GREMLIN Database
YRDR - Uncharacterized transporter YrdR
UniProt: O07086 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 321 (277)
Sequences: 38744 (28301)
Seq/√Len: 1700.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
91_G166_I3.4161.00
12_T248_Y2.9471.00
102_T163_I2.8891.00
248_Y252_I2.7751.00
273_M278_Y2.6811.00
90_L165_F2.5391.00
48_T197_L2.4691.00
26_V233_F2.4571.00
133_S294_G2.4001.00
87_L168_I2.3821.00
41_F204_G2.3671.00
248_Y251_K2.2721.00
124_V181_Q2.2171.00
113_L170_V2.1881.00
28_D278_Y2.1621.00
87_L165_F2.1141.00
104_S269_T2.0921.00
117_I178_M2.0841.00
225_A229_Y2.0801.00
21_G268_T2.0501.00
46_V235_I2.0481.00
13_C249_G1.9841.00
66_L69_K1.9591.00
95_M99_G1.9321.00
27_A89_F1.9211.00
118_L124_V1.9011.00
119_W126_P1.8671.00
45_G200_T1.8661.00
83_I172_G1.8471.00
52_V193_T1.8241.00
115_I134_I1.8101.00
95_M162_S1.7981.00
95_M163_I1.7851.00
235_I240_I1.7681.00
109_L113_L1.7661.00
164_L168_I1.7641.00
114_S259_I1.7601.00
21_G272_I1.7561.00
127_K130_T1.7341.00
94_L161_F1.7061.00
22_A233_F1.6461.00
296_I300_I1.6421.00
87_L172_G1.6281.00
201_A205_I1.6271.00
205_I208_A1.6231.00
187_S190_R1.6031.00
69_K185_E1.6001.00
48_T200_T1.6001.00
18_M268_T1.5711.00
113_L174_V1.5691.00
224_I227_I1.5561.00
34_V227_I1.5501.00
137_A263_N1.5401.00
254_S257_N1.5301.00
281_T284_D1.5111.00
133_S298_N1.4941.00
53_I56_L1.4921.00
90_L94_L1.4721.00
103_A166_I1.4541.00
16_A249_G1.4071.00
180_G247_N1.4011.00
67_E71_K1.3911.00
41_F200_T1.3901.00
113_L171_L1.3831.00
68_G71_K1.3821.00
54_L58_R1.3781.00
282_A286_V1.3701.00
100_I273_M1.3601.00
19_S237_L1.3451.00
133_S297_L1.3291.00
160_L163_I1.3291.00
118_L122_K1.3251.00
12_T245_S1.3171.00
52_V56_L1.3151.00
101_M270_L1.3141.00
47_V196_C1.3011.00
30_A39_F1.2971.00
20_W242_A1.2941.00
33_F227_I1.2931.00
90_L93_R1.2901.00
268_T272_I1.2881.00
50_M240_I1.2831.00
285_I289_L1.2801.00
143_M290_F1.2721.00
49_I53_I1.2721.00
29_H230_D1.2711.00
95_M102_T1.2671.00
117_I121_Y1.2661.00
25_P272_I1.2651.00
174_V178_M1.2621.00
137_A294_G1.2591.00
94_L165_F1.2571.00
67_E70_A1.2491.00
72_W179_G1.2491.00
225_A228_K1.2481.00
140_G287_G1.2431.00
39_F234_M1.2431.00
128_K132_I1.2361.00
68_G72_W1.2331.00
10_A261_F1.2231.00
131_M135_L1.2151.00
202_I205_I1.2131.00
53_I57_V1.2071.00
264_F268_T1.2021.00
117_I175_V1.2001.00
71_K75_L1.1981.00
105_I288_T1.1971.00
289_L293_I1.1971.00
226_A229_Y1.1931.00
129_Y297_L1.1931.00
35_D38_Y1.1921.00
99_G102_T1.1901.00
229_Y233_F1.1731.00
226_A230_D1.1721.00
143_M283_F1.1621.00
135_L139_L1.1621.00
160_L164_L1.1571.00
280_I285_I1.1511.00
75_L179_G1.1411.00
74_I198_F1.1391.00
94_L162_S1.1291.00
272_I275_I1.1281.00
28_D32_E1.1271.00
82_T202_I1.1261.00
41_F45_G1.1251.00
43_R239_G1.1201.00
181_Q254_S1.1141.00
41_F207_T1.1111.00
48_T193_T1.1101.00
26_V230_D1.1071.00
161_F165_F1.1051.00
78_V202_I1.1051.00
144_V287_G1.0961.00
92_Q103_A1.0901.00
16_A245_S1.0881.00
218_V221_I1.0871.00
11_L15_V1.0841.00
37_F206_M1.0821.00
114_S255_S1.0801.00
100_I276_K1.0791.00
