Cytochrom_C_asm - PFAM28P - GREMLIN Contacts

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Cytochrom_C_asm - Cytochrome C assembly protein

PFAM:	PF01578	Sequences: WGNLYGSLLLWAWLLALLGLLLERFYRRLPLRLLGAVLLPLALLLLGFALFLLLPLPPDGAGLNPLLQSPWLAIHVPLLYLGYAAFAVAFAFAIAYLLQERRLKRKRLGGLLRRLPPLETLDRLARRWLLVGFPFLTLGIILGAIWAELGWGGYWGWDPKENWSLIPWLVYAALLHSRLERGWRGRWAALLAILGFALVLLGYFGVRSLLEGLH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	214 (207)
Sequences:	41109 (22715)
Seq/√Len:	1578.8
META:	0.883

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
133_F	172_A	5.365	1.00
137_T	168_W	5.152	1.00
79_L	139_G	4.272	1.00
86_F	171_Y	4.200	1.00
170_V	195_G	3.126	1.00
153_G	156_G	3.043	1.00
170_V	198_L	2.838	1.00
89_A	129_L	2.546	1.00
129_L	174_L	2.429	1.00
90_F	196_F	2.408	1.00
86_F	132_G	2.403	1.00
87_A	196_F	2.190	1.00
123_R	127_R	2.117	1.00
132_G	171_Y	2.076	1.00
171_Y	195_G	2.009	1.00
10_L	14_L	1.875	1.00
174_L	192_A	1.805	1.00
34_L	38_L	1.755	1.00
85_A	132_G	1.734	1.00
36_A	40_P	1.720	1.00
81_L	135_F	1.686	1.00
183_W	187_W	1.677	1.00
117_P	120_T	1.673	1.00
122_D	178_R	1.671	1.00
37_V	40_P	1.666	1.00
47_G	50_L	1.604	1.00
126_R	130_L	1.594	1.00
85_A	131_V	1.586	1.00
133_F	137_T	1.577	1.00
182_G	185_G	1.576	1.00
181_R	184_R	1.549	1.00
45_L	49_A	1.545	1.00
36_A	39_L	1.545	1.00
126_R	178_R	1.523	1.00
46_L	50_L	1.516	1.00
35_G	38_L	1.510	1.00
133_F	168_W	1.503	1.00
174_L	191_L	1.488	1.00
38_L	42_A	1.487	1.00
129_L	192_A	1.465	1.00
25_F	28_R	1.462	1.00
13_W	17_L	1.456	1.00
52_L	55_P	1.456	1.00
32_R	35_G	1.454	1.00
165_L	169_L	1.439	1.00
27_R	30_P	1.439	1.00
100_E	186_R	1.416	1.00
47_G	51_F	1.415	1.00
18_L	85_A	1.398	1.00
92_F	124_L	1.384	1.00
140_I	168_W	1.369	1.00
156_G	161_E	1.366	1.00
96_Y	189_A	1.353	1.00
34_L	37_V	1.334	1.00
173_A	177_S	1.319	1.00
33_L	40_P	1.306	1.00
174_L	188_A	1.299	1.00
9_L	13_W	1.292	1.00
80_Y	84_A	1.292	1.00
130_L	175_L	1.281	1.00
55_P	58_P	1.269	1.00
85_A	128_W	1.266	1.00
42_A	46_L	1.263	1.00
78_L	138_L	1.255	1.00
24_R	27_R	1.248	1.00
92_F	125_A	1.236	1.00
40_P	43_L	1.218	1.00
33_L	37_V	1.217	1.00
46_L	49_A	1.214	1.00
48_F	51_F	1.211	1.00
101_R	105_R	1.200	1.00
70_P	73_A	1.188	1.00
120_T	123_R	1.163	1.00
114_R	117_P	1.160	1.00
90_F	193_I	1.157	1.00
35_G	42_A	1.150	1.00
110_G	113_R	1.142	1.00
44_L	48_F	1.141	1.00
57_P	60_G	1.139	1.00
122_D	185_G	1.131	1.00
41_L	44_L	1.122	1.00
16_A	20_L	1.121	1.00
196_F	200_L	1.120	1.00
208_S	212_G	1.117	1.00
186_R	190_L	1.116	1.00
90_F	94_I	1.116	1.00
35_G	39_L	1.115	1.00
38_L	41_L	1.106	1.00
93_A	192_A	1.104	1.00
204_F	208_S	1.101	1.00
137_T	141_I	1.091	1.00
89_A	192_A	1.091	1.00
82_G	164_S	1.073	1.00
177_S	188_A	1.072	1.00
