252_F256_L0.9521.00
289_I300_L0.9441.00
124_R128_V0.9441.00
294_L297_K0.9431.00
161_E164_K0.9401.00
256_L260_L0.9391.00
78_M81_L0.9371.00
230_R234_T0.9341.00
275_V281_H0.9341.00
181_E185_K0.9331.00
28_A127_T0.9311.00
182_D185_K0.9311.00
270_I275_V0.9201.00
265_Y269_R0.9061.00
138_V142_F0.9051.00
102_A105_T0.9021.00
295_L301_K0.9001.00
50_I54_Q0.8981.00
175_E179_L0.8921.00
192_K196_T0.8901.00
30_I127_T0.8891.00
54_Q128_V0.8881.00
273_R283_D0.8861.00
62_A66_T0.8841.00
109_I121_A0.8841.00
99_I103_L0.8801.00
163_M167_R0.8651.00
54_Q61_G0.8641.00
18_L22_S0.8621.00
252_F255_T0.8621.00
175_E178_I0.8591.00
261_D264_L0.8571.00
14_I33_G0.8571.00
259_E262_Y0.8501.00
163_M268_E0.8431.00
173_S179_L0.8411.00
169_S235_L0.8401.00
99_I102_A0.8370.99
200_Y204_R0.8350.99
13_A134_S0.8350.99
287_E293_Q0.8290.99
226_I231_A0.8280.99
264_L274_F0.8260.99
86_V93_L0.8240.99
204_R208_K0.8230.99
88_T91_L0.8150.99
32_A131_G0.8140.99
84_V88_T0.8080.99
291_Y297_K0.8080.99
74_P83_A0.8040.99
273_R277_K0.8040.99
80_G84_V0.8020.99
167_R272_M0.8010.99
13_A17_A0.8000.99
266_W270_I0.7990.99
241_L245_I0.7980.99
239_H242_E0.7980.99
298_S301_K0.7970.99
292_K300_L0.7960.99
31_F35_A0.7950.99
50_I124_R0.7940.99
222_R225_I0.7930.99
234_T238_L0.7910.99
277_K280_P0.7890.99
285_V289_I0.7870.99
223_Q226_I0.7870.99
98_T108_A0.7860.99
222_R228_A0.7800.99
285_V296_T0.7790.99
259_E264_L0.7790.99
253_Q260_L0.7730.99
199_L205_S0.7680.99
226_I232_L0.7660.99
86_V104_V0.7620.99
37_I40_I0.7590.99
253_Q259_E0.7590.99
124_R131_G0.7580.99
256_L266_W0.7560.99
293_Q298_S0.7560.99
289_I292_K0.7530.99
299_F302_N0.7530.99
281_H284_A0.7500.99
134_S138_V0.7460.99
161_E182_D0.7400.99
219_V223_Q0.7360.99
106_V111_E0.7350.99
266_W269_R0.7340.99
225_I228_A0.7330.99
271_L278_I0.7310.99
121_A125_T0.7300.99
51_I54_Q0.7280.99
251_E264_L0.7280.99
290_R297_K0.7260.99
32_A134_S0.7260.99
218_L222_R0.7250.99
224_A233_D0.7190.98
297_K301_K0.7180.98
278_I281_H0.7180.98
154_N192_K0.7170.98
267_H270_I0.7160.98
82_T86_V0.7150.98
161_E185_K0.7120.98
292_K298_S0.7110.98
130_L133_L0.7100.98
17_A24_I0.7090.98
183_I193_L0.7060.98
9_K13_A0.7030.98
237_K241_L0.7000.98
203_E206_Y0.6980.98
293_Q302_N0.6980.98
264_L270_I0.6960.98
229_N233_D0.6960.98
48_F51_I0.6950.98
275_V284_A0.6950.98
271_L275_V0.6940.98
99_I110_L0.6930.98
104_V109_I0.6920.98
272_M279_K0.6910.98
42_P47_S0.6880.98
180_K187_K0.6870.98
201_K205_S0.6870.98
47_S128_V0.6840.98
226_I229_N0.6840.98
173_S177_S0.6820.98
51_I132_V0.6790.98
34_I37_I0.6780.98
280_P283_D0.6770.98
65_A110_L0.6760.98
147_Y200_Y0.6740.98
182_D186_L0.6720.98
63_V67_V0.6650.97
34_I40_I0.6630.97
249_P253_Q0.6630.97
61_G124_R0.6620.97
225_I234_T0.6610.97
62_A121_A0.6580.97
241_L244_E0.6530.97
234_T242_E0.6530.97
57_A124_R0.6500.97
279_K282_D0.6490.97
