GREMLIN Database
YDFM - Uncharacterized transporter YdfM
UniProt: C0SP78 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 297 (274)
Sequences: 10418 (7279)
Seq/√Len: 439.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
183_Y187_I3.4861.00
198_K202_E3.1781.00
209_D214_K3.0211.00
253_V289_I2.8991.00
228_I253_V2.8451.00
238_D254_R2.7671.00
227_V280_Q2.7321.00
225_K229_F2.5491.00
30_F119_A2.4331.00
99_I103_L2.3551.00
28_V43_G2.3241.00
98_L190_A2.2691.00
228_I273_I2.1901.00
68_D75_H2.1771.00
275_N279_R2.1521.00
87_G204_I2.1021.00
205_R209_D2.0661.00
262_T265_Q2.0441.00
78_A212_M2.0361.00
138_G147_I2.0101.00
31_G40_F2.0011.00
231_C276_E1.9991.00
235_K258_D1.9881.00
118_F122_I1.9811.00
223_E280_Q1.9721.00
227_V281_F1.9501.00
227_V276_E1.9281.00
10_R64_N1.9191.00
222_E226_A1.9111.00
259_H264_K1.8811.00
169_L184_A1.8771.00
98_L193_A1.8541.00
117_L164_F1.8361.00
103_L107_K1.8221.00
221_I242_A1.8121.00
231_C273_I1.8081.00
231_C272_E1.7671.00
135_I139_K1.7531.00
77_K213_E1.7501.00
71_H75_H1.7431.00
29_F33_V1.7301.00
217_D220_L1.7071.00
255_L273_I1.6891.00
267_H290_H1.6871.00
268_D272_E1.6841.00
265_Q268_D1.6641.00
168_L172_I1.6541.00
10_R61_G1.6531.00
14_L18_I1.6501.00
201_M205_R1.6461.00
97_I189_S1.6301.00
95_V99_I1.6261.00
136_K140_K1.6261.00
276_E280_Q1.6221.00
263_I266_G1.5921.00
236_R256_S1.5661.00
28_V32_L1.5321.00
102_I106_V1.5251.00
194_Y198_K1.5211.00
190_A194_Y1.5161.00
14_L57_L1.4941.00
266_G291_V1.4841.00
54_I58_A1.4551.00
128_E132_R1.4221.00
101_A189_S1.4131.00
202_E205_R1.3971.00
147_I206_P1.3961.00
168_L171_I1.3881.00
19_A126_A1.3871.00
223_E227_V1.3871.00
242_A251_L1.3821.00
21_L50_V1.3751.00
166_G188_A1.3671.00
114_Y171_I1.3571.00
73_F252_D1.3561.00
251_L284_V1.3561.00
117_L171_I1.3471.00
121_L164_F1.3381.00
238_D292_N1.3261.00
162_A188_A1.3191.00
135_I150_A1.3131.00
183_Y186_A1.3061.00
117_L168_L1.2931.00
272_E276_E1.2891.00
121_L125_V1.2861.00
226_A230_Q1.2731.00
270_A274_R1.2621.00
45_H152_D1.2551.00
115_S118_F1.2521.00
34_G116_A1.2401.00
257_L269_I1.2381.00
15_I133_Y1.2321.00
240_I253_V1.2321.00
68_D71_H1.2291.00
27_K46_S1.2271.00
59_V82_S1.2171.00
257_L263_I1.2161.00
105_F186_A1.2101.00
31_G43_G1.2011.00
277_I284_V1.2011.00
96_Y99_I1.1951.00
222_E225_K1.1931.00
223_E281_F1.1871.00
94_S197_F1.1771.00
220_L223_E1.1761.00
129_I132_R1.1661.00
91_V200_S1.1621.00
149_I152_D1.1601.00
229_F236_R1.1591.00
216_V242_A1.1531.00
213_E250_L1.1491.00
274_R278_K1.1391.00
260_D264_K1.1371.00
105_F183_Y1.1341.00
24_M47_A1.1331.00
62_I78_A1.1311.00
19_A130_L1.1271.00
270_A290_H1.1271.00
224_Y277_I1.1201.00
231_C269_I1.1191.00
137_Q140_K1.1091.00
254_R292_N1.1081.00
117_L167_V1.1071.00
264_K268_D1.1051.00
17_L50_V1.1031.00
125_V129_I1.0981.00
18_I22_I1.0971.00
218_P222_E1.0921.00
238_D256_S1.0921.00
37_E101_A1.0881.00
233_Q265_Q1.0881.00
76_G248_Y1.0861.00
223_E226_A1.0831.00
241_R286_E1.0791.00
55_A82_S1.0681.00
71_H209_D1.0641.00
91_V95_V1.0601.00
267_H270_A1.0591.00
