MotA_ExbB - PFAM28P - GREMLIN Contacts

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MotA_ExbB - MotA/TolQ/ExbB proton channel family

PFAM:	PF01618	Sequences: QNSPLARVLAAGLRELARDPEAIERALERAIAREVARLERGLSFLATIGSVAPFLGLLGTVWGIINAFQAIAAAGSASLAVVAPGIAEALITTAAGLAVAIPAVIAYNYLSRRVDRLVAEMEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	123 (118)
Sequences:	45316 (22401)
Seq/√Len:	2062.1
META:	0.864

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_N	88_E	3.052	1.00
35_V	118_V	2.988	1.00
109_Y	113_R	2.595	1.00
12_G	27_L	2.401	1.00
11_A	30_A	2.076	1.00
7_R	34_E	2.047	1.00
10_A	14_R	2.028	1.00
34_E	37_R	1.968	1.00
69_Q	87_A	1.895	1.00
49_G	104_V	1.889	1.00
112_R	116_R	1.850	1.00
19_D	22_A	1.838	1.00
66_N	70_A	1.819	1.00
30_A	34_E	1.789	1.00
59_G	92_T	1.782	1.00
42_L	114_V	1.763	1.00
65_I	94_A	1.722	1.00
52_A	99_V	1.693	1.00
62_W	88_E	1.690	1.00
66_N	85_G	1.664	1.00
62_W	94_A	1.661	1.00
113_R	117_L	1.659	1.00
51_V	105_I	1.643	1.00
38_L	114_V	1.629	1.00
61_V	93_T	1.616	1.00
107_Y	111_S	1.600	1.00
69_Q	73_A	1.547	1.00
99_V	103_A	1.492	1.00
36_A	119_A	1.450	1.00
20_P	24_E	1.400	1.00
70_A	81_V	1.396	1.00
18_R	22_A	1.364	1.00
81_V	84_P	1.356	1.00
34_E	38_L	1.350	1.00
78_S	81_V	1.345	1.00
29_R	33_R	1.344	1.00
47_T	108_N	1.326	1.00
70_A	73_A	1.326	1.00
72_A	87_A	1.307	1.00
24_E	28_E	1.296	1.00
74_A	81_V	1.267	1.00
58_L	94_A	1.263	1.00
46_A	107_Y	1.246	1.00
113_R	116_R	1.243	1.00
44_F	48_I	1.230	1.00
45_L	106_A	1.221	1.00
7_R	10_A	1.206	1.00
31_I	35_V	1.181	1.00
22_A	26_A	1.162	1.00
63_G	85_G	1.153	1.00
30_A	33_R	1.140	1.00
9_L	13_L	1.137	1.00
114_V	118_V	1.125	1.00
28_E	32_A	1.111	1.00
35_V	114_V	1.088	1.00
26_A	30_A	1.079	1.00
25_R	28_E	1.050	1.00
72_A	84_P	1.044	1.00
58_L	98_A	1.043	1.00
117_L	120_E	1.032	1.00
73_A	81_V	1.021	1.00
45_L	103_A	1.020	1.00
111_S	115_D	1.014	1.00
66_N	69_Q	1.012	1.00
36_A	116_R	1.008	1.00
35_V	39_E	1.002	1.00
91_I	95_A	0.992	1.00
47_T	105_I	0.987	1.00
67_A	85_G	0.984	1.00
38_L	117_L	0.980	1.00
75_G	78_S	0.977	1.00
32_A	36_A	0.975	1.00
70_A	74_A	0.968	1.00
50_S	104_V	0.958	1.00
70_A	85_G	0.949	1.00
108_N	111_S	0.932	1.00
21_E	25_R	0.924	1.00
73_A	80_A	0.914	1.00
79_L	84_P	0.906	1.00
106_A	110_L	0.897	1.00
48_I	103_A	0.896	1.00
42_L	46_A	0.884	1.00
43_S	112_R	0.881	1.00
97_L	101_I	0.874	1.00
22_A	25_R	0.869	1.00
23_I	26_A	0.856	1.00
58_L	97_L	0.855	1.00
58_L	62_W	0.854	1.00
62_W	66_N	0.847	1.00
11_A	15_E	0.820	1.00
67_A	70_A	0.820	1.00
