GREMLIN Database
YDBO - Uncharacterized transporter YdbO
UniProt: P96610 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 290 (273)
Sequences: 10472 (7330)
Seq/√Len: 443.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
178_W182_V3.4821.00
193_K197_D3.0751.00
204_H209_G2.9161.00
247_M282_V2.9041.00
232_K248_V2.8471.00
222_V247_M2.7591.00
219_K223_G2.5781.00
31_I121_T2.4431.00
221_T275_H2.4061.00
99_L185_F2.3191.00
100_I104_K2.3081.00
29_L44_G2.3051.00
221_T274_E2.2981.00
69_D76_H2.2191.00
222_V267_V2.1551.00
88_S199_F2.1211.00
171_S179_V2.1161.00
200_K204_H2.0721.00
32_G41_R2.0151.00
79_A207_T1.9891.00
229_H252_D1.9811.00
120_W124_G1.9481.00
256_T259_E1.9381.00
216_E220_Q1.8841.00
253_P258_E1.8671.00
170_F174_L1.8631.00
99_L188_G1.8601.00
225_I267_V1.8541.00
211_H214_D1.8481.00
11_E65_Q1.8471.00
72_H76_H1.8221.00
269_D273_H1.8121.00
119_A166_F1.7691.00
225_I270_K1.7581.00
78_R208_D1.7251.00
217_P274_E1.7241.00
221_T270_K1.7231.00
261_H283_H1.7041.00
11_E62_R1.6981.00
104_K108_G1.6941.00
249_I267_V1.6811.00
30_V34_L1.6651.00
259_E262_G1.6631.00
215_L236_A1.6521.00
138_R142_S1.6361.00
230_R250_T1.6241.00
262_G266_E1.6161.00
137_K141_A1.6131.00
15_L19_F1.6131.00
96_I100_I1.6121.00
185_F189_I1.6011.00
225_I266_E1.5851.00
98_V184_A1.5831.00
196_W200_K1.5731.00
257_V260_G1.5461.00
189_I193_K1.5381.00
55_V59_I1.5241.00
119_A173_Q1.5171.00
168_G183_T1.5141.00
46_N154_D1.5131.00
29_L33_I1.5001.00
103_G107_A1.4881.00
20_A128_F1.4681.00
102_G184_A1.4621.00
260_G284_V1.4561.00
270_K274_E1.4551.00
149_M201_D1.4481.00
236_A245_I1.4371.00
15_L58_L1.4101.00
170_F173_Q1.4021.00
130_Y134_L1.3961.00
164_G183_T1.3911.00
119_A170_F1.3811.00
137_K152_A1.3751.00
22_V51_I1.3711.00
197_D200_K1.3711.00
232_K285_E1.3591.00
266_E270_K1.3561.00
74_Y246_E1.3461.00
35_Y118_A1.3231.00
217_P221_T1.3121.00
123_L127_V1.2951.00
264_A283_H1.2861.00
178_W181_P1.2821.00
28_K47_N1.2811.00
123_L166_F1.2671.00
116_L120_W1.2591.00
264_A268_E1.2561.00
220_Q224_R1.2561.00
16_L135_Y1.2541.00
251_V257_V1.2531.00
119_A169_V1.2321.00
60_G83_S1.2221.00
131_G134_L1.2161.00
251_V263_V1.2151.00
97_E100_I1.2091.00
127_V131_G1.2021.00
106_I181_P1.1981.00
69_D72_H1.1941.00
215_L219_K1.1901.00
63_I79_A1.1891.00
32_G44_G1.1851.00
224_R270_K1.1791.00
208_D244_H1.1791.00
151_A154_D1.1751.00
248_V285_E1.1731.00
92_M195_A1.1711.00
38_E102_G1.1691.00
134_L138_R1.1631.00
216_E219_K1.1611.00
234_V247_M1.1591.00
95_G192_C1.1461.00
223_G230_R1.1461.00
258_E262_G1.1441.00
261_H264_A1.1281.00
72_H204_H1.1271.00
235_K279_H1.1241.00
24_L28_K1.1201.00
25_A48_G1.1191.00
20_A132_I1.1121.00
257_V284_V1.0971.00
19_F23_I1.0941.00
106_I178_W1.0921.00
217_P275_H1.0911.00
225_I263_V1.0801.00
227_N259_E1.0771.00
131_G135_Y1.0771.00
77_Y242_T1.0691.00
268_E283_H1.0691.00
264_A284_V1.0681.00
217_P220_Q1.0681.00
268_E272_K1.0671.00
25_A44_G1.0651.00
126_A166_F1.0621.00
134_L137_K1.0591.00
18_I51_I1.0561.00
56_A83_S1.0561.00
