DMSB - HALSA - GREMLIN Contacts

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DMSB - Putative dimethyl sulfoxide reductase iron-sulfur subunit B

UniProt:	Q9HR73	Sequences: MTNYGLVIDQERCIGCQSCSLTCKQENNVPMGQFWNRVLTQGGDHVDTPSGDYPEGGDGGTLEMTYQPTACQHCENAPCVKVCPVNATYTRDDGIVEIDYDKCMGCRYCMAACPYNARVFNWDEPEHRPEDGTGDVAERPQGVVEKCTFCSHRVEDGLDPACVVNCPADARIFGDLDDDDSTVSKYIAEYDTHQLLDEKGTDPSTYYINGEMSPGRPWKSKKLESELDDDEAAKAARRRSGSVENGYDVTPHVPAETAGGDD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	262 (201)
Sequences:	1298 (720)
Seq/√Len:	50.8

ECOLI - FDNH FDOH HYBA NRFC YDHX YNFG DMSB HYFA HYCB YDHY NARH NARY HYDN YGFS YSAA
BACSU - NARH
HALSA - DMSB
SULSO - Q97V38 Q97XX9 Q97V75

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
160_P	163_V	4.038	1.00
6_L	149_F	4.000	1.00
149_F	205_T	3.624	1.00
26_E	152_H	3.132	1.00
69_T	195_L	3.097	1.00
194_Q	197_D	3.069	1.00
13_C	19_C	2.752	1.00
88_T	118_R	2.586	1.00
13_C	16_C	2.526	1.00
57_G	60_G	2.509	1.00
16_C	19_C	2.186	1.00
95_I	154_V	2.163	1.00
13_C	166_C	2.143	1.00
107_R	122_W	2.141	1.00
77_A	90_T	2.109	1.00
163_V	171_R	2.093	1.00
27_N	148_T	2.062	1.00
82_V	108_Y	2.039	1.00
172_I	186_Y	2.008	1.00
180_D	185_K	2.002	1.00
83_C	103_C	1.989	1.00
182_T	185_K	1.958	0.99
107_R	120_F	1.946	0.99
83_C	109_C	1.908	0.99
153_R	164_V	1.843	0.99
178_D	181_S	1.836	0.99
14_I	168_A	1.824	0.99
103_C	109_C	1.792	0.99
80_V	88_T	1.776	0.99
8_I	171_R	1.774	0.99
11_E	190_Y	1.761	0.99
183_V	186_Y	1.743	0.99
16_C	166_C	1.710	0.99
175_D	178_D	1.683	0.98
22_T	161_A	1.650	0.98
98_I	118_R	1.642	0.98
107_R	110_M	1.626	0.98
194_Q	202_D	1.615	0.98
110_M	144_V	1.614	0.98
3_N	204_S	1.591	0.98
139_R	145_E	1.587	0.98
82_V	88_T	1.586	0.98
195_L	201_T	1.583	0.98
47_D	51_G	1.572	0.98
10_Q	68_P	1.565	0.97
151_S	155_E	1.538	0.97
83_C	105_G	1.536	0.97
5_G	176_L	1.531	0.97
70_A	205_T	1.527	0.97
47_D	50_S	1.515	0.97
57_G	61_T	1.504	0.97
8_I	70_A	1.493	0.97
121_N	145_E	1.490	0.97
91_R	97_E	1.473	0.96
90_T	96_V	1.471	0.96
75_E	204_S	1.454	0.96
89_Y	99_D	1.448	0.96
70_A	149_F	1.444	0.96
105_G	109_C	1.430	0.96
19_C	166_C	1.409	0.95
185_K	189_E	1.408	0.95
22_T	165_N	1.394	0.95
82_V	112_A	1.393	0.95
172_I	182_T	1.359	0.94
88_T	98_I	1.352	0.94
159_D	163_V	1.329	0.94
194_Q	206_Y	1.296	0.93
78_P	112_A	1.291	0.93
194_Q	199_K	1.289	0.93
181_S	184_S	1.279	0.92
27_N	152_H	1.278	0.92
24_K	29_V	1.248	0.91
192_T	208_I	1.239	0.91
26_E	161_A	1.222	0.90
96_V	112_A	1.220	0.90
91_R	155_E	1.216	0.90
7_V	183_V	1.213	0.90
98_I	144_V	1.211	0.90
108_Y	111_A	1.190	0.89
26_E	153_R	1.177	0.89
13_C	167_P	1.171	0.88
46_V	50_S	1.164	0.88
213_S	216_R	1.155	0.88
85_V	106_C	1.123	0.86
37_R	73_H	1.117	0.86
185_K	188_A	1.112	0.86