39_E	114_V	0.818	1.00
20_P	25_R	0.812	1.00
50_S	53_P	0.800	1.00
62_W	65_I	0.799	1.00
52_A	103_A	0.789	1.00
29_R	36_A	0.788	1.00
92_T	99_V	0.786	1.00
11_A	14_R	0.786	1.00
31_I	118_V	0.779	1.00
58_L	101_I	0.778	1.00
118_V	122_E	0.773	1.00
65_I	91_I	0.773	1.00
43_S	47_T	0.771	1.00
6_A	10_A	0.769	1.00
67_A	90_L	0.758	1.00
89_A	93_T	0.749	1.00
71_I	83_A	0.749	1.00
25_R	29_R	0.748	1.00
13_L	16_L	0.747	1.00
69_Q	72_A	0.745	1.00
15_E	26_A	0.736	1.00
61_V	90_L	0.729	1.00
32_A	35_V	0.726	1.00
23_I	27_L	0.726	1.00
105_I	109_Y	0.725	1.00
74_A	77_A	0.719	1.00
19_D	23_I	0.714	1.00
76_S	80_A	0.710	1.00
51_V	104_V	0.706	1.00
43_S	46_A	0.697	1.00
42_L	110_L	0.691	1.00
26_A	29_R	0.688	1.00
54_F	100_A	0.683	1.00
42_L	111_S	0.680	1.00
118_V	121_M	0.678	1.00
61_V	94_A	0.667	1.00
55_L	101_I	0.660	1.00
46_A	50_S	0.654	1.00
8_V	121_M	0.654	1.00
106_A	109_Y	0.645	1.00
84_P	88_E	0.642	1.00
29_R	32_A	0.633	1.00
46_A	108_N	0.630	1.00
12_G	16_L	0.625	1.00
73_A	77_A	0.620	1.00
31_I	121_M	0.618	1.00
48_I	52_A	0.616	1.00
112_R	115_D	0.612	1.00
102_P	106_A	0.611	1.00
21_E	24_E	0.610	1.00
46_A	111_S	0.609	1.00
73_A	76_S	0.602	1.00
70_A	79_L	0.600	1.00
94_A	98_A	0.591	1.00
115_D	118_V	0.589	1.00
95_A	99_V	0.585	1.00
116_R	120_E	0.579	1.00
15_E	18_R	0.575	1.00
98_A	102_P	0.573	1.00
119_A	122_E	0.573	1.00
7_R	37_R	0.566	1.00
33_R	36_A	0.565	1.00
104_V	108_N	0.561	1.00
12_G	15_E	0.560	1.00
99_V	102_P	0.555	1.00
39_E	43_S	0.554	1.00
76_S	79_L	0.550	1.00
27_L	30_A	0.549	1.00
74_A	78_S	0.549	1.00
37_R	40_R	0.547	1.00
51_V	101_I	0.547	1.00
40_R	43_S	0.544	1.00
44_F	47_T	0.538	1.00
67_A	82_V	0.535	1.00
57_L	86_I	0.534	1.00
42_L	107_Y	0.533	1.00
6_A	9_L	0.532	1.00
109_Y	112_R	0.531	1.00
60_T	94_A	0.528	1.00
57_L	93_T	0.525	1.00
20_P	23_I	0.520	1.00
88_E	91_I	0.508	1.00
54_F	64_I	0.504	1.00
68_F	85_G	0.504	1.00
16_L	19_D	0.502	1.00
49_G	107_Y	0.500	1.00

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

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
2kluA	1	0.3659	13.3	0.889	Contact Map
4tllB	2	0.6098	12.2	0.89	Contact Map
4tllA	1	0.4553	9.5	0.896	Contact Map
1ji6A	1	0.4878	9.1	0.897	Contact Map
4cbkA	3	0.4959	8.8	0.897	Contact Map
4ev6A	3	0.8293	8.5	0.898	Contact Map
4u2pA	4	0.6423	8.1	0.899	Contact Map
3eb7A	2	0.5203	7.8	0.899	Contact Map
4aurA	1	0.9106	7.4	0.9	Contact Map
4v1gA	3	0.6423	7.3	0.901	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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