APPB - BACSU - GREMLIN Contacts

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APPB - Oligopeptide transport system permease protein AppB

UniProt:	P42062	Sequences: MAAYIIRRTLMSIPILLGITILSFVIMKAAPGDPMTLMMDPKISQADREQFIEKYGLNDPQYVQYLKWLGNMVQGDFGTSIVRKGTPVSELIMARLPNTLLLMLVSTILALMISIPFGVLSAKRPYSKIDYGITFTSFIGLAIPNFWFGLILIMVLSVNLGWFPTGGVETLNTEFNIFDRIHHLILPAFVLATADMAGLTRYTRSNMLDVLNQDYIRTARAKGFKENRVLFKHGLRNALLPVITIFGLMIPSFIGGSVVVEQIFTWPGLGKLFVDSAFQRDYPVIMAMTVISAVLVVVGNLIADILYAIVDPRIEY	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

ECOLI - DPPB YEJB DDPB NIKB GSIC OPPB SAPB YEJE DPPC SAPC NIKC DDPC GSID OPPC
BACSU - APPB OPPB DPPB DPPC APPC OPPC
HALSA - Q9HMX0 Q9HMI2 Q9HMW3 Q9HMW2 Q9HMI1 Q9HMX1
SULSO - Q97YQ0 Q97VF8 Q97UH1 Q97VK6 Q97UG4 Q97YP1 Q97VK7 Q97UG3 Q97UH2 Q97YP2 Q97YP9 Q97VF6

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_D	63_V	3.379	1.00
59_D	67_K	3.309	1.00
28_K	64_Q	3.295	1.00
66_L	70_G	2.955	1.00
70_G	74_Q	2.803	1.00
20_T	65_Y	2.781	1.00
207_M	234_G	2.660	1.00
45_Q	49_E	2.646	1.00
53_E	58_N	2.599	1.00
33_D	52_I	2.473	1.00
220_R	226_E	2.448	1.00
105_V	188_A	2.448	1.00
228_R	232_K	2.434	1.00
98_N	266_W	2.424	1.00
21_I	65_Y	2.357	1.00
271_K	275_D	2.336	1.00
216_I	234_G	2.259	1.00
210_V	215_Y	2.193	1.00
62_Y	66_L	2.131	1.00
91_L	272_L	2.095	1.00
210_V	213_Q	2.069	1.00
87_P	90_E	2.016	1.00
225_K	228_R	2.000	1.00
247_G	303_A	1.996	1.00
117_F	133_I	1.990	1.00
48_R	52_I	1.946	1.00
19_I	293_A	1.937	1.00
211_L	234_G	1.930	1.00
84_K	91_L	1.928	1.00
163_F	182_H	1.914	1.00
227_N	231_F	1.896	1.00
47_D	50_Q	1.886	1.00
112_M	116_P	1.850	1.00
109_L	192_A	1.850	1.00
163_F	185_I	1.825	1.00
44_S	47_D	1.808	1.00
130_D	204_R	1.804	1.00
124_R	127_S	1.768	1.00
157_S	165_T	1.753	1.00
86_T	90_E	1.751	1.00
50_Q	54_K	1.742	1.00
63_V	67_K	1.734	1.00
243_I	310_V	1.733	1.00
216_I	229_V	1.709	1.00
16_L	294_V	1.699	1.00
128_K	132_G	1.680	1.00
218_T	222_K	1.679	1.00
88_V	287_A	1.672	1.00
49_E	53_E	1.664	1.00
49_E	52_I	1.660	1.00
224_F	228_R	1.655	1.00
122_A	207_M	1.654	1.00
67_K	70_G	1.651	1.00
71_N	76_D	1.646	1.00
120_L	124_R	1.618	1.00
168_V	266_W	1.604	1.00
89_S	93_M	1.580	1.00
244_T	307_Y	1.577	1.00
123_K	230_L	1.574	1.00
129_I	133_I	1.564	1.00
154_M	159_N	1.536	1.00
10_L	14_P	1.528	1.00
