DsbD_2 - PFAM28P - GREMLIN Contacts

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DsbD_2 - Cytochrome C biogenesis protein transmembrane region

PFAM:	PF13386	Sequences: AAFLAGLLGSLPCVLPCGPIVLAYIAGQPKRALLSLLYVLGRALTYTLLGALAGLLGSLLGLAGQLPWLRGILGILLGLLGLLLGLSLLGLRGLLRLERLGRRLSRRLGPLSKRLGGLLGAFLLGLLFGLLPCGPLYAALLLAAATGSALLGALLLFAFGLGTGPPLLLLGLLAGRLLPKLRRRIVRVAGVLLILLGIY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	199 (196)
Sequences:	41550 (30037)
Seq/√Len:	2145.5
META:	0.875

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_L	122_F	4.368	1.00
183_R	186_V	3.227	1.00
183_R	187_R	2.821	1.00
51_A	153_A	2.787	1.00
81_G	85_G	2.747	1.00
47_T	157_F	2.718	1.00
184_R	187_R	2.630	1.00
78_G	81_G	2.592	1.00
73_L	77_L	2.243	1.00
37_L	118_L	2.192	1.00
77_L	81_G	2.160	1.00
43_A	160_G	2.136	1.00
190_G	193_L	2.131	1.00
74_G	78_G	2.091	1.00
103_R	106_R	2.055	1.00
148_S	151_L	2.045	1.00
98_E	101_G	2.013	1.00
47_T	153_A	1.957	1.00
39_V	164_G	1.941	1.00
29_P	32_A	1.856	1.00
75_I	79_L	1.774	1.00
96_R	99_R	1.771	1.00
41_G	122_F	1.752	1.00
74_G	81_G	1.730	1.00
45_T	126_L	1.703	1.00
107_R	110_P	1.695	1.00
189_A	193_L	1.609	1.00
93_G	96_R	1.592	1.00
43_A	47_T	1.579	1.00
35_S	171_G	1.560	1.00
116_G	120_G	1.557	1.00
95_L	98_E	1.539	1.00
135_P	138_A	1.535	1.00
68_W	71_G	1.532	1.00
190_G	194_I	1.530	1.00
39_V	168_L	1.519	1.00
37_L	122_F	1.502	1.00
103_R	107_R	1.501	1.00
9_G	135_P	1.490	1.00
100_L	103_R	1.464	1.00
51_A	149_A	1.458	1.00
150_L	153_A	1.443	1.00
70_R	74_G	1.441	1.00
12_P	17_C	1.431	1.00
2_A	155_L	1.411	1.00
37_L	121_A	1.407	1.00
72_I	75_I	1.405	1.00
108_L	111_L	1.397	1.00
189_A	192_L	1.380	1.00
4_L	8_L	1.371	1.00
104_L	107_R	1.370	1.00
102_R	105_S	1.369	1.00
97_L	100_L	1.363	1.00
12_P	16_P	1.358	1.00
85_G	88_L	1.356	1.00
71_G	75_I	1.346	1.00
85_G	89_L	1.344	1.00
9_G	159_F	1.340	1.00
106_R	109_G	1.334	1.00
186_V	189_A	1.331	1.00
10_S	166_P	1.321	1.00
137_Y	141_L	1.320	1.00
117_G	120_G	1.314	1.00
178_L	182_R	1.314	1.00
12_P	15_L	1.301	1.00
56_L	59_L	1.285	1.00
92_R	95_L	1.274	1.00
69_L	73_L	1.265	1.00
149_A	153_A	1.264	1.00
3_F	165_P	1.246	1.00
146_T	151_L	1.230	1.00
47_T	160_G	1.226	1.00
99_R	102_R	1.225	1.00
71_G	74_G	1.223	1.00
37_L	41_G	1.209	1.00
52_L	55_L	1.208	1.00
134_G	137_Y	1.202	1.00
101_G	105_S	1.202	1.00
3_F	162_G	1.192	1.00
102_R	106_R	1.173	1.00
34_L	121_A	1.172	1.00
68_W	72_I	1.165	1.00
39_V	42_R	1.161	1.00
5_A	139_A	1.160	1.00
75_I	78_G	1.145	1.00
83_L	87_S	1.143	1.00
80_L	84_L	1.138	1.00
141_L	145_A	1.134	1.00
84_L	87_S	1.114	1.00