12_R	169_D	1.108	0.85
85_V	104_M	1.108	0.85
15_G	19_C	1.105	0.85
84_P	103_C	1.099	0.85
181_S	185_K	1.092	0.85
77_A	96_V	1.085	0.84
7_V	208_I	1.067	0.83
84_P	109_C	1.066	0.83
3_N	75_E	1.052	0.82
153_R	158_L	1.049	0.82
80_V	90_T	1.038	0.81
97_E	151_S	1.036	0.81
159_D	164_V	1.034	0.81
120_F	142_G	1.027	0.81
77_A	80_V	1.027	0.81
19_C	167_P	1.021	0.80
184_S	188_A	1.021	0.80
69_T	72_Q	1.016	0.80
48_T	51_G	1.000	0.79
120_F	141_Q	0.998	0.79
203_P	207_Y	0.995	0.79
5_G	81_K	0.990	0.78
7_V	186_Y	0.989	0.78
115_Y	201_T	0.986	0.78
78_P	115_Y	0.980	0.77
37_R	92_D	0.973	0.77
179_D	184_S	0.969	0.77
187_I	192_T	0.955	0.76
182_T	186_Y	0.947	0.75
121_N	139_R	0.946	0.75
18_S	25_Q	0.945	0.75
6_L	70_A	0.933	0.74
4_Y	95_I	0.930	0.74
177_D	185_K	0.930	0.74
8_I	68_P	0.923	0.73
18_S	26_E	0.923	0.73
38_V	41_Q	0.921	0.73
42_G	45_H	0.915	0.72
106_C	109_C	0.900	0.71
76_N	81_K	0.900	0.71
33_Q	36_N	0.900	0.71
68_P	207_Y	0.894	0.71
14_I	169_D	0.887	0.70
106_C	112_A	0.871	0.69
12_R	18_S	0.870	0.69
78_P	201_T	0.865	0.68
196_L	199_K	0.863	0.68
38_V	43_G	0.859	0.68
187_I	206_Y	0.856	0.67
28_N	145_E	0.849	0.67
8_I	170_A	0.847	0.67
186_Y	189_E	0.843	0.66
190_Y	208_I	0.841	0.66
93_D	155_E	0.835	0.65
58_D	61_T	0.829	0.65
84_P	105_G	0.824	0.64
68_P	115_Y	0.819	0.64
26_E	164_V	0.818	0.64
36_N	40_T	0.800	0.62
59_G	62_L	0.799	0.62
5_G	184_S	0.796	0.62
160_P	171_R	0.793	0.61
40_T	43_G	0.783	0.60
17_Q	20_S	0.779	0.60
11_E	208_I	0.777	0.60
7_V	187_I	0.772	0.59
18_S	165_N	0.770	0.59
10_Q	69_T	0.768	0.59
100_Y	120_F	0.764	0.59
139_R	142_G	0.759	0.58
204_S	209_N	0.758	0.58
176_L	180_D	0.754	0.57
169_D	188_A	0.750	0.57
45_H	48_T	0.749	0.57
195_L	203_P	0.743	0.56
82_V	111_A	0.742	0.56
172_I	179_D	0.742	0.56
102_K	139_R	0.737	0.56
83_C	106_C	0.734	0.55
106_C	110_M	0.733	0.55
43_G	49_P	0.732	0.55
7_V	163_V	0.718	0.54
36_N	41_Q	0.716	0.54
91_R	95_I	0.711	0.53
4_Y	73_H	0.708	0.53
103_C	106_C	0.706	0.53
203_P	213_S	0.701	0.52
44_D	48_T	0.700	0.52
73_H	117_A	0.700	0.52
15_G	166_C	0.700	0.52
42_G	48_T	0.696	0.52
46_V	49_P	0.694	0.51
95_I	151_S	0.688	0.51
211_E	216_R	0.687	0.51
21_L	24_K	0.684	0.50
15_G	68_P	0.684	0.50
157_G	187_I	0.682	0.50
99_D	102_K	0.678	0.50
35_W	43_G	0.678	0.50
108_Y	112_A	0.677	0.50
5_G	204_S	0.677	0.50
149_F	173_F	0.675	0.49
7_V	179_D	0.674	0.49
27_N	170_A	0.669	0.49
68_P	171_R	0.665	0.48
35_W	39_L	0.664	0.48
34_F	41_Q	0.662	0.48
153_R	168_A	0.661	0.48
38_V	45_H	0.657	0.48
30_P	158_L	0.649	0.47
28_N	139_R	0.649	0.47
174_G	178_D	0.649	0.47
139_R	143_V	0.642	0.46
18_S	168_A	0.639	0.46
43_G	47_D	0.639	0.46
108_Y	143_V	0.638	0.46
49_P	77_A	0.629	0.45
212_M	215_G	0.622	0.44
88_T	121_N	0.620	0.44
106_C	144_V	0.614	0.43