117_I174_V1.0631.00
22_A272_I1.0611.00
15_V245_S1.0601.00
219_P222_K1.0581.00
140_G291_V1.0571.00
124_V130_T1.0561.00
106_A170_V1.0551.00
9_G249_G1.0541.00
82_T203_T1.0541.00
20_W246_W1.0511.00
94_L159_H1.0511.00
126_P131_M1.0421.00
16_A20_W1.0411.00
128_K131_M1.0401.00
206_M210_L1.0301.00
250_I258_G1.0271.00
27_A92_Q1.0211.00
40_S89_F1.0211.00
119_W125_K1.0201.00
250_I254_S1.0171.00
88_I92_Q1.0121.00
72_W76_F1.0091.00
115_I126_P1.0071.00
181_Q255_S1.0051.00
114_S177_T1.0041.00
122_K178_M1.0031.00
117_I171_L0.9871.00
232_L235_I0.9871.00
72_W183_F0.9831.00
100_I278_Y0.9831.00
129_Y301_Y0.9811.00
129_Y300_I0.9761.00
106_A163_I0.9731.00
19_S245_S0.9711.00
30_A227_I0.9691.00
36_P40_S0.9681.00
161_F164_L0.9651.00
106_A166_I0.9581.00
146_T281_T0.9561.00
109_L141_A0.9401.00
229_Y232_L0.9361.00
228_K232_L0.9341.00
95_M166_I0.9341.00
30_A230_D0.9321.00
9_G252_I0.9301.00
205_I209_I0.9301.00
37_F86_V0.9291.00
117_I120_G0.9291.00
60_G187_S0.9291.00
38_Y207_T0.9271.00
282_A285_I0.9271.00
254_S258_G0.9241.00
162_S166_I0.9241.00
127_K131_M0.9221.00
69_K186_W0.9211.00
114_S174_V0.9161.00
74_I77_G0.9071.00
136_I294_G0.9041.00
17_S21_G0.9031.00
170_V174_V0.8981.00
253_L258_G0.8961.00
45_G204_G0.8911.00
142_S146_T0.8851.00
50_M236_T0.8841.00
125_K129_Y0.8841.00
25_P275_I0.8841.00
105_I142_S0.8831.00
69_K72_W0.8811.00
81_F176_Y0.8811.00
120_G123_H0.8671.00
79_M175_V0.8631.00
77_G198_F0.8621.00
267_I288_T0.8581.00
56_L59_E0.8571.00
86_V90_L0.8531.00
56_L60_G0.8491.00
25_P273_M0.8481.00
17_S268_T0.8471.00
71_K74_I0.8471.00
206_M209_I0.8441.00
33_F224_I0.8441.00
72_W182_I0.8421.00
44_Y199_G0.8391.00
253_L257_N0.8271.00
125_K128_K0.8251.00
14_L268_T0.8251.00
139_L143_M0.8231.00
75_L78_V0.8231.00
197_L201_A0.8111.00
208_A211_T0.8061.00
249_G258_G0.8021.00
139_L290_F0.7881.00
79_M172_G0.7831.00
82_T86_V0.7821.00
283_F286_V0.7811.00
230_D233_F0.7741.00
141_A145_I0.7711.00
264_F267_I0.7711.00
198_F201_A0.7701.00
40_S203_T0.7661.00
270_L280_I0.7651.00
13_C261_F0.7651.00
51_L240_I0.7641.00
52_V197_L0.7641.00
182_I185_E0.7621.00
175_V179_G0.7621.00
159_H163_I0.7611.00
270_L288_T0.7591.00
143_M286_V0.7581.00
274_V280_I0.7551.00
112_M137_A0.7551.00
237_L241_I0.7531.00
132_I136_I0.7511.00
173_W177_T0.7511.00
57_V60_G0.7421.00
56_L61_K0.7371.00
17_S264_F0.7321.00
166_I170_V0.7311.00
286_V290_F0.7261.00
42_I46_V0.7251.00
50_M53_I0.7241.00
288_T292_I0.7221.00
84_Y172_G0.7211.00
114_S178_M0.7211.00
13_C253_L0.7191.00
190_R194_L0.7181.00
109_L112_M0.7181.00
126_P130_T0.7171.00
113_L167_F0.7121.00
232_L236_T0.7081.00
241_I245_S0.7041.00
231_F235_I0.7011.00
24_F88_I0.7011.00
50_M235_I0.7001.00
140_G294_G0.7001.00
274_V279_N0.6991.00
193_T197_L0.6981.00
25_P100_I0.6961.00
72_W75_L0.6951.00
106_A167_F0.6921.00
124_V256_I0.6901.00
48_T52_V0.6881.00
83_I87_L0.6841.00
217_S220_S0.6831.00
293_I297_L0.6811.00
119_W123_H0.6811.00
186_W191_Y0.6801.00
116_V120_G0.6751.00
73_I186_W0.6741.00
38_Y42_I0.6741.00
10_A257_N0.6721.00
