Collagen_mid - PFAM28P - GREMLIN Contacts

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Collagen_mid - Bacterial collagen, middle region

PFAM:	PF15984	Sequences: LPGVSSQTTQGLGGVVTSTGNAVSTLGNGVSNGLGQLGTNPNPVGTTVASVGNVVSDLGNAVSSLGGLVSSLGSGPLAPLAPVTTPVGGVVSTVGQAVTMLGDTLGTALSSGPVQQVTQTLSSAIVPVTSTVTGTTQTVGTATGLGAPVNGLLGTVGGAVAGAGTQVTGATGNPVTSGVGGVVTGVGNTVASAGGLVNG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	199 (194)
Sequences:	517 (323)
Seq/√Len:	23.2
META:	0.416

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_A	61_A	4.270	1.00
63_S	92_S	3.747	1.00
18_S	64_S	3.131	1.00
66_G	88_G	3.087	1.00
179_V	182_V	3.042	1.00
26_L	54_V	2.744	0.99
56_S	99_T	2.530	0.99
193_A	196_L	2.470	0.98
117_V	188_N	2.423	0.98
59_G	95_G	2.415	0.98
66_G	95_G	2.411	0.98
88_G	91_V	2.394	0.98
65_L	68_L	2.314	0.97
151_G	154_G	2.272	0.97
7_Q	71_S	2.201	0.96
22_A	58_L	2.133	0.96
15_V	68_L	2.123	0.95
30_V	167_V	2.117	0.95
22_A	54_V	2.098	0.95
52_G	102_G	2.082	0.95
168_T	184_T	2.020	0.94
8_T	11_G	1.999	0.94
146_G	194_G	1.992	0.94
161_A	184_T	1.970	0.93
21_N	57_D	1.970	0.93
11_G	71_S	1.932	0.93
125_I	128_V	1.925	0.92
142_A	145_L	1.870	0.91
80_L	86_P	1.823	0.90
160_V	163_A	1.798	0.89
179_V	197_V	1.755	0.88
34_L	48_V	1.753	0.88
157_G	187_G	1.722	0.87
51_V	54_V	1.690	0.86
14_G	18_S	1.675	0.86
87_V	90_V	1.641	0.85
34_L	53_N	1.627	0.84
40_N	46_T	1.600	0.83
143_T	148_P	1.549	0.81
10_Q	36_Q	1.538	0.80
27_G	95_G	1.529	0.80
31_S	44_V	1.514	0.79
47_T	118_T	1.504	0.79
63_S	99_T	1.500	0.79
28_N	32_N	1.464	0.77
50_S	71_S	1.424	0.75
91_V	95_G	1.422	0.75
156_V	163_A	1.412	0.74
85_T	97_A	1.400	0.74
94_V	97_A	1.395	0.73
135_T	139_V	1.379	0.73
59_G	88_G	1.379	0.73
121_L	124_A	1.367	0.72
90_V	165_T	1.353	0.71
136_T	143_T	1.352	0.71
42_N	45_G	1.345	0.71
11_G	65_L	1.343	0.70
80_L	83_V	1.341	0.70
186_V	197_V	1.330	0.70
26_L	50_S	1.326	0.70
29_G	50_S	1.318	0.69
82_P	86_P	1.310	0.69
43_P	82_P	1.293	0.68
141_T	179_V	1.267	0.66
77_L	84_T	1.206	0.62
143_T	160_V	1.187	0.61
67_G	101_L	1.185	0.61
78_A	82_P	1.181	0.60
136_T	148_P	1.174	0.60
43_P	129_T	1.166	0.59
91_V	132_V	1.160	0.59
167_V	183_V	1.160	0.59
97_A	101_L	1.158	0.59
56_S	160_V	1.150	0.58
30_V	169_G	1.148	0.58
42_N	46_T	1.147	0.58
27_G	66_G	1.144	0.58
173_N	176_T	1.122	0.56
20_G	59_G	1.112	0.56
149_V	152_L	1.087	0.54
114_V	129_T	1.086	0.54
114_V	128_V	1.085	0.54
69_V	72_L	1.066	0.52
106_G	109_L	1.062	0.52
21_N	25_T	1.059	0.52
69_V	73_G	1.057	0.52
62_V	98_V	1.057	0.52
130_S	179_V	1.046	0.51
25_T	57_D	1.039	0.51
