DUF2239 - PFAM28P - GREMLIN Contacts

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DUF2239 - Uncharacterized protein conserved in bacteria (DUF2239)

PFAM:	PF09998	Sequences: TCTAFAGHRRIASGPLAEVALAVKAALDRGPAAPVLIFDDATGRQVDLDLRGSAADVLARLAAPAAAAAAAAPPAPRGPGRPKLGVVAREVTLLPRHWEWLAAQPGGASVALRKLVEEARRANGGRDRARAAQEAAYRFMSAMAGNLPGFEEASRALFAGDRARFEALIAAWPADVRDHALRLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	184 (182)
Sequences:	2513 (1888)
Seq/√Len:	139.9
META:	0.844

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_T	40_D	4.060	1.00
110_V	114_K	3.345	1.00
164_R	168_L	3.049	1.00
139_F	143_M	3.039	1.00
123_N	127_D	2.624	1.00
150_F	154_S	2.457	1.00
8_H	147_L	2.375	1.00
137_Y	158_F	2.233	1.00
140_M	180_A	2.221	1.00
36_L	45_Q	2.135	1.00
21_L	54_A	2.114	1.00
141_S	150_F	2.084	1.00
162_R	166_E	2.056	1.00
161_D	164_R	2.029	1.00
52_G	60_R	2.023	1.00
133_Q	160_G	1.994	1.00
15_P	18_E	1.975	1.00
58_L	61_L	1.956	1.00
118_E	122_A	1.939	1.00
117_E	120_R	1.935	1.00
24_K	28_D	1.918	1.00
88_A	92_T	1.877	1.00
52_G	57_V	1.877	1.00
169_I	181_L	1.864	1.00
43_G	47_D	1.832	1.00
53_S	56_D	1.829	1.00
96_R	117_E	1.827	1.00
37_I	48_L	1.818	1.00
4_A	19_V	1.816	1.00
91_V	112_L	1.804	1.00
103_A	131_A	1.783	1.00
139_F	179_H	1.748	1.00
16_L	48_L	1.707	1.00
139_F	180_A	1.687	1.00
165_F	180_A	1.682	1.00
140_M	153_A	1.673	1.00
40_D	179_H	1.622	1.00
43_G	179_H	1.616	1.00
43_G	135_A	1.609	1.00
2_C	16_L	1.558	1.00
165_F	181_L	1.528	1.00
137_Y	141_S	1.489	1.00
144_A	176_V	1.481	1.00
137_Y	154_S	1.475	1.00
40_D	43_G	1.461	1.00
3_T	13_S	1.393	1.00
178_D	181_L	1.373	1.00
3_T	179_H	1.371	1.00
44_R	138_R	1.362	1.00
140_M	154_S	1.362	1.00
56_D	60_R	1.361	1.00
144_A	147_L	1.352	1.00
20_A	48_L	1.347	1.00
179_H	183_L	1.345	1.00
154_S	158_F	1.333	1.00
3_T	10_R	1.318	1.00
152_E	164_R	1.299	1.00
166_E	181_L	1.296	1.00
106_G	110_V	1.277	1.00
38_F	142_A	1.271	1.00
52_G	56_D	1.271	1.00
57_V	60_R	1.267	1.00
11_I	26_A	1.266	1.00
97_H	117_E	1.225	1.00
10_R	182_R	1.221	1.00
23_V	26_A	1.216	1.00
147_L	176_V	1.216	1.00
45_Q	142_A	1.201	1.00
2_C	46_V	1.190	1.00
134_E	158_F	1.175	1.00
53_S	60_R	1.174	1.00
154_S	180_A	1.169	0.99
129_A	133_Q	1.165	0.99
6_A	33_A	1.160	0.99
144_A	169_I	1.142	0.99
134_E	137_Y	1.134	0.99
137_Y	150_F	1.126	0.99
25_A	54_A	1.125	0.99
4_A	23_V	1.114	0.99
10_R	13_S	1.098	0.99
164_R	167_A	1.090	0.99
141_S	154_S	1.078	0.99