38_Y	128_F	1.111	1.00
122_F	126_L	1.108	1.00
55_L	59_L	1.104	1.00
179_P	182_R	1.095	1.00
67_P	70_R	1.090	1.00
138_A	141_L	1.087	1.00
191_V	195_L	1.086	1.00
74_G	77_L	1.084	1.00
43_A	157_F	1.079	1.00
54_G	149_A	1.068	1.00
109_G	113_K	1.068	1.00
188_V	191_V	1.052	1.00
21_V	24_Y	1.052	1.00
45_T	129_G	1.042	1.00
54_G	57_G	1.037	1.00
138_A	142_L	1.027	1.00
3_F	158_A	1.021	1.00
97_L	101_G	1.020	1.00
90_G	93_G	1.014	1.00
104_L	108_L	1.012	1.00
49_L	140_L	1.006	1.00
42_R	46_Y	1.000	1.00
72_I	76_L	0.998	1.00
84_L	88_L	0.996	1.00
173_L	176_R	0.993	1.00
67_P	71_G	0.983	1.00
136_L	140_L	0.977	1.00
111_L	114_R	0.975	1.00
79_L	83_L	0.967	1.00
25_I	28_Q	0.963	1.00
17_C	20_I	0.959	1.00
50_G	156_L	0.948	1.00
77_L	80_L	0.947	1.00
135_P	139_A	0.946	1.00
120_G	123_L	0.944	1.00
21_V	25_I	0.939	1.00
151_L	154_L	0.939	1.00
110_P	113_K	0.934	1.00
109_G	112_S	0.931	1.00
2_A	139_A	0.929	1.00
78_G	82_L	0.928	1.00
150_L	154_L	0.927	1.00
123_L	126_L	0.919	1.00
178_L	181_L	0.914	1.00
106_R	110_P	0.908	1.00
99_R	103_R	0.900	1.00
105_S	108_L	0.900	1.00
73_L	81_G	0.899	1.00
142_L	145_A	0.892	1.00
136_L	139_A	0.876	1.00
98_E	102_R	0.875	1.00
169_L	173_L	0.868	1.00
151_L	155_L	0.858	1.00
101_G	104_L	0.858	1.00
105_S	112_S	0.856	1.00
153_A	157_F	0.851	1.00
184_R	188_V	0.841	1.00
78_G	197_G	0.837	1.00
140_L	144_A	0.835	1.00
187_R	190_G	0.823	1.00
61_G	64_G	0.823	1.00
188_V	192_L	0.822	1.00
59_L	63_A	0.816	1.00
92_R	96_R	0.814	1.00
98_E	103_R	0.814	1.00
86_L	89_L	0.813	1.00
96_R	100_L	0.812	1.00
91_L	95_L	0.809	1.00
56_L	60_L	0.809	1.00
58_S	62_L	0.809	1.00
18_G	21_V	0.790	1.00
107_R	111_L	0.784	1.00
164_G	167_L	0.777	1.00
85_G	90_G	0.775	1.00
166_P	170_L	0.773	1.00
105_S	109_G	0.770	1.00
24_Y	35_S	0.769	1.00
20_I	23_A	0.759	1.00
4_L	7_L	0.757	1.00
103_R	108_L	0.757	1.00
69_L	72_I	0.752	1.00
71_G	81_G	0.751	1.00
119_L	122_F	0.749	1.00
36_L	40_L	0.748	1.00
166_P	169_L	0.745	1.00
141_L	144_A	0.742	1.00
40_L	157_F	0.737	1.00
35_S	39_V	0.736	1.00
36_L	168_L	0.734	1.00
52_L	56_L	0.729	1.00
40_L	122_F	0.729	1.00
34_L	118_L	0.724	1.00
176_R	179_P	0.721	1.00
175_G	178_L	0.719	1.00
3_F	7_L	0.716	1.00
185_I	189_A	0.709	1.00
100_L	104_L	0.706	1.00
172_L	176_R	0.705	1.00
55_L	58_S	0.704	1.00
96_R	101_G	0.703	1.00
10_S	21_V	0.696	1.00
94_L	97_L	0.695	1.00
50_G	152_G	0.695	1.00
170_L	174_A	0.692	1.00
70_R	73_L	0.677	1.00
98_E	105_S	0.674	1.00
153_A	156_L	0.671	1.00
85_G	194_I	0.669	1.00
157_F	161_L	0.668	1.00
15_L	18_G	0.668	1.00
40_L	44_L	0.666	1.00
31_R	34_L	0.663	1.00
17_C	21_V	0.663	1.00
154_L	158_A	0.662	1.00
