DsbD - PFAM28P - GREMLIN Contacts

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DsbD - Cytochrome C biogenesis protein transmembrane region

PFAM:	PF02683	Sequences: AFLAGLLSFLSPCVLPLLPIYLSYISGQSAGDRRAGKGRLRALLLSLAFVLGFALVFVALGALAAALGSLLGAYQPWLRIVAGVLLILFGLSLLGVFEIPLLSRERRLARLSRRRGGGLLGAFLLGLLFALVWTPCTGPILGAILALAATQGSALRGALLLLAYSLGLGLPFLLLALFPGRLLRRLPRLGRWMRWVKRVSGVLLIAVGILLLT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	213 (209)
Sequences:	55902 (36748)
Seq/√Len:	2541.9
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
55_L	123_F	4.371	1.00
194_R	198_R	3.964	1.00
2_F	170_L	2.913	1.00
195_W	198_R	2.887	1.00
102_L	105_E	2.605	1.00
192_W	195_W	2.502	1.00
76_P	80_I	2.383	1.00
77_W	80_I	2.323	1.00
74_Y	77_W	2.307	1.00
105_E	108_L	2.286	1.00
48_A	119_L	2.285	1.00
187_P	190_G	2.248	1.00
62_A	158_A	2.216	1.00
151_Q	156_R	2.191	1.00
50_V	169_G	2.144	1.00
76_P	79_R	2.132	1.00
188_R	192_W	2.072	1.00
103_S	106_R	2.068	1.00
68_G	71_L	2.030	1.00
104_R	107_R	2.022	1.00
95_G	98_E	1.984	1.00
77_W	81_V	1.923	1.00
58_V	162_L	1.859	1.00
80_I	84_V	1.837	1.00
32_D	35_A	1.833	1.00
79_R	82_A	1.829	1.00
195_W	199_V	1.742	1.00
99_I	102_L	1.719	1.00
50_V	173_L	1.702	1.00
8_S	164_Y	1.691	1.00
194_R	197_K	1.651	1.00
103_S	107_R	1.639	1.00
101_L	104_R	1.622	1.00
42_A	45_L	1.603	1.00
54_A	58_V	1.563	1.00
45_L	122_A	1.535	1.00
90_G	94_L	1.528	1.00
41_R	44_L	1.490	1.00
189_L	192_W	1.479	1.00
87_I	205_I	1.458	1.00
41_R	45_L	1.443	1.00
143_A	146_A	1.435	1.00
198_R	202_V	1.429	1.00
146_A	149_A	1.424	1.00
54_A	165_S	1.410	1.00
185_R	188_R	1.400	1.00
43_L	177_L	1.390	1.00
190_G	193_M	1.377	1.00
48_A	52_G	1.365	1.00
189_L	193_M	1.359	1.00
67_L	70_L	1.357	1.00
180_G	183_L	1.347	1.00
11_S	14_V	1.343	1.00
90_G	205_I	1.330	1.00
202_V	206_A	1.325	1.00
100_P	103_S	1.324	1.00
104_R	108_L	1.324	1.00
188_R	191_R	1.323	1.00
140_I	143_A	1.315	1.00
78_L	81_V	1.315	1.00
112_S	115_R	1.312	1.00
56_V	127_L	1.307	1.00
91_L	96_V	1.300	1.00
63_L	66_A	1.293	1.00
159_L	163_A	1.281	1.00
48_A	123_F	1.275	1.00
87_I	208_G	1.274	1.00
101_L	105_E	1.269	1.00
100_P	104_R	1.238	1.00
109_A	112_S	1.235	1.00
45_L	49_F	1.234	1.00
69_S	72_G	1.228	1.00
44_L	48_A	1.226	1.00
153_S	156_R	1.204	1.00
50_V	53_F	1.203	1.00
46_S	176_A	1.199	1.00
110_R	113_R	1.185	1.00
113_R	116_G	1.178	1.00
118_G	121_G	1.153	1.00
155_L	158_A	1.152	1.00
73_A	76_P	1.151	1.00
192_W	196_V	1.142	1.00
155_L	159_L	1.134	1.00
92_S	95_G	1.128	1.00
142_G	146_A	1.122	1.00
143_A	147_L	1.118	1.00
58_V	165_S	1.115	1.00
158_A	161_L	1.115	1.00
84_V	88_L	1.113	1.00
2_F	163_A	1.099	1.00
184_R	187_P	1.092	1.00
50_V	54_A	1.091	1.00
4_A	140_I	1.091	1.00
123_F	127_L	1.090	1.00
144_I	160_L	1.087	1.00