120_L	129_I	1.522	1.00
273_F	288_M	1.517	1.00
306_L	309_I	1.503	1.00
124_R	129_I	1.496	1.00
12_S	297_V	1.492	1.00
101_L	168_V	1.485	1.00
119_V	207_M	1.481	1.00
113_I	116_P	1.473	1.00
86_T	94_A	1.468	1.00
17_L	65_Y	1.454	1.00
98_N	168_V	1.449	1.00
72_M	77_F	1.440	1.00
155_V	159_N	1.435	1.00
210_V	238_A	1.434	1.00
215_Y	237_N	1.422	1.00
110_A	195_D	1.421	1.00
147_W	151_I	1.419	1.00
188_A	192_A	1.418	1.00
113_I	196_M	1.417	1.00
214_D	217_R	1.415	1.00
152_L	190_V	1.408	1.00
210_V	216_I	1.398	1.00
222_K	233_H	1.388	1.00
67_K	71_N	1.383	1.00
35_M	48_R	1.359	1.00
192_A	196_M	1.350	1.00
91_L	284_V	1.349	1.00
51_F	54_K	1.344	1.00
17_L	21_I	1.340	1.00
6_I	10_L	1.340	1.00
126_Y	130_D	1.335	1.00
20_T	68_W	1.329	1.00
276_S	284_V	1.320	1.00
63_V	66_L	1.316	1.00
51_F	55_Y	1.300	1.00
60_P	63_V	1.297	1.00
272_L	284_V	1.294	1.00
155_V	160_L	1.288	1.00
111_L	246_F	1.273	1.00
118_G	122_A	1.267	1.00
33_D	36_T	1.258	1.00
114_S	203_T	1.244	1.00
94_A	97_P	1.229	1.00
240_L	307_Y	1.228	1.00
79_T	87_P	1.226	1.00
118_G	203_T	1.224	1.00
114_S	199_L	1.217	1.00
107_T	246_F	1.210	1.00
203_T	242_V	1.204	1.00
77_F	287_A	1.200	1.00
143_I	148_F	1.197	1.00
101_L	105_V	1.188	1.00
86_T	91_L	1.185	1.00
98_N	101_L	1.183	1.00
77_F	89_S	1.183	1.00
210_V	234_G	1.179	1.00
56_G	59_D	1.168	1.00
140_G	197_A	1.166	1.00
181_I	185_I	1.166	1.00
202_Y	245_I	1.162	1.00
204_R	208_L	1.148	1.00
59_D	62_Y	1.147	1.00
305_I	309_I	1.142	1.00
56_G	67_K	1.140	1.00
122_A	211_L	1.138	1.00
170_T	183_H	1.134	1.00
123_K	226_E	1.130	1.00
133_I	200_T	1.125	1.00
21_I	25_V	1.122	1.00
12_S	301_L	1.121	1.00
101_L	184_L	1.118	1.00
36_T	48_R	1.117	1.00
288_M	292_S	1.115	1.00
82_V	279_Q	1.109	1.00
17_L	69_L	1.105	1.00
199_L	249_M	1.097	1.00
122_A	208_L	1.092	1.00
151_I	155_V	1.090	1.00
145_N	260_V	1.087	1.00
152_L	186_L	1.087	1.00
121_S	133_I	1.086	1.00
93_M	97_P	1.081	1.00
274_V	278_F	1.079	1.00
80_S	281_D	1.073	1.00
5_I	305_I	1.068	1.00
90_E	94_A	1.061	1.00
299_G	303_A	1.052	1.00
21_I	61_Q	1.049	1.00
117_F	200_T	1.041	1.00
16_L	297_V	1.038	1.00
156_L	160_L	1.038	1.00
9_T	301_L	1.037	1.00
28_K	61_Q	1.035	1.00
50_Q	53_E	1.031	1.00
4_Y	308_A	1.025	1.00
91_L	94_A	1.023	1.00
106_S	192_A	1.017	1.00
275_D	279_Q	1.016	1.00
190_V	194_A	1.009	1.00
163_F	186_L	1.004	1.00
39_M	51_F	1.003	1.00
