FtsX - PFAM28P - GREMLIN Contacts

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FtsX - FtsX-like permease family

PFAM:	PF02687	Sequences: ILFAGLALLVACIGIMNLMLASVTERTREIGIRKALGASRRQILRQFLTESLLLALIGGLLGLLLGLLLARLLSSLLPAGLPLALPISIDPWVLLLALLLSLLVGLLAGLYPARRAARLDP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	121 (118)
Sequences:	111278 (76346)
Seq/√Len:	7028.2
META:	0.781

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_I	47_F	3.099	1.00
39_S	42_Q	2.966	1.00
110_L	114_R	2.614	1.00
51_S	109_G	2.540	1.00
90_D	93_V	2.127	1.00
26_R	50_E	2.109	1.00
49_T	53_L	2.085	1.00
44_L	114_R	2.083	1.00
118_R	121_P	2.005	1.00
114_R	118_R	1.962	1.00
45_R	49_T	1.896	1.00
91_P	95_L	1.859	1.00
71_R	75_S	1.851	1.00
59_G	98_L	1.850	1.00
33_R	46_Q	1.846	1.00
71_R	74_S	1.824	1.00
33_R	38_A	1.735	1.00
59_G	63_L	1.730	1.00
83_L	86_P	1.728	1.00
68_L	71_R	1.667	1.00
55_A	105_G	1.590	1.00
34_K	40_R	1.584	1.00
92_W	96_L	1.545	1.00
62_G	66_G	1.542	1.00
92_W	95_L	1.525	1.00
84_A	87_I	1.487	1.00
7_A	14_G	1.484	1.00
88_S	92_W	1.441	1.00
41_R	45_R	1.435	1.00
113_A	117_A	1.425	1.00
12_C	104_V	1.412	1.00
40_R	117_A	1.405	1.00
26_R	29_E	1.389	1.00
19_M	51_S	1.382	1.00
59_G	101_S	1.356	1.00
64_L	68_L	1.345	1.00
52_L	106_L	1.306	1.00
24_T	27_T	1.283	1.00
64_L	67_L	1.278	1.00
68_L	72_L	1.256	1.00
67_L	71_R	1.234	1.00
60_L	64_L	1.224	1.00
42_Q	45_R	1.209	1.00
44_L	110_L	1.203	1.00
38_A	42_Q	1.202	1.00
88_S	91_P	1.202	1.00
72_L	76_L	1.200	1.00
40_R	118_R	1.190	1.00
72_L	75_S	1.161	1.00
29_E	33_R	1.156	1.00
95_L	99_L	1.154	1.00
61_L	64_L	1.128	1.00
114_R	117_A	1.124	1.00
108_A	112_P	1.119	1.00
44_L	117_A	1.073	1.00
98_L	102_L	1.072	1.00
16_M	20_L	1.047	1.00
84_A	88_S	1.046	1.00
44_L	113_A	1.038	1.00
17_N	21_A	1.008	1.00
67_L	89_I	1.005	1.00
58_G	62_G	1.000	1.00
103_L	107_L	0.994	1.00
16_M	108_A	0.993	1.00
75_S	78_P	0.976	1.00
55_A	101_S	0.970	1.00
34_K	43_I	0.969	1.00
38_A	43_I	0.964	1.00
50_E	53_L	0.962	1.00
95_L	98_L	0.956	1.00
57_I	60_L	0.954	1.00
40_R	44_L	0.953	1.00
70_A	74_S	0.947	1.00
55_A	59_G	0.937	1.00
21_A	25_E	0.936	1.00
74_S	78_P	0.934	1.00
93_V	97_A	0.931	1.00
94_L	98_L	0.917	1.00
115_R	119_L	0.898	1.00
109_G	113_A	0.898	1.00
48_L	110_L	0.897	1.00
27_T	31_G	0.896	1.00
49_T	52_L	0.892	1.00
5_G	9_L	0.892	1.00
113_A	116_A	0.886	1.00
28_R	32_I	0.877	1.00
46_Q	49_T	0.876	1.00
100_L	104_V	0.875	1.00
51_S	55_A	0.874	1.00
65_L	69_L	0.865	1.00
