GREMLIN Database
YFMD - Fe(3+)-citrate import system permease protein YfmD
UniProt: O34933 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 333 (317)
Sequences: 13873 (9884)
Seq/√Len: 555.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
217_S276_H4.0161.00
75_A285_A3.7181.00
26_G294_Y3.5091.00
111_S125_F3.5061.00
83_L209_A3.3791.00
27_L67_T3.2881.00
232_N235_G3.1991.00
76_S202_S3.0251.00
83_L240_I3.0141.00
71_V289_A2.8831.00
269_V287_F2.7871.00
70_G187_I2.7651.00
42_D55_E2.7641.00
69_I190_S2.5351.00
79_V285_A2.5221.00
76_S247_L2.4331.00
76_S251_S2.4261.00
27_L71_V2.4191.00
106_L165_M2.4091.00
42_D45_K2.4071.00
223_D237_R2.3521.00
23_F290_I2.3011.00
73_V251_S2.2271.00
22_I290_I2.2151.00
82_A284_S2.1921.00
79_V206_I2.1681.00
273_I283_F2.1171.00
71_V293_V2.0981.00
215_S236_I2.0751.00
32_S40_I2.0601.00
73_V255_A2.0481.00
23_F71_V2.0381.00
52_G55_E2.0361.00
39_S42_D2.0111.00
72_F199_A2.0021.00
201_F250_A1.9991.00
110_A114_I1.9421.00
106_L162_L1.9191.00
41_I45_K1.9111.00
212_F215_S1.8841.00
30_N67_T1.8791.00
218_V231_Q1.8701.00
86_A277_Y1.8681.00
84_M244_I1.8351.00
26_G290_I1.8061.00
66_R296_D1.8041.00
208_L243_I1.8031.00
217_S277_Y1.8001.00
109_V166_T1.7901.00
16_F283_F1.7821.00
56_Q60_S1.7501.00
205_G247_L1.7171.00
212_F239_L1.7171.00
53_S56_Q1.6841.00
190_S194_D1.6181.00
68_L195_V1.6001.00
235_G239_L1.5921.00
196_I200_P1.5811.00
191_N194_D1.5791.00
82_A280_V1.5621.00
261_V292_L1.5511.00
29_L32_S1.5411.00
212_F236_I1.5361.00
298_L302_I1.5291.00
46_Y60_S1.5211.00
19_A286_L1.5211.00
205_G246_I1.4961.00
108_V126_A1.4861.00
26_G293_V1.4711.00
29_L33_V1.4601.00
130_A249_G1.4561.00
23_F286_L1.4321.00
279_Y282_P1.4221.00
15_M283_F1.4061.00
187_I292_L1.4031.00
107_F125_F1.3891.00
30_N297_V1.3881.00
299_A310_V1.3831.00
134_G245_L1.3791.00
205_G243_I1.3631.00
298_L313_V1.3521.00
269_V283_F1.3481.00
19_A283_F1.3321.00
23_F289_A1.3281.00
44_L48_F1.3241.00
19_A287_F1.3191.00
133_G162_L1.3051.00
200_P204_I1.3001.00
208_L212_F1.2971.00
80_A247_L1.2851.00
196_I199_A1.2841.00
212_F240_I1.2641.00
69_I254_V1.2551.00
105_S166_T1.2441.00
72_F195_V1.2351.00
265_V287_F1.2291.00
265_V291_L1.2231.00
57_L61_T1.2201.00
161_F319_T1.2191.00
227_K234_N1.2171.00
269_V280_V1.2141.00
37_D40_I1.2121.00
46_Y56_Q1.2091.00
225_T228_G1.2031.00
101_N248_S1.2021.00
255_A258_I1.2011.00
16_F279_Y1.1941.00
78_A265_V1.1941.00
19_A290_I1.1921.00
235_G238_I1.1911.00
107_F129_G1.1841.00
218_V229_L1.1791.00
198_I254_V1.1711.00
54_K57_L1.1701.00
125_F129_G1.1691.00
236_I239_L1.1631.00
70_G293_V1.1541.00