55_V	118_T	1.022	0.49
26_L	29_G	1.022	0.49
140_G	146_G	1.013	0.49
36_Q	39_T	1.013	0.49
171_T	176_T	1.000	0.48
136_T	153_L	0.998	0.48
119_Q	123_S	0.991	0.47
22_A	88_G	0.979	0.46
154_G	158_G	0.973	0.46
25_T	30_V	0.972	0.46
193_A	197_V	0.971	0.46
139_V	193_A	0.968	0.46
49_A	83_V	0.965	0.45
192_S	195_G	0.961	0.45
19_T	49_A	0.959	0.45
10_Q	32_N	0.958	0.45
145_L	168_T	0.953	0.45
40_N	128_V	0.953	0.45
186_V	192_S	0.948	0.44
12_L	81_A	0.947	0.44
131_T	159_A	0.937	0.43
43_P	122_S	0.933	0.43
186_V	189_T	0.931	0.43
82_P	119_Q	0.924	0.43
5_S	9_T	0.915	0.42
165_T	184_T	0.910	0.42
101_L	104_T	0.909	0.42
136_T	146_G	0.908	0.41
37_L	41_P	0.902	0.41
52_G	119_Q	0.893	0.40
96_Q	100_M	0.888	0.40
66_G	91_V	0.888	0.40
43_P	182_V	0.886	0.40
116_Q	127_P	0.886	0.40
29_G	95_G	0.883	0.40
18_S	68_L	0.871	0.39
39_T	132_V	0.871	0.39
148_P	153_L	0.865	0.39
29_G	91_V	0.865	0.39
44_V	72_L	0.863	0.38
74_S	85_T	0.859	0.38
43_P	84_T	0.857	0.38
28_N	156_V	0.856	0.38
19_T	104_T	0.849	0.38
33_G	55_V	0.835	0.37
128_V	192_S	0.835	0.37
132_V	135_T	0.833	0.36
18_S	60_N	0.832	0.36
5_S	130_S	0.825	0.36
88_G	95_G	0.812	0.35
37_L	135_T	0.812	0.35
59_G	66_G	0.808	0.35
137_Q	140_G	0.807	0.35
11_G	15_V	0.800	0.34
48_V	83_V	0.794	0.34
23_V	26_L	0.792	0.34
116_Q	137_Q	0.791	0.34
33_G	44_V	0.787	0.34
149_V	155_T	0.784	0.33
54_V	90_V	0.783	0.33
57_D	128_V	0.782	0.33
73_G	79_P	0.780	0.33
89_G	160_V	0.776	0.33
138_T	155_T	0.766	0.32
142_A	153_L	0.765	0.32
140_G	194_G	0.765	0.32
101_L	151_G	0.762	0.32
121_L	181_G	0.752	0.31
157_G	164_G	0.750	0.31
11_G	83_V	0.747	0.31
71_S	74_S	0.746	0.31
51_V	83_V	0.742	0.31
9_T	26_L	0.739	0.31
79_P	84_T	0.736	0.30
152_L	168_T	0.733	0.30
123_S	130_S	0.733	0.30
145_L	149_V	0.733	0.30
94_V	166_Q	0.726	0.30
9_T	170_A	0.724	0.30
80_L	84_T	0.722	0.30
16_V	180_G	0.718	0.29
11_G	167_V	0.711	0.29
17_T	23_V	0.710	0.29
185_G	188_N	0.709	0.29
45_G	88_G	0.708	0.29
137_Q	148_P	0.707	0.29
130_S	175_V	0.706	0.29
168_T	176_T	0.705	0.29
98_V	101_L	0.705	0.29
100_M	104_T	0.703	0.29
8_T	129_T	0.699	0.28
46_T	118_T	0.698	0.28
36_Q	40_N	0.698	0.28
105_L	108_A	0.692	0.28
190_V	194_G	0.690	0.28
17_T	21_N	0.688	0.28
12_L	32_N	0.688	0.28
192_S	198_N	0.685	0.28
183_V	190_V	0.680	0.27
10_Q	39_T	0.679	0.27
83_V	111_S	0.679	0.27
168_T	183_V	0.675	0.27
11_G	68_L	0.675	0.27
114_V	125_I	0.674	0.27
105_L	160_V	0.667	0.27
30_V	108_A	0.667	0.27
156_V	169_G	0.667	0.27
9_T	17_T	0.665	0.26
158_G	193_A	0.655	0.26
159_A	163_A	0.655	0.26
18_S	177_S	0.653	0.26
29_G	51_V	0.652	0.26
9_T	12_L	0.647	0.25
