DUF155 - PFAM28P - GREMLIN Contacts

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DUF155 - Uncharacterised ACR, YagE family COG1723

PFAM:	PF02582	Sequences: VFLFRYGVVVFWGLSEEEEEEFLRRLKEEPETEEFEFEEDEPRIEGDVIVLKDLSPERLLVIADALAQSVALAYYERRVAKLFDRTEPLAEELAKTGRLPLSRRELLKFIGEALLVRHRINLRLELLDKPDLLWDDPELERLYARLRDEFELKERYRALN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	160 (159)
Sequences:	3949 (2586)
Seq/√Len:	205.1
META:	0.752

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_E	20_E	3.156	1.00
15_S	18_E	2.922	1.00
33_E	37_F	2.729	1.00
24_R	27_K	2.701	1.00
33_E	39_E	2.587	1.00
14_L	18_E	2.575	1.00
64_D	68_Q	2.532	1.00
12_W	63_A	2.500	1.00
91_E	95_K	2.483	1.00
140_E	144_A	2.386	1.00
105_E	108_K	2.252	1.00
21_E	24_R	2.128	1.00
92_E	100_P	2.079	1.00
42_P	52_K	2.064	1.00
33_E	36_E	1.948	1.00
35_F	39_E	1.925	1.00
93_L	111_G	1.913	1.00
11_F	14_L	1.904	1.00
38_E	48_V	1.896	1.00
94_A	112_E	1.892	1.00
31_E	73_A	1.891	1.00
11_F	23_L	1.817	1.00
14_L	19_E	1.802	1.00
104_R	108_K	1.777	1.00
102_S	105_E	1.761	1.00
20_E	24_R	1.742	1.00
3_L	26_L	1.636	1.00
3_L	9_V	1.607	1.00
17_E	20_E	1.607	1.00
94_A	115_L	1.605	1.00
92_E	96_T	1.604	1.00
93_L	107_L	1.551	1.00
4_F	67_A	1.528	1.00
71_A	124_L	1.513	1.00
23_L	27_K	1.511	1.00
18_E	21_E	1.499	1.00
12_W	59_L	1.488	1.00
140_E	143_Y	1.482	1.00
53_D	58_R	1.476	1.00
140_E	151_E	1.473	1.00
81_K	84_D	1.473	1.00
70_V	73_A	1.427	1.00
79_V	120_I	1.424	1.00
97_G	111_G	1.415	1.00
147_R	153_K	1.406	1.00
28_E	31_E	1.400	1.00
97_G	108_K	1.399	1.00
43_R	50_V	1.392	1.00
129_K	140_E	1.361	1.00
143_Y	147_R	1.347	1.00
11_F	19_E	1.330	1.00
151_E	154_E	1.318	1.00
10_V	67_A	1.318	1.00
65_A	146_L	1.280	1.00
86_T	114_L	1.273	1.00
34_E	37_F	1.272	1.00
3_L	22_F	1.259	1.00
73_A	76_E	1.251	1.00
81_K	85_R	1.248	1.00
89_L	106_L	1.244	1.00
85_R	109_F	1.231	1.00
133_L	140_E	1.226	1.00
17_E	21_E	1.225	1.00
6_Y	75_Y	1.189	1.00
34_E	38_E	1.185	1.00
44_I	49_I	1.181	1.00
71_A	127_L	1.157	1.00
70_V	118_H	1.137	1.00
70_V	136_D	1.128	1.00
68_Q	151_E	1.120	1.00
17_E	25_R	1.111	1.00
94_A	108_K	1.099	1.00
87_E	91_E	1.090	1.00
90_A	114_L	1.087	1.00
137_P	149_E	1.058	1.00
109_F	112_E	1.057	1.00
131_D	134_W	1.047	1.00
47_D	50_V	1.042	1.00
54_L	59_L	1.025	1.00
36_E	40_D	1.007	1.00
36_E	48_V	1.002	1.00
61_V	132_L	0.996	1.00
66_L	150_F	0.992	1.00
32_T	37_F	0.986	1.00
63_A	122_L	0.975	1.00
8_V	67_A	0.969	1.00
76_E	143_Y	0.963	1.00
82_L	112_E	0.961	0.99
42_P	126_L	0.954	0.99
5_R	10_V	0.952	0.99
31_E	39_E	0.943	0.99
96_T	100_P	0.942	0.99
6_Y	67_A	0.940	0.99
131_D	135_D	0.939	0.99
129_K	151_E	0.937	0.99
120_I	123_R	0.928	0.99
135_D	138_E	0.925	0.99
100_P	106_L	0.924	0.99
68_Q	147_R	0.921	0.99
39_E	59_L	0.918	0.99
36_E	39_E	0.913	0.99
85_R	112_E	0.909	0.99
134_W	140_E	0.903	0.99
148_D	154_E	0.902	0.99
85_R	105_E	0.899	0.99
107_L	110_I	0.890	0.99
34_E	39_E	0.887	0.99
45_E	50_V	0.885	0.99
20_E	25_R	0.878	0.99
121_N	124_L	0.871	0.99
144_A	147_R	0.856	0.99
33_E	40_D	0.854	0.99
130_P	134_W	0.832	0.99
55_S	58_R	0.831	0.99
28_E	38_E	0.824	0.98
82_L	109_F	0.822	0.98
78_R	119_R	0.818	0.98
116_V	119_R	0.816	0.98
18_E	25_R	0.814	0.98
6_Y	126_L	0.813	0.98