19_M	22_S	0.859	1.00
69_L	72_L	0.853	1.00
99_L	103_L	0.849	1.00
27_T	119_L	0.827	1.00
104_V	108_A	0.820	1.00
93_V	96_L	0.815	1.00
31_G	35_A	0.813	1.00
12_C	108_A	0.798	1.00
48_L	52_L	0.792	1.00
73_L	76_L	0.786	1.00
96_L	100_L	0.774	1.00
52_L	105_G	0.773	1.00
22_S	50_E	0.760	1.00
115_R	118_R	0.759	1.00
26_R	47_F	0.756	1.00
74_S	87_I	0.750	1.00
66_G	70_A	0.737	1.00
89_I	94_L	0.732	1.00
91_P	94_L	0.731	1.00
63_L	94_L	0.731	1.00
100_L	103_L	0.720	1.00
111_Y	115_R	0.715	1.00
52_L	55_A	0.709	1.00
89_I	93_V	0.709	1.00
71_R	87_I	0.708	1.00
65_L	68_L	0.707	1.00
56_L	60_L	0.699	1.00
30_I	43_I	0.698	1.00
80_G	83_L	0.696	1.00
27_T	115_R	0.694	1.00
41_R	44_L	0.694	1.00
53_L	56_L	0.688	1.00
18_L	22_S	0.686	1.00
56_L	59_G	0.676	1.00
83_L	87_I	0.675	1.00
10_V	14_G	0.674	1.00
20_L	111_Y	0.670	1.00
81_L	84_A	0.667	1.00
97_A	101_S	0.666	1.00
55_A	102_L	0.665	1.00
99_L	102_L	0.663	1.00
96_L	99_L	0.656	1.00
107_L	110_L	0.653	1.00
63_L	98_L	0.651	1.00
19_M	54_L	0.646	1.00
56_L	102_L	0.638	1.00
78_P	84_A	0.636	1.00
29_E	32_I	0.631	1.00
24_T	115_R	0.618	1.00
44_L	48_L	0.612	1.00
14_G	33_R	0.602	1.00
32_I	35_A	0.597	1.00
40_R	114_R	0.597	1.00
78_P	81_L	0.592	1.00
73_L	77_L	0.591	1.00
77_L	83_L	0.586	1.00
53_L	57_I	0.584	1.00
48_L	106_L	0.580	1.00
111_Y	114_R	0.577	1.00
63_L	67_L	0.574	1.00
55_A	109_G	0.572	1.00
19_M	23_V	0.568	1.00
57_I	61_L	0.565	1.00
70_A	73_L	0.564	1.00
85_L	88_S	0.563	1.00
3_F	21_A	0.563	1.00
52_L	56_L	0.549	1.00
82_P	85_L	0.549	1.00
98_L	101_S	0.546	1.00
18_L	33_R	0.543	1.00
61_L	65_L	0.541	1.00
23_V	47_F	0.536	1.00
60_L	63_L	0.535	1.00
20_L	24_T	0.533	1.00
23_V	30_I	0.531	1.00
83_L	88_S	0.530	1.00
33_R	42_Q	0.526	1.00
50_E	54_L	0.526	1.00
107_L	111_Y	0.522	1.00
51_S	113_A	0.521	1.00
67_L	70_A	0.511	1.00
106_L	110_L	0.511	1.00
4_A	7_A	0.511	1.00
85_L	89_I	0.509	1.00
15_I	58_G	0.501	1.00
67_L	94_L	0.500	1.00
101_S	105_G	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
3tuiA	2	0.9752	30.4	0.84	Contact Map
3rlfF	1	0.9091	18.5	0.856	Contact Map
4av3A	2	0.7851	16.8	0.859	Contact Map
4tquM	1	0.9835	15.6	0.861	Contact Map
4ymuD	2	0.9669	12.7	0.866	Contact Map
4il3A	1	0.843	7.5	0.879	Contact Map
2onkC	2	0.9504	6.7	0.882	Contact Map
3d31C	2	0.9008	5.1	0.888	Contact Map
4eneA	2	0.7107	4.2	0.893	Contact Map
4aw6A	2	0.9008	4.1	0.893	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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