169_E	183_H	0.996	1.00
184_L	188_A	0.995	1.00
20_T	290_V	0.991	1.00
46_A	50_Q	0.989	1.00
226_E	229_V	0.989	1.00
32_G	280_R	0.982	1.00
53_E	59_D	0.981	1.00
25_V	28_K	0.980	1.00
128_K	131_Y	0.980	1.00
224_F	229_V	0.970	1.00
302_I	306_L	0.966	1.00
72_M	290_V	0.959	1.00
130_D	208_L	0.957	1.00
203_T	207_M	0.952	1.00
90_E	93_M	0.950	1.00
137_S	200_T	0.949	1.00
125_P	212_N	0.948	1.00
185_I	189_F	0.947	1.00
126_Y	131_Y	0.944	1.00
219_A	229_V	0.944	1.00
103_M	253_F	0.935	1.00
251_P	296_V	0.934	1.00
149_G	190_V	0.927	1.00
25_V	61_Q	0.925	1.00
71_N	74_Q	0.923	1.00
109_L	188_A	0.920	1.00
219_A	224_F	0.919	1.00
104_L	108_I	0.917	1.00
70_G	73_V	0.915	1.00
250_I	299_G	0.912	1.00
308_A	314_I	0.910	1.00
220_R	229_V	0.906	1.00
95_R	272_L	0.906	1.00
14_P	17_L	0.905	1.00
39_M	43_I	0.904	1.00
18_G	22_L	0.904	1.00
66_L	69_L	0.901	1.00
65_Y	69_L	0.899	1.00
28_K	282_Y	0.894	1.00
116_P	119_V	0.890	1.00
189_F	192_A	0.887	1.00
243_I	303_A	0.887	1.00
229_V	234_G	0.885	1.00
79_T	85_G	0.883	1.00
114_S	118_G	0.880	1.00
238_A	241_P	0.880	1.00
156_L	163_F	0.880	1.00
272_L	276_S	0.874	1.00
228_R	231_F	0.870	1.00
134_T	200_T	0.869	1.00
73_V	76_D	0.868	1.00
35_M	39_M	0.867	1.00
119_V	230_L	0.867	1.00
149_G	263_I	0.853	1.00
68_W	72_M	0.851	1.00
114_S	200_T	0.851	1.00
81_I	283_P	0.850	1.00
307_Y	314_I	0.849	1.00
136_T	140_G	0.843	1.00
148_F	193_T	0.841	1.00
107_T	250_I	0.840	1.00
231_F	234_G	0.840	1.00
106_S	191_L	0.840	1.00
207_M	238_A	0.838	1.00
101_L	104_L	0.833	1.00
24_F	28_K	0.826	1.00
124_R	226_E	0.826	1.00
132_G	136_T	0.824	1.00
35_M	51_F	0.823	1.00
123_K	231_F	0.820	1.00
206_N	238_A	0.820	1.00
92_I	288_M	0.820	1.00
115_I	203_T	0.819	1.00
105_V	266_W	0.819	1.00
298_V	302_I	0.818	1.00
35_M	52_I	0.817	1.00
116_P	120_L	0.817	1.00
262_Q	271_K	0.815	1.00
99_T	103_M	0.811	1.00
118_G	207_M	0.810	1.00
145_N	193_T	0.807	1.00
9_T	13_I	0.807	1.00
92_I	287_A	0.805	1.00
257_S	260_V	0.805	1.00
131_Y	134_T	0.804	1.00
45_Q	48_R	0.803	1.00
111_L	116_P	0.798	1.00
46_A	49_E	0.797	1.00
23_S	289_T	0.792	1.00
104_L	250_I	0.788	1.00
282_Y	286_M	0.786	1.00
273_F	276_S	0.785	1.00
168_V	184_L	0.780	1.00
102_L	188_A	0.779	1.00
251_P	299_G	0.779	1.00
21_I	62_Y	0.775	1.00
106_S	110_A	0.775	1.00
196_M	200_T	0.774	1.00
129_I	132_G	0.772	1.00
140_G	193_T	0.769	1.00