20_I	24_Y	0.658	1.00
185_I	193_L	0.654	1.00
192_L	195_L	0.652	1.00
43_A	164_G	0.651	1.00
42_R	45_T	0.649	1.00
94_L	98_E	0.649	1.00
192_L	196_L	0.648	1.00
117_G	121_A	0.647	1.00
121_A	125_G	0.646	1.00
140_L	156_L	0.645	1.00
82_L	197_G	0.642	1.00
169_L	172_L	0.641	1.00
48_L	51_A	0.641	1.00
53_A	140_L	0.639	1.00
19_P	22_L	0.638	1.00
158_A	162_G	0.636	1.00
35_S	172_L	0.635	1.00
193_L	196_L	0.634	1.00
107_R	112_S	0.630	1.00
39_V	167_L	0.628	1.00
118_L	121_A	0.627	1.00
91_L	94_L	0.626	1.00
180_K	184_R	0.619	1.00
134_G	159_F	0.612	1.00
185_I	188_V	0.611	1.00
22_L	26_A	0.611	1.00
81_G	194_I	0.608	1.00
95_L	99_R	0.603	1.00
6_G	9_G	0.599	1.00
139_A	143_A	0.597	1.00
87_S	90_G	0.594	1.00
73_L	80_L	0.594	1.00
170_L	173_L	0.593	1.00
14_V	166_P	0.593	1.00
19_P	23_A	0.590	1.00
45_T	48_L	0.590	1.00
81_G	87_S	0.586	1.00
2_A	158_A	0.584	1.00
93_G	97_L	0.582	1.00
17_C	42_R	0.581	1.00
76_L	79_L	0.579	1.00
80_L	83_L	0.578	1.00
168_L	171_G	0.578	1.00
72_I	81_G	0.576	1.00
37_L	40_L	0.573	1.00
44_L	48_L	0.572	1.00
40_L	43_A	0.571	1.00
99_R	105_S	0.571	1.00
146_T	149_A	0.568	1.00
42_R	163_T	0.568	1.00
110_P	114_R	0.563	1.00
119_L	123_L	0.562	1.00
143_A	152_G	0.561	1.00
83_L	86_L	0.561	1.00
44_L	47_T	0.559	1.00
39_V	171_G	0.555	1.00
108_L	112_S	0.554	1.00
12_P	18_G	0.552	1.00
28_Q	34_L	0.552	1.00
64_G	67_P	0.551	1.00
49_L	53_A	0.546	1.00
101_G	108_L	0.546	1.00
137_Y	140_L	0.545	1.00
39_V	43_A	0.544	1.00
2_A	6_G	0.544	1.00
9_G	17_C	0.543	1.00
65_Q	68_W	0.542	1.00
142_L	146_T	0.540	1.00
53_A	144_A	0.538	1.00
191_V	194_I	0.537	1.00
73_L	76_L	0.534	1.00
182_R	186_V	0.533	1.00
66_L	71_G	0.524	1.00
173_L	177_L	0.523	1.00
168_L	172_L	0.522	1.00
101_G	106_R	0.521	1.00
185_I	190_G	0.521	1.00
50_G	54_G	0.521	1.00
22_L	174_A	0.520	1.00
155_L	158_A	0.516	1.00
54_G	147_G	0.512	1.00
70_R	80_L	0.512	1.00
73_L	79_L	0.511	1.00
77_L	84_L	0.511	1.00
181_L	184_R	0.509	1.00
16_P	21_V	0.509	1.00
54_G	152_G	0.507	1.00
95_L	101_G	0.505	1.00
87_S	91_L	0.504	1.00
72_I	78_G	0.501	1.00
142_L	155_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
4m64A	1	0.9397	60.3	0.89	Contact Map
3o7qA	1	0.9648	55.4	0.893	Contact Map
2gfpA	2	0.9196	40.7	0.902	Contact Map
3wdoA	1	0.9246	33.5	0.907	Contact Map
1pw4A	1	0.9146	31.2	0.908	Contact Map
2cfqA	1	0.9146	21.5	0.915	Contact Map
4p6vE	1	0.8593	18.1	0.918	Contact Map
4xnjA	1	0.9146	16.8	0.919	Contact Map
2xq2A	2	0.4523	15	0.921	Contact Map
3llqA	3	0.4121	11.6	0.925	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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