33_R	36_G	1.085	1.00
66_A	69_S	1.085	1.00
154_A	158_A	1.085	1.00
99_I	103_S	1.084	1.00
111_L	114_R	1.075	1.00
138_G	141_L	1.067	1.00
191_R	194_R	1.052	1.00
53_F	57_F	1.043	1.00
65_A	68_G	1.040	1.00
156_R	160_L	1.039	1.00
183_L	186_L	1.039	1.00
94_L	205_I	1.035	1.00
162_L	166_L	1.032	1.00
47_L	51_L	1.032	1.00
193_M	197_K	1.030	1.00
46_S	49_F	1.021	1.00
48_A	122_A	1.016	1.00
75_Q	79_R	1.005	1.00
148_A	157_G	1.001	1.00
105_E	109_A	1.000	1.00
53_F	56_V	1.000	1.00
181_R	185_R	0.998	1.00
2_F	167_G	0.993	1.00
43_L	47_L	0.984	1.00
102_L	107_R	0.981	1.00
97_F	100_P	0.981	1.00
29_S	32_D	0.978	1.00
51_L	123_F	0.973	1.00
58_V	158_A	0.972	1.00
23_S	26_S	0.967	1.00
181_R	184_R	0.966	1.00
31_G	35_A	0.966	1.00
81_V	85_L	0.962	1.00
61_G	64_A	0.962	1.00
3_L	7_L	0.959	1.00
99_I	105_E	0.954	1.00
49_F	53_F	0.954	1.00
45_L	48_A	0.953	1.00
147_L	151_Q	0.950	1.00
75_Q	78_L	0.949	1.00
47_L	173_L	0.937	1.00
102_L	106_R	0.935	1.00
78_L	82_A	0.932	1.00
61_G	161_L	0.932	1.00
72_G	75_Q	0.930	1.00
171_P	174_L	0.928	1.00
68_G	72_G	0.923	1.00
186_L	189_L	0.917	1.00
106_R	109_A	0.910	1.00
44_L	119_L	0.900	1.00
44_L	47_L	0.900	1.00
79_R	83_G	0.890	1.00
175_L	186_L	0.879	1.00
106_R	110_R	0.879	1.00
64_A	67_L	0.873	1.00
49_F	57_F	0.864	1.00
29_S	33_R	0.862	1.00
107_R	110_R	0.861	1.00
17_L	20_I	0.861	1.00
196_V	200_S	0.858	1.00
88_L	97_F	0.857	1.00
32_D	36_G	0.853	1.00
156_R	159_L	0.849	1.00
65_A	154_A	0.840	1.00
77_W	82_A	0.839	1.00
154_A	157_G	0.838	1.00
206_A	210_L	0.837	1.00
52_G	56_V	0.835	1.00
67_L	71_L	0.834	1.00
63_L	67_L	0.833	1.00
178_F	181_R	0.832	1.00
61_G	65_A	0.829	1.00
90_G	93_L	0.823	1.00
59_A	62_A	0.820	1.00
92_S	97_F	0.817	1.00
62_A	65_A	0.816	1.00
92_S	98_E	0.815	1.00
98_E	103_S	0.811	1.00
100_P	105_E	0.806	1.00
182_L	186_L	0.805	1.00
147_L	150_T	0.801	1.00
88_L	92_S	0.794	1.00
57_F	61_G	0.788	1.00
47_L	50_V	0.788	1.00
191_R	195_W	0.783	1.00
48_A	51_L	0.782	1.00
75_Q	80_I	0.773	1.00
58_V	61_G	0.771	1.00
186_L	190_G	0.757	1.00
43_L	46_S	0.754	1.00
30_A	33_R	0.753	1.00
52_G	123_F	0.751	1.00
141_L	164_Y	0.751	1.00
54_A	162_L	0.749	1.00
187_P	192_W	0.746	1.00
51_L	162_L	0.746	1.00
140_I	144_I	0.745	1.00
73_A	77_W	0.744	1.00
109_A	113_R	0.743	1.00
59_A	63_L	0.741	1.00
46_S	50_V	0.739	1.00
51_L	55_L	0.735	1.00
168_L	172_F	0.729	1.00
175_L	178_F	0.727	1.00
99_I	104_R	0.726	1.00
179_P	183_L	0.721	1.00
42_A	46_S	0.720	1.00
69_S	73_A	0.719	1.00
36_G	39_R	0.719	1.00
8_S	11_S	0.719	1.00
13_C	136_C	0.717	1.00
56_V	59_A	0.715	1.00
40_L	44_L	0.714	1.00
115_R	118_G	0.713	1.00
65_A	69_S	0.711	1.00
178_F	182_L	0.710	1.00
94_L	198_R	0.701	1.00
98_E	197_K	0.700	1.00
28_Q	32_D	0.700	1.00
193_M	196_V	0.699	1.00
83_G	87_I	0.698	1.00