116_V	119_A	1.077	0.99
10_R	178_D	1.064	0.99
45_Q	146_N	1.061	0.99
149_G	168_L	1.060	0.99
124_G	127_D	1.042	0.99
39_D	42_T	1.039	0.99
3_T	43_G	1.038	0.99
27_L	50_L	1.019	0.99
169_I	177_R	1.015	0.99
6_A	9_R	1.014	0.99
54_A	58_L	1.011	0.99
23_V	37_I	1.011	0.99
23_V	35_V	1.010	0.99
114_K	117_E	1.009	0.99
24_K	54_A	1.005	0.98
170_A	181_L	1.001	0.98
38_F	139_F	0.998	0.98
136_A	180_A	0.996	0.98
13_S	40_D	0.990	0.98
117_E	121_R	0.988	0.98
56_D	59_A	0.985	0.98
23_V	27_L	0.985	0.98
6_A	30_G	0.973	0.98
105_P	114_K	0.971	0.98
30_G	33_A	0.960	0.98
156_A	164_R	0.959	0.98
118_E	121_R	0.956	0.98
152_E	168_L	0.948	0.98
26_A	30_G	0.939	0.98
40_D	182_R	0.935	0.98
180_A	184_A	0.923	0.97
27_L	30_G	0.915	0.97
129_A	160_G	0.903	0.97
24_K	52_G	0.902	0.97
36_L	142_A	0.886	0.97
31_P	34_P	0.885	0.97
50_L	57_V	0.869	0.96
107_G	111_A	0.867	0.96
153_A	169_I	0.865	0.96
17_A	58_L	0.863	0.96
127_D	130_R	0.858	0.96
165_F	169_I	0.856	0.96
38_F	143_M	0.855	0.96
39_D	44_R	0.850	0.96
6_A	29_R	0.850	0.96
130_R	134_E	0.850	0.96
105_P	130_R	0.845	0.96
37_I	50_L	0.843	0.95
24_K	57_V	0.838	0.95
27_L	31_P	0.838	0.95
89_R	107_G	0.831	0.95
21_L	58_L	0.826	0.95
22_A	26_A	0.821	0.95
20_A	61_L	0.814	0.95
54_A	57_V	0.811	0.94
87_V	120_R	0.801	0.94
177_R	181_L	0.796	0.94
62_A	68_A	0.794	0.94
132_A	136_A	0.789	0.94
8_H	143_M	0.788	0.94
24_K	58_L	0.781	0.93
27_L	35_V	0.779	0.93
123_N	126_R	0.778	0.93
57_V	61_L	0.776	0.93
21_L	24_K	0.776	0.93
23_V	50_L	0.775	0.93
111_A	127_D	0.772	0.93
140_M	169_I	0.768	0.93
20_A	52_G	0.760	0.92
45_Q	48_L	0.756	0.92
8_H	146_N	0.744	0.91
24_K	50_L	0.737	0.91
88_A	102_A	0.736	0.91
66_A	70_A	0.735	0.91
136_A	140_M	0.734	0.91
30_G	34_P	0.731	0.91
125_G	128_R	0.727	0.91
4_A	37_I	0.726	0.90
76_P	79_P	0.721	0.90
21_L	61_L	0.718	0.90
28_D	54_A	0.718	0.90
163_A	181_L	0.714	0.90
11_I	23_V	0.712	0.90
163_A	166_E	0.709	0.89
174_A	178_D	0.707	0.89
132_A	135_A	0.701	0.89
44_R	146_N	0.697	0.89
47_D	51_R	0.695	0.88
134_E	138_R	0.693	0.88
179_H	182_R	0.693	0.88
11_I	19_V	0.692	0.88
17_A	57_V	0.689	0.88
38_F	43_G	0.689	0.88
2_C	47_D	0.687	0.88
54_A	62_A	0.686	0.88
99_E	102_A	0.680	0.87
62_A	65_A	0.680	0.87
162_R	165_F	0.678	0.87
10_R	175_D	0.677	0.87
168_L	171_A	0.677	0.87
143_M	176_V	0.677	0.87
149_G	152_E	0.671	0.87
8_H	176_V	0.667	0.86
111_A	123_N	0.665	0.86
52_G	61_L	0.665	0.86
103_A	127_D	0.662	0.86
149_G	171_A	0.660	0.86
