GREMLIN Database
APPB - Oligopeptide transport system permease protein AppB
UniProt: P42062 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 316 (301)
Sequences: 18539 (11789)
Seq/√Len: 679.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
59_D63_V3.3791.00
59_D67_K3.3091.00
28_K64_Q3.2951.00
66_L70_G2.9551.00
70_G74_Q2.8031.00
20_T65_Y2.7811.00
207_M234_G2.6601.00
45_Q49_E2.6461.00
53_E58_N2.5991.00
33_D52_I2.4731.00
220_R226_E2.4481.00
105_V188_A2.4481.00
228_R232_K2.4341.00
98_N266_W2.4241.00
21_I65_Y2.3571.00
271_K275_D2.3361.00
216_I234_G2.2591.00
210_V215_Y2.1931.00
62_Y66_L2.1311.00
91_L272_L2.0951.00
210_V213_Q2.0691.00
87_P90_E2.0161.00
225_K228_R2.0001.00
247_G303_A1.9961.00
117_F133_I1.9901.00
48_R52_I1.9461.00
19_I293_A1.9371.00
211_L234_G1.9301.00
84_K91_L1.9281.00
163_F182_H1.9141.00
227_N231_F1.8961.00
47_D50_Q1.8861.00
112_M116_P1.8501.00
109_L192_A1.8501.00
163_F185_I1.8251.00
44_S47_D1.8081.00
130_D204_R1.8041.00
124_R127_S1.7681.00
157_S165_T1.7531.00
86_T90_E1.7511.00
50_Q54_K1.7421.00
63_V67_K1.7341.00
243_I310_V1.7331.00
216_I229_V1.7091.00
16_L294_V1.6991.00
128_K132_G1.6801.00
218_T222_K1.6791.00
88_V287_A1.6721.00
49_E53_E1.6641.00
49_E52_I1.6601.00
224_F228_R1.6551.00
122_A207_M1.6541.00
67_K70_G1.6511.00
71_N76_D1.6461.00
120_L124_R1.6181.00
168_V266_W1.6041.00
89_S93_M1.5801.00
244_T307_Y1.5771.00
123_K230_L1.5741.00
129_I133_I1.5641.00
154_M159_N1.5361.00
10_L14_P1.5281.00
120_L129_I1.5221.00
273_F288_M1.5171.00
306_L309_I1.5031.00
124_R129_I1.4961.00
12_S297_V1.4921.00
101_L168_V1.4851.00
119_V207_M1.4811.00
113_I116_P1.4731.00
86_T94_A1.4681.00
17_L65_Y1.4541.00
98_N168_V1.4491.00
72_M77_F1.4401.00
155_V159_N1.4351.00
210_V238_A1.4341.00
215_Y237_N1.4221.00
110_A195_D1.4211.00
147_W151_I1.4191.00
188_A192_A1.4181.00
113_I196_M1.4171.00
214_D217_R1.4151.00
152_L190_V1.4081.00
210_V216_I1.3981.00
222_K233_H1.3881.00
67_K71_N1.3831.00
35_M48_R1.3591.00
192_A196_M1.3501.00
91_L284_V1.3491.00
51_F54_K1.3441.00
17_L21_I1.3401.00
6_I10_L1.3401.00
126_Y130_D1.3351.00
20_T68_W1.3291.00
276_S284_V1.3201.00
63_V66_L1.3161.00
51_F55_Y1.3001.00
60_P63_V1.2971.00
272_L284_V1.2941.00
155_V160_L1.2881.00
111_L246_F1.2731.00
118_G122_A1.2671.00
33_D36_T1.2581.00
114_S203_T1.2441.00
94_A97_P1.2291.00
240_L307_Y1.2281.00
79_T87_P1.2261.00
118_G203_T1.2241.00
114_S199_L1.2171.00
107_T246_F1.2101.00
203_T242_V1.2041.00