277_Y280_V1.1511.00
87_M240_I1.1501.00
207_G211_V1.1441.00
75_A289_A1.1421.00
14_M17_I1.1391.00
234_N237_R1.1311.00
103_G133_G1.1231.00
208_L239_L1.1131.00
105_S183_M1.1061.00
234_N238_I1.1051.00
118_S121_S1.1041.00
135_A139_M1.0891.00
109_V179_V1.0861.00
36_S58_I1.0781.00
70_G292_L1.0761.00
209_A243_I1.0741.00
159_H163_S1.0731.00
106_L110_A1.0651.00
113_V169_I1.0641.00
124_I128_A1.0611.00
68_L192_W1.0611.00
69_I195_V1.0601.00
72_F198_I1.0591.00
75_A78_A1.0551.00
282_P285_A1.0471.00
82_A281_L1.0441.00
102_A162_L1.0351.00
142_S234_N1.0331.00
222_G226_A1.0301.00
273_I279_Y1.0291.00
82_A277_Y1.0231.00
300_R307_E1.0211.00
198_I202_S1.0211.00
32_S43_S1.0161.00
168_A172_L1.0151.00
299_A313_V1.0061.00
110_A169_I1.0041.00
137_V158_V1.0041.00
216_V240_I0.9961.00
127_F246_I0.9961.00
236_I240_I0.9941.00
204_I207_G0.9931.00
33_V301_W0.9901.00
60_S64_L0.9891.00
290_I294_Y0.9881.00
279_Y283_F0.9781.00
51_D56_Q0.9731.00
103_G129_G0.9701.00
20_L24_I0.9671.00
21_I25_F0.9651.00
27_L293_V0.9651.00
298_L301_W0.9651.00
205_G250_A0.9611.00
46_Y55_E0.9611.00
46_Y59_I0.9611.00
101_N257_P0.9591.00
303_A306_Y0.9491.00
320_P324_Y0.9451.00
132_A136_I0.9391.00
20_L286_L0.9371.00
258_I292_L0.9371.00
67_T297_V0.9331.00
113_V173_N0.9331.00
28_G32_S0.9321.00
106_L166_T0.9291.00
200_P203_V0.9231.00
31_L67_T0.9221.00
296_D300_R0.9191.00
280_V284_S0.9171.00
43_S59_I0.9131.00
197_T200_P0.9111.00
265_V269_V0.9101.00
45_K49_V0.9061.00
28_G40_I0.9031.00
50_W56_Q0.9021.00
56_Q61_T0.9011.00
122_S125_F0.9001.00
272_L287_F0.8931.00
26_G297_V0.8901.00
231_Q236_I0.8871.00
192_W195_V0.8831.00
15_M19_A0.8831.00
238_I242_L0.8821.00
100_V130_A0.8791.00
34_G63_R0.8741.00
276_H279_Y0.8731.00
223_D227_K0.8731.00
15_M18_I0.8701.00
75_A206_I0.8701.00
315_A320_P0.8701.00
14_M18_I0.8701.00
321_F324_Y0.8681.00
294_Y298_L0.8681.00
72_F202_S0.8671.00
251_S255_A0.8661.00
45_K48_F0.8631.00
217_S278_Q0.8581.00
46_Y51_D0.8551.00
38_I59_I0.8531.00
80_A244_I0.8471.00
45_K50_W0.8441.00
24_I28_G0.8431.00
224_E227_K0.8381.00
81_G266_P0.8351.00
106_L169_I0.8321.00
122_S126_A0.8301.00
179_V183_M0.8271.00
108_V122_S0.8261.00
33_V37_D0.8261.00
208_L211_V0.8241.00
53_S57_L0.8201.00
193_Q196_I0.8191.00
127_F131_A0.8181.00
233_M237_R0.8141.00
104_A130_A0.8131.00
32_S37_D0.8101.00
111_S122_S0.8061.00
67_T293_V0.8051.00
209_A240_I0.8041.00
23_F27_L0.8031.00
194_D254_V0.8021.00
76_S80_A0.7971.00
241_S245_L0.7961.00
112_L122_S0.7941.00
203_V207_G0.7911.00
223_D233_M0.7911.00
299_A309_P0.7901.00
64_L192_W0.7891.00
270_R280_V0.7881.00