115_I130_T0.6651.00
84_Y176_Y0.6641.00
224_I228_K0.6641.00
194_L198_F0.6631.00
200_T204_G0.6631.00
23_M238_P0.6621.00
73_I77_G0.6611.00
74_I78_V0.6601.00
146_T149_N0.6601.00
34_V39_F0.6601.00
198_F202_I0.6601.00
79_M179_G0.6561.00
91_G103_A0.6551.00
70_A73_I0.6521.00
81_F243_L0.6521.00
63_S66_L0.6501.00
173_W246_W0.6491.00
58_R187_S0.6481.00
233_F237_L0.6461.00
108_A141_A0.6461.00
45_G49_I0.6451.00
227_I230_D0.6421.00
70_A74_I0.6411.00
64_F67_E0.6381.00
273_M276_K0.6351.00
77_G82_T0.6351.00
244_L248_Y0.6311.00
280_I284_D0.6311.00
88_I103_A0.6281.00
70_A198_F0.6261.00
54_L189_L0.6251.00
260_L298_N0.6221.00
24_F104_S0.6191.00
27_A31_L0.6171.00
136_I297_L0.6171.00
294_G298_N0.6161.00
284_D288_T0.6151.00
111_P263_N0.6151.00
9_G253_L0.6151.00
81_F195_T0.6131.00
197_L200_T0.6131.00
279_N283_F0.6121.00
58_R61_K0.6121.00
66_L70_A0.6091.00
105_I145_I0.6071.00
29_H276_K0.6071.00
46_V50_M0.6061.00
91_G162_S0.6051.00
19_S242_A0.6051.00
55_L59_E0.6041.00
87_L169_G0.6041.00
88_I169_G0.6011.00
72_W77_G0.5971.00
281_T285_I0.5931.00
211_T219_P0.5921.00
176_Y247_N0.5901.00
31_L92_Q0.5901.00
115_I119_W0.5891.00
192_S247_N0.5891.00
55_L193_T0.5891.00
60_G63_S0.5881.00
177_T246_W0.5831.00
263_N295_L0.5821.00
15_V19_S0.5821.00
192_S195_T0.5811.00
158_D161_F0.5801.00
89_F93_R0.5761.00
70_A194_L0.5731.00
145_I163_I0.5731.00
95_M103_A0.5711.00
109_L170_V0.5681.00
108_A111_P0.5651.00
165_F168_I0.5631.00
181_Q184_R0.5621.00
73_I76_F0.5621.00
201_A204_G0.5621.00
194_L197_L0.5611.00
270_L274_V0.5591.00
47_V240_I0.5591.00
222_K225_A0.5591.00
23_M89_F0.5561.00
73_I191_Y0.5561.00
199_G203_T0.5541.00
116_V134_I0.5531.00
177_T259_I0.5521.00
262_I265_V0.5511.00
17_S265_V0.5491.00
19_S238_P0.5481.00
130_T254_S0.5441.00
34_V38_Y0.5431.00
55_L190_R0.5411.00
82_T206_M0.5401.00
122_K182_I0.5391.00
171_L175_V0.5381.00
81_F199_G0.5361.00
13_C246_W0.5341.00
108_A170_V0.5311.00
285_I288_T0.5291.00
121_Y175_V0.5261.00
118_L256_I0.5261.00
274_V285_I0.5251.00
55_L58_R0.5231.00
57_V61_K0.5231.00
295_L298_N0.5231.00
143_M284_D0.5211.00
127_K301_Y0.5181.00
23_M234_M0.5171.00
81_F85_N0.5161.00
24_F28_D0.5151.00
140_G290_F0.5151.00
10_A14_L0.5141.00
204_G208_A0.5131.00
249_G253_L0.5131.00
109_L137_A0.5121.00
42_I231_F0.5111.00
112_M134_I0.5101.00
58_R189_L0.5081.00
122_K181_Q0.5081.00
279_N284_D0.5081.00
105_I144_V0.5061.00
54_L57_V0.5051.00
245_S248_Y0.5041.00
188_T192_S0.5031.00
21_G269_T0.5001.00
104_S108_A0.5001.00
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  
2i68A 2 0.2368 98.6 0.789 Contact Map
3b5dA 2 0.3146 98.1 0.816 Contact Map
1pw4A 1 0.9408 81.3 0.907 Contact Map
3wdoA 1 0.9252 77.1 0.91 Contact Map
4pypA 1 0.891 68 0.917 Contact Map
4he8J 1 0.486 58.4 0.921 Contact Map
3zuxA 1 0.8785 58.4 0.921 Contact Map
4j05A 3 0.9097 51.6 0.925 Contact Map
4tphA 2 0.8567 49.3 0.926 Contact Map
4w6vA 1 0.9034 36.3 0.931 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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