77_F287_A1.2001.00
143_I148_F1.1971.00
101_L105_V1.1881.00
86_T91_L1.1851.00
98_N101_L1.1831.00
77_F89_S1.1831.00
210_V234_G1.1791.00
56_G59_D1.1681.00
140_G197_A1.1661.00
181_I185_I1.1661.00
202_Y245_I1.1621.00
204_R208_L1.1481.00
59_D62_Y1.1471.00
305_I309_I1.1421.00
56_G67_K1.1401.00
122_A211_L1.1381.00
170_T183_H1.1341.00
123_K226_E1.1301.00
133_I200_T1.1251.00
21_I25_V1.1221.00
12_S301_L1.1211.00
101_L184_L1.1181.00
36_T48_R1.1171.00
288_M292_S1.1151.00
82_V279_Q1.1091.00
17_L69_L1.1051.00
199_L249_M1.0971.00
122_A208_L1.0921.00
151_I155_V1.0901.00
145_N260_V1.0871.00
152_L186_L1.0871.00
121_S133_I1.0861.00
93_M97_P1.0811.00
274_V278_F1.0791.00
80_S281_D1.0731.00
5_I305_I1.0681.00
90_E94_A1.0611.00
299_G303_A1.0521.00
21_I61_Q1.0491.00
117_F200_T1.0411.00
16_L297_V1.0381.00
156_L160_L1.0381.00
9_T301_L1.0371.00
28_K61_Q1.0351.00
50_Q53_E1.0311.00
4_Y308_A1.0251.00
91_L94_A1.0231.00
106_S192_A1.0171.00
275_D279_Q1.0161.00
190_V194_A1.0091.00
163_F186_L1.0041.00
39_M51_F1.0031.00
169_E183_H0.9961.00
184_L188_A0.9951.00
20_T290_V0.9911.00
46_A50_Q0.9891.00
226_E229_V0.9891.00
32_G280_R0.9821.00
53_E59_D0.9811.00
25_V28_K0.9801.00
128_K131_Y0.9801.00
224_F229_V0.9701.00
302_I306_L0.9661.00
72_M290_V0.9591.00
130_D208_L0.9571.00
203_T207_M0.9521.00
90_E93_M0.9501.00
137_S200_T0.9491.00
125_P212_N0.9481.00
185_I189_F0.9471.00
126_Y131_Y0.9441.00
219_A229_V0.9441.00
103_M253_F0.9351.00
251_P296_V0.9341.00
149_G190_V0.9271.00
25_V61_Q0.9251.00
71_N74_Q0.9231.00
109_L188_A0.9201.00
219_A224_F0.9191.00
104_L108_I0.9171.00
70_G73_V0.9151.00
250_I299_G0.9121.00
308_A314_I0.9101.00
220_R229_V0.9061.00
95_R272_L0.9061.00
14_P17_L0.9051.00
39_M43_I0.9041.00
18_G22_L0.9041.00
66_L69_L0.9011.00
65_Y69_L0.8991.00
28_K282_Y0.8941.00
116_P119_V0.8901.00
189_F192_A0.8871.00
243_I303_A0.8871.00
229_V234_G0.8851.00
79_T85_G0.8831.00
114_S118_G0.8801.00
238_A241_P0.8801.00
156_L163_F0.8801.00
272_L276_S0.8741.00
228_R231_F0.8701.00
134_T200_T0.8691.00
73_V76_D0.8681.00
35_M39_M0.8671.00
119_V230_L0.8671.00
149_G263_I0.8531.00
68_W72_M0.8511.00
114_S200_T0.8511.00
81_I283_P0.8501.00
307_Y314_I0.8491.00
136_T140_G0.8431.00
148_F193_T0.8411.00
107_T250_I0.8401.00
231_F234_G0.8401.00
106_S191_L0.8401.00
207_M238_A0.8381.00
101_L104_L0.8331.00
24_F28_K0.8261.00
124_R226_E0.8261.00
132_G136_T0.8241.00
35_M51_F0.8231.00
123_K231_F0.8201.00
206_N238_A0.8201.00