132_R136_K1.0581.00
98_L102_I1.0471.00
70_D75_H1.0431.00
87_G203_L1.0401.00
24_M28_V1.0391.00
61_G64_N1.0371.00
23_L126_A1.0361.00
62_I65_K1.0331.00
100_E103_L1.0231.00
24_M43_G1.0231.00
224_Y242_A1.0171.00
23_L27_K1.0151.00
150_A154_K1.0141.00
129_I133_Y1.0141.00
132_R135_I1.0141.00
263_I291_V1.0131.00
80_V210_V1.0121.00
118_F121_L1.0061.00
270_A291_V1.0051.00
230_Q276_E0.9961.00
251_L287_V0.9961.00
11_K15_I0.9931.00
91_V201_M0.9841.00
227_V230_Q0.9821.00
28_V40_F0.9781.00
226_A229_F0.9771.00
91_V197_F0.9721.00
16_A130_L0.9711.00
274_R290_H0.9701.00
25_A29_F0.9681.00
152_D155_G0.9681.00
267_H293_P0.9661.00
105_F190_A0.9621.00
266_G270_A0.9541.00
17_L57_L0.9491.00
178_W183_Y0.9491.00
120_A164_F0.9451.00
221_I225_K0.9451.00
213_E245_H0.9261.00
37_E189_S0.9241.00
37_E104_S0.9231.00
245_H250_L0.9141.00
101_A190_A0.9131.00
42_D160_S0.9091.00
152_D156_D0.9041.00
56_V145_A0.9041.00
166_G184_A0.8991.00
58_A62_I0.8961.00
233_Q269_I0.8951.00
42_D45_H0.8941.00
17_L54_I0.8921.00
239_R254_R0.8911.00
81_I212_M0.8901.00
257_L291_V0.8881.00
32_L40_F0.8791.00
271_R275_N0.8781.00
70_D214_K0.8721.00
215_S221_I0.8701.00
137_Q141_W0.8691.00
88_I92_I0.8691.00
131_Y150_A0.8661.00
227_V231_C0.8661.00
161_L165_I0.8631.00
270_A289_I0.8581.00
56_V148_A0.8551.00
210_V244_E0.8541.00
100_E104_S0.8501.00
257_L266_G0.8441.00
79_E143_S0.8401.00
102_I190_A0.8361.00
216_V249_K0.8341.00
276_E279_R0.8301.00
112_P115_S0.8301.00
124_Y164_F0.8291.00
21_L25_A0.8261.00
239_R286_E0.8231.00
26_G122_I0.8221.00
213_E243_R0.8111.00
12_V133_Y0.8001.00
187_I191_I0.7921.00
48_A93_V0.7921.00
266_G269_I0.7911.00
277_I287_V0.7861.00
159_A163_A0.7821.00
229_F237_I0.7821.00
224_Y251_L0.7801.00
234_V255_L0.7791.00
151_Y154_K0.7791.00
237_I253_V0.7781.00
237_I240_I0.7771.00
45_H49_D0.7751.00
37_E100_E0.7741.00
128_E154_K0.7721.00
72_P215_S0.7661.00
20_N46_S0.7621.00
225_K237_I0.7611.00
188_A192_V0.7611.00
92_I96_Y0.7611.00
92_I99_I0.7571.00
131_Y135_I0.7561.00
284_V287_V0.7531.00
271_R274_R0.7481.00
96_Y100_E0.7471.00
84_A204_I0.7461.00
228_I237_I0.7461.00
233_Q272_E0.7461.00
136_K139_K0.7441.00
103_L106_V0.7431.00
184_A188_A0.7381.00
128_E157_I0.7381.00
95_V197_F0.7371.00
117_L121_L0.7321.00
73_F243_R0.7311.00
269_I273_I0.7301.00
274_R287_V0.7281.00
24_M50_V0.7271.00
124_Y161_L0.7241.00
244_E249_K0.7221.00
38_A188_A0.7171.00
77_K243_R0.7131.00
241_R252_D0.7091.00
130_L153_H0.7091.00
26_G119_A0.7081.00
28_V47_A0.7061.00
116_A167_V0.7061.00
220_L249_K0.7001.00
32_L43_G0.6951.00
234_V237_I0.6951.00
84_A88_I0.6941.00
24_M46_S0.6891.00
228_I255_L0.6881.00
84_A207_S0.6861.00
58_A61_G0.6851.00
63_S79_E0.6841.00
144_K210_V0.6841.00
111_V114_Y0.6811.00
273_I289_I0.6811.00
216_V220_L0.6801.00
255_L291_V0.6791.00
27_K43_G0.6761.00
272_E275_N0.6721.00
153_H156_D0.6711.00
81_I85_I0.6701.00
14_L17_L0.6691.00
127_K130_L0.6691.00
156_D162_A0.6691.00
147_I151_Y0.6691.00
103_L109_P0.6651.00
60_I145_A0.6641.00
83_E203_L0.6591.00