245_I277_V1.0541.00
71_D76_H1.0531.00
176_L179_V1.0491.00
24_L128_F1.0441.00
120_W123_L1.0441.00
245_I280_V1.0341.00
133_Y137_K1.0331.00
25_A29_L1.0301.00
92_M96_I1.0291.00
232_K250_T1.0271.00
88_S198_I1.0251.00
99_L103_G1.0181.00
81_T205_S1.0171.00
254_K258_E1.0141.00
62_R65_Q1.0131.00
218_Y236_A1.0131.00
92_M196_W1.0111.00
101_G104_K0.9991.00
152_A156_R0.9981.00
163_A167_I0.9971.00
12_K16_L0.9911.00
138_R141_A0.9871.00
109_G112_E0.9841.00
63_I66_R0.9801.00
43_D46_N0.9801.00
260_G264_A0.9791.00
92_M192_C0.9781.00
218_Y271_I0.9781.00
38_E184_A0.9701.00
43_D162_S0.9701.00
118_A169_V0.9701.00
17_N132_I0.9701.00
261_H286_P0.9681.00
208_D239_L0.9661.00
29_L41_R0.9641.00
18_I58_L0.9621.00
122_A166_F0.9561.00
38_E105_A0.9511.00
102_G185_F0.9461.00
117_I120_W0.9411.00
116_L173_Q0.9351.00
18_I55_V0.9341.00
57_V150_A0.9301.00
57_V147_A0.9271.00
271_I277_V0.9111.00
141_A144_K0.9041.00
80_E145_S0.9041.00
265_D269_D0.9031.00
71_D209_G0.9021.00
103_G185_F0.9001.00
133_Y152_A0.8941.00
26_V30_V0.8911.00
114_P117_I0.8901.00
208_D237_R0.8891.00
33_I41_R0.8851.00
210_F214_D0.8801.00
205_S238_Y0.8791.00
106_I185_F0.8791.00
251_V284_V0.8761.00
82_I207_T0.8711.00
214_D243_V0.8701.00
101_G105_A0.8691.00
59_I63_I0.8671.00
239_L244_H0.8661.00
89_F93_A0.8631.00
251_V260_G0.8611.00
233_D279_H0.8551.00
130_Y156_R0.8521.00
46_N50_D0.8501.00
220_Q223_G0.8421.00
22_V26_V0.8381.00
227_N263_V0.8331.00
233_D248_V0.8321.00
265_D268_E0.8301.00
27_V124_G0.8291.00
231_L234_V0.8261.00
78_R237_R0.8251.00
228_V249_I0.8221.00
93_A97_E0.8201.00
182_V186_I0.8201.00
21_Y47_N0.8191.00
154_D158_D0.8181.00
210_F243_V0.8161.00
221_T225_I0.8141.00
126_A163_A0.8081.00
221_T224_R0.8071.00
264_A282_V0.8061.00
270_K273_H0.8021.00
104_K107_A0.7981.00
125_S129_M0.7981.00
38_E101_G0.7981.00
168_G179_V0.7941.00
271_I280_V0.7931.00
13_G135_Y0.7921.00
61_L147_A0.7871.00
132_I135_Y0.7821.00
227_N266_E0.7801.00
218_Y245_I0.7781.00
132_I155_S0.7771.00
263_V267_V0.7771.00
129_M132_I0.7771.00
35_Y117_I0.7751.00
179_V183_T0.7671.00
115_N173_Q0.7591.00
29_L48_G0.7541.00
223_G231_L0.7451.00
85_L199_F0.7451.00
97_E101_G0.7431.00
261_H285_E0.7381.00
27_V121_T0.7381.00
74_Y237_R0.7381.00
25_A47_N0.7361.00
37_S180_D0.7341.00
153_K156_R0.7331.00
222_V231_L0.7311.00
39_A183_T0.7301.00
260_G263_V0.7291.00
93_A100_I0.7291.00
33_I44_G0.7191.00
25_A51_I0.7191.00
11_E58_L0.7181.00
219_K231_L0.7171.00
271_I282_V0.7171.00
266_E269_D0.7161.00
157_S194_T0.7151.00
235_K246_E0.7131.00
136_N151_A0.7111.00
183_T187_I0.7111.00
49_T94_V0.7091.00
228_V231_L0.7081.00
238_Y243_V0.7081.00
210_F236_A0.7071.00
130_Y159_A0.7041.00
150_A198_I0.7031.00
28_K44_G0.7011.00
133_Y156_R0.7001.00
132_I136_N0.6971.00
82_I86_V0.6941.00
231_L247_M0.6921.00
64_S80_E0.6911.00
59_I62_R0.6911.00
268_E280_V0.6901.00
17_N155_S0.6861.00
17_N136_N0.6841.00
85_L89_F0.6841.00
119_A123_L0.6781.00
190_I194_T0.6761.00
212_L216_E0.6761.00
222_V249_I0.6721.00