136_A	157_L	0.659	0.86
77_R	92_T	0.658	0.86
49_D	60_R	0.647	0.85
6_A	26_A	0.643	0.84
9_R	33_A	0.642	0.84
48_L	61_L	0.640	0.84
80_G	86_V	0.640	0.84
2_C	15_P	0.639	0.84
171_A	174_A	0.630	0.83
6_A	31_P	0.629	0.83
2_C	43_G	0.626	0.83
150_F	153_A	0.625	0.83
24_K	27_L	0.624	0.82
102_A	106_G	0.620	0.82
163_A	167_A	0.619	0.82
126_R	133_Q	0.611	0.81
80_G	85_G	0.610	0.81
22_A	25_A	0.610	0.81
64_P	70_A	0.609	0.81
81_R	86_V	0.606	0.81
82_P	86_V	0.605	0.81
112_L	116_V	0.604	0.80
25_A	29_R	0.602	0.80
2_C	19_V	0.602	0.80
132_A	142_A	0.599	0.80
55_A	88_A	0.596	0.80
139_F	176_V	0.596	0.80
6_A	35_V	0.590	0.79
169_I	180_A	0.589	0.79
166_E	170_A	0.586	0.78
39_D	45_Q	0.586	0.78
41_A	135_A	0.585	0.78
133_Q	154_S	0.583	0.78
79_P	147_L	0.577	0.77
67_A	70_A	0.575	0.77
38_F	47_D	0.575	0.77
105_P	117_E	0.573	0.77
80_G	84_L	0.572	0.77
45_Q	138_R	0.570	0.76
16_L	52_G	0.570	0.76
36_L	46_V	0.570	0.76
4_A	35_V	0.569	0.76
38_F	45_Q	0.565	0.76
21_L	55_A	0.560	0.75
41_A	131_A	0.559	0.75
21_L	57_V	0.558	0.75
129_A	132_A	0.557	0.75
141_S	153_A	0.556	0.75
165_F	184_A	0.556	0.75
131_A	167_A	0.554	0.74
18_E	25_A	0.551	0.74
170_A	174_A	0.551	0.74
20_A	57_V	0.550	0.74
69_A	72_A	0.550	0.74
128_R	135_A	0.549	0.74
70_A	74_P	0.548	0.74
62_A	69_A	0.544	0.73
91_V	111_A	0.542	0.73
56_D	61_L	0.542	0.73
62_A	70_A	0.541	0.73
39_D	138_R	0.539	0.72
66_A	69_A	0.539	0.72
135_A	138_R	0.535	0.72
142_A	147_L	0.534	0.72
16_L	39_D	0.532	0.71
133_Q	158_F	0.532	0.71
19_V	37_I	0.530	0.71
102_A	108_A	0.526	0.71
111_A	120_R	0.524	0.70
4_A	24_K	0.523	0.70
78_G	128_R	0.520	0.70
147_L	174_A	0.518	0.69
13_S	182_R	0.517	0.69
143_M	169_I	0.516	0.69
118_E	126_R	0.514	0.69
153_A	165_F	0.513	0.69
67_A	72_A	0.510	0.68
89_R	102_A	0.507	0.68
150_F	168_L	0.505	0.68
17_A	180_A	0.502	0.67
6_A	11_I	0.502	0.67
2_C	40_D	0.500	0.67
54_A	71_A	0.500	0.67
89_R	111_A	0.500	0.67

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
2jokA	1	0.3913	53	0.952	Contact Map
3ff0A	2	0.3696	11.1	0.966	Contact Map
2o7gA	2	0.2337	11.1	0.966	Contact Map
2ov9A	2	0.5543	10.2	0.966	Contact Map
4uzzA	1	0.2935	9	0.967	Contact Map
4xc8A	2	0.9022	8.3	0.968	Contact Map
1wekA	5	0.3261	7.4	0.968	Contact Map
3sbxA	2	0.3207	7.4	0.968	Contact Map
4us5A	3	0.4674	7.2	0.969	Contact Map
3quaA	2	0.3261	7	0.969	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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