144_K206_P0.6581.00
104_S109_P0.6551.00
16_A134_S0.6500.99
138_G141_W0.6490.99
167_V170_A0.6480.99
233_Q258_D0.6480.99
163_A166_G0.6470.99
29_F32_L0.6460.99
268_D271_R0.6460.99
267_H292_N0.6440.99
148_A203_L0.6440.99
155_G159_A0.6430.99
147_I150_A0.6400.99
18_I21_L0.6400.99
240_I251_L0.6360.99
57_L61_G0.6360.99
195_L199_I0.6360.99
159_A162_A0.6350.99
113_Q171_I0.6340.99
47_A51_V0.6330.99
45_H90_L0.6300.99
273_I276_E0.6300.99
134_S149_I0.6290.99
52_A89_I0.6280.99
130_L134_S0.6260.99
36_S185_D0.6260.99
35_D109_P0.6260.99
10_R57_L0.6250.99
101_A193_A0.6240.99
81_I208_V0.6220.99
10_R14_L0.6220.99
131_Y153_H0.6200.99
70_D209_D0.6170.99
155_G199_I0.6160.99
163_A170_A0.6150.99
90_L153_H0.6120.99
20_N49_D0.6110.99
27_K42_D0.6100.99
244_E247_H0.6100.99
198_K201_M0.6100.99
135_I138_G0.6040.99
209_D217_D0.6020.99
94_S200_S0.5990.99
31_G34_G0.5980.99
231_C234_V0.5960.99
266_G293_P0.5960.99
52_A56_V0.5940.99
72_P241_R0.5910.99
215_S242_A0.5910.99
51_V54_I0.5910.99
123_S127_K0.5900.99
133_Y137_Q0.5890.99
267_H271_R0.5890.99
16_A53_S0.5860.99
87_G207_S0.5860.99
138_G150_A0.5850.99
83_E145_A0.5820.99
169_L172_I0.5810.99
162_A170_A0.5810.99
252_D286_E0.5810.99
191_I195_L0.5770.99
270_A273_I0.5730.99
278_K285_E0.5720.99
265_Q272_E0.5700.99
114_Y118_F0.5680.99
34_G115_S0.5660.99
215_S244_E0.5650.99
143_S146_I0.5650.99
20_N50_V0.5620.99
124_Y128_E0.5610.99
188_A191_I0.5580.98
120_A123_S0.5570.98
278_K287_V0.5570.98
156_D159_A0.5560.98
13_A56_V0.5550.98
197_F201_M0.5540.98
232_D272_E0.5540.98
53_S149_I0.5540.98
219_E242_A0.5540.98
162_A166_G0.5520.98
83_E207_S0.5520.98
165_I169_L0.5500.98
154_K158_V0.5490.98
163_A167_V0.5480.98
130_L133_Y0.5470.98
126_A130_L0.5460.98
195_L198_K0.5430.98
228_I234_V0.5410.98
116_A170_A0.5410.98
118_F125_V0.5410.98
109_P112_P0.5380.98
13_A17_L0.5360.98
78_A82_S0.5360.98
281_F284_V0.5330.98
101_A186_A0.5310.98
12_V137_Q0.5300.98
227_V273_I0.5300.98
23_L26_G0.5290.98
255_L289_I0.5260.98
162_A192_V0.5260.98
226_A280_Q0.5250.98
84_A211_L0.5240.98
61_G65_K0.5240.98
235_K257_L0.5230.98
16_A153_H0.5230.98
65_K75_H0.5230.98
37_E40_F0.5220.98
278_K286_E0.5210.98
122_I126_A0.5180.97
164_F168_L0.5180.97
52_A152_D0.5140.97
127_K153_H0.5140.97
22_I26_G0.5140.97
92_I95_V0.5120.97
208_V212_M0.5090.97
277_I289_I0.5090.97
93_V96_Y0.5090.97
67_P75_H0.5060.97
269_I272_E0.5050.97
193_A200_S0.5050.97
23_L130_L0.5020.97
84_A208_V0.5000.97
131_Y157_I0.5000.97
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  
3j1zP 8 0.9731 100 0.117 Contact Map
3h90A 3 0.9495 100 0.133 Contact Map
2zztA 2 0.2727 99.6 0.749 Contact Map
3bypA 2 0.2694 99.5 0.755 Contact Map
3w61A 2 0.2694 99.4 0.774 Contact Map
3lnoA 1 0.2795 52.2 0.942 Contact Map
3cq1A 2 0.2862 43 0.945 Contact Map
2jsxA 1 0.2761 32.8 0.948 Contact Map
1ji6A 1 0.404 31.2 0.949 Contact Map
3ne5A 3 0.4343 28.3 0.95 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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