92_I288_M0.8201.00
115_I203_T0.8191.00
105_V266_W0.8191.00
298_V302_I0.8181.00
35_M52_I0.8171.00
116_P120_L0.8171.00
262_Q271_K0.8151.00
99_T103_M0.8111.00
118_G207_M0.8101.00
145_N193_T0.8071.00
9_T13_I0.8071.00
92_I287_A0.8051.00
257_S260_V0.8051.00
131_Y134_T0.8041.00
45_Q48_R0.8031.00
111_L116_P0.7981.00
46_A49_E0.7971.00
23_S289_T0.7921.00
104_L250_I0.7881.00
282_Y286_M0.7861.00
273_F276_S0.7851.00
168_V184_L0.7801.00
102_L188_A0.7791.00
251_P299_G0.7791.00
21_I62_Y0.7751.00
106_S110_A0.7751.00
196_M200_T0.7741.00
129_I132_G0.7721.00
140_G193_T0.7691.00
117_F196_M0.7671.00
125_P208_L0.7621.00
100_L104_L0.7581.00
305_I308_A0.7561.00
70_G75_G0.7501.00
115_I242_V0.7481.00
262_Q274_V0.7451.00
190_V260_V0.7421.00
69_L73_V0.7421.00
294_V298_V0.7371.00
272_L288_M0.7331.00
219_A233_H0.7311.00
43_I48_R0.7291.00
195_D198_G0.7261.00
113_I117_F0.7251.00
226_E230_L0.7231.00
203_T238_A0.7231.00
156_L162_W0.7221.00
97_P100_L0.7211.00
206_N210_V0.7181.00
159_N162_W0.7181.00
156_L186_L0.7171.00
119_V235_L0.7171.00
47_D51_F0.7161.00
154_M158_V0.7141.00
15_I297_V0.7121.00
185_I188_A0.7091.00
203_T206_N0.7071.00
275_D278_F0.7071.00
38_M51_F0.7041.00
296_V300_N0.7021.00
69_L72_M0.6961.00
203_T235_L0.6941.00
243_I306_L0.6861.00
166_G265_T0.6821.00
96_L100_L0.6811.00
8_R304_D0.6811.00
267_P271_K0.6801.00
110_A192_A0.6801.00
181_I184_L0.6791.00
182_H185_I0.6791.00
286_M289_T0.6781.00
273_F292_S0.6701.00
152_L189_F0.6661.00
285_I289_T0.6651.00
25_V29_A0.6631.00
91_L95_R0.6631.00
121_S130_D0.6621.00
23_S27_M0.6611.00
219_A222_K0.6601.00
153_I165_T0.6601.00
141_L197_A0.6591.00
105_V181_I0.6511.00
13_I17_L0.6511.00
23_S28_K0.6511.00
287_A291_I0.6491.00
97_P101_L0.6491.00
137_S197_A0.6481.00
164_P167_G0.6411.00
63_V70_G0.6391.00
262_Q275_D0.6391.00
132_G135_F0.6351.00
4_Y8_R0.6351.00
35_M55_Y0.6341.00
28_K286_M0.6331.00
105_V185_I0.6331.00
113_I192_A0.6301.00
215_Y219_A0.6281.00
133_I137_S0.6281.00
80_S86_T0.6281.00
105_V109_L0.6271.00
84_K284_V0.6261.00
192_A195_D0.6251.00
27_M285_I0.6241.00
303_A307_Y0.6201.00
224_F233_H0.6181.00
258_V274_V0.6171.00
209_D213_Q0.6171.00
95_R271_K0.6121.00
130_D134_T0.6121.00
43_I47_D0.6101.00
167_G183_H0.6101.00
108_I112_M0.6091.00
93_M96_L0.6091.00
135_F139_I0.6081.00
197_A200_T0.6071.00
164_P183_H0.6051.00
247_G299_G0.6051.00
308_A315_E0.6001.00
124_R130_D0.6001.00
49_E58_N0.5971.00
7_R11_M0.5961.00
292_S296_V0.5951.00
239_L243_I0.5931.00