45_L	48_F	1.067	1.00
40_P	46_L	1.066	1.00
130_L	134_P	1.063	1.00
93_A	125_A	1.051	1.00
180_E	184_R	1.038	1.00
29_L	32_R	1.037	1.00
167_P	199_V	1.029	1.00
92_F	121_L	1.026	1.00
32_R	36_A	1.002	1.00
183_W	186_R	0.997	1.00
12_A	16_A	0.989	1.00
24_R	28_R	0.986	1.00
40_P	44_L	0.984	1.00
119_E	123_R	0.982	1.00
13_W	19_G	0.975	1.00
184_R	187_W	0.968	1.00
78_L	142_L	0.957	1.00
97_L	193_I	0.952	1.00
187_W	190_L	0.940	1.00
133_F	175_L	0.936	1.00
157_W	161_E	0.935	1.00
121_L	125_A	0.933	1.00
52_L	56_L	0.925	1.00
205_G	208_S	0.922	1.00
80_Y	83_Y	0.918	1.00
89_A	128_W	0.911	1.00
125_A	174_L	0.907	1.00
62_G	65_P	0.906	1.00
202_G	205_G	0.901	1.00
7_S	203_Y	0.900	1.00
39_L	43_L	0.899	1.00
53_L	58_P	0.889	1.00
33_L	36_A	0.886	1.00
36_A	41_L	0.884	1.00
21_L	25_F	0.884	1.00
125_A	192_A	0.877	1.00
14_L	84_A	0.877	1.00
42_A	49_A	0.873	1.00
94_I	193_I	0.868	1.00
147_A	151_W	0.867	1.00
99_Q	102_R	0.867	1.00
37_V	41_L	0.860	1.00
26_Y	29_L	0.860	1.00
174_L	178_R	0.860	1.00
37_V	42_A	0.857	1.00
206_V	210_L	0.857	1.00
203_Y	207_R	0.855	1.00
43_L	47_G	0.854	1.00
201_L	210_L	0.852	1.00
53_L	56_L	0.849	1.00
30_P	33_L	0.845	1.00
61_A	64_N	0.844	1.00
193_I	197_A	0.839	1.00
138_L	142_L	0.839	1.00
14_L	18_L	0.838	1.00
148_E	154_Y	0.832	1.00
71_W	145_I	0.831	1.00
185_G	189_A	0.829	1.00
19_G	23_E	0.825	1.00
31_L	35_G	0.824	1.00
160_K	207_R	0.821	1.00
96_Y	118_L	0.816	1.00
108_L	112_L	0.813	1.00
188_A	192_A	0.805	1.00
42_A	45_L	0.803	1.00
82_G	136_L	0.796	1.00
136_L	139_G	0.794	1.00
169_L	173_A	0.793	1.00
92_F	128_W	0.793	1.00
184_R	188_A	0.792	1.00
131_V	135_F	0.789	1.00
177_S	183_W	0.780	1.00
39_L	46_L	0.776	1.00
147_A	155_W	0.776	1.00
34_L	42_A	0.771	1.00
190_L	194_L	0.769	1.00
46_L	51_F	0.767	1.00
33_L	38_L	0.760	1.00
83_Y	160_K	0.756	1.00
35_G	43_L	0.755	1.00
167_P	202_G	0.754	1.00
149_L	153_G	0.752	1.00
147_A	150_G	0.752	1.00
116_P	120_T	0.751	1.00
73_A	77_P	0.751	1.00
54_L	57_P	0.751	1.00
34_L	41_L	0.749	1.00
13_W	16_A	0.748	1.00
115_L	118_L	0.747	1.00
30_P	34_L	0.746	1.00
44_L	47_G	0.746	1.00
13_W	20_L	0.744	1.00
102_R	107_R	0.743	1.00
53_L	57_P	0.741	1.00
39_L	42_A	0.739	1.00
14_L	81_L	0.739	1.00
122_D	189_A	0.737	1.00
31_L	38_L	0.735	1.00
64_N	67_L	0.733	1.00
83_Y	136_L	0.732	1.00
129_L	171_Y	0.729	1.00
109_G	113_R	0.728	1.00
183_W	188_A	0.725	1.00
171_Y	192_A	0.722	1.00
148_E	151_W	0.720	1.00
187_W	191_L	0.716	1.00
148_E	153_G	0.715	1.00
108_L	113_R	0.712	1.00
163_W	166_I	0.711	1.00
205_G	209_L	0.704	1.00
102_R	109_G	0.701	1.00
157_W	162_N	0.700	1.00
23_E	26_Y	0.698	1.00
182_G	187_W	0.695	1.00
30_P	40_P	0.692	1.00
176_H	180_E	0.691	1.00
122_D	125_A	0.690	1.00
182_G	188_A	0.689	1.00
28_R	31_L	0.687	1.00