38_G	41_R	0.691	1.00
80_I	83_G	0.691	1.00
108_L	112_S	0.682	1.00
103_S	108_L	0.674	1.00
124_L	127_L	0.672	1.00
92_S	96_V	0.671	1.00
190_G	194_R	0.670	1.00
52_G	57_F	0.667	1.00
64_A	69_S	0.667	1.00
65_A	71_L	0.661	1.00
31_G	36_G	0.661	1.00
119_L	122_A	0.657	1.00
64_A	68_G	0.651	1.00
185_R	189_L	0.651	1.00
81_V	84_V	0.651	1.00
158_A	162_L	0.633	1.00
64_A	70_L	0.631	1.00
98_E	101_L	0.630	1.00
22_L	25_I	0.624	1.00
114_R	117_G	0.623	1.00
31_G	34_R	0.619	1.00
55_L	58_V	0.619	1.00
89_F	92_S	0.618	1.00
89_F	142_G	0.617	1.00
24_Y	27_G	0.616	1.00
137_T	168_L	0.615	1.00
196_V	199_V	0.609	1.00
199_V	202_V	0.606	1.00
86_L	211_L	0.602	1.00
187_P	191_R	0.599	1.00
173_L	176_A	0.598	1.00
71_L	74_Y	0.597	1.00
157_G	160_L	0.594	1.00
100_P	106_R	0.594	1.00
43_L	48_A	0.594	1.00
112_S	117_G	0.590	1.00
183_L	187_P	0.589	1.00
64_A	71_L	0.589	1.00
152_G	156_R	0.588	1.00
180_G	184_R	0.587	1.00
49_F	52_G	0.587	1.00
120_L	123_F	0.585	1.00
145_L	149_A	0.584	1.00
2_F	6_L	0.580	1.00
4_A	7_L	0.576	1.00
60_L	64_A	0.574	1.00
34_R	38_G	0.574	1.00
35_A	38_G	0.572	1.00
41_R	46_S	0.567	1.00
188_R	193_M	0.566	1.00
113_R	117_G	0.564	1.00
153_S	157_G	0.560	1.00
12_P	15_L	0.559	1.00
203_L	207_V	0.558	1.00
41_R	49_F	0.557	1.00
133_W	137_T	0.556	1.00
127_L	131_L	0.554	1.00
21_Y	24_Y	0.551	1.00
94_L	202_V	0.551	1.00
120_L	124_L	0.549	1.00
43_L	173_L	0.548	1.00
89_F	93_L	0.548	1.00
139_P	143_A	0.547	1.00
175_L	179_P	0.547	1.00
182_L	185_R	0.541	1.00
201_G	205_I	0.541	1.00
102_L	108_L	0.539	1.00
5_G	167_G	0.538	1.00
108_L	111_L	0.537	1.00
119_L	123_F	0.537	1.00
2_F	166_L	0.535	1.00
62_A	66_A	0.535	1.00
146_A	150_T	0.533	1.00
161_L	165_S	0.532	1.00
22_L	175_L	0.531	1.00
43_L	49_F	0.531	1.00
94_L	97_F	0.530	1.00
133_W	138_G	0.529	1.00
21_Y	25_I	0.528	1.00
9_F	21_Y	0.525	1.00
20_I	24_Y	0.524	1.00
110_R	114_R	0.524	1.00
20_I	23_S	0.518	1.00
61_G	68_G	0.517	1.00
85_L	89_F	0.516	1.00
86_L	90_G	0.516	1.00
159_L	162_L	0.515	1.00
91_L	94_L	0.515	1.00
52_G	55_L	0.514	1.00
9_F	171_P	0.513	1.00
124_L	128_L	0.512	1.00
114_R	118_G	0.509	1.00
49_F	61_G	0.507	1.00
83_G	86_L	0.507	1.00
78_L	83_G	0.506	1.00
51_L	54_A	0.505	1.00
101_L	107_R	0.503	1.00
66_A	70_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
3wdoA	1	0.8545	6.7	0.934	Contact Map
2gfpA	2	0.8592	5.9	0.935	Contact Map
4lz6A	1	0.8404	4.2	0.94	Contact Map
1pw4A	1	0.8592	4.1	0.94	Contact Map
3rlbA	1	0.446	3.5	0.942	Contact Map
2xq2A	2	0.8357	3.4	0.943	Contact Map
2mmuA	1	0.2347	2.3	0.947	Contact Map
3hzqA	3	0.3662	1.9	0.95	Contact Map
3dh4A	3	0.4225	1.9	0.95	Contact Map
4dveA	3	0.4742	1.9	0.95	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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