198_G245_I0.5921.00
295_L299_G0.5921.00
145_N194_A0.5911.00
143_I147_W0.5891.00
199_L203_T0.5891.00
258_V262_Q0.5881.00
127_S132_G0.5871.00
230_L234_G0.5841.00
103_M107_T0.5821.00
99_T257_S0.5811.00
88_V272_L0.5801.00
199_L242_V0.5801.00
276_S285_I0.5781.00
34_P282_Y0.5781.00
206_N209_D0.5761.00
145_N148_F0.5751.00
127_S130_D0.5741.00
119_V231_F0.5731.00
103_M250_I0.5721.00
109_L189_F0.5701.00
20_T69_L0.5691.00
135_F138_F0.5681.00
240_L314_I0.5671.00
11_M14_P0.5671.00
88_V284_V0.5661.00
147_W150_L0.5631.00
54_K85_G0.5621.00
284_V288_M0.5621.00
75_G79_T0.5621.00
14_P18_G0.5601.00
35_M43_I0.5601.00
101_L266_W0.5601.00
24_F27_M0.5591.00
7_R10_L0.5581.00
10_L13_I0.5561.00
92_I269_L0.5561.00
127_S131_Y0.5551.00
157_S161_G0.5531.00
283_P286_M0.5521.00
297_V300_N0.5521.00
186_L190_V0.5511.00
191_L257_S0.5501.00
199_L245_I0.5491.00
105_V184_L0.5471.00
198_G249_M0.5451.00
121_S134_T0.5441.00
239_L242_V0.5441.00
99_T261_E0.5431.00
312_P315_E0.5431.00
181_I188_A0.5411.00
301_L305_I0.5411.00
189_F193_T0.5411.00
217_R220_R0.5391.00
107_T111_L0.5371.00
227_N230_L0.5361.00
170_T182_H0.5361.00
293_A297_V0.5351.00
111_L199_L0.5351.00
231_F236_R0.5351.00
198_G202_Y0.5341.00
261_E268_G0.5341.00
8_R11_M0.5321.00
225_K229_V0.5301.00
202_Y206_N0.5301.00
80_S84_K0.5281.00
123_K211_L0.5271.00
106_S257_S0.5271.00
112_M115_I0.5241.00
160_L163_F0.5241.00
4_Y301_L0.5220.99
145_N149_G0.5220.99
61_Q64_Q0.5210.99
5_I301_L0.5190.99
36_T40_D0.5190.99
21_I69_L0.5170.99
4_Y314_I0.5160.99
52_I57_L0.5160.99
103_M257_S0.5150.99
12_S16_L0.5150.99
77_F92_I0.5150.99
307_Y311_D0.5140.99
249_M252_S0.5140.99
245_I249_M0.5140.99
111_L115_I0.5110.99
124_R231_F0.5110.99
156_L159_N0.5110.99
286_M290_V0.5080.99
201_R205_S0.5060.99
258_V273_F0.5060.99
4_Y305_I0.5050.99
122_A130_D0.5050.99
216_I220_R0.5050.99
121_S204_R0.5040.99
274_V277_A0.5010.99
79_T84_K0.5000.99
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  
3tuiA 2 0.6614 99.9 0.653 Contact Map
4tquM 1 0.8481 99.9 0.665 Contact Map
3rlfF 1 0.8418 99.8 0.684 Contact Map
4ymuD 2 0.6646 99.8 0.698 Contact Map
2onkC 2 0.788 99.8 0.699 Contact Map
3d31C 2 0.7816 99.8 0.7 Contact Map
4tquN 1 0.807 99.7 0.721 Contact Map
3rlfG 1 0.8196 99.7 0.734 Contact Map
2nq2A 2 0.8418 4.8 0.965 Contact Map
1q16C 2 0.3734 4.3 0.966 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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