212_F243_I0.7871.00
96_Q101_N0.7791.00
213_S278_Q0.7781.00
133_G137_V0.7761.00
103_G162_L0.7761.00
121_S124_I0.7741.00
269_V273_I0.7731.00
286_L290_I0.7721.00
177_E180_L0.7701.00
45_K51_D0.7691.00
139_M142_S0.7651.00
138_Y238_I0.7621.00
78_A82_A0.7611.00
38_I55_E0.7581.00
75_A202_S0.7561.00
142_S146_M0.7551.00
303_A308_S0.7531.00
102_A105_S0.7491.00
30_N300_R0.7491.00
210_L213_S0.7461.00
142_S145_G0.7461.00
110_A165_M0.7431.00
84_M98_F0.7411.00
202_S251_S0.7401.00
24_I27_L0.7371.00
198_I250_A0.7371.00
201_F205_G0.7361.00
100_V134_G0.7321.00
211_V215_S0.7301.00
57_L60_S0.7301.00
215_S231_Q0.7291.00
261_V314_T0.7291.00
226_A233_M0.7271.00
43_S46_Y0.7261.00
120_Y124_I0.7231.00
301_W304_F0.7231.00
25_F28_G0.7221.00
292_L314_T0.7211.00
278_Q282_P0.7181.00
269_V272_L0.7181.00
110_A115_L0.7181.00
277_Y282_P0.7161.00
302_I305_P0.7151.00
324_Y328_K0.7141.00
66_R300_R0.7141.00
31_L64_L0.7111.00
68_L72_F0.7111.00
316_I320_P0.7111.00
219_L233_M0.7091.00
23_F293_V0.7081.00
88_T152_A0.7081.00
66_R307_E0.7081.00
206_I210_L0.7061.00
138_Y234_N0.7051.00
109_V170_I0.7051.00
69_I198_I0.7041.00
128_A132_A0.7021.00
52_G56_Q0.7001.00
227_K233_M0.7001.00
79_V209_A0.6971.00
137_V141_A0.6961.00
80_A248_S0.6951.00
250_A253_A0.6931.00
271_K325_L0.6921.00
199_A203_V0.6871.00
289_A293_V0.6871.00
36_S40_I0.6871.00
94_S97_I0.6861.00
292_L310_V0.6841.00
112_L178_D0.6841.00
19_A23_F0.6801.00
129_G133_G0.6781.00
173_N176_G0.6781.00
130_A245_L0.6741.00
250_A254_V0.6731.00
170_I180_L0.6721.00
187_I310_V0.6701.00
198_I201_F0.6691.00
31_L59_I0.6671.00
258_I310_V0.6661.00
57_L62_L0.6651.00
205_G209_A0.6631.00
261_V291_L0.6621.00
78_A285_A0.6581.00
192_W196_I0.6561.00
268_I271_K0.6551.00
27_L31_L0.6551.00
77_L261_V0.6541.00
105_S257_P0.6501.00
111_S121_S0.6481.00
266_P284_S0.6471.00
86_A220_G0.6471.00
15_M272_L0.6461.00
102_A159_H0.6461.00
33_V297_V0.6451.00
36_S39_S0.6441.00
295_A313_V0.6431.00
268_I291_L0.6421.00
180_L183_M0.6411.00
167_Q171_I0.6411.00
79_V281_L0.6361.00
291_L295_A0.6331.00
268_I287_F0.6321.00
131_A249_G0.6321.00
128_A131_A0.6321.00
163_S183_M0.6311.00
291_L317_I0.6301.00
107_F111_S0.6291.00
134_G241_S0.6291.00
264_L322_F0.6281.00
64_L68_L0.6271.00
30_N293_V0.6261.00
175_S178_D0.6231.00
28_G44_L0.6211.00
59_I64_L0.6181.00
167_Q182_W0.6171.00
83_L243_I0.6161.00
201_F246_I0.6151.00
49_V52_G0.6141.00
18_I22_I0.6141.00
40_I44_L0.6121.00
39_S55_E0.6101.00
38_I46_Y0.6091.00
75_A79_V0.6091.00
73_V187_I0.6081.00
240_I244_I0.6081.00
136_I139_M0.6061.00
285_A289_A0.6061.00