291_Y300_L0.6470.97
41_Q54_Q0.6470.97
268_E272_M0.6460.97
220_L223_Q0.6430.97
94_K97_H0.6380.97
94_K102_A0.6370.97
132_V136_F0.6350.97
20_L130_L0.6330.97
236_K239_H0.6330.97
42_P45_Y0.6320.97
31_F57_A0.6320.97
217_K224_A0.6320.97
230_R236_K0.6290.96
105_T111_E0.6290.96
271_L277_K0.6290.96
103_L107_I0.6290.96
289_I296_T0.6280.96
220_L226_I0.6270.96
168_L182_D0.6260.96
54_Q131_G0.6260.96
10_T14_I0.6240.96
224_A227_T0.6230.96
220_L227_T0.6230.96
274_F278_I0.6220.96
65_A199_L0.6220.96
50_I128_V0.6190.96
76_P80_G0.6190.96
293_Q299_F0.6170.96
234_T237_K0.6170.96
251_E259_E0.6140.96
79_I87_I0.6120.96
221_F225_I0.6100.96
255_T258_E0.6100.96
276_G283_D0.6090.96
183_I186_L0.6030.96
252_F257_T0.5990.95
174_T178_I0.5990.95
243_N246_Y0.5990.95
274_F277_K0.5980.95
234_T240_R0.5980.95
191_I195_Q0.5960.95
99_I104_V0.5960.95
50_I61_G0.5950.95
154_N193_L0.5930.95
247_H250_E0.5930.95
185_K188_E0.5910.95
6_R40_I0.5900.95
193_L201_K0.5890.95
228_A237_K0.5880.95
108_A128_V0.5870.95
65_A144_P0.5870.95
44_I143_L0.5850.95
202_E207_F0.5840.95
200_Y208_K0.5780.94
247_H252_F0.5760.94
270_I274_F0.5750.94
68_F72_F0.5750.94
43_S47_S0.5710.94
26_L29_P0.5700.94
285_V290_R0.5670.94
291_Y302_N0.5670.94
83_A91_L0.5660.94
109_I113_A0.5630.94
293_Q300_L0.5610.93
103_L108_A0.5600.93
77_I80_G0.5600.93
190_M194_D0.5580.93
60_I102_A0.5570.93
98_T109_I0.5560.93
260_L271_L0.5550.93
120_F124_R0.5520.93
99_I108_A0.5520.93
41_Q53_D0.5480.93
264_L280_P0.5470.93
99_I106_V0.5470.93
31_F128_V0.5460.93
289_I297_K0.5430.92
7_I31_F0.5400.92
178_I182_D0.5400.92
254_E259_E0.5400.92
99_I107_I0.5390.92
135_S144_P0.5390.92
46_R50_I0.5370.92
236_K242_E0.5360.92
289_I294_L0.5350.92
107_I110_L0.5340.92
255_T264_L0.5310.91
102_A108_A0.5290.91
230_R238_L0.5280.91
35_A57_A0.5270.91
274_F280_P0.5270.91
45_Y50_I0.5240.91
287_E297_K0.5220.91
42_P147_Y0.5210.91
85_I92_K0.5180.90
277_K281_H0.5180.90
39_A54_Q0.5180.90
275_V291_Y0.5160.90
41_Q45_Y0.5130.90
98_T106_V0.5130.90
66_T82_T0.5120.90
191_I194_D0.5080.90
45_Y51_I0.5080.90
292_K301_K0.5070.90
29_P32_A0.5040.89
252_F259_E0.5030.89
43_S87_I0.5030.89
64_I86_V0.5030.89
245_I248_M0.5030.89
285_V291_Y0.5020.89
46_R54_Q0.5020.89
184_E194_D0.5010.89
125_T129_I0.5010.89
277_K282_D0.5000.89
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  
2oltA 5 0.5439 79.9 0.907 Contact Map
3ne5A 3 0.4306 49.7 0.925 Contact Map
4k0jA 3 0.4136 42.8 0.928 Contact Map
3l39A 3 0.5581 41 0.928 Contact Map
4cgkA 3 0.4986 40.2 0.929 Contact Map
4q4gX 1 0 39.4 0.929 Contact Map
3w9iA 3 0.4334 35.2 0.931 Contact Map
4dx5A 3 0.4306 31.5 0.933 Contact Map
4bgnA 3 0.2776 26.1 0.935 Contact Map
4i5sA 2 0.5524 23.9 0.937 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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