149_M153_K0.6711.00
96_I192_C0.6701.00
46_N91_M0.6691.00
267_V282_V0.6671.00
30_V33_I0.6671.00
277_V280_V0.6671.00
95_G195_A0.6671.00
104_K110_T0.6641.00
85_L202_A0.6611.00
146_S205_S0.6611.00
102_G188_G0.6591.00
249_I284_V0.6541.00
19_F22_V0.6531.00
53_A57_V0.6480.99
272_K278_T0.6470.99
54_S151_A0.6450.99
267_V270_K0.6440.99
186_I190_I0.6440.99
272_K280_V0.6430.99
193_K196_W0.6420.99
53_A90_I0.6400.99
11_E15_L0.6380.99
71_D204_H0.6370.99
227_N252_D0.6370.99
165_A168_G0.6370.99
128_F132_I0.6360.99
141_A149_M0.6350.99
48_G52_V0.6350.99
116_L119_A0.6340.99
21_Y50_D0.6340.99
15_L18_I0.6310.99
32_G35_Y0.6300.99
58_L62_R0.6300.99
262_G265_D0.6270.99
84_S147_A0.6270.99
149_M152_A0.6260.99
260_G286_P0.6240.99
28_K43_D0.6220.99
171_S174_L0.6200.99
13_G138_R0.6190.99
259_E266_E0.6140.99
31_I117_I0.6130.99
62_R66_R0.6110.99
17_N54_S0.6090.99
108_G111_T0.6090.99
36_H110_T0.6090.99
264_A267_V0.6070.99
112_E115_N0.6040.99
88_S202_A0.6010.99
28_K125_S0.5980.99
238_Y241_S0.5980.99
146_S201_D0.5970.99
234_V245_I0.5950.99
122_A125_S0.5940.99
133_Y155_S0.5930.99
73_P235_K0.5920.99
129_M155_S0.5900.99
94_V97_E0.5900.99
129_M136_N0.5890.99
261_H265_D0.5880.99
84_S198_I0.5870.99
17_N151_A0.5850.99
82_I203_S0.5840.99
52_V55_V0.5800.99
246_E279_H0.5790.99
14_A57_V0.5780.99
156_R160_F0.5750.99
38_E41_R0.5730.99
85_L206_L0.5640.99
190_I193_K0.5640.99
225_I228_V0.5640.99
124_G128_F0.5630.99
79_A83_S0.5610.99
183_T186_I0.5610.99
126_A130_Y0.5570.98
66_R76_H0.5570.98
40_L91_M0.5570.98
160_F163_A0.5570.98
164_G187_I0.5550.98
18_I54_S0.5550.98
269_D272_K0.5540.98
84_S202_A0.5530.98
222_V225_I0.5530.98
111_T177_P0.5520.98
105_A110_T0.5500.98
222_V234_V0.5490.98
245_I278_T0.5490.98
40_L169_V0.5450.98
14_A18_I0.5440.98
40_L122_A0.5390.98
29_L45_L0.5390.98
136_N155_S0.5380.98
53_A154_D0.5370.98
118_A168_G0.5360.98
85_L203_S0.5350.98
272_K279_H0.5350.98
214_D217_P0.5330.98
21_Y51_I0.5330.98
113_T116_L0.5330.98
67_P76_H0.5310.98
203_S207_T0.5280.98
167_I171_S0.5270.98
38_E42_A0.5260.98
83_S147_A0.5250.98
171_S176_L0.5240.98
102_G181_P0.5240.98
73_P210_F0.5200.98
137_K156_R0.5200.98
16_L20_A0.5170.98
214_D218_Y0.5140.97
70_S215_L0.5140.97
129_M154_D0.5120.97
118_A172_S0.5120.97
225_I282_V0.5110.97
222_V228_V0.5100.97
16_L19_F0.5100.97
161_V165_A0.5090.97
249_I282_V0.5070.97
101_G185_F0.5060.97
259_E263_V0.5060.97
21_Y155_S0.5030.97
229_H251_V0.5030.97
250_T285_E0.5010.97
47_N161_V0.5000.97
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 0.9966 100 0.11 Contact Map
3h90A 3 0.9724 100 0.123 Contact Map
2zztA 2 0.2724 99.4 0.766 Contact Map
3bypA 2 0.2724 99.4 0.768 Contact Map
3w61A 2 0.2724 99.3 0.78 Contact Map
3cq1A 2 0.2897 27.3 0.95 Contact Map
3lnoA 1 0.2793 26.7 0.95 Contact Map
1mhsA 2 0.7724 25 0.95 Contact Map
4k0jA 3 0.3793 24.3 0.951 Contact Map
4mt1A 3 0.4207 23.1 0.951 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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