112_L179_V0.6051.00
264_L268_I0.6031.00
219_L236_I0.6031.00
111_S115_L0.6031.00
294_Y297_V0.6021.00
147_T150_K0.6001.00
134_G138_Y0.6001.00
154_S157_A0.5981.00
46_Y50_W0.5981.00
25_F29_L0.5971.00
327_R330_R0.5971.00
41_I44_L0.5941.00
263_L325_L0.5941.00
163_S167_Q0.5941.00
101_N104_A0.5931.00
215_S218_V0.5931.00
133_G158_V0.5931.00
239_L243_I0.5901.00
94_S262_G0.5901.00
299_A307_E0.5891.00
140_I154_S0.5891.00
141_A154_S0.5891.00
40_I43_S0.5881.00
84_M93_A0.5861.00
193_Q197_T0.5841.00
268_I321_F0.5841.00
187_I255_A0.5811.00
89_R223_D0.5801.00
202_S206_I0.5780.99
146_M150_K0.5780.99
264_L321_F0.5780.99
15_M273_I0.5780.99
211_V214_G0.5760.99
88_T91_P0.5750.99
16_F20_L0.5740.99
102_A163_S0.5730.99
195_V198_I0.5710.99
131_A245_L0.5710.99
43_S48_F0.5700.99
245_L249_G0.5680.99
248_S252_V0.5670.99
249_G253_A0.5640.99
69_I73_V0.5620.99
29_L297_V0.5610.99
232_N238_I0.5610.99
214_G217_S0.5600.99
239_L242_L0.5590.99
84_M100_V0.5570.99
197_T201_F0.5570.99
287_F290_I0.5570.99
49_V53_S0.5560.99
149_V152_A0.5540.99
16_F286_L0.5540.99
141_A151_L0.5530.99
83_L244_I0.5530.99
232_N239_L0.5520.99
26_G29_L0.5510.99
282_P286_L0.5500.99
51_D55_E0.5480.99
37_D41_I0.5470.99
132_A135_A0.5470.99
178_D181_Y0.5440.99
204_I208_L0.5440.99
217_S220_G0.5440.99
70_G310_V0.5430.99
195_V199_A0.5410.99
299_A302_I0.5400.99
43_S47_L0.5390.99
119_P123_V0.5350.99
42_D51_D0.5340.99
108_V125_F0.5340.99
50_W53_S0.5330.99
293_V297_V0.5330.99
114_I117_A0.5310.99
170_I176_G0.5300.99
82_A269_V0.5300.99
69_I255_A0.5300.99
296_D307_E0.5280.99
103_G158_V0.5270.99
154_S158_V0.5260.99
297_V301_W0.5250.99
197_T250_A0.5230.99
123_V126_A0.5220.99
36_S55_E0.5200.99
138_Y142_S0.5180.99
274_G278_Q0.5180.99
170_I179_V0.5150.99
79_V202_S0.5130.99
164_S315_A0.5130.99
324_Y327_R0.5110.99
176_G179_V0.5090.99
22_I26_G0.5090.99
54_K58_I0.5080.99
170_I183_M0.5080.99
18_I21_I0.5070.99
32_S44_L0.5060.99
100_V137_V0.5050.99
35_A305_P0.5040.99
17_I21_I0.5020.99
209_A213_S0.5020.99
118_S123_V0.5000.99
269_V284_S0.5000.99
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  
4g1uA 2 0.8829 100 0.206 Contact Map
2nq2A 2 0.9189 100 0.209 Contact Map
2qi9A 2 0.958 100 0.211 Contact Map
3rlbA 1 0.5045 17.2 0.965 Contact Map
4xtrG 1 0.0661 15.5 0.965 Contact Map
2m20A 2 0.0841 13.4 0.966 Contact Map
2l9uA 2 0.0871 11.2 0.968 Contact Map
4huqS 1 0.4715 10.5 0.968 Contact Map
3hd7A 1 0.1021 9.7 0.968 Contact Map
3w4tA 1 0.8979 9.3 0.969 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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