189_E	192_T	0.611	0.43
55_E	62_L	0.611	0.43
49_P	69_T	0.604	0.42
38_V	42_G	0.602	0.42
100_Y	143_V	0.600	0.42
116_N	119_V	0.598	0.42
12_R	185_K	0.597	0.41
100_Y	151_S	0.597	0.41
154_V	173_F	0.595	0.41
120_F	144_V	0.595	0.41
91_R	96_V	0.595	0.41
32_G	82_V	0.593	0.41
121_N	142_G	0.591	0.41
18_S	21_L	0.591	0.41
106_C	211_E	0.590	0.41
147_C	162_C	0.590	0.41
3_N	177_D	0.590	0.41
77_A	91_R	0.588	0.41
120_F	200_G	0.586	0.40
82_V	118_R	0.586	0.40
44_D	52_D	0.586	0.40
183_V	206_Y	0.585	0.40
153_R	161_A	0.584	0.40
115_Y	203_P	0.584	0.40
195_L	200_G	0.581	0.40
8_I	205_T	0.580	0.40
104_M	112_A	0.579	0.40
11_E	213_S	0.578	0.40
6_L	205_T	0.577	0.39
116_N	148_T	0.576	0.39
92_D	178_D	0.573	0.39
4_Y	93_D	0.573	0.39
171_R	195_L	0.572	0.39
37_R	42_G	0.571	0.39
45_H	50_S	0.569	0.39
92_D	97_E	0.566	0.38
14_I	34_F	0.564	0.38
200_G	214_P	0.562	0.38
22_T	159_D	0.560	0.38
76_N	86_N	0.559	0.38
27_N	48_T	0.559	0.38
85_V	98_I	0.555	0.37
192_T	205_T	0.553	0.37
177_D	187_I	0.551	0.37
61_T	185_K	0.548	0.37
176_L	184_S	0.548	0.37
11_E	66_Y	0.544	0.36
38_V	88_T	0.544	0.36
85_V	107_R	0.543	0.36
169_D	172_I	0.542	0.36
69_T	207_Y	0.542	0.36
72_Q	194_Q	0.541	0.36
81_K	204_S	0.539	0.36
45_H	51_G	0.539	0.36
102_K	145_E	0.539	0.36
212_M	216_R	0.532	0.35
98_I	171_R	0.532	0.35
42_G	47_D	0.527	0.35
22_T	25_Q	0.527	0.35
121_N	140_P	0.526	0.35
67_Q	78_P	0.526	0.35
7_V	192_T	0.525	0.34
56_G	86_N	0.523	0.34
7_V	65_T	0.522	0.34
101_D	211_E	0.522	0.34
78_P	120_F	0.522	0.34
4_Y	142_G	0.521	0.34
63_E	210_G	0.520	0.34
10_Q	67_Q	0.520	0.34
152_H	161_A	0.519	0.34
6_L	173_F	0.519	0.34
179_D	182_T	0.519	0.34
39_L	42_G	0.518	0.34
142_G	199_K	0.516	0.34
78_P	199_K	0.516	0.34
75_E	176_L	0.515	0.33
159_D	182_T	0.515	0.33
13_C	170_A	0.515	0.33
88_T	144_V	0.513	0.33
52_D	55_E	0.513	0.33
16_C	167_P	0.512	0.33
80_V	144_V	0.512	0.33
91_R	197_D	0.511	0.33
187_I	202_D	0.511	0.33
5_G	181_S	0.510	0.33
141_Q	170_A	0.509	0.33
9_D	208_I	0.509	0.33
25_Q	164_V	0.509	0.33
3_N	176_L	0.509	0.33
4_Y	177_D	0.508	0.33
176_L	204_S	0.508	0.33
68_P	142_G	0.506	0.33
63_E	189_E	0.505	0.33
163_V	187_I	0.504	0.32
162_C	166_C	0.503	0.32
182_T	192_T	0.500	0.32

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
2ivfB	1	0.9351	100	0.456	Contact Map
1ti6B	2	0.874	100	0.492	Contact Map
1kqfB	3	0.8893	100	0.502	Contact Map
1h0hB	1	0.7748	100	0.51	Contact Map
2vpzB	2	0.7328	100	0.53	Contact Map
1q16B	2	0.9351	100	0.531	Contact Map
4z3xE	2	0.6374	100	0.679	Contact Map
3mm5B	2	0.8435	99.8	0.774	Contact Map
3gyxB	1	0.5496	99.4	0.837	Contact Map
3i9v9	1	0.5802	99.4	0.838	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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