113_P	116_Q	0.636	0.25
74_S	130_S	0.634	0.25
96_Q	121_L	0.633	0.25
46_T	58_L	0.632	0.25
55_V	98_V	0.631	0.25
47_T	59_G	0.629	0.25
6_S	10_Q	0.629	0.25
33_G	118_T	0.627	0.24
44_V	193_A	0.624	0.24
13_G	19_T	0.618	0.24
10_Q	17_T	0.614	0.24
68_L	71_S	0.614	0.24
164_G	180_G	0.611	0.24
83_V	158_G	0.609	0.24
38_G	73_G	0.607	0.23
50_S	197_V	0.607	0.23
93_T	173_N	0.606	0.23
14_G	165_T	0.606	0.23
74_S	172_G	0.606	0.23
18_S	23_V	0.604	0.23
137_Q	157_G	0.603	0.23
185_G	198_N	0.603	0.23
5_S	10_Q	0.602	0.23
25_T	43_P	0.602	0.23
174_P	182_V	0.601	0.23
68_L	80_L	0.601	0.23
6_S	17_T	0.600	0.23
185_G	195_G	0.596	0.23
24_S	108_A	0.595	0.23
35_G	42_N	0.590	0.23
14_G	66_G	0.590	0.23
81_A	163_A	0.587	0.22
78_A	84_T	0.586	0.22
160_V	192_S	0.586	0.22
126_V	174_P	0.586	0.22
136_T	140_G	0.585	0.22
5_S	31_S	0.578	0.22
42_N	118_T	0.577	0.22
147_A	155_T	0.576	0.22
139_V	152_L	0.573	0.22
164_G	187_G	0.572	0.22
68_L	179_V	0.567	0.21
68_L	133_T	0.567	0.21
56_S	145_L	0.564	0.21
25_T	50_S	0.564	0.21
190_V	193_A	0.563	0.21
85_T	91_V	0.563	0.21
15_V	167_V	0.563	0.21
111_S	166_Q	0.562	0.21
151_G	169_G	0.562	0.21
17_T	60_N	0.555	0.21
42_N	47_T	0.554	0.21
19_T	58_L	0.554	0.21
173_N	177_S	0.554	0.21
83_V	98_V	0.552	0.21
26_L	51_V	0.549	0.21
37_L	78_A	0.549	0.21
47_T	105_L	0.546	0.20
39_T	46_T	0.546	0.20
80_L	115_Q	0.545	0.20
30_V	34_L	0.544	0.20
144_G	148_P	0.541	0.20
36_Q	179_V	0.540	0.20
37_L	133_T	0.538	0.20
23_V	112_G	0.538	0.20
13_G	17_T	0.536	0.20
177_S	193_A	0.534	0.20
35_G	118_T	0.530	0.20
67_G	70_S	0.529	0.20
142_A	159_A	0.528	0.20
181_G	188_N	0.527	0.20
104_T	112_G	0.523	0.19
69_V	84_T	0.521	0.19
14_G	50_S	0.518	0.19
15_V	18_S	0.515	0.19
114_V	121_L	0.514	0.19
130_S	134_G	0.512	0.19
99_T	103_D	0.511	0.19
73_G	125_I	0.510	0.19
56_S	63_S	0.508	0.19
69_V	81_A	0.508	0.19
144_G	152_L	0.507	0.19
51_V	55_V	0.505	0.19
188_N	192_S	0.505	0.19
161_A	165_T	0.504	0.19
6_S	39_T	0.503	0.19
26_L	53_N	0.503	0.19
18_S	166_Q	0.502	0.19
114_V	137_Q	0.500	0.18

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
2ieqA	3	0.4523	26.8	0.906	Contact Map
2ch7A	2	0.8392	13.4	0.918	Contact Map
3g67A	2	0.9045	12.9	0.918	Contact Map
4f7gB	1	0.6683	10.8	0.921	Contact Map
3zx6A	2	0.9749	9.1	0.924	Contact Map
2b9bA	3	0.9497	9.1	0.924	Contact Map
2l7nA	1	0.6332	7.5	0.927	Contact Map
2bezC	3	0.3869	7.5	0.927	Contact Map
1g5gA	3	0.6683	7.3	0.927	Contact Map
3zqeA	1	0.5528	6.4	0.929	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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