86_F	136_L	0.683	1.00
140_I	164_S	0.682	1.00
95_A	121_L	0.680	1.00
34_L	39_L	0.679	1.00
176_H	179_L	0.679	1.00
40_P	47_G	0.671	1.00
7_S	11_W	0.669	1.00
56_L	59_D	0.669	1.00
17_L	21_L	0.668	1.00
41_L	47_G	0.666	1.00
74_I	77_P	0.666	1.00
105_R	108_L	0.661	1.00
109_G	112_L	0.658	1.00
70_P	74_I	0.656	1.00
86_F	195_G	0.654	1.00
93_A	97_L	0.653	1.00
40_P	45_L	0.650	1.00
31_L	36_A	0.648	1.00
36_A	49_A	0.647	1.00
38_L	43_L	0.646	1.00
151_W	156_G	0.646	1.00
65_P	68_Q	0.644	1.00
9_L	12_A	0.643	1.00
54_L	58_P	0.643	1.00
195_G	199_V	0.640	1.00
122_D	126_R	0.633	1.00
186_R	189_A	0.632	1.00
182_G	186_R	0.632	1.00
116_P	119_E	0.629	1.00
149_L	152_G	0.627	1.00
152_G	155_W	0.623	1.00
52_L	57_P	0.621	1.00
7_S	80_Y	0.618	1.00
31_L	34_L	0.616	1.00
140_I	165_L	0.615	1.00
144_A	147_A	0.614	1.00
27_R	32_R	0.614	1.00
112_L	116_P	0.610	1.00
34_L	40_P	0.608	1.00
185_G	188_A	0.607	1.00
118_L	121_L	0.605	1.00
20_L	23_E	0.604	1.00
90_F	93_A	0.601	1.00
16_A	19_G	0.600	1.00
69_S	72_L	0.600	1.00
111_L	115_L	0.597	1.00
78_L	135_F	0.596	1.00
180_E	183_W	0.595	1.00
79_L	140_I	0.594	1.00
144_A	148_E	0.591	1.00
44_L	51_F	0.587	1.00
88_V	128_W	0.585	1.00
58_P	61_A	0.585	1.00
97_L	189_A	0.585	1.00
44_L	49_A	0.581	1.00
72_L	76_V	0.580	1.00
160_K	164_S	0.579	1.00
106_K	109_G	0.575	1.00
129_L	178_R	0.575	1.00
34_L	46_L	0.573	1.00
136_L	167_P	0.573	1.00
15_L	87_A	0.572	1.00
133_F	171_Y	0.571	1.00
30_P	35_G	0.570	1.00
111_L	114_R	0.570	1.00
102_R	112_L	0.567	1.00
154_Y	157_W	0.565	1.00
36_A	46_L	0.561	1.00
190_L	193_I	0.561	1.00
113_R	116_P	0.560	1.00
33_L	39_L	0.560	1.00
7_S	10_L	0.559	1.00
139_G	164_S	0.554	1.00
202_G	207_R	0.553	1.00
189_A	192_A	0.552	1.00
20_L	24_R	0.545	1.00
42_A	48_F	0.544	1.00
189_A	193_I	0.541	1.00
14_L	17_L	0.540	1.00
154_Y	161_E	0.538	1.00
40_P	51_F	0.535	1.00
11_W	80_Y	0.534	1.00
26_Y	30_P	0.532	1.00
198_L	202_G	0.532	1.00
35_G	40_P	0.532	1.00
36_A	43_L	0.531	1.00
96_Y	122_D	0.530	1.00
35_G	41_L	0.524	1.00
172_A	176_H	0.523	1.00
4_L	8_L	0.515	1.00
30_P	36_A	0.514	1.00
151_W	155_W	0.508	1.00
176_H	181_R	0.506	1.00
32_R	42_A	0.505	1.00
116_P	121_L	0.502	1.00
38_L	45_L	0.501	1.00
29_L	33_L	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
1zcdA	1	0.4159	5.6	0.945	Contact Map
3ayfA	2	0.9206	4.2	0.948	Contact Map
2m20A	2	0.2804	3.1	0.951	Contact Map
4o6yA	2	0.743	2.8	0.952	Contact Map
3giaA	1	0.4252	2.3	0.954	Contact Map
2l2tA	2	0.2056	2.1	0.955	Contact Map
1q16C	2	0.6402	1.8	0.957	Contact Map
1mhsA	2	0.6075	1.7	0.957	Contact Map
3rkoL	1	0.8785	1.6	0.958	Contact Map
4px7A	1	0.4065	1.6	0.958	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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