101_L	105_E	0.801	0.98
16_E	19_E	0.796	0.98
46_G	61_V	0.791	0.98
31_E	35_F	0.789	0.98
57_E	139_L	0.789	0.98
65_A	143_Y	0.786	0.98
153_K	157_R	0.782	0.98
65_A	150_F	0.771	0.98
109_F	125_E	0.768	0.98
76_E	130_P	0.764	0.97
51_L	62_I	0.761	0.97
49_I	142_L	0.758	0.97
67_A	112_E	0.751	0.97
49_I	58_R	0.750	0.97
4_F	60_L	0.746	0.97
155_R	159_L	0.745	0.97
46_G	137_P	0.742	0.97
51_L	58_R	0.738	0.97
22_F	26_L	0.734	0.97
2_F	12_W	0.729	0.97
30_P	33_E	0.722	0.96
32_T	36_E	0.722	0.96
49_I	146_L	0.716	0.96
145_R	148_D	0.715	0.96
52_K	58_R	0.712	0.96
8_V	71_A	0.711	0.96
94_A	97_G	0.709	0.96
22_F	25_R	0.699	0.96
85_R	92_E	0.695	0.96
128_D	133_L	0.688	0.95
41_E	47_D	0.681	0.95
91_E	148_D	0.678	0.95
129_K	154_E	0.675	0.95
60_L	82_L	0.674	0.95
124_L	152_L	0.673	0.95
39_E	54_L	0.671	0.95
2_F	63_A	0.661	0.94
58_R	61_V	0.658	0.94
129_K	133_L	0.657	0.94
35_F	38_E	0.652	0.94
63_A	89_L	0.652	0.94
4_F	7_G	0.649	0.94
143_Y	158_A	0.646	0.94
86_T	115_L	0.645	0.93
60_L	133_L	0.644	0.93
86_T	117_R	0.643	0.93
107_L	139_L	0.641	0.93
68_Q	97_G	0.640	0.93
47_D	149_E	0.635	0.93
11_F	69_S	0.634	0.93
32_T	94_A	0.633	0.93
31_E	36_E	0.632	0.93
11_F	22_F	0.632	0.93
38_E	50_V	0.631	0.93
90_A	113_A	0.631	0.93
34_E	40_D	0.628	0.93
113_A	117_R	0.624	0.92
111_G	115_L	0.620	0.92
21_E	25_R	0.617	0.92
44_I	50_V	0.616	0.92
31_E	37_F	0.613	0.92
121_N	125_E	0.607	0.91
95_K	104_R	0.607	0.91
86_T	109_F	0.606	0.91
129_K	147_R	0.602	0.91
60_L	103_R	0.601	0.91
109_F	120_I	0.599	0.91
84_D	87_E	0.597	0.91
29_E	32_T	0.593	0.90
109_F	113_A	0.585	0.90
56_P	96_T	0.585	0.90
9_V	23_L	0.584	0.90
57_E	136_D	0.583	0.90
45_E	48_V	0.582	0.89
53_D	95_K	0.575	0.89
92_E	95_K	0.573	0.89
120_I	143_Y	0.569	0.88
90_A	117_R	0.568	0.88
29_E	33_E	0.558	0.87
122_L	125_E	0.557	0.87
49_I	150_F	0.556	0.87
41_E	44_I	0.556	0.87
147_R	151_E	0.553	0.87
70_V	78_R	0.552	0.87
6_Y	68_Q	0.550	0.87
135_D	145_R	0.549	0.87
90_A	111_G	0.548	0.86
56_P	119_R	0.546	0.86
18_E	22_F	0.544	0.86
36_E	95_K	0.544	0.86
1_V	22_F	0.541	0.86
86_T	110_I	0.539	0.86
133_L	139_L	0.535	0.85
86_T	113_A	0.533	0.85
60_L	156_Y	0.531	0.85
59_L	121_N	0.526	0.84
39_E	51_L	0.525	0.84
85_R	158_A	0.524	0.84
108_K	112_E	0.524	0.84
31_E	34_E	0.523	0.84
111_G	114_L	0.522	0.84
9_V	81_K	0.521	0.84
93_L	118_H	0.520	0.83
102_S	127_L	0.519	0.83
144_A	148_D	0.519	0.83
39_E	50_V	0.518	0.83
22_F	30_P	0.517	0.83
68_Q	75_Y	0.516	0.83
38_E	81_K	0.515	0.83
32_T	38_E	0.515	0.83
24_R	53_D	0.512	0.83
11_F	66_L	0.508	0.82
120_I	147_R	0.508	0.82
86_T	107_L	0.508	0.82
45_E	51_L	0.507	0.82
127_L	156_Y	0.505	0.82
78_R	116_V	0.503	0.81
136_D	140_E	0.500	0.81

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
1dgsA	1	0.3625	11.3	0.934	Contact Map
3oiqB	1	0.1875	11.2	0.934	Contact Map
3sgiA	1	0.3438	7.4	0.939	Contact Map
3j8bC	1	0.2938	6.6	0.941	Contact Map
4lh6A	1	0.3875	5	0.944	Contact Map
3c0uA	2	0.45	4.6	0.945	Contact Map
3qneA	2	0.9375	4.1	0.946	Contact Map
3uq8A	1	0.3375	3.6	0.948	Contact Map
1mp9A	2	0.7625	3.4	0.948	Contact Map
1m2dA	2	0.2375	3.4	0.948	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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