117_F	196_M	0.767	1.00
125_P	208_L	0.762	1.00
100_L	104_L	0.758	1.00
305_I	308_A	0.756	1.00
70_G	75_G	0.750	1.00
115_I	242_V	0.748	1.00
262_Q	274_V	0.745	1.00
190_V	260_V	0.742	1.00
69_L	73_V	0.742	1.00
294_V	298_V	0.737	1.00
272_L	288_M	0.733	1.00
219_A	233_H	0.731	1.00
43_I	48_R	0.729	1.00
195_D	198_G	0.726	1.00
113_I	117_F	0.725	1.00
226_E	230_L	0.723	1.00
203_T	238_A	0.723	1.00
156_L	162_W	0.722	1.00
97_P	100_L	0.721	1.00
206_N	210_V	0.718	1.00
159_N	162_W	0.718	1.00
156_L	186_L	0.717	1.00
119_V	235_L	0.717	1.00
47_D	51_F	0.716	1.00
154_M	158_V	0.714	1.00
15_I	297_V	0.712	1.00
185_I	188_A	0.709	1.00
203_T	206_N	0.707	1.00
275_D	278_F	0.707	1.00
38_M	51_F	0.704	1.00
296_V	300_N	0.702	1.00
69_L	72_M	0.696	1.00
203_T	235_L	0.694	1.00
243_I	306_L	0.686	1.00
166_G	265_T	0.682	1.00
96_L	100_L	0.681	1.00
8_R	304_D	0.681	1.00
267_P	271_K	0.680	1.00
110_A	192_A	0.680	1.00
181_I	184_L	0.679	1.00
182_H	185_I	0.679	1.00
286_M	289_T	0.678	1.00
273_F	292_S	0.670	1.00
152_L	189_F	0.666	1.00
285_I	289_T	0.665	1.00
25_V	29_A	0.663	1.00
91_L	95_R	0.663	1.00
121_S	130_D	0.662	1.00
23_S	27_M	0.661	1.00
219_A	222_K	0.660	1.00
153_I	165_T	0.660	1.00
141_L	197_A	0.659	1.00
105_V	181_I	0.651	1.00
13_I	17_L	0.651	1.00
23_S	28_K	0.651	1.00
287_A	291_I	0.649	1.00
97_P	101_L	0.649	1.00
137_S	197_A	0.648	1.00
164_P	167_G	0.641	1.00
63_V	70_G	0.639	1.00
262_Q	275_D	0.639	1.00
132_G	135_F	0.635	1.00
4_Y	8_R	0.635	1.00
35_M	55_Y	0.634	1.00
28_K	286_M	0.633	1.00
105_V	185_I	0.633	1.00
113_I	192_A	0.630	1.00
215_Y	219_A	0.628	1.00
133_I	137_S	0.628	1.00
80_S	86_T	0.628	1.00
105_V	109_L	0.627	1.00
84_K	284_V	0.626	1.00
192_A	195_D	0.625	1.00
27_M	285_I	0.624	1.00
303_A	307_Y	0.620	1.00
224_F	233_H	0.618	1.00
258_V	274_V	0.617	1.00
209_D	213_Q	0.617	1.00
95_R	271_K	0.612	1.00
130_D	134_T	0.612	1.00
43_I	47_D	0.610	1.00
167_G	183_H	0.610	1.00
108_I	112_M	0.609	1.00
93_M	96_L	0.609	1.00
135_F	139_I	0.608	1.00
197_A	200_T	0.607	1.00
164_P	183_H	0.605	1.00
247_G	299_G	0.605	1.00
308_A	315_E	0.600	1.00
124_R	130_D	0.600	1.00
49_E	58_N	0.597	1.00
7_R	11_M	0.596	1.00
292_S	296_V	0.595	1.00
239_L	243_I	0.593	1.00
198_G	245_I	0.592	1.00
295_L	299_G	0.592	1.00
145_N	194_A	0.591	1.00
143_I	147_W	0.589	1.00
199_L	203_T	0.589	1.00
258_V	262_Q	0.588	1.00
127_S	132_G	0.587	1.00
230_L	234_G	0.584	1.00
103_M	107_T	0.582	1.00
99_T	257_S	0.581	1.00
88_V	272_L	0.580	1.00
199_L	242_V	0.580	1.00
276_S	285_I	0.578	1.00
34_P	282_Y	0.578	1.00
206_N	209_D	0.576	1.00
145_N	148_F	0.575	1.00
127_S	130_D	0.574	1.00
119_V	231_F	0.573	1.00
103_M	250_I	0.572	1.00
109_L	189_F	0.570	1.00
20_T	69_L	0.569	1.00
135_F	138_F	0.568	1.00
240_L	314_I	0.567	1.00
11_M	14_P	0.567	1.00
88_V	284_V	0.566	1.00
147_W	150_L	0.563	1.00
54_K	85_G	0.562	1.00
284_V	288_M	0.562	1.00
75_G	79_T	0.562	1.00
14_P	18_G	0.560	1.00
35_M	43_I	0.560	1.00
101_L	266_W	0.560	1.00
24_F	27_M	0.559	1.00
7_R	10_L	0.558	1.00
10_L	13_I	0.556	1.00
92_I	269_L	0.556	1.00
127_S	131_Y	0.555	1.00
157_S	161_G	0.553	1.00
283_P	286_M	0.552	1.00
297_V	300_N	0.552	1.00
186_L	190_V	0.551	1.00
191_L	257_S	0.550	1.00
199_L	245_I	0.549	1.00
105_V	184_L	0.547	1.00
198_G	249_M	0.545	1.00
121_S	134_T	0.544	1.00
239_L	242_V	0.544	1.00
99_T	261_E	0.543	1.00
312_P	315_E	0.543	1.00
181_I	188_A	0.541	1.00
301_L	305_I	0.541	1.00
189_F	193_T	0.541	1.00
217_R	220_R	0.539	1.00
107_T	111_L	0.537	1.00
227_N	230_L	0.536	1.00
170_T	182_H	0.536	1.00
293_A	297_V	0.535	1.00
111_L	199_L	0.535	1.00
231_F	236_R	0.535	1.00
198_G	202_Y	0.534	1.00
261_E	268_G	0.534	1.00
8_R	11_M	0.532	1.00
225_K	229_V	0.530	1.00
202_Y	206_N	0.530	1.00
80_S	84_K	0.528	1.00
123_K	211_L	0.527	1.00
106_S	257_S	0.527	1.00
112_M	115_I	0.524	1.00
160_L	163_F	0.524	1.00
4_Y	301_L	0.522	0.99
145_N	149_G	0.522	0.99
61_Q	64_Q	0.521	0.99
5_I	301_L	0.519	0.99
36_T	40_D	0.519	0.99
21_I	69_L	0.517	0.99
4_Y	314_I	0.516	0.99
52_I	57_L	0.516	0.99
103_M	257_S	0.515	0.99
12_S	16_L	0.515	0.99
77_F	92_I	0.515	0.99
307_Y	311_D	0.514	0.99
249_M	252_S	0.514	0.99
245_I	249_M	0.514	0.99
111_L	115_I	0.511	0.99
124_R	231_F	0.511	0.99
156_L	159_N	0.511	0.99
286_M	290_V	0.508	0.99
201_R	205_S	0.506	0.99
258_V	273_F	0.506	0.99
4_Y	305_I	0.505	0.99
122_A	130_D	0.505	0.99
216_I	220_R	0.505	0.99
121_S	204_R	0.504	0.99
274_V	277_A	0.501	0.99
79_T	84_K	0.500	0.99

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

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

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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